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LDMS User Manual - Frontier Science website

1. ses sssssssssssessssssersssssstesssssssersssssreessssssresss 31 Co enrolling a primary SpeciMEe Mrenea 33 Modifying a primary SpeciMen s ss esssssseerssssseeessssseeesssssseesssssseeessssseerssosseresssssseresss 35 Aliguot SPECIMENS isoen e cuban aaa aae SEELE SS 35 Adding aliquots to a primary SpeciMen ssssssssssssssssrssssssersssssseesssssssessssssreessses 35 Entering cryopreservation information sesssssssessssssssesssssreessssssressssssseesssssreesss 37 010S a EREA E S E EE E EA E E E AEE TRA 37 Adding specimens using QUICK ACh essessessessssscessssessesessessessesesesscstesteaceseenes 38 LDMS User Manual Contents TBD in QUICK AdA tEMPlAte ce ceesssssssssesssssssssssessessessessssesessescecseceeseecsseesecseeseseess 39 QUICK Add templates meann inarin O Eaa AR TAE 39 Differences between primaries and ALIQUOTS cecsssesessesesesessecscseescesceseeseeeeseeees 40 Specimen aVAILADILIY noranai ataaeas ds cab AE ai a acd AEA 41 Specimen tecord details oeri aaa aeaa EE R 42 Specimen conditions ersen aE AARS EET EA A EEEE NAE 45 Destroying A SPECIMEN cccsssscsssssssssessessessasssssssssssessesssssssscescescescescascascascassussassessees 46 Procedural conditions essiensa ni 46 Specimen container conditionS sss eesssssseesssssseeessseseerssssseeessssestessnessterssesseersssessees 47 TEMPELatUre conditionSseusnesre a 47 SIPPING CONGITIONS aeaa A a E AO RRR 48 Qualitative conditions neronnnnetir
2. LDMS USRMANOO3 Code BRN BRS BUC BUF CAN ccc CcD4 CD8 CDN CDP CEL CEN CGN CIO CLI CLN CMV CRY CSF CSR CTB CTC CTS CVL Cvs CXS DBE DBS DPE DPL DPS DSP DUR DWB ED4 END EPP FHR FLD FPL Codes units and abbreviations Description Brain Tissue Breast Tissue Buccal Unficolled Cryopreserved Buffy Coat Viable Candida Cryopreserved Cells from a Culture Viable CD4 Positive T Cells CD8 cells Copy DNA Dry Pellet from a Culture Non Viable PBMC Cells Viable Fresh Cells from a Non Blood Spec Type Cells in GITC Cells in Other Solution Non Viable Cell Lines Cryopreserved primary cells from Non Blood Spec Type Viable CytoMegaloVirus Isolate Generic Cryptococcus Cerebro Spinal Fluid Serum Chilled Cytobrush Cells from a CTL Assay Supernatant generated from a CTL Assay Cervical Vaginal Lavage CVL Supernatant Cervical Swab Dried Blood Extract Dried Blood Spot Spray Dried EDTA Plasma Dried Dried Plasma Spot Digested Sputum Dried Urine Dried Whole Blood Effector Memory CD4 T cells Endometrial Tissue Endodontic Paper Point Hair Facial Fluid Portion from a Non Blood Specimen Type Plasma Filtered Page 147 LDMS User Manual LDMS USRMANOO3 Code FSI FSO GMI HAR HRT ICK IPK IVR LAV LIV LPD LPK LYM LYS MCL MCS MD4 MDC MEC MPE MTB MUC N A NCL ND4 NKC NON NPE NPW NTM NXD OPC OTH PCC PDC PED PEL PEN PEO PER Description
3. lf using a date range specify the Start Date and End Date 5 Leave the File Type as PDF pdf LDMS USRMANOO3 Page 66 LDMS User Manual Storage This report is not intended to be generated in a format other than PDF 6 Click Generate Move Report What to do next Each row in the Storage Move Report will represent one specimen that has changed locations with its original Location and its now Location Use the report to find the specimen in its original location so that it can be related to the new position Removing items from storage Storage items and specimens can be removed from storage Background Removing a storage item removes all of the items that it contains If the location being removed contains specimens you will be given the opportunity to change their condition and apply comments to them which can be accessed when viewing the specimens Removing a storage item that contains specimens does not delete the specimens They will still be visible on the Specimen Management page and unless you chose to make them unavailable they can be added to a different storage container Warning Removing a storage item cannot be undone Procedure 1 Click Storage from the LDMS menu bar 2 Find the storage item or specimen that you want to remove Use the filters on the left side of the Storage page to help locate the items to be removed 3 From the Edit combo button to the right of the item select Delete N
4. Description NDVNS1 Newcastle disease virus with NS1 influenza protein NDVB1 Newcastle disease virus wild type Newcastle disease virus with W influenza protein Negative Control Natural Killer cells Sodium Hydroxide None Neuropepsidase Inhibitor Normal Saline Nucleotides Optimum Cutting Temperature Medium OKT3 Treated Other P24 Parrafin Phosphate Buffered Saline PreserveCytSolution Pre Infusion Paraformaldahyde PHA Treated S8820 Sigma SIGMAFAST Protease Inhibitor Tablets Plasma Depleted Phorbol Myristate Acetate Ionomycin Phosphoric Acid Piperaquine Protamine Sulfate Post infusion Proteinase K Polyvinyl alcohol Pokeweed Mitogen RNAse free water Right RNAlater RNA Protect RPMI 1640 Medium Reverse Transcriptase buffer Sendai 52 virus with defective infectious particules Sodium Carbonate Second Spin Sigma Staphylococcus Enterotoxin B Page 153 LDMS User Manual Codes units and abbreviations Code Description SNP Snap Flash Freeze STG Skim milk Tryptone Glucose Glycerin Medium STGG STM Stimulated by Multiple Antigens SUP Cultural Supernatant TBD Specimen type to be defined TBS Tris buffered saline TCA 1 Thimersol 6 6 EACA Epsilon Amino Caproic Acid TCL T cell Lymphoblastoid Cell Line TCM Trichrome stain TEM Tempus Tube TFM Tissue Freezing Medium TMD Myeloid dendritic cell non infected and treated with TSST TMS Transport Medium Stuarts TND Myeloid dendritic cell
5. Penis Foreskin Inner Tissue Penis Foreskin Outer Tissue Gastro Intestinal Mucosa Hair Heart Supernatant generated from Inducible Cytokines Methanol Extract Supernatant Intra vaginal Ring Lavage Liver Tissue Lipid Layer Leukopak Lymph Node Biopsy Aspirate Lysed whole blood Macrophage Cells Viable Microbiology Culture Slant Central Memory CD4 T cells Myeloid Dendritic Cells Meconium Macrophage Dried Cell Pellet Non Viable MTB Isolates Mucins Not Applicable Same as Primary Specimen Type Neutrophil PMN Viable cells Naive CD4 T cells Natural Killer Cells None Neutrophil PMN Dried Cell Pellet Non Viable Nasopharyngeal Wash Nontuberculous mycobacteria Non extracted DNA Ova and Parasite Concentrate Other Culture Supernatant and Cells Plasmacytoid Dendritic Cells Dried Pellet Digene Non viable PBMC s Non viable cells from non blood specimen type Wet Pellet Prep Organon Teknika Dried Pellet Roche Codes units and abbreviations Page 148 LDMS User Manual LDMS USRMANOO3 Code PHR PL PL1 PL2 PLA PLC PLH PLM PLP PLT PPS QAG QMT ONL RBC REC RD4 SAL SDI SDO SEC SEI SEM SEO SER SHR SKN SLD SMR SNO SPG SPI SPQ SPT SRH STK STL SUP SWB TBD Description Hair Pubic Plasma All Plasma Single Spun Plasma Double Spun Plasma Unknown Processing Placental Tissue Plasma High Spin Placenta Membrane Slice Supernatant and Cells from a Qua
6. Primary Project Sub Add Der Visit Unit Visit Value Lab 485 specimen count report Information displayed on report e Project e PID ID1 e Protocol e SID ID3 e Visit e Visit Unit e Clinic e Received Date e Draw Date e Draw Time e Import Date e Specimen ID e Global Specimen ID e Primary e Additive e Derivative e Sub Additive Derivative e Volume e Volume Unit e Condition e Time e Time Unit e Other Specimen ID e Test e Comments e Ship Date e Ship Batch e Ship to Laboratory Provides the number of specimens with a unique primary additive derivative sub A D combination LDMS USRMANOO3 Page 94 LDMS User Manual Reports Sorting Filter criteria Information displayed on report 1 Project and study combination 2 Participant 3 Visit ACTG PID ID1 ACTG Protocol ACTG Protocol Type Additive Derivative Non ACTG PID ID1 Non ACTG Prot ID2 Primary PID Visit Visit Unit Primary Additive Derivative Sub Additive Derivative Count Project Sub Add Der Visit Unit Visit Value Volume Volume unit Lab 485 specimen count with volume report Provides the number of specimens with a unique primary additive derivative sub A D combination along with total volume Sorting Filter criteria Information displayed on report 1 Project and study ACTG PID ID1 e PID combination ACTG Protocol e Visit 2 Participant ACTG Protocol Type e Visit Unit 3 Visit Addit
7. protocol and SID combination If you do not have a specimen time recorded on your CRF contact the clinic that collected the specimen from the participant This field is required for specimens with a specimen date of 01 January 2004 or later it is optional for specimens prior to that date This requirement can be overridden for specimens after this date if necessary e ACTG IMPAACT uses the standard LDMS Shipping File format to ship between ACTG and IMPAACT laboratories using LDMS e ACTG IMPAACT requires specimens to be labeled with a 2D barcode and label from LDMS LDMS comes with label formats for ACTG setup and ready to use e ACTG and IMPAACT are listed as a combined project throughout LDMS ACTG IMPACT e Preloads are permitted for the ACTG IMPAACT project but users are not permitted to create their own All ACTG preloads are created by Frontier Science in collaboration with network leadership For more information about preloads see the section called Preloads Templates for Expected Specimen Collections LDMS USRMANOO3 Page 119 LDMS User Manual AERAS Preset projects The AERAS preset project has these requirements Data entry requirements Field ID1 PID ID2 Study ID3 Visit OPID Clinic Specimen Time Received Time Notes Quick Add templates can be used for Aeras AIEDRP Required Required Required Disabled Required Disabled Required Required Opt
8. pum a 7 For each item being moved select a position in the destination If you want to automatically place the items being moved into the destination select a position and then select the Auto fill all from selected position option This will cause all remaining storage items to be placed into the destination based on the destination s fill order 8 Click the Continue button Related sections Listing specimens that moved in storage on page 66 After moving specimens in LDMS s storage you can print a list of these changes so that you can move the actual specimens Listing specimens that moved in storage After moving specimens in LDMS s storage you can print a list of these changes so that you can move the actual specimens Background When specimens are moved in LDMS they also need to be moved in your actual specimen storage area so that the storage location assignments in LDMS remain accurate To help you keep LDMS and your storage in sync you can print a list of specimens that have been assigned new storage locations in LDMS Procedure 1 In the menu bar click Storage gt Stored Samples 2 From the action menu in the upper left corner click Print Move Report 3 Next to Generate for select one of the following e Select This Login Session if you want to see all specimens that you have moved while signed in e Select Date Rage if you want to see all specimens that have been moved during a given date range
9. FOR GEN GIT GLT GRB H20 HEP Description Acid Citrate Dextrose ESAT 6 free cocktail 1 ESAT 6 free Cherry pick Ammonium Heparin CultureSwab Kit Bacterial Freezing Media Boric Acid Biopsy Transport Media Citrate Phosphate Dextrose Cell Preparation Tube Heparin Cell Preparation Tube SCI Culture Transport Kit Desferoxamine Double dosage of Heparin Spray Dried Potassium EDTA Spray Dried Sodium EDTA EDTA Endometrial Tissue Ethanol Fetal Fibronectin Buffer Formaldehyde Formalin GenAptima Media Guanidine Isothiocyanate GITC Glutaraldehyde Guanidine Reduction Buffer Water Heparin Page 144 LDMS User Manual LDMS USRMANOO3 Code ISO IST LHG LHP LPE LSE LYB MBK MPA NOH NON NOR NSL OCT ORA ORG OTH PAC PAX PBS PED PFM PIL PLP PPT PRO QAG QTF QMT ONL RBE RBN RLS RNL RNP ROC RPM SCC SCI SED Description Isohelix kit Internal Standard Lithium Heparin and Gel for Plasma Lithium Heparin Liquid Potassium EDTA Liquid Sodium EDTA Lysis Buffer Microbank tube Metaphosphoric Acid Sodium Hydroxide None Normasol Normal Saline Optimum Cutting Temperature Medium OraSure Collection Container Oragene Collection Container Other Port a cul Transport Tube PAXgene Blood RNA tube Phosphate Buffered Saline Potassium EDTA Paraformaldahyde S8820 Sigma SIGMAFAST Protease Inhibitor Tablets PLP Fixative Plasma Preparation Tube ProbeTec Media QFT TB Ag Red Cap QuantiF
10. Global Spec ID 17 ID 1 PID 15 Spec Date 10 Spec Time 5 Primary 3 Additive 3 Derivative 3 Sub Add Der 3 Volume 6 Val Units 3 E a Row 6 Column 1 Ship Batch No 8 SetField Clear Field Procedure 1 Click Labels from the LDMS menu bar Select a locally defined project from the Project box Select the label format to be customized from the Format box Click the Modify Format button The Create Format window will open 5 Modify the label format as needed Poa N LDMS USRMANOO3 Page 113 LDMS User Manual 6 Administration e To add afield to a label select a box from the Fields section where you want the information to appear Select an item from the box below the Fields section and then click the Set Field button e To remove a field select it from the Fields section and then click the Clear Field button Click the Modify Format button Your changes will be saved and the Create Format window will close Setting the default label format for a project The default label format and stock size can be set for individual projects Background This means that when you print labels for that project the default format and size will automatically be selected If you typically use the same format and size for a specific project s labels then you can save time by defining these defaults Procedure 1 From the menu bar click Labels gt Label Setup 2 In the Project box
11. Modify any participant information as needed The Enrollments section of this window was not present when the participant was first created It lists protocols in which the participant is enrolled and provides a link to view and modify that enrollment if needed 5 Click the Save button If you modified the participant identifier LDMS will check to ensure that it does not already exist for another participant Enrollments An enrollment associates a participant with a protocol For example a participant in the Frontier project may be participating in a study called F1526 The combination of that participant identifier on that study is called the enrollment A protocol is called ID2 in LDMS Like ID1 for participant identifiers the name for ID2 will vary depending on the project For example a vaccine project may call the protocol box in LDMS STUDY whereas a pharmacology project may call it TEST PANEL Also like ID1 a project may have rules for how its ID2 is formatted For example a vaccine project may require that protocols are in the format STUDY 201 STUDY 202 and so on a pharmacology project may use TEST PANEL A0003 TEST PANEL A0004 etc If the project has specified these rules they will be enforced by LDMS A participant can be enrolled in more than one ID2 for a project however because participants are specific to a project they cannot be enrolled in protocols across multiple proje
12. Note Draw Time Optional a Received Time Optional Only required if the draw date is after 01 Jan 2004 IRC The IRC preset project has these requirements Data entry requirements Field Required ID1 PID Required ID2 Protocol Required ID3 SID Required Visit Required OPID Optional Clinic Required Draw Time Required Received Time Optional MACS The MACS preset project has these requirements Data entry requirements Field Required ID1 MACSID Required ID2 Study Required ID3 Optional Visit Optional OPID Optional LDMS USRMANOO3 Note MACS Identifier Previously entered ID3s will be automatically populated by LDMS for the MACSID and study combination Select from pre defined List of visit units Page 131 LDMS User Manual Field Required Preset projects Note Clinic Optional Previously entered clinics will be automatically populated by LDMS for the MACSID and study combination Specimen Time Optional Received Time Optional e Notes e Quick Add templates are permitted for MACS e When sending shipments to the MACS repository the SeraCare shipping file format should be used The MAVRC preset project must meet these requirements MAVRC Data entry requirements Field Required ID1 PID Required ID2 Protocol Optional ID3 ID3 Optional Visit Optional OPID Optional Clinic Optional Draw Time Optional Received Time Optional MTCT The MTCT preset proje
13. Use filters from the left side of the screen to narrow down the participants that are displayed 3 Select the ID2 from the fID2 box The label for the ID2 box will depend on the project Common labels are study and protocol 4 To modify the enrollment a Click Edit ID2 where Protocol is the appropriate label for the project b Modify the enrollment as needed c Click Save 5 To remove the enrollment a From the Edit ID2 menu click Delete D2 Figure 9 The Edit Study menu Edit 027 v Add Visit Print Labels Delete i202 In this image ID2 is Study b Click Delete A visit is a specimen collection event associated with an enrollment A visit typically involves the collection of specimens defined by the protocol For example a visit may specify that you collect 3 tubes of blood from the participant In LDMS you would add the visit to the participant and then add the specimens to the visit LDMS USRMANOO3 Page 26 LDMS User Manual Specimen Management Visit identifiers A visit identifier defines the type of visit A visit is identified by two pieces of information the visit value and visit unit The visit value is a sequential identifier such as a number The visit unit is the type of visit For example a visit of 3 WK indicates that it is the third visit of the week type The 3 is the visit value and WK is the visit unit The protocol in which the participant
14. You can still modify this information if needed Any changes made will only affect the containers that you are creating 6 Enter the number of rows and columns for the new container into the Number of rows and Number of columns boxes This represents the size and capacity of the new container in terms of the number of specimens that the container can hold For example if you are creating a box that can hold 25 specimens you might have 5 columns and 5 rows 7 Select or deselect the Positions only option as desired If the positions only option is selected each specimen in the container will be identified by a number If it is not selected each specimen will be identified by its coordinates LDMS USRMANOO3 Page 59 LDMS User Manual 10 11 12 Storage If Positions only is not selected Define how specimens in the new container should be identified a Select either Row CoLumn or CoLumn Row from the Coordinate order box If Row CoLumn is selected each specimen s position will be identified in the format row column Select how columns and rows are to be labeled from the Column labeling and Row labeling boxes b To use letters to identify rows or columns select Alphabetic to use numbers select numeric c Select the fill order for the new level from the Fill order box Fill order will be used when adding new specimens to the container and you chose to use automatic positioning While you must specify a
15. rtable Te POrtss icenean a a i Aces EE A Aete sotine hans 93 Databases dump repart noraini E E e A 93 Lab 485 aliguot Tepi terioa a aa seaesnassapsansts 94 Lab 485 specimen count repOrt sssssseeessseseeessseseeesssssseesssseseeessssseeesssesseesssseseressss 94 Lab 485 specimen count with volume repofrt ssssssssessssssssessssssreesssssrersssssee 95 Primary specimen database dump repofrt s sesssssssessssssseessssssersssssreessssssresssssse 95 Sample counts for specified group POPOL ececsccsessessessessesesesestesessteseeseseecs 95 SPECIMEN export repor beamais AAE EE A R E 96 Storage export reporna a A 96 Miscellaneous reparis coracao a A RAO URN 97 Cime contact reportes a a a a 97 LDMS abbreviated codes repOft sssssseeessssseeesssesteesssssseesssssseeessssseeessneseeesssesseesssss 97 LDMS primary additive derivative sub additive derivative codes RE DOTT a T EEEE ROA A 98 Participant EP ONES anran ANAA T A A E A AT 98 Participant identifiers FePOFta sesssssssssssssssssssssssssessssssessessssssesssssesseseeceeceeceseesees 98 Quick Add Term Plates ransono NA A ARRE 98 Quick Add Template List Report esssssseeessssseeessssseeesssssseeessseseeessssseeessssssersssssseee 98 Shipping Tepos n EAE E AAEE KEE AA 99 Daily imported specimen LOG repO0ft ssssseeessssseeesssssseeessseseeessseseeesssesseesssseseeessses 99 Detailed imported specimen report ssssseeeessssseeessssseeesssseseesssss
16. visit value visit unit For a visit the type of visit such as the week number ex 1 WK where wk is the visit unit visit value For a visit an identifier that represents the step or sequence of the visit within a protocol such as the week number ex 1 WK where 1 is the visit value LDMS USRMANOO3 Page 173 LDMS User Manual Index lt gt 110 21 CFR Part 11 9 A accessibility information 169 account management 117 additional time 31 42 additive type 31 42 additives color icons 54 Adobe Reader 10 aliquot specimen adding 35 assigning storage location 60 sequence number in global specimen ID 29 ANM 49 ANP 41 46 assistive technology 169 availability 31 35 41 67 available 18 42 available volume 42 B barcode 110 barcode labels 109 barcode scanner 10 barcodes scanning 109 BKV 47 browse 14 browser tabs 12 BSS 10 bulk specimen modification 68 C cascading changes 35 35 CEL 37 challenge code 15 changing participant information 23 Chrome 10 clinic 27 42 CLT 48 co enrolled 35 42 co enrollment 25 co enrollments 33 COC 49 coenrollment 18 comments 31 35 42 68 compatibility with LDMS 30 Index conditions 41 container adding 59 moving 65 containers removing 67 corrections 33 68 cryopreservation 37 CTM 48 D database 11 derivative type 35 42 destroying a specimen 46 DIM 47 DMC 10 DMG 47 dot matrix labels 109 downloads 13 draw date 27 33 42 dra
17. AR 80 LDMS User Manual Contents RECEIVING SNIPMENTS se scscccvessecesesMascadessesd E n N E RANO 81 SHIPPING ANA PrOje Cts esecsecsessessecsecsessessesessesessessesscscescessssesessessesseseseesesesseseeees 82 IMPO aS Sereas er E sens dutnsedess A au davise vice nana 82 Handling non LDMS shipping FILES sesssssssseessesteseesssescesssseecesceecenceeseseesees 83 Shipment QA O Corsa sss scestson zi aa aan ee A a chtdbons dolce coacec dhe audawhclsta asda cuasthabeekdobeosdeces 83 Performing QA O Co ces iee renra a aa AERA a 84 Shipment MSTO ariran AAA Se Saleen dl Sede ead dee 85 REMOVING a received ShIpmMent s eessssseeesssssseesssssseeessssseeessssseeesssseseeesssssreessssseeess 86 UN SENCING shipments narini AAA AERA AEn 86 CETT a e 225 AAEN AEA AEE AE E A EE 87 Repos n a E a A oak ENA A 87 CUSTOM Report BULLAE essessessesscsscsscsscssessessessesesessesesscsussussucscescesceseeseesessesassesessesneees 87 EXAMPLE CUSTOM LE DOM sanserss de ccstorsteiestaseteccsedestacoetots EA ANRA 88 Modifying Or deleting a saved FEPOF ta essessecsecsccsccscesessessessessecsestestestestesteses 89 RUNNING A SAVEC report seise a 89 Creating a CUSEOM reportase aa 89 Generating a PEP OM Ecin ran NRA S el cel AERO 90 Available report format Saeni arata a Ea E E NA 92 ACMINiStratiVe reports oeann eA AAT A AR EAA 93 User permissions FEPOPT cesessessessesssssecsecsecsessessessessesecsessecseescessescescseessessesestestestenses 93 Exp
18. Add templates available to your laboratory Sorting Available filters Information on report Alphabetical by template name 1D2 protocol e Quick add template name Project e Type local or preset Quick Add Template Name byFrontier Science Quick Add template Type e list of enrollment and specimen data that will be populated by the template this will vary by template LDMS USRMANOO3 Page 98 LDMS User Manual Shipping reports Daily imported specimen log report Reports Shows a list of specimens for a project protocol combination that have been received from another laboratory in a shipping file Sorting This report is sorted by project protocol combination and then by specimen date Detailed imported specimen report Filter criteria ACTG protocol ACTG protocol type Clinic ID Condition Global specimen ID Import date Non ACTG PID ID1 Non ACTG Prot ID2 Project SID ID3 Sending lab ID Specimen date Specimen ID Visit unit Visit value Information displayed on report e Specimen ID e First global specimen ID e Second global specimen ID e Clinic e PID ID1 e SID ID3 e Visit e Specimen date e Import date e Sending laboratory e Specimen condition Shows specimens received through a shipping file from another laboratory sorted by shipment number Sorting This report is sorted by shipment number and then by specimen ID LDMS USRMANOO3 Filter criteria ACTG PID ACTG prot
19. Gel Inf OFP ONP PDT PE POR Pos POX PPt Prf Pri Pst Qul Rdw RRV RRV LDMS USRMANOO3 Description A Autopsy B Baseline Birth Cord Blood Post Study Confirmation Test Challenge Days Event Driven Visit Entry Baseline End of Study and redraw End Of Study End of Study and possible recent exposure Extension Phase Recent Exposure Exit Discontinuation Failure Confirmation Follow up Test On study without gel Infected Participant Testing D Labor and Delivery Months Off PrEP On PrEP Product Discontinuation Pre entry Post study and redraw Post Study Post study and possible recent exposure Post Partum Proficiency Pre Infusion Post Infusion Qualification Redraw Retrospective Retrospective Codes units and abbreviations Page 157 LDMS User Manual Release notes Code Description RWK R Week SC Seroconversion SCK Sick Scr Screening SD Study Day SP Sero Positive Sps Special Studies SRV Post Study Service Test UnK Unknown Uns Unscheduled Vst Visit Wk Weeks Yr Years Release notes LDMS release 08 Oct 2015 version 3 0 These are the enhancements made to LDMS release 08 Oct 2015 version 3 0 New features e R 17763 The ability to edit multiple specimens at once has been added to the Specimen Management page e R 22175 Added new Custom Report Builder feature to LDMS e R 22431 The website www webldms org now directs to a general website about LDMS rather th
20. LDMS USRMANOO3 Page 60 LDMS User Manual Storage Before you begin You must create the specimens on the Specimen Management page prior to adding them to a container You must also have created the container to which the specimens will be added Background Individuals specimens are stored in containers You cannot add specimens to a Level or storage unit without a container Procedure 1 2 LDMS USRMANOO3 Click Storage gt Stored specimens from the LDMS menu bar Find the storage container to which you want to add specimens in the storage tree Use the filters on the Left side of the screen to assist in finding the container From the Edit menu to the right of the container select Store specimens Figure 27 The Edit container menu Edit Store Specimens Set Condition Code Print labels Delete The Store Specimens window will open Optional Use any of the filters available to narrow down the specimens available for storage While this is not required if a filter is not applied all specimens that can be stored at your laboratory will be displayed In some cases this will be a lot of specimens From the Available specimens list select each specimen to store and then click Add at the bottom of the list I I Tip To select multiple specimens in a row hold down the Shift key to E select multiple specimens that are not together hold down the Ctrl key Specimens will be added to the conta
21. LHP LPE T LSE o NON PED T SCI B SED SFL SST amp THM Assigning storage locations Adding a new storage unit A storage unit is the largest type of storage item and is used to hold levels Background A new storage unit is created by defining various properties for it such as its size and temperature You can manually define these properties for the storage unit as you create it or you can use a template that applies default settings for you LDMS USRMANOO3 Page 55 LDMS User Manual Storage Procedure 1 Click Storage gt Stored Specimens from the LDMS menu bar 2 From the action menu select Add storage unit Figure 24 The LDMS action menu Add Storage Unit Move Storage Item s Print Move Report The Create storage unit window will open 3 Optional Select a template to use for the new storage unit from the From template box All settings from the template will be set for you You can override any settings from the template if needed Any changes made will only affect the new storage unit the template will not be modified 4 Optional Click the Empty Structure button to remove any levels that were automatically added by a template This is only necessary if you do not want to use the default Levels if present from a template All levels added by a template will be removed 5 Enter a descriptive name for the new storage unit in to Name box This is the name for the new storage unit as it
22. Optional Optional Optional Optional Optional Page 121 LDMS User Manual Field Required Preset projects Note Received Time ATN Optional The ATN preset project has these requirements Data entry requirements Field ID1 PID ID2 Protocol ID3 SID Visit OPID Clinic Specimen Time Received Time Notes Quick Add templates can be used for ATN BM Required Required Required Required Required Available Optional Required Optional Note A 6 digit number between 10001 and 999999 If the PID is less than 6 digits leading zeros will automatically be added LDMS will check that the PID is valid Must be a 3 digit number between 004 and 999 An 8 digit number between 40001 and 999999999 If the SID is less than 8 digits leading zeros will automatically be added 7 digit SIDs can still be imported by LDMS If the same PID protocol combination has been entered LDMS will automatically default to the previously used SID NOSID is a valid entry for ATN Select from pre defined List of visit units The BM preset project has these requirements LDMS USRMANOO3 Page 122 LDMS User Manual Preset projects Data entry requirements Field Required Note ID1 studyID Required Must be in the BM studyID format ID2 ID2 Optional ID3 ID3 Optional Visit Optional OPID Optional Clinic Optional Draw Time Optional Received Time Optional aS BM
23. RT PCR for Sequencing Extracted total nucleic acid Sub additive derivative codes This section lists the sub additive derivative codes available in LDMS LDMS USRMANOO3 Code 562 ADA AEB AFS APR ASC ATC ATG Atorvast 20H Atorvast 40H Atorvast LAC Description K562 Cell Line Adenosine Deaminase Qiagen AE Buffer Alsever s Freezing Solution Aprotinin Ascorbate Vit C Animal Tumor Cell Line TB Antigen 2 hydroxy Atorvastatin 4 hydroxy Atorvastatin Atorvastatin Lactone Page 150 LDMS User Manual LDMS USRMANOO3 Code Atorvast LAC20H Atorvast LAC40OH AUO AVE BCG BCL BFM BHT BML BMR BTM CAN CCM CD4 CD8 CDN CME CMV CON CSP CSC CUP CYT DCF DEA DMS DPH DPL DTM DTT EDT ETH FBS FMD FOR FPR FRS FUN GAG Codes units and abbreviations Description 2 hydroxy Atorvastatin Lactone 4 hydroxy Atorvastatin Lactone Auramine O en Buffer AVE Bacille Calmette Gu rin B cell Lymphoblastoid Cell Line Bacterial freezing media lated hydroxytoluene Breast Left Breast Right Biopsy Transfer Media Candida CASTA CareHPV Collection Medium CD4 cells CD8 cells cDNA Culture Media CytoMegaloVirus Control Cytospin Slides Cervical secretions CUP Cytokines 2 deoxycoformycin DEACTIVATED Dimethylsulfoxide DMSO used in cryopreservation solution CPS Wyeth Ayerst Diphtheria Antigen Depleted Cell Populations Digene Qiagen Specimen Transport Medium Di
24. Rectal Biopsy by Anoscopy Breast Areola Arterial Blood Draw Bronchoalveolar Lavage Hair Body Blood Whole Bone Marrow Aspirate Bone Marrow Core Biopsy Breast Milk Breast Milk Left Breast Milk Right Bronchoscopy Brush Brain Tissue Breast Tissue Buccal Cervix Cord Blood Cervical Secretion Cerebro Spinal Fluid Cervical Biopsy Aspirate Cervicovaginal Fluid Cervical Vaginal Lavage Cervical Culturette Codes units and abbreviations Page 141 LDMS User Manual LDMS USRMANOO3 Code CXS DIA DPL DTC DWB EBC END EPS EYE FHR FSC FSI FSK FSO FSR FST GAS GCF GLN GLU GMI HAR HRT HST INT INW IVR KID LBT LIV LPK LUE LUF LYM MEC MSB NAS NPH NPW NRH Description Cervical Swab Dialysate Dried Plasma Distal colon Dried Whole Blood Exhaled Breath Condensate Endometrium Expressed Prostatic Secretions Corneal Tissue Hair Facial Sigmoid Colon Biopsy by Flexible Sigmoidoscopy Penis Foreskin Inner Tissue Penis Foreskin Whole Tissue Penis Foreskin Outer Tissue Rectal Biopsy by Flexible Sigmoidoscopy Blood from Fingerstick Gastric Secretions Gingival Crevicular Fluid Glans Genital Lesion Ulcer Gastro Intestinal Mucosa Hair Heart Blood from Heelstick Intestinal Biopsy Aspirate Induction Waste Intra vaginal Ring Kidney Biopsy Lateral Border of the Tongue Liver Tissue Leukopak Lung Excised Lung Filter Paper Lymph Node Biopsy Aspirate Meconium Main Ste
25. Required ID number for the laboratory sending the shipping file Receiving Lab Required ID number for the laboratory receiving the shipping file Setup Date Optional Date shipping file was created Ship Date Optional Date specimens were shipped Temperature Optional Temperature of the shipment Shipment Comment Optional Notes about the shipment Container Optional Name of container holding specimen Row Optional Position of specimen in container Column Optional Position of specimen in container QA Performed Optional Whether shipping file was compared to the actual shipment to ensure specimens were correct and included in the correct container locations Project Required Name of project for which the specimen was collected LDMS USRMANOO3 Page 78 LDMS User Manua Shipping container report LDMS USRMANOO3 l Column ID1 ID2 ID3 Visit Visit Unit Clinic Specimen Date Specimen Time Received Date Received Time Specimen ID Global Spec ID Other Spec ID Primary Additive Derivative Sub A D Volume Volume Units Condition Comments Tests Required Required Required Required Required Required Required Required Required Optional Optional Optional Optional Required Required Required Optional Required Required Optional Optional Optional Notes Shipping Participant or specimen source ID Protocol ID Sub protocol ID Value for visi
26. Specimen conditions on page 45 A specimen condition is a 3 letter code that indicates the status of a specimen Shipping Shipping The Shipping page in LDMS is where you create shipping data files and receive shipping data files from other laboratories The shipping page is organized into three sections Pending shipments This page is where you create new data shipments view and modify shipments that have been created but not yet sent and generate shipping files Receive shipments This page is where you will import shipping data files Shipment history This page shows a record of all shipping files created and received for your laboratory Shipments that are still pending will not be shown LDMS shipping file compatibility LDMS for the web shipping files are compatible with certain version of LDMS for Windows The format of the shipping files used by LDMS for the web is an encrypted XML data file LDMS for Windows support will vary based on the version of LDMS for Windows LDMS for Windows Can ship and receive shipping files with laboratories using version 10 0 or LDMS for the web without restriction higher LDMS for Windows Can ship specimens to but not receive specimens from LDMS for version 9 x the web LDMS for Windows No shipping compatibility with LDMS for the web version 8 x or earlier Related sections Specimen identifiers in LDMS for Windows on page 30 LDMS for Windows handles specimen identifiers in a few way
27. are marked with a large X indicate locations in the container that are empty Figure 34 The Shipping Container Report Proiect Prot Imported Shipping Container Report Batch Number 126 Legend Sidal Specimen m Aadi Sending Lab Batch Number 43 301 Shipping Box 0 Box Size 4X5 Sorted by Prot ID2 Specimen ID ELD Batch storage report This report lists the specimens in a shipment and their assigned storage location This report is intended to be printed and be used to help locate and pull specimens from storage This would only be applicable if you assigned a storage location to the specimens being shipped on the Storage page The shipping container report can be found on either the Pending Shipments or Shipment History page To the right of the shipment click the down arrow next to the button and click Shipping Container Report If you are sending the shipment the Batch Storage Report must be created before you generate a shipping file One the shipping file has been created the report will no longer be available This is because specimens are removed from their assigned storage location and their availability changed to unavailable during shipping file creation Once this happens LDMS will not know where the specimens were located Information displayed on report e Shipment number LDMS USRMANOO3 Page 80 LDMS User Manual Shipping Shipment setup date Specimen ID Global specimen ID Other specimen ID Pr
28. asked if they want to update the aliquots as well LDMS USRMANOO3 Page 40 LDMS User Manual Specimen Management e Frozen date e Frozen time e Comments e Internal comments e Tech initials If a comment is cascaded from a primary to an aliquot it will be added to any existing comment the aliquot already has Related sections Primary specimens on page 29 A primary specimen is a specimen that was collected from a participant during a visit Aliquot specimens on page 35 An aliquot is a specimen that is derived from a primary specimen Specimen availability Availability refers to whether or not a specimen exists at a laboratory A specimen s physical availability may change for a variety of reasons For example if a primary specimen was processed into aliquots the primary specimen no longer exists and is thus not available Likewise if an aliquot s tube was damaged and its contents could not be recovered it is also not available If a specimen is available it can be added to a shipment and it can be assigned a storage location If it is not available LDMS will prevent you from shipping or storing the specimen B Note In LDMS for Windows availability is called never store Availability is a property of both primary specimens and aliquot specimens By default new specimens are available until you change them to unavailable or a specific condition automatically changes them There are several times where LDMS wi
29. click Add New c In the row that appeared enter the information for the aliquot specimen to be created 7 Atthe bottom of the page click Save Template Modifying or deleting a quick add template Quick add templates can be changed or deleted without affecting specimens added using the template Background When a template is modified the changes will be reflected when new visits are created using the template existing entries will not be changed If a template is deleted it will be permanently removed however any entries made using the template will remain Procedure 1 From the LDMS menu bar click Specimen Management gt Quick Add Templates 2 Inthe Saved Templates box select the template to be modified or deleted 3 Doone of the following e Make any changes to the template and then click Save Template at the bottom of the page e At the bottom of the page click Delete Template Differences between primaries and aliquots This section describes the differences between how LDMS treats primaries and aliquots Table 1 Primary and aliquot comparison Primary Aliquot Global Specimen ID Ends in 00 Ends in 01 02 etc Processing date Entered by user Uses value from primary Enrollment Can be associated with more Must select exactly one than one visit or protocol associated enrollment Certain information can be cascaded from primaries to derived aliquots specimens so that if the primary is updated users will be
30. containers in the new level should be identified a Select either Row CoLumn or CoLumn Row from the Coordinate order box If Row Column is selected each level or container position will be identified in the format row column b Select how columns and rows are to be labeled from the Column labeling and Row labeling boxes To use letters to identify rows or columns select Alphabetic to use numbers select numeric Select the fill order for the new Level from the Fill order box Fill order can be used when adding a new level or container to the level While you must specify a fill order you can override it when adding items to the level Optional Select a position s in the level to be excluded from the Excluded positions box Excluded positions are used to help identify the orientation of the container meaning which side is the front and which is the back Review the Preview of the new storage item Click the Continue button The Select position window will open Specify the position within the storage unit for the new Level by doing one of the following e Select a position for the new level from the Position box e Click ona position in the Preview section Positions that cannot be selected are either already occupied by another Level or empty by exclusion rules for the storage unit Gray positions are occupied black positions are excluded Click the Save button Related sections The storage tree on page 51 Th
31. file generate by WebLDMS that contains data for specimens being shipped to another laboratory Also known as shipping data file sort order How specimens are sorted before they are put into a shipping container specimen ID An identifier that was assigned to primary specimens and aliquot specimens by LDMS and other laboratory data systems WebLDMS using global specimen ID instead specimen record A collection of information for a specific derived specimen produced from a collected specimen for a particular participant visit storage container The storage item in the WebLDMS storage system that contains specimens such as a box Also known as box storage level An intermediary item in the WebLDMS storage system such as a shelf within a freezer or a rack on a shelf Also known as level storage unit The highest level in the WebLDMS storage system such as a freezer Also known as freezer stored Whether or not a specimen has been assigned a storage location in WebLDMS sub level On the Storage page a storage level that is within another storage level LDMS USRMANOO3 Page 172 LDMS User Manual Terms storage template A storage item such as a container that is set up in WebLDMS in advance so that it can be used as the basis of creating new storage items thaw count The number of times that a specimen has been removed from cold storage visit An event at which a specimen is collected from a patient comprised of a visit unit and
32. fill order using the automatic positioning feature is optional Optional Select a position s in the container to be excluded from the Excluded positions box d D Excluded positions are used to help identify the orientation of the container meaning which side is the front and which is the back Click the Continue button The Select position window will open Enter a descriptive name for the first container into the Name box This is the label for the new container as it will appear in the storage tree Specify the position for the new container on its parent level by doing one of the following e Select a position for the new container from the Position box e Click ona position in the Preview section Positions that cannot be selected are either already occupied by another container or empty by exclusion rules for the parent level Gray positions are occupied black positions are excluded Click the Continue button You will need to specify the Name and position for each new container that you are creating Results The new containers will be created in the positions specified Related sections The storage tree on page 51 The storage system in LDMS is a hierarchy of storage items Storage templates on page 63 Templates allow you to add commonly used storage items quickly by defining them in advance Assigning a storage location to specimens Individual specimens are added to containers on the Storage page
33. has no rules or validation and can be manually assigned by a laboratory patient The source of a specimen in WebLDMS typically a person enrolled in a study Also known as participant source preset project A project in LDMS that cannot be modified by users and has requirements and rules that are built into LDMS primary specimen The raw specimen that is collected from a patient during a visit the specimen from which aliquots are created Also known as primary primary type The kind of primary specimen that was collected from a patient such as blood represented in WebLDMS as a 3 letter code LDMS USRMANOO3 Page 171 LDMS User Manual Terms processing date The date that a primary specimen was processed into aliquot specimens project The larger clinical trial government group or research organization in which a participant is enrolled reason specimen not collected The reason that an expected primary specimen was not collected from a patient during a visit received date The date that a primary specimen was received by a laboratory from the collection site where the visit occurred response code A password provide to you from LDMS User Support to access a feature that is restricted with a challenge code Also known as challenge code challenge password shipped A status for a specimen that was once considered at your laboratory but has since been added to a shipping file and sent to another laboratory shipping file A data
34. is configured by default to save file downloads to a default location without asking you where to save them There are many times that LDMS will provide a file for you to download such as a shipping file Since you need to know where the file is on your computer in order to provide it to another laboratory it is helpful to understand how your web browser handles file downloads How to view and modify your browser s behavior for downloading files or opening files automatically will vary by browser and version For instructions consult the help documentation for your web browser The LDMS user interface The LDMS user interface has many common elements across different pages Figure 1 The main LDMS user interface m admin Lab 500 Training DB change Logout EDT UTC 04 00 Specimen Management Storage Shipping Reports Labels Administration Help Specimen Management m me Participant 1 of 23 gt aiaa Project FRONTIER Edit Participant Y Applied 1 filter 7 PID 123456 Participant Filters O 4 OPIDs Project Study METABOLIC Edit Study gt FRONTIER X O D1 Visits Visit Collection Date 1D3 Clinic Action 0 Ser 17 May 2013 9910 Euit El OPID Primary Global Specimen ID Status Collection Primary Additive Specime Action Specimens Time Type Type Condition Enrollment Fitters HEQO067G 00 07 45 BLD HEP SAT Eat gt ID2 4 v Aliquots Global Specimen ID Status Derivative SubAdd Specime Action Visit F
35. is enrolled likely has defined specimen collections for this visit The available visit units are defined by various projects that use LDMS Users cannot create their own visit units Related sections LDMS abbreviated codes report on page 97 Provides a list of LDMS unit visit time specimen condition codes used in LDMS and their meaning Adding a visit to an enrollment Visits are added to an enrollment on the Specimen Management page Background A visit must be created before you can enter specimen information in LDMS I I Tip If you want to create a new visit for a specimen that already exists you should co enroll the primary specimen instead of adding a new visit to the enrollment During the co enrollment process you will have the opportunity to create a new visit Procedure 1 Click Specimen Management from the LDMS menu bar 2 Find the participant to which a visit will be added Use filters from the left side of the page to find the participant 3 Select the ID2 from the list The label for the ID2 box will depend on the project Common labels are study and protocol LDMS USRMANOO3 Page 27 LDMS User Manual 9 Specimen Management Click the down arrow next to the Edit ID2 button and then click Add Visit Figure 10 The Edit Study menu lt m Participant 250 of 250 gt Project FRONTIER Edit Participant l PID 01111110 OPIDs Study Edit Stu
36. issue where units and their associated help tooltip could not be displayed correctly if the unit contained a special character R 20534 Fixed issue where clicking a specific button on the Labels page caused other information entered on the screen to reset R 20569 Fixed message that appears when attempting to assign an item to an excluded storage or shipping container position so that it displays the correct number R 20659 Fixed issue where co enrolled specimens could not be assigned different clinics R 20667 Fixed issue where if the user modified a specimen s draw date on the Edit Primary page it would not automatically be refreshed on the Specimen Management page R 20866 Fixed issue where certain fields were shown in the interface as required when creating a new shipment however the fields are not actually required until the shipment is sent not when saving a pending shipment R 21300 Fixed issue where if a primary specimen is shipped to another laboratory and then shipped back to the original laboratory any new aliquot specimens added to it would be erroneously assigned a global specimen ID that does not match the parent R 21305 Fixed issue with the Storage Detail Report where the label for the visit column was not being displayed correctly Page 165 LDMS User Manual Release notes R 21562 Fixed inconsistencies with how specimens were being sorted on shipments when there was a mix of specimens using LDMS for Windows and L
37. menu bar click Specimen Management Using filters on the left locate the specimen to be destroyed To the right of the specimen click Edit Change Specimen Condition to DSR If the specimen has been assigned a storage location Write down the storage location of the specimen if it has not already been physically removed ie eS Warning The specimen will automatically be un assigned from its storage location in LDMS This is your last chance to get the specimen s storage location 6 Inthe Comments box enter an explanation of why the specimen was destroyed What to do next If you have not already done so use the storage location that was noted by LDMS to find the specimen and physically remove it from storage The specimen was automatically removed from storage in LDMS Procedural conditions These specimen condition codes describe issues that can occur in the collection and processing environment Table 3 Procedural conditions Code Description Usage ANP Aliquot Not Prepared Indicate that an expected aliquot was not processed but no other more specific condition code applies The reason specimen not collected box should be used in conjunction with ANP EQF Equipment Failure There was an issue with the processing equipment such as a power failure during processing INV Invalid The specimen is not valid for testing purposes Generally another condition code such as LBE or PST would be more appropriate LDMS
38. of aliquot specimen created The project ID2 combination associated with an aliquot The date the specimen was frozen The time the specimen was frozen A unique identifier for the specimen A sub protocol or study Additional details about the specimen Indicates if the specimen is available The enrollment that owns a primary specimen A laboratory defined identifier The type of primary specimen Example PL2 Project ID2 04 Jun 2014 15 00 500 AEQ0052R 01 A502505621 Project ID2 BLD Specimen Management Notes Selected from a pre defined List of codified values Hover the mouse pointer over a type for a more detailed description The enrollment is in the format project ID2 This is generally used to indicate the date the freezing process began This is generally used to indicate the time the freezing process began This will be unique for the specimen LDMS will never generate the same global specimen ID even at two different laboratories Global specimen IDs for primaries always end in 00 global specimen IDs for aliquots will have the same ID as their parent primary but end in 01 02 and so forth Specimens added in LDMS will have the originating laboratory s ID number as the first 3 digits Global specimen IDs generated by LDMS will lack this feature Used by some projects to further identify the protocol This is typically se
39. received date b Select the logic for how the filter should be applied from the middle box EB Note The operator lt gt means not equal to c Select the filter value from the third box d Click the Add button LDMS USRMANOO3 Page 111 LDMS User Manual Labels The filter will appear at the bottom of the page To remove a filter click the Delete button to its right 5 Optional If you want to skip some labels enter a number into the Skip box This will skip the number of spaces specified which is useful if you need to print labels on a partial sheet For example if you have sheet where you already used the first 3 labels you can skip them so that printing begins on the 4th label 6 Click the Generate button Results You will be prompted to save a PDF file that contains the labels or it may open automatically depending on the default behavior of your web browser B Note Specimens that are not available will not have labels generated Related sections Printing labels anywhere on page 109 Specimen labels can be printed in many places in LDMS not just the Labels page Defining new label formats You can create new label formats Procedure 1 Optional Select a Project and Format that you want to use as the basis for your new label If you chose a Project and Format you can copy all of the information from this label to your new label to use as a Starting point 2 Click the Create Format button The
40. shipment number and then by ACTG Protocol Type global specimen ID Additive Clinic ID Condition Derivative Destination Lab NON ACTG PID ID1 NON ACTG PROT ID2 Other Spec ID Primary Project Shipment Date Shipment Number Shipping Temp Spec Date Spec ID Specimen Time Sub Add Der Visit Unit Visit Value Volume Volume Unit Shipped specimen report summary report Information displayed on report e Shipment batch number e Shipment date e Laboratory shipped to e Clinic e Specimen ID e Other specimen ID e Project prot e Global specimen ID e PID ID1 e VID e Specimen Date e Specimen time e Primary e Additive e Derivative e Sub additive derivative e Volume e Condition Shows the number of specimens of a specific derivative type on a shipment that was sent LDMS USRMANOO3 Page 100 LDMS User Manual Sorting This report is sorted by shipment number and then grouped by derivative Filter criteria ACTG protocol ACTG protocol type Clinic ID Derivative Destination laboratory Non ACTG prot ID2 Project Reports Information displayed on report e Batch number e Ship date e Destination e Project protocol e Derivative e Number of specimens shipped Shipment date Shipment number Shipping temperature Shipping laboratory contact report Shows contact information for a given laboratory Sorting Filter criteria Information displayed on report This report is sorte
41. storage item 3 Click the down arrow next to the Edit button to the right of the intended parent storage unit or level and then click Add new level Figure 25 The Edit Storage Unit button Edit Add New Level Set Condition Code Print labels Delete The Select position for new level window will open LDMS USRMANOO3 Page 57 LDMS User Manual 10 11 12 13 14 Storage Optional Select a template to use for the new Level from the From template box All settings from the template will be set for you You can override any settings from the template if needed Any changes made will only affect the new level the template will not be modified Enter a descriptive name for the new level in to Name box This is the name for the new level as it will appear in the storage tree in LDMS Enter the number of rows and columns for the new Level into the Number of rows and Number of columns boxes This represents the size and capacity of the new level in terms of the number of levels or containers that it can hold For example if you are creating a shelf that can hold 5 boxes side by side you might have 5 columns and 1 rows Select or deselect the Positions only option as desired If the positions only option is selected each item in the new level will be identified by a number If it is not selected each level will be identified by its coordinates If Positions only is not selected Define how levels or
42. template button Deleting a template makes it unavailable to be used for new storage items Existing storage items that were based on the template will not be affected 4 Click the Save template button Results The template will modified and any new storage items based on it will reflect the changes Existing storage items that were based on the template will not be modified Moving items in storage Storage items can be moved to a different location or rearranged in their current location Background Any storage item can be moved to another location in LDMS Moving a storage item will require you to specify its position in its new location If you move a storage item from its current location to its current location you will be given the opportunity to rearrange its contents LDMS USRMANOO3 Page 65 LDMS User Manual Storage Procedure 1 Click Storage gt Stored specimens from the LDMS menu bar 2 Click Move storage item s from the action menu The Move storage items window will open 3 Select the storage items to be moved The storage items selected must be moved to the same destination You cannot move two storage items at once that cannot occupy the same location For example you cannot select to move a specimen and a level at the same time Click the Next button Locate the storage location that will be the destination Click the Select button to the right of the destination The Select Positions window will open
43. time Sub add der System entry date Test ordered Time Time unit Visit unit Visit value Volume Volume unit aliquots in a laboratory s database LDMS USRMANOO3 Sorting This report is sorted by project protocol combination then by draw date and then grouped by primary Filter criteria ACTG PID ID1 ACTG protocol ACTG protocol type Additive Derivative Global specimen ID Import date Non ACTG PID ID1 Non ACTG Prot ID2 Other specimen ID Primary Project Received date SID ID3 Specimen date Specimen ID Visit unit Visit value Reports Information displayed on report e Received date e Primary volume e Time time unit e Other specimen ID e Comments for primary specimen e Aliquot specimen ID e Global specimen ID e Other specimen ID e Primary additive e Derivative Sub additive derivative e Current volume e Condition e Group prot e Test s ordered e Shipped e Comments Provides processing information processing date frozen date etc for primaries and Information displayed on report e PID ID1 e Project Prot e SID ID3 e VID e Clinic e OPID e Primary specimen ID e Global specimen ID e Other specimen ID e Primary e Additive e Volume e Specimen date e Specimen time e Received date e Received time e Total cell count e Proc essing date e Proc essing time e Proc essed by e Aliquot specimen ID e Global specimen ID e Other specimen I
44. units Level templates This is where you can define templates for commonly used storage levels Container templates This is where you can define templates for commonly used storage containers Navigation on the Storage page The Storage page shows a representation of your real life storage as a collapsible tree LDMS USRMANOO3 Page 50 LDMS User Manua The storage tr LDMS USRMANOO3 l Storage This tree is called the storage tree view and shows all of the items in storage as you have defined them in LDMS Figure 19 The Storage page Em M icon roin E F 7 E 80 FREEZER Edit v g ABC FREEZER Edit 01 SxS level Edit v o2 55 level Edit o3 J 55 level Edit v mE C04 5x6 eel gy Edit v 01 BOXKI Edit 1 1 0777 001MWK00 209 OE Gpeeimans Set Condition Code 1 2 0777 001MWK00 210 Print labels C2 3 0777 001MWK00 211 Aa i 4 0777 001MWK00 212 ferfe Sas fm CHEST Edit m i e of 11 Page 1 72 P m 1 Navigate between pages if your storage page does not fit on one 2 The storage tree view 3 Edit menu for storage item named BOX 1 4 The location of the specimen in BOX 1 The storage units in the storage tree are sorted alphabetically by name The contents within storage units are sorted by position Click on the button to the left of a storage item to open it The contents in the square bracket
45. wasn t intended In addition when you apply a template any information that you already entered on the Quick Add screen will be cleared This means that the template must be applied first before you enter any other information Creating quick add templates Create quick add templates by defining the information for the visit Procedure 1 From the LDMS menu bar click Specimen Management gt Quick Add Templates 2 Complete the Template Information section The Name is the name of your template as it will appear when selecting it when using the quick add feature The Comments is a brief description of the template that will appear when the template is selected and can be used to provide the person entering data if additional information or instructions such as a reminder to remove an optional specimen if it was not collected 3 Inthe Participant Information section select a Project Optional In the Enrollment Information section select an ID2 to be applied LDMS USRMANOO3 Page 39 LDMS User Manual Specimen Management 5 Optional Add a primary specimen a In the Primary Information section click Add New b In the row that appeared enter the information for the primary specimen to be created c Optional To view and modify all of the information for the primary click Edit in the right column 6 Optional Add an aliquot specimen a Highlight the primary specimen for the aliquot b In the Aliquot Information section
46. will appear in the storage tree in LDMS 6 Select the type of storage unit from the Type box 7 Select the temperature of the new storage unit from the Temperature box 8 Enter the number of rows and columns for the new storage unit into the Number of rows and Number of columns boxes This represents the size and capacity of the new storage unit in terms of the number of levels that it can hold For example if you are creating a freezer that can hold 5 shelves vertically you might have 1 column and 5 rows 9 Select or deselect the Positions only option as desired If the positions only option is selected each item in the level in the new storage unit will be identified by a number If it is not selected each level will be identified by its coordinates 10 If Positions only is not selected Define how levels in the new unit should be LDMS USRMANOO3 identified a Select either Row CoLumn or CoLumn Row from the Coordinate order box If Row Column is selected each level s position will be identified in the format row column b Select how columns and rows are to be labeled from the Column labeling and Row labeling boxes To use letters to identify rows or columns select Alphabetic to use numbers select numeric c Select the fill order for the new unit from the Fill order box Page 56 LDMS User Manual Storage Fill order can be used when adding a new level to the unit While you must specify a fill order you can ove
47. you will need to transfer to the laboratory that will be receiving the specimens You can either email this file to the receiving laboratory or provide it on removable media such as a USB drive with the physical shipment of specimens Related sections Un sending shipments on page 86 After a shipping file has been generated and a shipment changed to sent in LDMS it is possible to change the shipment back to a pending state Generating a shipping manifest Shipping manifests contain an overview of the contents of a shipment and are intended to be printed and included with shipments Background A shipping manifest should be printed and included with all shipments This will help the laboratory receiving the shipment to identify its contents and match it to the shipping file that you provided to them You can also save the manifest as a PDF file and then send it to the receiving laboratory long with the shipping file LDMS USRMANOO3 Page 76 LDMS User Manual Shipping The shipping manifest can be generated before or after a shipment is sent Figure 33 A typical shipping manifest Shipping Manifest Batch Number 119 QA QC Not Performed Setup Date 08 Sep 2015 Shipped No Ship Date 08 Sep 2015 Shipped From Shipped To Lab ID 500 Lab ID 300 Lab Name Frontier Laboratories Lab Name University 4033 Maple Road Pathology Bldg Room 31 600 University St Amherst NY 14226 Baltimore Country Country United States C
48. 210 When receiving a shipping file LDMS will now show a preview of the shipment s contents R 17264 When a shipping file is received that contains storage items LDMS can now add those storage items as is to a storage unit at the receiving laboratory R 18229 Added support for cross LIMS shipping files R 18230 Added support for shipment QA QC a feature that allows users to verify that the specimens that are included in a shipping file match the physical specimens in the real world shipment R 18231 After a shipping file has been generated and all of the specimens changed to sent a shipment can now be un sent returning it and its specimens back to their previous state R 18232 After a shipping file has been received and loaded by a laboratory it can now be un received removing all of the specimens from the shipment from the laboratory R 18443 It is now possible to specify logic for selecting data when generating reports on the Reports page R 20049 It is now possible to generate a report showing where specimens have moved in storage R 20162 Added support for numerous preset projects Requirements and validations for these projects are determine by individual projects working with Frontier Science R 20200 Added support for the SeraCare shipping file format for sending shipments only R 20391 Added the ability to enter cryopreservation information for specimens Page 162 LDMS User Manual Release notes Improvements LDMS U
49. 3 Optional Visit Optional OPID Optional Clinic Optional Draw Time Optional Received Time Optional WIHS Preset projects The WIHS preset project has these requirements Data entry requirements Field Required ID1 PID Required ID2 Protocol Required ID3 SID Optional Visit Required OPID Optional Clinic Optional Specimen Time Optional Received Time Optional WIHS PID format Note Must meet WIHS PID format requirements Select from pre populated List The visit unit will default to VST and the visit number will be automatically populated based on an algorithm that uses the current date Site_Number Recruitment_Number Participant_Number Check_Digit Site_Number LDMS USRMANOO3 NYC Bronx Brooklyn Page 138 LDMS User Manual Recruitment_Number Check_Digit Notes 2B OB 1B Preset projects Washington D C Los Angeles San Francisco Chicago New recruit Original recruit Original recruit Any character an algorithm will determine if the character is valid based on the read of the PID e The SeraCare shipping file formatshould be used when shipping specimen to the MACS repository e Quick Add templates are permitted for WIHS and users are expected to create and use template for WIHS data entry e Draw Date and Received Date will automatically be set to your local date WITS The WITS preset project has these requirements Data entry requirements F
50. A saved custom report can be modified and re saved or deleted Procedure 1 From the menu bar click Reports gt Custom Report Builder 2 In the Saved Queries box select the report you want to run 3 Do one of the following e To remove the saved report click the Delete button e To modify the report make changes to its fields sort order or selection criteria and then click Save e To modify the report and save it as a new report enter a new name into the Saved Queries box and then click Save Running a saved report Saved custom report can be run at any time Procedure 1 From the menu bar click Reports gt Custom Report Builder 2 In the Saved Queries box select the report you want to run 3 Optional Make any changes needed to the report s fields sort order or selection criteria Changes will not be permanently saved unless you click Save at the top of the page 4 Do one of the following e To view the first 100 records of the report in your browser click Preview e To generate and save the report in the indicated file type click Generate Report Creating a custom report Custom reports are created by indicating the information that should appear on the report how the report should be sorted and any special logic for selecting specimens Procedure 1 From the menu bar click Reports gt Custom Report Builder 2 In the All Fields section do the following e For items that you want to appea
51. Create Format window will open If you selected a label format to use as the basis for your new format you will see the name of that label in the Source format box If you did not select a base label then the Source format will not appear 3 Enter a name for your new label format into the Name box Optional If you want to copy the fields from the source format select the Copy Fields box 5 Click the Create Format button Results Your new label format will be created and will be available for selection What to do next You will want to customize your new label format and define the information that will appear on it LDMS USRMANOO3 Page 112 LDMS User Manual Labels Related sections Terms used in LDMS on page 16 Specimen records are stored as a hierarchy of related participant enrollment and information All of this information for a participant project combination comprise a record in LDMS Customizing label formats You can customize that information that appears on label formats created by your laboratory Background New label formats are blank when they are created You must customize the format to show the information that you want displayed New labels and existing labels are modified the same way Only label formats that your laboratory created can be modified Label formats that are pre defined in LDMS cannot be changed Figure 43 The label modification page Name FRONTIER Barcode LDMS Standard Fields
52. D e Derivative e Sub additive derivative e Volume e Group prot Page 103 LDMS User Manual Reports Sorting Filter criteria Information displayed on report e Frozen date e Frozen time e Proc essing date e Proc essing time e Proc essing by Specimens for a given group report Shows the aliquots for a given project protocol combination then by specimen ID Additive Clinic ID Derivative Import date Non ACTG PID ID1 Non ACTG prot ID2 OPID Other specimen ID Primary Project Received date SID ID3 Specimen date Specimen ID Specimen time Sub additive derivative Visit unit Visit value Sorting Filter criteria Information displayed on report This report is grouped by ACTG PID e Protocol and project project protocol combination ACTG protocol e PID ID1 and then sorted by ID1 and ACTG protocol type e OPID Specimen ID Global specimen ID Specimen date Specimen time Primary Additive Derivative Sub additive derivative Received date Received time Import date VID visit value and unit Other specimen ID Specimens for a given group 2 Shows the aliquots for a given project protocol combination in aggregate form with the number of aliquots with a given specimen ID LDMS USRMANOO3 Derivative Import date Non ACTG PID ID1 Non ACTG prot ID2 OPID Other specimen ID Primary Project Sorting Filter criteria Information displayed on report This report is grouped by e ACTG P
53. D2 Protocol ID3 Visit OPID Clinic Specimen Time Received Time Notes e Throughout LDMS HVTN is listed as VTN Required Required Required Disabled Required Disabled Required Optional but required by VTN Required Note LDMS checks that the PID is valid A PID cannot be changed without approval from VTN Laboratory Leadership LDMS checks that the PID and protocol combination are valid Use VST for routine HIV diagnostic visits otherwise use the appropriate visit unit This visit unit is used by certain laboratories for driving testing algorithms The clinic is automatically populated based on the PID the same clinical location can be associated with multiple clinic IDs e g for Phase I II or Phase II III VTN clinics start with the letter V such as V101 instead of 101 LDMS will verify that a VTN clinic was selected While completion of this field is optional in LDMS VTN requires laboratories to complete it e The volume for VTN specimens will default to ML e Within VTN LDMS Shipping files are sometimes called e manifests e Barcodes must be printed on labels for VTN specimens e Quick Add templates are not permitted for VTN specimens WHIN The WHIN preset project must meet these requirements LDMS USRMANOO3 Page 137 LDMS User Manual Data entry requirements Field Required ID1 ParticipantID Required ID2 Protocol Optional ID3 ID
54. DMS format global specimen IDs R 21564 Fixed issue where a specimen with the same global specimen ID could be received in a shipping file even if it was already in a laboratory s database R 21578 Added labels to some date and time boxes on the new specimen screens that did not have labels R 21593 Fixed issue where modifying the draw date for a specimen on the Quick Add screen did not update the specimen s received date as expected R 21623 Fixed issue where the Specimens Not In Storage report did not show the full global specimen ID if it was in the LDMS format R 21852 Fixed an issue where an error would prevent updating an existing visit using the Quick Add feature R 19579 Fixed formatting of date time fields on the Aliquot Edit page R 19803 Fixed Z order of LDMS s menu bar R 19973 Fixed alignment of fields on the Change Password page R 20159 Fixed security vulnerability where users with a temporary password were not subject to the lock out rules for successive sign in failures LDMS release 19 Mar 2015 version 1 1 These are the enhancements made to LDMS release 19 Mar 2015 version 1 1 New features R 17271 A shipping file can now be re generated R 20201 New quick add feature This allows users to quickly add specimens visits and even new participants on a single screen Templates for common visits and draws can be used to automatically fill in some information R 20303 Specimen labels can now be generated in ma
55. ERON TB Gold Assay QFT Mitogen Purple Cap QTF Nil Grey Cap Royal blue EDTA Royal blue no anticoagulant Ringer s Lactate Solution RNALater RNAprotect Roche Media RPMI 1640 Medium Steck Cyto Chex tubes stabilized Sodium Citrate Sodium EDTA Codes units and abbreviations Page 145 LDMS User Manua l Code SFL Description Codes units and abbreviations Sodium Fluoride SKM SNP SPH SPO SPS SST STG TBD TBS TEM TFM THM TMS UNK VTM Derivative codes LDMS USRMANOO3 This section lists the derivative codes available in LDMS Code AD4 ADL AG1 AG2 AMN APL ASP BAL BCL BHR BLD BLK BMA BMC BMK BML BMR BMS BMW BPS Skim Milk Snap Flash Frozen Sucrose Phosphate Sodium Fluoride Potassium Oxalate Sodium Polyanetholesulfonate Serum Separator Skim milk Tryptone Glucose Glycerin Medium STGG Specimen type to be defined Tris buffered saline Tempus Tube Tissue Freezing Medium Thrombin Transport Medium Stuarts Unknown Additive Viral Transport Media Description Activated CD4 Adipose Tissue Layer ESAT 6 free cocktail 1 ESAT 6 free Cherry pick Amniotic Fluid Applicator Tip Aspirate Bronchoalveolar Lavage B cell Lymphoblastoid Cell Line Hair Body Blood Whole Tissue Block Bone Marrow Aspirate Bone Marrow Core Biopsy Breast Milk Breast Milk Left Breast Milk Right Breast Milk Spun Breast Milk Whole Biopsy Page 146 LDMS User Manual
56. For LDMS USRMANOO3 Page 53 LDMS User Manual Storage example if you know that the upper right corner of a container will be empty you know where to start inserting specimens Figure 23 Configuring a storage item layout Positions Only Coordinate Order Row Column Column Labeling Alphabetic Left to Right Row Labeling Alphabetic Top to Bottom Fill Order Leftto Right Top to Bottom Reset Excluded Positions Corners Upper Left Preview X The preview shows how these settings will be interpreted by LDMS A A black is an excluded position A B to C A gray contain another storage item or specimen C B to E B tan are empty positions All of these properties of storage items can be configured when adding new items to the storage tree They can also be defined in advance by using a storage template Icons and their meaning The icons next to the items in the storage tree indicate the type of storage item and special properties such as its additive or whether the item is part of a pending shipment Table 10 Storage item icons Icon Meaning O Storage unit w Co Level C Sub level an v7 Container a Specimen Specimen be that is part of a pending shipment Table 11 Additives with colored tubes on the storage page Any additive not listed in this table uses a black icon LDMS USRMANOO3 Page 54 LDMS User Manual Storage Additive Icon ACD C AHP DPE T DSE EDT D HEP e LHG T
57. ID 5000V13000001 Specimen ID 5000V13000001 Global Specimen ID HEQ00676 01 Global Specimen ID HEQ00676 01 WebLDMS Shipped LDMS for Windows Shipped WebLDMS Specimen ID None Specimen ID 5000V13000001 Specimen ID 5000V13000001 Global Specimen ID 0500 HEQ00676 001 Global Specimen ID 0500 HEQ00676 001 Global Specimen ID 0500 HEQ00676 001 This image shows how specimen IDs and global specimen IDs are affected as specimens are shipped between LDMS and LDMS for Windows The global specimen ID of a primary specimen can be different LDMS for Windows does not permit the shipping or storage of primary specimens these are features that are exclusive to LDMS In LDMS for Windows users would generally create aliquots commonly called ghost aliquots that were identical to the primary specimen the aliquot which was really just the primary could then be shipped and stored When a primary specimen is shipped to LDMS for Windows an aliquot will automatically be created This aliquot will have the global specimen ID of the primary specimen and the primary specimen ID will have no global specimen ID Figure 14 Primary specimens shipped to LDMS for Windows WebLDMS LDMS for Windows Primary Primary Specimen ID None Shipped Specimen ID 5000V13000001 Global Specimen ID 0500 HEQ00676 000 Global Specimen ID None Aliquot p Aliquot None Specimen ID 5000V13000001 Global Specimen ID 0500 HEQ00676 000 Th
58. ID e Protocol and project project protocol combination e ACTG protocol e PID ID1 then grouped by Specimen ID acteG protocol type e OPID and then sorted by ID1 and e Additive Specimen ID then by specimen ID on e Clinic ID e Count Specimen date Specimen time SID ID3 Primary Additive Derivative Sub additive derivative Received date Page 104 LDMS User Manual Reports Sorting Filter criteria Information displayed on report Received date e Received time SID ID3 e Import date Specimen date e VID visit value and unit Specimen ID e Other specimen ID Specimen time Sub additive derivative Visit unit Visit value Time to freeze QA QC summary report Shows the time to freeze for aliquots along with a graph and summary of overall time to freeze Sorting Filter criteria Information displayed on report ACTG protocol e Patid ACTG protocol type e Draw date Non ACTG prot ID2 e Draw time Project e Frozen date Specimen date e Frozen time Tech initials e Time to freeze in minutes e Tech e Additive e Derivative e Comments Time to process QA QC summary report Shows the time to process for aliquots along with a graph and summary of overall time to process Sorting Filter criteria Information displayed on report a ACTG protocol e Patid ACTG protocol type e Draw date Non ACTG prot ID2 e Draw time Project e Process time Specimen date e Frozen time Tech initials e Time to process in minutes e T
59. ID1 requirements The SNRP preset project has these requirements Data entry requirements Field ID1 PID ID2 Study ID3 SID Visit OPID Clinic Draw Time LDMS USRMANOO3 Required Required Optional Optional Optional Optional Optional Optional Page 135 LDMS User Manual Preset projects Field Required Note Received Time Optional s5 VOA The VOA preset project has these requirements Data entry requirements Field Required Note ID1 PanelID Required LDMS will determine if this field is valid Specimens entered or received in a shipping file prior to 01 July 2007 will not be validated ID2 N A This field is not used by VQA ID3 N A This field is not used by VQA Visit N A This field is not used by VQA OPID N A This field is not used by VQA Clinic N A This field is not used by VOA Specimen Time N A This field is not used by VOA Received Time N A This field is not used by VQA PanellD format Assay_Category Panel_Number Panel_Subtype Num Panel_Configuration Assay_Category RNA DNA or CUL Panel_Number A number between 000 and 999 paler ops UM Ultrasensitive RNA SM Standard RNA RT DNA proficiency panel PQ DNA pre qualification panel cc Culture panel Num A number between 01 and 99 Panel_Configuration A B or C LDMS USRMANOO3 Page 136 LDMS User Manual VIN Preset projects The VTN preset project has these requirements Data entry requirements Field ID1 PID I
60. ID1 they will be run at this time If the ID1 that you entered is not valid for the project you will be prompted to correct it before you can save the new participant LDMS will also verify that the participant with the same ID1 does not already exist in the project If the participant does exist you will receive an error message Close the window and use the filters on the Specimen Management to locate the existing participant Results The new participant will be created and added to the end of your laboratory s database For example if your laboratory previously had 250 participants the new participant will be 251 LDMS will automatically open the record for the newly created participant so that you can add enrollment information Related sections Entering specimen information Overview on page 20 LDMS USRMANOO3 Page 22 LDMS User Manual Specimen Management Records are added to LDMS from the top down starting with the creation of a new participant Quick add on page 37 The quick add feature allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS Adding participants using Quick Add The Quick Add feature can be used to add a new participant along with other information on a single page Background If adding a participant in this way at least one visit must have occurred as the date of the visit the Collection Date is required Procedur
61. ID1 format BM XXX Y BM Must be BM XXX Any 3 digits Y O for mother 1 to 9 for child CEMALB The CEMALB preset project must meet these requirements Data entry requirements Field Required Note ID1 PID Required Must be 5 characters ID2 Protocol Required ID3 Visit Optional a2 Visit Optional lt 5 OPID Optional os Clinic Optional Draw Time Optional Received Time Optional 7 LDMS USRMANOO3 Page 123 LDMS User Manual CHAVI Preset projects The CHAVI preset project must meet these requirements Data entry requirements Field ID1 PID ID2 Protocol ID3 ID3 Visit OPID Clinic Draw Time Received Time CIPRA HT Required Required Required Optional Required Optional Optional Optional Required Note Must pass HPTN ID1 validation and must be 9 characters in length Validated using ID1 where ID2 is embedded into ID1 as either the 4th or 4th and 5th digits depending on the protocol The CIPRA HT preset project has these requirements Data entry requirements Field ID1 PID ID2 Protocol ID3 SID Visit OPID Clinic Draw Time Received Time LDMS USRMANOO3 Required Required Required Required Optional Optional Required Optional Optional Note Must pass HPTN ID1 validation Must pass ACTG IMPAACT ID3 validation Page 124 LDMS User Manual Preset projects CIPRA ZA Short reference description Data entry requiremen
62. In aweb browser go to https Awww webldms org 2 In the upper right corner of the page click LDMS Login 3 Enter your user name and password and then click the Login button The Select Laboratory page will open 4 Select the laboratory from which you want to work from the Select Lab oratory box You will be working out of the selected laboratory s database for your session You will only be able to select a laboratory to which you have access What to do next If you want to change to a different laboratory s database after signing in click the Change link next to the laboratory name in the upper right corner LDMS USRMANOO3 Page 11 LDMS User Manual Getting started Changing users To switch users from the same web browser you must log out and log in as a different user Background Although multiple users can sign in and access data from one laboratory s database at the same time you cannot sign in with multiple users from the same web browser on the same computer For example you can sign in as two different users on two different computers using Firefox but you cannot open a new tab on the same computer and Sign in as a different user Doing so would cause problems with the tab in which you were originally signed in Procedure 1 In the upper left corner of any page in LDMS click the Logout button 2 Signin as a different user Saving changes when automatically signed out It is possible to save change
63. LOMS LDMS User Manual LDMS for the web version 3 0 Copyright 2015 Frontier Science Foundation Inc Distribution of this document to persons or organizations outside of Frontier Science Foundation is strictly prohibited All trademarks trade names service marks and logos referenced herein belong to their respective companies LDMS USRMANOO03 Document version 3 0 Last updated 28 Sep 2015 Summary This manual explains how to use LDMS LDMS User Manual Contents Contents PE OUE EIS NAN M hLaeoe ix 2 oe cece seen deca ernas e LE LE EESE Er OE ES eo EEE tn 9 Getting started sonsu ne aa A cov a E E aaaea EE ee 9 Getting started enei a A a A e S 9 About LDMSimerarenio arin ari e A RER A A 9 About Frontier ScienCe msscnsciiniinieciininiceini nna 10 SYSTEM reguirene nE eina ar A N EA 10 SIQMING si to LDM Seriea ana a E AE i 11 Changing Users onnea ERE E A EA E lees ceden ts c00 12 Saving changes when automatically signed Ut esssessesssscssceseesessessessesseseseseens 12 Downloading FILES i sssvecsssasasshesassessesesaassonndtustusnwesuenuniustartadl R tdi deaths as 13 THE LDMS user interface esscsscsesscsseccoseds covcctsehcvathscuech ceded adbacsbe cevconteavesdautevassescetae asseda 13 Applying filters to a Pag eneore rn NE T EN AT 14 Challenge COdeSoneuiinranni lus a NENA A a r a E a tis 15 Specimen Managements ciscccsciccccscsncested cenccacsedesbuccchcnesdetSecidecasacscesuewssenkcstsaniverencs 16 SPECIMEN MANAGE
64. Longer be made blank R 22376 When applying a Quick Add template validation errors that were present before the template was applied will now be cleared R 22148 Fixed issue where the filter criteria on the Reports page could be activated before the desired report was selected R 22152 When assigning storage locations to specimens selecting and adding specimens will move then from the Available Specimens list to the Selected Specimens list R 22153 A SHIMS ID3 will now appear correctly on the Manage Enrollments screen R 22207 VQA ID1 will now be validated when using the Quick Add feature R 22247 Removed ability to move specimens from a container that is part of a pending shipment to another container that is part of another pending shipment R 22289 Fixed error triggered by adding a date filter without selecting a date R 22305 Quick Add template filters will now only show filters used by existing Quick Add templates R 22363 Specimens that are moved within a container will now appear on the Move Report R 22415 An appropriate error message will now appear when an incorrect challenge response code is provided R 22553 On the Storage page unknown specimen types will no longer generate an error due to a missing icon R 22577 Fixed issue where pre defined lists and values were erroneously available for VQA specimens R 22580 It is now possible to generate aliquot labels using Internet Explorer 9 R 22857 Fixed issue where a specimen that wa
65. MENL cscssccscsscesssssssssssesssssesssssscsscescsscascascascascasssssssssessssussssseescascascascaseases 16 Trims used WA LDM S cece cscseessaciecks tesacabuss ass avicisssaasasanesdvasdennedactsesneabsdscnabsedtavastestadtespseisanaasease 16 Navigation on the Specimen Management Ppage scsssssscsecsesessessessssessessessceseesceseenes 18 Entering Specimen information OvervieW sesssssseesssssseesssssssessssssreesssssreessssssressssss 20 Participants seeker aT E E teal dcdecadhash uesta te dhaatandas dor Briatetrnesaas toasts 21 Participant identifie Ssp T a a EE RE 21 Adding participants using the Specimen Management paGe ssssecsseeee 21 Adding participants USING QUICK ACC iesssssssssssseseesssssesssssscssessesceseeseeseeses 23 Modifying A participanta ssania a aaia as 23 Enrollments an a aE aeaea a aaea EE S E E 24 Adding enrollments using the Specimen Management Page csssecseeees 24 MOdifyiNg enrolmen S ians aa a a a 25 VISITS cscs emenn e eana s i a ia obo con sutuesoasubieaiensbosecsneseatentaaieogeiee 26 Visit identifier Senesi aiii aaie 27 Adding a visit to an enrollMent esssseessssssseessseseeessssseeesssssseesssesseeessseseeessssseeesssses 27 Modifying Vissiin nan AA T NENEA 29 Primary specimen Sossi e ENEO NE 29 SPECIMEN Identifier n a RET A N EANA A 29 Specimen identifiers in LDMS for WiNdOWG c cccssssssesessssessecscescesseseseesesees 30 Adding a primary specimen tO a ViSit
66. MS will no longer create labels for unavailable specimens R 19969 Fixed issue where it was not possible to add specimens to shipping containers that already contained a large number of specimens Page 164 LDMS User Manual LDMS USRMANOO3 Release notes R 20113 If a specimen is part of a pending shipment LDMS will no longer allow a user to delete it without first removing it from the shipment R 20123 The Storage Unit Template page now clearly shows the hierarchy of storage items contained in the storage unit R 19137 When modifying a shipping container LDMS will now correctly sort specimens using the shipments fill order R 20324 Unless otherwise enforced by a project ID3 is no longer considered a required field for specimens being sent or received in a shipment R 20333 The Specimens Not in Storage report will now correctly show primary specimens as well as aliquots R 20337 When a specimen s condition is changed to a condition that makes it unavailable such as DSR for destroyed the Available option will be disabled for the specimen R 21508 When a specimen s condition is changed to a condition that makes it available after being unavailable the specimen will now be changed back to available R 20348 Fixed issue where the positions of specimens in CSV shipping files were not calculated correctly R 20486 Fixed issue where storage items holding too many items were not displayed properly in the interface R 20527 Fixed
67. NOO3 Page 84 LDMS User Manual Shipping Procedure 1 Do one of the following e To QA QC a pending shipment click Shipping gt Pending Shipments e To QA QC a received shipment click Shipping gt Shipment History On the button to the right of the shipment click the triangle and select QA QC With the first specimen select which is the default do one of the following e Scan the specimen s barcode recommended e Manually compare the Global Specimen ID on the screen with the global specimen ID on the specimen s label If they match click Pass Specimen otherwise click Fail Specimen If there are multiple shipment containers After each specimen in the container has been reviewed select the next item from the Select a Container List After all specimens in the shipment have been reviewed click Save at the bottom of the page What to do next Confirm that QA QC has been completed for the shipment by looking at the QA QC column on the Pending Shipments or Received Shipments page Shipment history A record of shipments sent and received can be found on the Shipment History page In terms of LDMS a shipment received is one for which you have uploaded a shipping data file from another laboratory in LDMS and a shipment sent is when you have generated the shipping data file Figure 36 The Shipment History page Shipment Shipment Shipment Format Destination Sending Shipment Setup Date Ship Date Rec
68. New Primary Figure 15 Adding a new primary to a visit Add New Primary Print Labels Delete The Create Specimen window will open Fill in the information for the new primary specimen Items marked with a red are required Optional Enter additional information about the primary specimens into the Comments box Information that is typically included here includes details for specimens that were not collected an explanation of a condition or an explanation of why a specimen is not available Optional Enter additional information about the primary specimens into the Internal only comments box These comments will be include if the specimen s information is shipped to another laboratory Comments entered here is for your laboratory s use only These comments will not be included if the specimen s information is shipped to another laboratory At the bottom of the window click Save The information you entered will be checked for completeness and validity If there is an issue with one of your entries it will be highlighted with a brief explanation of how to correct it Page 32 LDMS User Manual Specimen Management Results A new primary specimen is now available It will automatically be assigned a global specimen ID ending in 00 by LDMS I i Note The new primary will not have a specimen ID assigned to it Specimen ID is only used by LDMS LDMS uses the global specimen ID not specimen ID to iden
69. RoundNo ID3 ExpDate Visit OPID Clinic Specimen Time Received Time Notes e CPQA use the LDMS shipping file format Required Required Required Optional Optional Optional Optional Optional Optional Note Must be five characters in Length in the format Round_ Panel_alpha_ID 2_numbers such as 22A00 This is the same as the first 2 digits of the PanellD This field will automatically be populated by LDMS Select from pre defined List of visit units e There are CPQA barcode options available in LDMS e Quick Add templates can be used for CPQA however users are not expected to use this feature e ThePharmacology Proficiency Results report can be generated from LDMS for Clinical Laboratory Improvement Amendments CLIA This is sometimes referred to as the CLIA Report FACTS The FACTS preset project has these requirements Data entry requirements Field ID1 PID LDMS USRMANOO3 Required Required Note A 7 digit number LDMS will verify that the PID is valid Page 127 LDMS User Manual Preset projects Field Required Note ID2 Study Required Select from pre populated List ID3 Disabled This field is not used by FACTS Visit Required Select from pre defined List of visit units OPID Disabled This field is not used by FACTS Clinic Disabled This field is not used by FACTS Specimen Time Required Received Time Optional Notes e Quick Add t
70. SRMANOO3 R 17879 Improved the readability of specimen information on the Specimen Management page R 19056 Updated interface to more consistently use the term specimen instead of sample R 19461 When selecting specimens to store or add to a shipment it is now possible to select more than one specimen at once R 19462 When a specimen is added to a pending shipment and has a storage location assigned its icon on the Storage page will indicate that it is part of a shipment R 19513 Improvements to the interface on the Labels page R 19568 Reordered data entry boxes on the New Specimen page so that more commonly used items appear near the top R 19968 Shipping manifests can now be generated prior to shipping a shipment R 20207 Added specimen validation checks to the ACTG IMPAACT project R 19037 The user is no longer required to specify a shipping destination before saving a pending shipment the destination is still required to send the shipment R 20216 Added logic to prevent users from inadvertently creating shipping files in the LDMS format for laboratories not using LDMS as well as a warning attempting to use a non LDMS format to ship to a laboratory that does use LDMS R 20284 When changing a specimen s condition to DSR destroyed LDMS will now show the specimen s storage location and prompt the user to enter a comment R 20308 Specimen validation will now be checked for specimens on shipments when they are sent and re
71. TN URINE BOX Che 1 11 eeao307 01 1 2 ior ie 1 4 AEQ00371 01 1 A storage unit 2 A level 3 A container 4 Specimens in the container 5 The name for this specific storage unit 6 The position of the item in its parent 7 The global specimen ID for each specimen Storage items Storage items in LDMS are represented as nested grids Each storage item contains rows and columns that represent individual locations within that storage item For example a shelf that can hold 10 boxes might have the LDMS USRMANOO3 Page 52 LDMS User Manual Storage dimensions of 2 x 5 2 rows with 5 columns to represent each box This is true of all storage items from big storage units to small containers Figure 22 Storage items as grids Unit Level Sub level Container Specimen gt l 1 1234 4 3 2 1 This visual illustrates the nested grid of storage items Below each item is a grid showing where the highlighted item is positioned Rows and columns can be represented as either numbers or letters Individual sections of a storage item can also be represented as a position number instead of coordinates For example if you have a 1 x 3 shelf each position could be represented as 1 2 and 3 rather than 1 1 1 2 and 1 3 Storage items can optionally have an excluded position An excluded position is useful for determining which side of the storage item is the front and which is the back
72. This means that only information for that project will be displayed 3 Select or enter the information to be shown from the filter box You can either select the information to filter from this list or enter it into the box Filters will automatically show available options as you type I I Note Filters do not affect other filters For example if you select the E FRONTIER group then try to apply a filter for ID1 all ID1 values in the laboratory s database will be available for selection even if they don t below to the FRONTIER group Results The filter will be applied immediately once it is selected and the page will automatically refresh to remove any records that do not meet the filter s criteria If two filters were selected they will both be applied using and logic For example if you selected FRONTIER from the Project filter and BLD from the Primary type filter only blood specimens for the FRONTIER project will be displayed What to do next To remove a filter that has been applied find it in the filter panel on the left side of the page and click on it It will be removed immediately and the page will automatically be refreshed to reflect the change Challenge codes A challenge code is password that you must give to LDMS User Support to perform certain actions in LDMS Access to certain features in LDMS may be restricted for a number of reasons For example changing all of the specimens in a storage uni
73. USRMANOO3 Page 46 LDMS User Manual Code LBE OPR OSW PST Description Laboratory Error Outside Protocol Requirements Outside Visit Window Processed After Specified Time Specimen container conditions These condition codes describe physical problems with the specimen s container If there is a qualitative issue with the specimen as a result of the container issue a qualitative code may be more appropriate Specimen Management Usage The laboratory made a general error during processing such as setting equipment up incorrectly or mislabeling specimens The specimen was drawn during the protocol defined window but not in a manner consistent with the protocol For example if a participant was supposed to be fasting but was not this code would apply The specimen was collected correctly but outside the window for the visit as specified by the protocol The specimen was collected and processed into aliquots but the processing was done after the time frame specified by the protocol This is commonly applicable for PBMC and pharmacology specimens Table 4 Specimen container conditions Code BKV DMG EXP INT LKD Description Broken Vial Damaged Expired Incorrect Tube Leaked Temperature conditions Temperature condition codes are typically applicable if there was an issue during shipping such as sublimed dry ice or if a piece of storage equipment failed Other codes are
74. additive time used for a primary specimen varies based on certain factors In these situations using the TBD code will require the user to select the correct code when the template is used Places where TBD can be used in quick add templates e Primary type e Additive type e Derivative type e Sub A D type Quick add templates Quick add templates are predefined specimen entry scenarios typically for specific study visits that can be used to automatically create some default specimens Templates are best used for specific study visits to create the expected specimen collections for the visit They can also be used to complete other information such as the ID2 and project that would be the same whenever the template is applied There are two types of templates templates created by Frontier Science and templates that are created by your laboratory Templates created by Frontier Science are designed in collaboration with leadership for projects and cannot be modified by users Templates created by users at your laboratory can be modified User created templates are only available at the laboratory where they were created they are not shipped or sharable with other laboratories Regardless of the type once a template is applied you will be prevented from changing the participant s project meaning you can t apply a template intended for one project and then change the project effectively using the template for a project for which it
75. al project requires you to specify what you are going to call D1 ID2 and D3 Table 14 Identifiers Identifier Description Example ID1 Uniquely identifies a participant or Participant ID specimen source ID2 Identifies the study in which the Study number participant is enrolled ID3 Used to further identify a branch or sub Sub study number unit in a study While there are no rules for what you can name each identifier they must be used for these purposes For some projects it may be more appropriate to think of ID1 as identifying the source from which specimens were collected such as a testing solution that you received rather than a participant Creating a new project New projects can be created on the Project Administration page Procedure 1 Click Administration gt Projects from the LDMS menu bar 2 From the LDMS action menu select Create project The Create Project window will open 3 Enter the name of the project as you would like it to appear in menus throughout LDMS into the Name box 4 Enter a brief description of the project into the Description box Page 115 LDMS User Manual Administration The description is generally used to provide the full name of the project especially when the project is an acronym 5 Enter the name that you want to use for ID1 for the group into the ID1 Name box and a brief description into the ID1 Description box ID1 is typically used as an identifier for a partic
76. an directly to the login screen Improvements e R 21567 Relaxed rules for assigning modifying or removing storage locations to specimens that are part of a shipment e R 22002 Added remove button to filters to make it more apparent how they are deactivated e R 22443 Added remove button to filters when adding specimens to storage to make it more apparent how they are deactivated e R 22010 Improved LDMS s Section 508 compliance in various areas e R 22094 Improved LDMS s Section 508 compliance by adding more links to appropriate plugins LDMS USRMANOO3 Page 158 LDMS User Manual LDMS USRMANOO3 Release notes R 22096 Improved LDMS s Section 508 compliance by adding aria Label Ledby attributes to various fields R 22020 The user can now remove cryopreservation information that was previously added R 22045 Re arranged display of information on several pages so that ID3 appears before clinic to accommodate projects where ID3 determines the clinic R 22058 It is now possible for certain specimen fields such as VTN s ID1 to be locked per project requiring a challenge code response from user support to modify R 22197 Quick Add templates can now be deactivated so that they can no longer be selected but are still preserved for historical purposes R 22368 Refactored images to increase application load time and responsiveness R 22377 Added client side validation for required comments when a specimen is made unavailabl
77. ange the shipment back to a pending state LDMS USRMANOO3 Page 86 LDMS User Manual Reports Reports Reports Background This would be necessary if you need to modify the shipment and re generate the shipping file This could happen for example if you discovered there were more specimens to be shipped and the shipment hasn t left your laboratory yet CAUTION A shipment should not be un sent if the receiving laboratory has A received and loaded the shipping file Doing so would cause the specimens to appear at both laboratories Contact the receiving laboratory and ensure that have not yet loaded the shipping file before continuing Procedure 1 Inthe menu bar click Shipping gt Shipment History 2 On the View button to the right of the shipment click the arrow and select Unship 3 Click Unship The Reports page is where you can retrieve data that is stored in your laboratory s LDMS database While you can browse specimen information for individual participant visits on the Specimen Management page you can t control what is displayed and how For example suppose you need a list of participant identifiers for all participants at your laboratory and what project those participants belong to You can t quickly get this information from the Specimen Management page This is where reports are helpful The Reports page allows you to generate pre defined reports about data in your laboratory s LDMS database while t
78. ant for example the unique participant identifier ID may be called PID for another project it may be PanellD LDMS USRMANOO3 Page 18 LDMS User Manual Specimen Management The main work area of the Specimen Management page will display the all the visits and associated specimens for a participant Use the navigation buttons to change between different participants Figure 5 The Specimen Management page lt Participanti of 1 gt Project Project Name Edit Participant gt D4 987123654 OPIDs 2 102 METABOLIC Edit 02 Visits Visit Draw Date 03 Clinic Action 1 Vst 18 Feb 2015 NONE Edit v 1 Vst 18 Feb 2015 Edit gt Primary Global Specimen ID Status Draw Primary Additive Specimen Action Specimens Time Type Type Condition O 0500 001NGJ00 000 BLD EDT SAT Edit x Add New Specimen Aliquots Manage Enrollments 5 Global Specimen ID Status O 0500 001NGIO0 001 v Print Aliquot Labels for Coenrollments Print Aliquot Labels for Selected Enrollment Delete 0500 001NGI00 002 oa PL2 N A SAT Edit v 0500 001NGI00 003 E PL2 N A SAT Edit v SSeS gt 1 Navigate between participants 2 The current participant s enrollment information 3 Visits for the current participant 4 Primary specimens for the currently selected visit 5 Aliquot specimens derived from the currently selected primary sp
79. applied as part of routine and expected handling of specimens For example the FRO condition code can be used to indicate that a specimen intended to be stored ambient or refrigerated was frozen Table 5 Temperature conditions Code DIM FRO LDMS USRMANOO3 Description Dry Ice Melted Frozen Usage The container was broken beyond recovery such as being dropped and shattered on the ground The container is not leaking but is damaged in another way such as a tear in a label or a dent in a plastic container The additive in a container or some other component used during specimen collection was expired A tube type other than the one specified by the protocol was used and the tube used was determined to be an acceptable alternative by the study team The specimen leaked from the container and it was placed inside another container and recovered Usage The specimen was kept on dry ice but the dry ice sublimed This does not necessary imply that the specimen was damaged or TNO The temperature of the specimen has been lowered below its freezing point This applies only to specimens that were not intended to be frozen such as Page 47 LDMS User Manual Specimen Management Code Description Usage specimens that were shipped at ambient temperature during the winter REF Refrigerated The specimen is cooler than room temperature but not below its freezing point This applies only to specimens that were no
80. are added to LDMS from the top down starting with the creation of a new participant Quick add on page 37 The quick add feature allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS Modifying enrollments Participant enrollments can be modified or removed after they are created on the Specimen Management page Before you begin e If removing an enrollment from a participant the enrollment must not have any associated visits e If you accidentally added a visit and specimens to the enrollment in error and you want to preserve them co enroll the specimen s in another enrollment first so that the erroneous enrollment can be removed LDMS USRMANOO3 Page 25 LDMS User Manual Specimen Management Visits Background The only property of an enrollment is the associated D2 If the incorrect ID2 was selected when the enrollment was created you can change it Doing so will add the participant to a new enrollment not change the existing For example if a participant is currently assigned an ID2 of STUDY3 and you change it to STUDY4 this change will only affect this participant not all participants in STUDY3 If the enrollment was added in error it can be deleted instead B Note Enrollments can also be modified using Quick Add Procedure 1 Inthe LDMS menu bar click Specimen Management 2 Find the participant with the enrollment to be modified
81. ary specimens A primary specimen is a specimen that was collected from a participant during a visit Primary specimens are generally larger specimens that are later processed into smaller specimens called aliquots New primary specimen are added to LDMS on the Specimen Management page They are always associated with at least one participant visit Specimen identifiers All specimens in LDMS are assigned a unique specimen identifier LDMS USRMANOO3 Page 29 LDMS User Manual Specimen Management There are three types of specimen identifiers that can appear in LDMS global specimen ID This is a unique identifier assigned to all specimens specimen ID This identifier may or may not be unique It is only used by LDMS LDMS will not assign a specimen ID to specimens added using LDMS other specimen ID This identifier is intended for laboratories to use to assign their own internal use identifiers as needed Important LDMS for Windows and LDMS for the web use different formats for the global specimen ID The format used by LDMS is longer and contains the originating laboratory s ID For example the global specimen ID 0500 0005JEO0 000 indicates that the specimen originated from LDMS laboratory 500 The global specimen ID assigned by LDMS links a primary specimen to any aliquot specimens created from it Primaries and aliquots derived from them will have the same global specimen ID up to the dash character The last three numbers a
82. ary type and the received date and time Each row on a label can hold up to four items and a label can have up to 8 rows Figure 40 Label definition and corresponding output Barcode Label Fields Global Spec ID 17 ID 1 PID 15 Spec Date 10 Spec Time 5 Primary 3 Additive 3 Derivative 3 Sub Add Der 3 Volume 6 Vol Units 3 A label as it is set up in LDMS left compared to a generated label right The colored background shows how each item in the label definition matches up to the item on the label LDMS USRMANOO3 Page 108 LDMS User Manual Barcodes Label sizes Labels LDMS supports generating 2D barcodes on labels If a label has a barcode it will appear as the first item on the label The barcodes generated by LDMS contain the specimen s global specimen ID Labels can be generated in a variety of common sizes The label s name in LDMS indicates information about its size manufacturer and use Figure 41 Example label name Barcode Label 20 2 75 x 1 Brady 300 MVP Horizontal 7 rows Type of label Name of label Dimensions of label Number of items that can fit on label There are three types of labels available Laser labels For printing using a desktop printer with special 8 5 by 11 inch paper Barcode labels For printers specifically made for printing labels Dot matrix labels For use with dot matrix printers I I Note If you choose a label format that has a barcode only
83. ate the pending shipment to be sent 3 Click the Edit Ship button to the right of the shipment The Pending Shipment Preview window will open 4 Click the Ship button LDMS will warn you that this is your last change to generate the Batch Storage Report If you want to view this report click the Cancel button On the Shipment Contents tab click the Batch Storage Report button to generate the report LDMS will check that the information for the shipment has been fully completed If there are any issues it will be highlighted in red and you will be prompted to correct it before continuing 5 When asked to confirm if you want to send the shipment click the OK button The shipping file will be generated When it is ready you will be prompted to save it to your computer Page 75 LDMS User Manual Shipping Warning Do not close the window until the shipping file has been saved 6 Click the Close button to go back to the Pending Shipments page 7 Optional Generate a shipping manifest a Click Shipping gt Shipment History from the LDMS menu bar b Locate the shipment that you sent c Click the arrow next to the View button and then click Generate Manifest Figure 32 Generate Manifest Generate Manifest Shipping Container Report QAC QA QC report Unship Download shipping file Results The shipping file is now saved at the location you specified on your computer What to do next This is the file
84. ative Non ACTG prot ID2 e Sub a dditive d erivative Project e Count Storage detail report Shows detailed information about the contents of containers in storage units Sorting Filter criteria Information displayed on report This report is sorted by storage ACTG PID e Storage location location and then by storage e ACTG protocol e Specimen ID position e ACTG protocol type e Global spec imen ID Additive Project prot Derivative PID ID1 Import date VID unit Non ACTG PID ID1 Prim ary Non ACTG Prot ID2 Add itive LDMS USRMANOO3 OPID Other specimen ID Primary Project Received date SID ID3 Shipment number Specimen date Der ivative Sub a dditive d erivative Volume Ship Storage date Spec cimen date Time Clinic Page 107 LDMS User Manual Labels Sorting Filter criteria Information displayed on report Specimen ID e Pos ition Specimen time e Other specimen ID Stored date Sub add itive der ivative Visit unit Visit value Volume Volume unit Labels Labels The Labels page is used to print labels for specimens and define what those labels should look like Understanding label formats Specimen labels can be produced that contain a wide array of information Label formats Labels are setup like grids with items that appear on the label occupying one cell Items that can appear are most of the information that can be found on the Specimen Management page such as the prim
85. atories using LDMS in a secure environment that meets the standards of 21 CFR Part 11 and NIST FISMA guidelines Related sections LDMS website LDMS USRMANOO3 Page 9 LDMS User Manual Getting started About Frontier Science Frontier Science develops and maintains LDMS and provides data hosting for laboratories Frontier Science and Technology Research Foundation Inc is a not for profit that provides data management services to research organizations LDMS is one of those data management services Frontier Science also develops and maintains LDMS a similar product that is not web based and requires installation on a computer at the users laboratory Many organizations that utilize LDMS and LDMS also utilize Frontier Science s data management center often referred to as the DMC in Amherst New York for long term data storage These organizations use LDMS and LDMS as a mechanism for sending specimen data for studies to Frontier Science Frontier Science is involved in many other statistical research efforts beyond LDMS and LDMS To learn more about the work that Frontier Science does visit https www fstrf org Related sections Frontier Science website System requirements This section lists the system requirements and recommendations for computers connecting to LDMS Supported web browsers e Firefox 24 or higher e Chrome 13 or higher e Internet Explorer 9 or higher For all browsers JavaScript must be enabled
86. ats erisha aiea ra R 112 CUSTOMIZING tabel FOFMALS cccecsssssssessesseseesscsecsecsecscssccssescssssessesseseessessesscsecsecseescesceneenses 113 Setting the default label format for a Project ecsessssssssssesessessssesesestssesseeseeees 114 Administrationen tecacasstcecbtatsccsscuuteechaceeseeuaicabseeestntetsatenetshataiars 114 Administrations insera i ie a aad 114 Projection aa R R ANE AE ATT E 114 Local projeciS nordon ra N N e AAA N NERA 115 Government projeti enron ea a a en 116 User managementom an EAA Ar EAE N R 117 CHANGING your PASSWOMC s csecseccsetsuscesceccusaeisseostesececsheussabsustasnastedcdeibcaucsdansevneasealesesdustbeabiasndbade 117 Password FEQUITEMENIG csscssessecssessessessecsecsecsecsecsecsecsecsecsesseeseesssussussussucsscsscsscess 118 Preset DIO COUS coe c2eatecssis cesesaesseseeosencsaeeearsessessvieectandoe een edie eoi Eiaeia erais 118 Preset PFO etts E OEE A 118 ACT G IMPAAG T ssscctcssotccesestutazisces tnats cy state cuntitesassaspidcueentioetadinass Subild od anaa a ae aa asta saasta 118 AERA S nnne ieii a st ole th0ite se abssatbbeeseuse aana oa aa aasan anana 120 AEDRP ni iii A T RE 120 AMGr ERA E R T AAA AAG 121 ATN ennie an a a aa a o ae a G A 122 EINA PAA EEEE EE A E T E E E A 122 CEMAL B ninien naaa tears a A A buon mmenteatealtts 123 E p NYA ETEA EEEE EAEE EE 124 QIPRA Hes oraaa ea a a chess lead aana a E i aaaea a EE 124 GIPRASZA cas cectaeiicts sot shadistesstatacotctuvesthacevetavsa
87. barcode labels can E be selected For laser and dot matrix labels the size of the label refers to the label itself not the paper it will be printed on These labels are generated in US letter size paper 8 5 by 11 inches with the assumption that the user is using special label paper that can be pealed apart Barcode labels on the other hand require special printers and label paper that are designed exclusively for printing labels How to use a barcode reader with LDMS LDMS supports using any Windows compatible barcode reader Barcode readers that are compatible with Windows will extract the global specimen ID from the 2D barcodes that are generated by LDMS You can test this yourself by opening Notepad and scanning a barcode Doing so will cause the global specimen ID from the barcode to appear in Notepad In any place in where you would need to type a global specimen ID you can use a barcode reader to input the ID instead Select the box where you want the global specimen ID to appear and then scan the barcode This can help avoid errors when trying to type out a global specimen ID using the keyboard Printing labels anywhere LDMS USRMANOO3 Specimen labels can be printed in many places in LDMS not just the Labels page Page 109 LDMS User Manual Labels Labels can be printed almost anywhere in LDMS where you can interact with specimens e On the Specimen Management page click the down arrow next to any of the Edit bu
88. ceived R 20321 Lab tech initials can now be set on aliquot specimens instead of just primary specimens R 20336 When receiving a shipping file that includes specimens without a global specimen ID assigned similar specimens will now be appropriately grouped together under a primary specimen R 20498 Added link to a PDF viewer on pages where the user can download a PDF file This was done to improve compliance with the Section 508 Amendment to the Rehabilitation Act of 1973 R 21640 Added alternative text to pagination buttons to improve compliance with Section 508 R 20660 Improved the interface of the Manage Enrollments page R 20854 The Shipping Manifest Shipping Container and Storage reports are now available in additional places on the Shipping page R 20855 LDMS can now import shipping files with a dat extension which is sometimes added automatically to shipping files by email clients when attaching them to messages Page 163 LDMS User Manual Release notes R 20208 For the preset projects added as part of R 20162 validation checks were also added R 21472 Added support for Quick Add template usage rules and restrictions for preset projects added as part of R 20162 R 21483 Users are now prevented from changing projects once a Quick Add template has been applied This is necessary to support using templates with preset projects R 21785 Added co enrollment usage rules for preset projects R 21837 Certain primary specim
89. cific project the name and format for an ID1 will vary depending on the project Also known as patient identifier Abbreviations PID protocol The plan that determines the collection of specimens types of collections timelines etc such as a study the label for which is dependent on the project Also known as D2 ID3 A sub protocol identifier not used by all projects label A small printed paper with an adhesive back that is placed on a specimen container to help identify its contents LDMS laboratory ID A number assigned by Frontier Science that is used to identify a laboratory to other laboratories can be assigned to laboratories that do and do not use LDMS Also known as laboratory ID labid laboratory number LDMS for Windows A locally installed Windows application developed and maintained by Frontier Science used by laboratories around the world to create specimen records track specimen shipment and storage and submit assay result data laboratory information management system LIMS A computer program that is used to manage laboratory data such as cataloging and shipping specimens Acronyms LIMS other patient identifier OPID A secondary identifier than can be applied to a patient typically in addition to an identifier in addition to one defined by the project Acronyms OPID original volume The initial amount of a specimen before any processing occurred other specimen ID An identifier for a primary specimen that
90. cimen assigning storage location 60 co enrolling 33 entering new 31 modifying 35 move to different visit 25 moving between enrollments 33 sequence number in global specimen ID 29 primary type 31 42 processing date 31 42 processing information 35 processing tech initials 31 42 project validation rules 21 projects creating 82 115 modifying 116 removing 116 shipping 82 protocol 24 24 25 PST 46 Q QA QC 83 QA QC status 83 ONS 41 49 LDMS User Manual R reason sample not collected 35 reason specimen not collected 42 46 received date 31 42 REF 47 reports 13 90 resolution 10 response code 15 S Safari 10 sample condition 31 SAT 49 SDAC 10 SDMC 10 search 14 searching 18 section 508 169 Shipment History page 86 shipment workflow 82 shipments checking for issues 83 pending icon 54 projects 82 receiving 82 83 sending 83 unship 86 shipped 18 42 shipping receiving 81 shipping file modifying after sending 86 shipping files 13 SHV 49 sign in 11 sign out 13 SNC 41 49 SNP 41 48 SNR 48 specimen assigning storage location 60 store 65 specimen condition 31 35 42 46 47 47 48 48 49 49 68 specimen entry 20 specimen ID 29 30 42 specimen management 14 16 31 Specimen Management 18 spreadsheet viewer 10 status indicators 18 storage 14 50 51 52 57 59 63 63 65 65 66 68 storage hierarchy 51 storage items icons 54 removing 67 Storage Move Report 66 storage position 52 s
91. cimens from a participant visit at once and is the preferred method for entering new visits in LDMS Modifying visits Visit information is modified or removed on the Specimen Management page Background You may need to modify a visit after it is created to correct an entry error for example using the incorrect clinic If the visit was added in error you can also remove it Procedure 1 Click Specimen Management gt Available Specimens from the LDMS menu bar 2 Find the participant with the visit to be modified Use filters from the Left side of the screen to narrow down the participants that are displayed 3 Select the protocol ID2 associated with the visit from the Protocol box The label for the Protocol box will depend on the project Common labels are study and protocol 4 To modify the visit a Click the Edit button to the right of the visit The Edit Visit window will open b Modify the visit information as needed If a primary specimen has already been entered for the visit it will be listed along with the visit information c Click the Save button 5 To remove the visit select Delete from the Edit menu to the right of the visit In order to remove the visit there must be no primary specimens added to it If you want to remove a visit without deleting the primary specimens you can co enroll the primary specimen This will allow you to associate the specimen with another visit Prim
92. co enrolled and then click Manage enrollments Figure 16 The Edit button for a primary Add New Specimen a Manage Enrollments Print Aliquot Labels for Coenrollments Delete The Manage Enrollments window will open Figure 17 The Manage Enrollments window Collection Date 17 May 2013 j Add Enrolment Project ID1 ID2 Visit Value Action FRONTIER amp 123456 METABOLIC o Remove FRONTIER 123456 56C 1 Remove bt sl Selected Enrollment x Project FRONTIER Note specimens enrolled in only non exportable projects may only be co enrolled with other non exportable projects k PID 123456 Study 56C r Visit Value 1 Visit Units Wk ID3 Clinic 9910 Q Update Aliquots Specimen ID Global Specimen ID Action 500V13000008 HEQOO676 01 fear El 500V13000008 HEQOO67G 02 Edit 500V13000008 HEQOO67G 03 Eait y ki 2 Save Cancel 1 Add a blank enrollment row 2 Enrollments for this primary specimen 3 Details for currently selected enrollments 4 Save changes to currently selected enrollment 5 ALl aliquots derived from this primary including all enrollments Click the Add Enrollment button Select the blank row created in the previous step by clicking on it Fill in the information in the Selected Enrollment section for the new enrollment Click Update Page 34 LDMS User Manual 8 Specimen Management The information for the enrollment will be updated in the list of
93. ct has these requirements Data entry requirements Field Required ID1 PID Required ID2 Protocol Optional LDMS USRMANOO3 Page 132 LDMS User Manual Field Required Preset projects Note ID3 ID3 Optional Visit Optional 3 OPID Optional S Clinic Optional Draw Time Optional Received Time Optional 9 characters long Select from a pre populated list Not used for MTN Visit unit defaults to VST but this can be overridden Not used for MTN Not used for MTN This field is not required but recommended This field is not required but recommended e There are two label options available for MTN one with a barcode and one without MTN The MTN preset project has these requirements Data entry requirements Field Required Note ID1 PID Required ID2 Protocol Required ID3 Disabled Visit Required OPID Disabled Clinic Disabled Specimen Time Optional Received Time Optional Notes e Primary and aliquot volume will default to ML for MTN specimens e Quick Add templates are permitted for MTN NICHD Westat The NICHD Westat has the same requirements the ACTG IMPAACT project LDMS USRMANOO3 Page 133 LDMS User Manual Preset projects 8 characters long 7 numbers with a letter at the Select from a pre populated list all protocols are in the format PHXXxX e g PH200 Not used by PHACS Select from pre defined List of visit units Will automatically populate using the previous clinic
94. cts Adding enrollments using the Specimen Management page Enrollments are added to an existing participant and associate that participant with a specific protocol Before you begin The participant must already exist in LDMS before an enrollment can be added Procedure 1 From the LDMS menu bar click Specimen Management 2 Find the participant Use filters from the left side of the page to narrow down the participants that are displayed LDMS USRMANOO3 Page 24 LDMS User Manual Specimen Management 3 From the Edit Participant menu click Add Enrollment Figure 8 Adding a new enrollment to a participant Is Participant 250 of 250 gt gt Project FRONTIER Edit Participant Add Enrollment Print Labels Delete Participant PID 01111110 OPIDs Study Edit Study Visits Primary Specimens Aliquots In this image ID2 is called Study The Create Enrollment window will open 4 Select or enter an ID2 in the box The label for this box will vary depending on the project It is most commonly called Study or Protocol 5 Click Save Results The participant is now enrolled in the protocol You will see the protocol listed in the ID2 box What to do next If the participant is enrolled in more than one protocol for a project you can create additional enrollments in the same way Related sections Entering specimen information Overview on page 20 Records
95. d box Re enter your new password into the Confirm Password box Click the Change Password button a a Related sections User management on page 117 User accounts are managed by Frontier Science LDMS USRMANOO3 Page 117 LDMS User Manual Preset projects Password requirements This section explains the requirements for user passwords e Passwords must contain at least one upper case letter one lower case letter one number and one special character e A password must not be the same as one of the your previous passwords e A password must be between 10 and 50 characters e Must not be similar to your current password user ID or display name Temporary passwords expire within 24 hours If you do not sign into LDMS using the temporary password before it expires you must have a new temporary password generated Related sections User management on page 117 User accounts are managed by Frontier Science Preset projects Preset projects Preset projects are projects that are built into LDMS that have special rules and requirements Preset projects and their requirements cannot be modified or removed by users These projects and designed based on the needs of a specific project working with Frontier Science An example of a preset project is ACTG IMPAACT Specimens created until this project have specific requirements which are defined by ACTG and IMPAACT These requirements are implemented in LDMS to accommodate the needs of the p
96. d by e Laboratory ID e Laboratory ID laboratory ID e Laboratory name e Contact with telephone number and email address e Address e Room number e Country e Laboratory telephone number e Laboratory fax number Specimen reports Cell yield QA QC summary report Provides a summary cell yield for viable PBMCs along with a graph of cell yeild by date mean standard deviation and range Filter criteria Sorting Information displayed on report This report is sorted by draw ACTG protocol e Patid date ACTG protocol type e Draw date Non ACTG prot ID2 e Draw time Project e Tech Specimen date e Additive Technician initials e Total cell count x106 e Total volume e Comments from Specimen Management e Cell yield x106 Primary specimens received report Provides a summary of all primary specimens within a laboratory s database and the total number of primaries LDMS USRMANOO3 Page 101 LDMS User Manual Reports Sorting Filter criteria Information displayed on report This report is sorted by project ACTG PID e Specimen ID protocol combination and then ACTG protocol e Project protocol by specimen ID Specimen count report ACTG protocol type PID ID1 Additive Clinic Clinic ID Global specimen ID Condition Visit Import date Non ACTG PID ID1 Non ACTG Prot ID2 OPID Other specimen ID Primary Project Received date SID ID3 Specimen date Specimen ID Visit unit Visit value V
97. d containers Background These templates can be selected when adding storage items to LDMS to save time Procedure 1 Hover the mouse pointer over Storage from the LDMS menu bar and then click either Storage unit templates Level templates or Container templates depending on the type of template you want to create 2 Enter a name for the template into the Name box This is the name for the template as it will appear when creating new storage items LDMS USRMANOO3 Page 63 LDMS User Manua LDMS USRMANOO3 l 10 Storage For storage units only Select the type of storage unit from the Type box and the temperature from the Temperature box Enter the number of rows and columns for storage items based on this template into the Number of rows and Number of columns boxes This represents the size and capacity of new storage items based on this template in terms of the number of levels or containers that it can hold For example if you are creating a shelf that can hold 5 boxes side by side you might have 5 columns and 1 rows Select or deselect the Positions only option as desired If the positions only option is selected each item in storage items based on this template will be identified by a number If it is not selected each storage item will be identified by its coordinates If Positions only is not selected Define how levels or containers in storage items based on this template should be identified a Select eithe
98. d to be printed they have been designed with PDF output in mind only If you select a different file format for the manifest you may experience formatting issues Results You will be prompted to save the manifest or it may open automatically depending on the default behavior of your web browser Supported shipping file formats These are the file formats that are supported for sending and receiving shipping files LDMS USRMANOO3 Page 77 LDMS User Manual Shipping Table 12 Supported shipping file formats Format Encrypted Intended destination LDMS Yes Laboratories using LDMS or LDMS for Windows CSV No Laboratories not using LDMS SeraCare No Specimens being sent to the SeraCare repository Cross LIMS Manifest No Laboratories not using LDMS CSV shipping files LDMS can generate and accept shipping files that are a standard CSV comma separated value format A CSV shipping file can be generated by many applications other than LDMS You can make the CSV file using Excel LibreOffice Calc a text editor or any other program that can generated comma separated data For LDMS to be able to read the CSV file it must meet the following requirements e header row is present and column headers are named correctly e required columns are present but can be in any order e fields are separated by commas e dates are in the format dd MMM yyyy e times are in 24 hour format Shipment Number ID number for the shipment Sending Lab
99. dd specimens to a single use shipping container in the Shipping Boxes section Add storage containers to the shipment a Click the Add New button to the right of the Storage Containers List The Storage Containers window will open b Locate the storage item to be shipped c Click the Select button next to the storage item The Storage Containers window will close The storage item will appear in the Storage Containers List Page 73 LDMS User Manual Shipping 9 Add individual specimens to the shipment a Click the Add New button to the right of Shipping Boxes The Create Shipping Container window will open b Enter the number of rows and columns for the container into the Number of rows and Number of columns boxes This represents the size and capacity of the container For example a container with 8 columns and 5 rows could hold up to 40 specimens The container as it is currently defined will appear in the Preview section c Select or deselect the Positions only option as desired If the positions only option is selected each specimen in the shipping container will be identified by a number If it is not selected each specimen will be identified by its coordinates If Positions only is not selected Define how specimens in the container should be organized d wa coordinate order This is how the specimens position will be identified such as 8 5 or 5 8 column labeling This is how rows and columns will be named in t
100. dows could not be imported under certain circumstances due to duplicate level and container names R 21057 Fixed issue where co enrollment information in a CSV shipping file was lost when receiving the shipping file R 21075 Fixed issue where Internet Explorer was not able to display some screens properly when creating a new shipment R 21088 Fixed issue where Internet Explorer needlessly scrolled horizontally in popup windows R 21196 Fixed issue where Internet Explorer version 9 was not able to add specimens to a shipment R 21097 Filters will no longer persist when switching between laboratories R 21099 Fixed issue where receiving a CSV shipping file would fail if the first specimen in the file was a primary specimen R 21194 Fixed issue where shipping files generated by LDMS for Windows could not be received by LDMS under certain circumstances R 21306 Fixed issue where primaries specimens could be inadvertently shown as not stored when trying to make an invalid change to a specimen record R 21331 Fixed issue where drop down menus would become inaccessible in certain circumstances R 21275 Fixed issue where the FreezerRemover and Level Remover classes were erroneously changed to be declared as BoxRemover R 21159 Fixed issue where error messages were not being correctly displayed due to an error inthe ErrorLayout template Page 168 LDMS User Manual Accessibility information e R 20650 Fixed issue where the LoginService class incorr
101. dy Add Visit Visits Visit Collection Date ID3 Clinic Print Labet Delete Study Primary Specimens Aliquots In this image the label for ID2 is Study The Add Visit window will open Figure 11 The Add Visit window Create Visit D3 1545 Clinic 4501 Collection Date 10 Jun 2015 i Visit Value 3 Visit Units Wk Save Cancel Select the clinical site where the visit occurred from the Clinic list If you want to know the name of the site hover over it with the mouse pointer Note The list of clinics and clinic ID numbers are maintained by Frontier Science and cannot be modified by users For more information contact LDMS User Support If required by the project Select the D3 from the ID3 list ID3 is typically used for a sub study or sub protocol Select the date that the visit occurred from the Draw Date list If the visit occurred over more than one day you must add a new visit for each date Enter the visit value and visit unit for the visit into the Visit Value boxes If you want to see what a particular visit unit means hover over it with the mouse pointer Click the Save button Related sections Entering specimen information Overview on page 20 LDMS USRMANOO3 Page 28 LDMS User Manual Specimen Management Records are added to LDMS from the top down starting with the creation of a new participant Quick add on page 37 The quick add feature allow you to create all of the spe
102. e R 22387 Changed the display widget on several screens to make LDMS faster R 22539 Added new REPRIEVE2 label format R 22551 Updated copyright statement in page footers R 22597 Added Quick Add Template List report which lists available Quick Add templates R 23039 Added new Database Dump 2 report R 22619 Added PHIA as an available preset project R 22666 When using a Quick Add template the frozen date will now default to the received date R 22742 The speed and responsiveness of the Storage page has been significantly improved R 22804 Improved speed and responsiveness of the Shipping page when a laboratory has a large number of specimens R 22788 It is now possible to add more than 100 containers to a storage level R 23021 Increased allowable length of tech initials on shipment QA QC from five to ten R 22000 Added unit tests for un shipping a sent shipment R 22011 Added unit tests for cryopreservation features R 22090 Added unit test cases for the classes that auto populate various specimen information based on project specific defaults R 20894 Improved appearance of the PopUpLayout view R 21085 LDMS now uses an optimized custom Dojo build to significantly reduce the number of files that are requested when initially accessing the application R 22086 Miscellaneous improvements and fixes to project specific initializations R 22286 Added robots txt file R 22287 Added lt meta gt to prevent Internet Explorer from reque
103. e 3 Only present if the user has system administrator privileges Related sections User management on page 117 User accounts are managed by Frontier Science Exportable reports Database dump report A general report that provides information from all specimens in a laboratory s LDMS database Sorting LDMS USRMANOO3 Available filters e ACTG PID e ACTG Protocol e ACTG Protocol Type e Additive e Clinic ID e Derivative e Global Spec ID e Non ACTG PID ID1 e Non ACTG Prot ID2 e Other Specimen ID e Primary e Project e Received Date e Ship to Lab Number e Specimen Date Information on report Project PID ID1 Protoco ID2 SID ID3 Visit Visit Unit Clinic Rec Date Rec Time Draw Date Draw Time Import Date Spec ID Global Spec ID PRI Page 93 LDMS User Manual Sorting Available filters Specimen ID Sub Add Der Visit Unit Visit Value Volume Volume Unit Lab 485 aliquot report Reports Information on report e ADD e DER e SUB e VOL e VOL Unit e Cond e Time e Time Unit e Other Spec ID e Test e Comments e Ship Date e Ship Batch Number e Ship to Lab Similar to the Specimen Export Report but sorts the results differently Sorting Filter criteria 1 Project ACTG PID ID1 2 Non ACTG Protocol ACTG Protocol 3 Non ACTG PID ACTG Protocol Type 4 Visit Value Additive 5 Primary Derivative 6 Additive Non ACTG PID ID1 7 Derivative Non ACTG Prot ID2
104. e 1 From the LDMS menu bar click Specimen Management gt Quick Add 2 Optional Select a template for the participant visit 3 Complete the information in the Participant Information section 4 In the Visit Information section enter the Collection Date 5 At the bottom of the page click Add 6 Optional Complete any additional enrollment visit or specimen information for this participant Results When the participant is successfully created a note will appear at the top of the page The participant will be available for select on the Specimen Management and Quick Add pages where new enrollments visits and specimens can be added Related sections Quick add on page 37 The quick add feature allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS Modifying a participant Modify participants on the Specimen Management page Background A participant may need to be modified to correct an error in the ID1 that was entered or to add and remove OPIDs as needed Procedure 1 Click Specimen Management from the LDMS menu 2 Find the participant to be modified LDMS USRMANOO3 Page 23 LDMS User Manual Specimen Management Use filters from the left side of the screen to narrow down the participants that are displayed 3 With the participant open in the work area click the Edit Participant button The Edit Participant window will open 4
105. e There are several HPTN label formats available e Primary and aliquot volumes with default to ML e Quick Add templates are not permitted for HPTN IPREX The IPREX preset project has these requirements LDMS USRMANOO3 Page 129 LDMS User Manual Data entry requirements Field ID1 PID ID2 Protocol ID3 SID Visit OPID Clinic Draw Time Received Time Notes Required Required Required Required Required Optional Required Optional Optional Preset projects Note Must by 5 to 7 characters long and a valid IPREX PID NOPID is a valid PID unless the SID is NOSID Must be 11 characters long with the first 2 digits being the clinic and the last five being the screening number in the range 80001 99999 Must be 3 characters long in the format I 86 to 97 such as 192 e IPREX using the LDMS Shipping File format e When entering sero conversion visits use the visit unit SC The visit value should be the same as the originally scheduled visit e When entering sero positive visits use the visit unit SP The visit value should be the number of weeks after the seroconversion visit The IQA preset project has these requirements Data entry requirements Field ID1 PID ID2 ID2 ID3 ID3 Visit OPID Clinic LDMS USRMANOO3 Required Required Optional Optional Optional Optional Optional Page 130 LDMS User Manual Field Required Preset projects
106. e storage system in LDMS is a hierarchy of storage items LDMS USRMANOO3 Page 58 LDMS User Manual Storage Storage templates on page 63 Templates allow you to add commonly used storage items quickly by defining them in advance Adding a container to a level A new storage container is added to an existing level or sub level Before you begin You must have created the storage units and levels for the container before adding the container In other words you cannot add a container to a freezer without a level nor can you create a container that is not within a freezer Procedure 1 Click Storage gt Stored Specimens from the LDMS menu bar 2 Find the storage unit to which you are adding a Level If you want to add a sub level to an existing level find that level instead 3 Click the down arrow next to the Edit button to the right of the level that will hold the container and then click Add New Container Figure 26 The Edit level button Add New Level Add New Container Set Condition Code Print labels Delete If the level has had sub levels added the Add new container option will not be available A container cannot be added side by side with a sub Level The Create container window will open Enter the number of new containers to add in the Number to add box 5 Optional Select a template to use from the From template box The information from the template will be populated into the remaining boxes
107. e teMPlAateS ccsscsecseseesesesscsecsesseeseencencenees 65 Moving items m St olagE srar raia E A 65 Listing SPECIMENS that moved IN StOFAGE cccescsecsssseseeseeseesecsessesscsceeceacesceneeses 66 REMOVING items from StOFAGE cccscsscsscsssssssessssscssccscsssssssscsscsssssessesseseesssascascaseeceecenceucesensees 67 Modifying the condition of stored SPECIMENS cccssssssssessessesessseesssecsesscscescesceseeseeses 68 SEV DUNG esse chececsecat esate tesce cateestenasino tien Siete reieenteicdacesin iaiebes Saath acnaubec da ieeeieendentons 69 SIMI PUIG aeree ra ieee cSt ok ee ceh terse E a A NNE A 69 LDMS Shipping file COMPAtIDILITY cc essesssestestesecsecsecssescescesccseesessessessesesesesssssseees 69 Shipments are data transfer cccccssscsscsssecssssssssssssssssesssssssssssssessessesscsessecscssescesceseesesseesesses 70 ShipmNent MUNDE enna A A E A 71 New shipments oeiee r castles E A 71 Creating new SHIPMENIG csssssessessecsecsessesssessessessessessessesssessessessecsecsecsecsecssessessess 72 Sending a pending Shipments sendera aa 75 Generating a SHIPPING ManifeSt e esssssseeessseseeessssseeesssseseesssssseeessssseeesssssseesssssse 76 Supported shipping file fOormats esssseeeessssseeesssseseesssseseeessssseeesssssseesssssseeessssseeessssseeesssssse 77 CSV SHIPPING Mesam riere AAAA TN NAAA A 78 Shipping container Tepon nnsa nen a R AEE E R 79 Batch Storage repo Eran ninna AETA E E A
108. e unit e Clinic e Time e Received date e Participant identifier ID1 e Protocol identifier ID2 e Source laboratory e Draw time e Received time Storage export report Provides a summary of specimens and their storage location in a laboratory s local database Sorting Filter criteria Information displayed on report LDMS USRMANOO3 ACTG PID ID1 ACTG protocol ACTG protocol type Additive Derivative Non ACTG PID ID1 Non ACTG Prot ID2 OPID Other specimen ID Primary Project Specimen date Specimen ID Project Prot PID ID1 OPID Primary Additive Derivative Sub additive derivative Specimen Date Visit ID Volume Time Page 96 LDMS User Manual Reports Sorting Filter criteria Information displayed on report Specimen ID e Shipped no Sub add der e Other specimen ID Visit unit e Storage location position Visit value Volume Volume unit Miscellaneous reports Clinic contact report Provides contact information for clinics by clinic ID number Sorting Filter criteria Information displayed on report This report is sorted by clinic e Clinic ID e Clinic ID ID e Clinic name e Address e Telephone number e Fax number e Contact s including name phone number fax number and email address LDMS abbreviated codes report Provides a list of LDMS unit visit time specimen condition codes used in LDMS and their meaning Information displayed on report I I Note The
109. eating or modifying a visit Page 167 LDMS User Manual LDMS USRMANOO3 Release notes R 20578 Fixed issue where tooltips did not always appear for certain types of text R 20779 Fixed issue where users that did not have permission to view the Specimen Management page could not access any other pages in LDMS since the Specimen Management page was the default when signing in R 20865 Fixed issue where Internet Explorer required the user to save between each step when creating a new shipment R 20881 Fixed issue where the Shipping Container Report would incorrectly indicate occupied positions in a container as empty R 20906 Corrected reports ported from LDMS for Windows that were using specimen ID for sorting grouping or filtering during report generation This caused issues for specimens added in LDMS for the web since it does not utilize the specimen ID R 20963 Fixed issue where a LDMS for the web shipment sent to a laboratory using LDMS for Windows and then shipped back to a LDMS Laboratory could not be received if it included a shipment container using positions only labeling R 20971 Fixed issue where the shipment temperature in a shipping file was handled in such a way that shipping files could not be imported by LDMS for Windows R 21018 When generating labels the skip box will now default to zero instead of requiring the user to enter a value which is typically zero R 21032 Fixed issue where shipments created in LDMS for Win
110. ech e Additive e Derivative e Comments Shipping reports Specimens not in storage report Shows specimens that are available in a laboratory s database but have not had a storage location assigned on the Storage page LDMS USRMANOO3 Page 105 LDMS User Manual Reports Sorting Filter criteria Information displayed on report This report is grouped by project protocol combination and then by specimen ID and then sorted by global specimen ID ACTG protocol ACTG protocol type Additive Condition Derivative Non ACTG PID ID1 Non ACTG prot ID2 Primary Project Specimen ID Status Sub additive derivative Visit unit Visit value Volume Volume unit Project prot Specimen ID Global specimen ID PID ID1 Specimen date Pri mary Add itive Der ivative Sub a dditive d erivative VID visit unit and value Volume Condition Status Related sections Assigning a storage location to specimens on page 60 Individual specimens are added to containers on the Storage page Specimens remaining in storage report Shows the number of aliquots for a given participant with a storage location assigned in a laboratory s database Sorting Filter criteria Information displayed on report This report is grouped and ACTG PID ID1 e Project sorted by project ID1 and ACTG protocol e PID protocol ACTG protocol type e Protocol Additive e Volume Non ACTG PID ID1 e Volume unit Non ACTG prot ID2 e Derivati
111. ecimen 6 Specimen status indicators 7 Actions for a primary Status Icon 4 pa lt To change Meaning Specimen is available Specimen is assigned a storage location Specimen has been shipped to another laboratory Specimen has an additional enrollment Click the navigation buttons at the top of the screen participants To view the visits for a different study LDMS USRMANOO3 Select the study from the Study drop down box Page 19 LDMS User Manual Specimen Management that the participant fil Note If the Study box is disabled then the participant is enrolled in E is only enrolled in one study To see the primary click a visit from the Visits section of the page specimens associated with a Visit To see the aliquots click a primary in the Primary Specimens section associated with a primary specimen To search for a use the filters on the left side of the page specific participant Related sections The LDMS user interface on page 13 The LDMS user interface has many common elements across different pages Entering specimen information Overview Records are added to LDMS from the top down starting with the creation of a new participant Background Because records in LDMS are hierarchical you need to enter information starting with a participant and then work you way down to aliquot specimens There are two ways to enter participant
112. ectly compared account lock expiration time as less than or equal to the current time Accessibility information Terms additional time additive type This section describes the accessibility of LDMS and its use with assistive technologies LDMS has been designed with the accessibility of everyone in mind Adherence to Section 508 of the Rehabilitation Act of 1973 is taken into account when planning new features for LDMS and making those features intuitive and useful to the greatest number of people possible Since LDMS runs within a web browser the level of accessibility can vary from browser to browser To the extent possible web pages in LDMS are made accessible to screen readers and users that work with assistive technologies For example different parts of the user interface provide metadata so that their purpose in the application can be discerned by assistive technology Some reports and files generated by LDMS require the use of additional software to open and view A list of these application can be found in LDMS s system requirements If you are experiencing difficult using certain features of LDMS with assistive technology please contact the Frontier Science Foundation Related sections System requirements on page 10 This section lists the system requirements and recommendations for computers connecting to LDMS Contact the Frontier Science Foundation A time stored with a specimen other than its collection pr
113. eived Date QAQC Number Type Lab Lab Temperature 132 Received LDMS ii 777 Ambient 30 0ct 2014 29 0ct 2014 15 Sep 2015 Not Performed 127 Received LDMS 10 777 Cold Packs 11 Apr 2015 10 Apr 2015 08 Sep 2015 Not Performed 126 Received LDMS 10 777 Cold Packs 09 Apr 2015 08 Apr 2015 08 Sep 2015 Not Performed 114 Received LDMS 15 1700 Ambient 21 Aug 2015 20 Aug 2015 24 Aug 2015 Nol Generate Manifest 110 Sent LDMS 17 195 Cold Packs 09 Nov 2011 09 Nov 2011 No Batch Storage Report 100 Sent Loms 999001 500 Dry Ice 24 Jun 2011 24 Jun 2011 a Shipping Container Report Print labels 94 Sent Loms 401 373 Cold Packs 06 Apr 2011 06 Apr 2011 q QANQC 92 Sent LDMS 17 373 Cold Packs 24 May 2010 13 3u1 2011 No Mes pul QwaC report 90 Sent Excel or Comma 17 500 Cold Packs 11May 2010 11 May 2010 No Unship Separated Text 1 0 Unimport 89 Sent Excel or Comma 17 500 Liquid Nitrogen 11 May 2010 11 May 2010 Not Performed View gt Separated Text 1 0 Shipment number An internal shipment number assigned to the shipment at your laboratory Shipment type Indicates whether the shipment was sent to another Laboratory or received from another laboratory Shipment format The type of shipping file LDMS USRMANOO3 Page 85 LDMS User Manual Destination laboratory Sending laboratory Shipment temperature Setup date Ship date Received date QA QC Removing a received shipment Background Shipping The laboratory ID of the destination that
114. elect the enrollment for the new aliquot from the Enrollment box An aliquot cannot be enrolled in more than one study 6 Fill in the information for the new aliquot specimens Items marked with a red are required 7 Optional Enter additional information about the aliquot into the Comments box Information that is typically included here includes details for specimens that were not collected an explanation of a condition or an explanation of why a specimen is not available 8 Optional Enter additional information about the aliquot into the Internal only comments box Comments entered here are for your laboratory s use only These comments will not be included if the specimen s information is shipped to another laboratory 9 Atthe bottom of the window click Save The information you entered will be checked for completeness and validity If there is an issue it will be highlighted with a brief explanation of how to correct it Results The number of aliquots that you specified will be added to the participant visit The primary specimen will automatically change to unavailable to indicate that the specimen was consumed during processing LDMS USRMANOO3 Page 36 LDMS User Manual Specimen Management What to do next If you added multiple aliquots and any of those aliquots differed from the others such as one aliquot having a different condition be sure to make those changes to the aliquot Related sections Enteri
115. emplates can be used for FACTS HN The HN preset project must meet these requirements Data entry requirements Field ID1 studyID ID2 ID2 ID3 ID3 Visit OPID Clinic Draw Time Received Time HPTN Required Required Optional Optional Optional Optional Optional Optional Optional The HPTN preset project has these requirements LDMS USRMANOO3 Page 128 LDMS User Manual Data entry requirements Field ID1 PID ID2 Protocol ID3 Visit OPID Clinic Specimen Time Received Time Notes Required Required Required Depends Required Disabled Disabled Required Optional Preset projects Note LDMS performs a checks to make sure the PID is valid Based on the protocol LDMS will determine whether a 9 digit or 10 digit PID must be used Special PID checks are enforced if the protocol is 043 0 For 043 0 the visit will also be set to 2 0 VST and the user will not be able to modify it This field is disabled for all protocols except 043 0 It allows up to 12 characters and should be scanned from the blood ID number Defaults to the visit unit of VST Interim unscheduled visits should be entered by incrementing the visit value e g 1 10 for the first unscheduled visit 1 20 for the second etc If the protocol is 043 0 the visit will also be set to 2 0 VST and the user will not be able to modify it You will be warned if received time is blank
116. en information can now be cascaded from a primary specimen to aliquots at the user s discretion R 19052 Improved page loading times by allowing certain HTTP requests to be run in parallel R 19005 Validation of excluded positions in containers is now performed at the server level R 19622 Removed ContainsUnavailableSamplLes property from storage view models R 20058 Removed support for CDC barcode R 20164 When a new field is added to a table and that field has a default value new transaction log entries will now be made for these record changes R 20328 Set up an automated process for generating builds nightly and after committing code changes as well as running test units on builds R 20488 In web config on development customErrors mode is now set to off R 21639 Added Lang en to generated HTML output for Frontier Science web standards Fixes LDMS USRMANOO3 R 19217 Fixed issue where some reports would list co enrolled specimens twice R 19474 Fixed issue where specimens were not being found on the Labels page when searching on a field that was not defined for the specimen R 19641 Fixed ambiguous message the appeared when removing items from storage R 19892 Fixed issue where freezer temperatures did not appear in order when they could be selected from a menu R 19923 Fixed issue where the Shipping Container Report did not correctly show the sort order for individual containers R 19941 When generating specimen labels LD
117. enrollment and specimen in LDMS e Using the Quick Add feature recommended e Adding new participant enrollment and specimen information one by one For most data entry in LDMS the Quick Add feature is strongly recommended since it allows you to enter all of the information at once Adding individual items on the Specimen Management page is recommended for minor changes such as adding a single aliquot specimen to a primary specimen Each of the steps below can be completed independently provided that the previous steps were completed For example you can create a new participant in LDMS without enrolling that participant in any protocols or creating any associated visits however you cannot create a generic enrollment that is not associated with a specific participant visit Likewise it is also not possible to create a primary specimen without associating it with a specimen participant s visit Procedure 1 Create a new participant LDMS USRMANOO3 Page 20 LDMS User Manual Specimen Management Participant s are specific to a project If a person is participating in more than one project then they would be considered two different participants in LDMS and would be entered separately 2 Add an enrollment to the participant This means that you are associating the participant with a specific protocol Participants can be associated with multiple protocols 3 Adda visit to the participant Add a primary specimen to the vi
118. enrollments At the bottom of the window click Save Modifying a primary specimen A primary specimen can be modified on the Specimen Management page Background After a primary has been created it may need to be modified for a variety of reasons such as correcting a data entry error or updating its current condition Procedure 1 Click Specimen Management from the LDMS menu 2 Find the participant with the primary specimen to be modified Use filters from the left side of the screen to narrow down the participants that are displayed 3 Select the protocol ID2 associated with the visit from the Protocol box The label for the Protocol box will depend on the project Common labels are study and protocol 4 Click the Edit button to the right of the primary specimen to be modified The Edit Specimen window will open 5 Modify the primary specimen as needed If any aliquot specimens were added for this primary it will appear at the bottom of the window 6 Click the Save button If there are any issues with the changes that you made such as an invalid entry you will be prompted to correct it An explanation will appear next to the information that needs to be corrected Aliquot specimens An aliquot is a specimen that is derived from a primary specimen An aliquot is created by processing the specimen collected at a participant s visit into smaller specimens For example if 10 mL of blood was collected dur
119. ey are received e All specimens without a global specimen ID will be treated like aliquot specimens and assigned to a new primary specimen e All specimens without a global specimen ID will be assigned one e Specimens with the same project ID1 ID2 visit draw date draw time primary type and additive time will be grouped until the same primary specimen Shipment QA QC Shipment QA QC is the process of comparing actual specimens in a shipping container to the specimen that is expected in that container position by LDMS This should be done for shipments before they are sent and after they are received You can view the current QA QC status of a shipment on the Pending Shipments or Shipment History page QA QC Status Action Needed Complete None In Progress Finish QA QC Complete with Errors Investigate the specimens that did not pass QA Qc Not Performed Start QA QC To perform QA QC you need to look at the global specimen ID on a physical specimen and then compare it to the global specimen ID in LDMS If they match the specimen has passed otherwise it has failed QA QC should be performed by scanning the specimen s barcode which will read the global specimen ID and do the comparison for LDMS USRMANOO3 Page 83 LDMS User Manual Shipping you This is the recommended process If you do not have a barcode scanner you can manually compare the two global specimen IDs instead Figure 35 The QA QC Entry page Select a con
120. for the group PID and protocol combination entered PHACS clinics range between 1 and 24 LDMS will check that a valid clinic was selected This field is optional but recommended This field is optional but recommended create their own templates All PHACS templates are created by Frontier Science in The REPRIEVE preset project has the same requirements as the ACTG IMPACCT project PHACS The PHACS preset project has these requirements Data entry requirements Field Required Note ID1 PID Required end ID2 Protocol Required 1D3 N A Visit Required OPID Optional Clinic Required Specimen Time Optional Received Time Optional Notes e PHACS uses the standard LDMS shipping file format e There are two label options for PHACS specimens one with a barcode and one without e Quick Add templates can be applied for PHACS but users are not permitted to collaboration with PHACS leadership REPRIEVE SHIMS The SHIMS preset project must meet these requirements LDMS USRMANOO3 Page 134 LDMS User Manual Data entry requirements Field ID1 PID ID2 Study ID3 Rapid Test Visit OPID Clinic Draw Time Received Time SHIMS ID1 format RAAAhhcpp R AAA hh c pp SNRP Required Required Required Required Required Optional Optional Required Required 1to4 001 to 599 01 to 26 Check digit 01 to 99 Note Preset projects Nine characters long that meets the SHIMS
121. he and row labeling container Alphabetic uses letters while numeric uses numbers The second option specifies where labeling should start e Select the fill order for the shipping container from the Fill order box The fill order is the logic that is used to determine where specimens will be placed in the container f Select the sort order for the container from the Primary Sort Order box This is how specimens will be sorted before they are put into the container g If Prot ID2 was selected for primary sort order Select a Secondary Sort Order h Click the Add Specimens button The Store Specimens window will open i From the Available specimens list select each specimen to store and then click Add at the bottom of the List Use the available filters to narrow down the number of specimens displayed Specimens that are not available will cannot be selected The selected specimens will appear in the Selected Specimens list They can be removed from the shipment by clicking the Remove button next to them j Click the Continue button The Store Specimens window will close The Preview section for the shipping contain will indicate the positions that now hold specimens If you added more specimens than could fit in the contain multiple containers will have been created You can switch between these containers using the arrow buttons in the Preview section Click the Add button The shipping contain will appear in the Shipping boxes Li
122. he content of these reports are predetermined you can often add criteria to filter what will be displayed For example you could generate a report that lets you see all participant identifiers at your laboratory but only for a specific project Custom Report Builder The Custom Report Builder allows you to export specimen data from LDMS into a wide variety of formats The custom report builder allows you to do the following e specify what data to use to select specimens to appear on the report e the information to appear on the report e how to sort information on the report e apply complex logic to reports LDMS USRMANOO3 Page 87 LDMS User Manual Reports e save custom reports so they can be re used Figure 37 The Custom Report Builder Saved Queries Qe TESTING 2 Save Delete All Fields Fields to display Sort results by Specimen Storage Shipping Up Down Up Down Name Description Category Display Sort Name Remove Name Remove i AP m z jm A Address Assigned Has a destination Shipping 2 adtvess assigned x moere fe es address been es assigned Batch Number x Batch Number Shipment batch Shipping 7 identifier Destination Lab ID x Destination Lab ID Lab ID of the Shipping 7 lab receiving la import Date x Import Date Date batch was Shipping imported received Source Lab ID x Original Batch Batch identifier from Shipping a let A Additional Time x Sta
123. i nen a 48 QUANTITATIVE conditi NS ssteissi rse eeki aseen ei eanan ia 49 Other CONGITIONS 25 55 scts sscsestscconseuesuestasangessseside sleaaden as e a aai a Sioa 49 Stora ga s r a a e a E a aeaa a eaaa a aaa S oe AE aes SEn Se 50 SLAT 1E PARIE AOE EE I OEEO EAEE E E ON 50 Navigation on the Storage page sessssssessssssssessssssseesssssrerssssssressssssreessssseeesssssrersssssse 50 qhe storage Tenere i NT EN N Ni 51 Storage EMS era Aa a AA ARA 52 ICONS ANA Their MEANING ccccsscscsesessessssecsecsscssssssssesseseessssessessssecsecsesssssscseeceees 54 ASSIGNING StOFAGE LOCATIONS ecsessssssssecsessecsessessestestesscsecsecsscscescescessesesseeseseseessestesseateseenses 55 Adding a NEW storage UN It ccsessssssessessesecsessesssesccsccscesccseeseesessessesessesesesseesneees 55 Adding a new Level in a storage UNIt ee esessessessessesseseesestesesscsessscscencesceneeees 57 Adding a container tO a l vel sssssseesssssseersssseeeesssssseesssseseeessseseeessssseeesssssseessssssee 59 ASSIGNING a storage LOCATION TO SPECIMENS ccsscssssssesesesessessessescescesseseeseeees 60 Generating a printable List Of What is IN StOFAGE eceesseseessesestesessesseeseeseenes 62 CONMEAINER RE DONE anae aE En EEEE desler ethan EA 62 Storage template Samirana A AEE A ET A T AE a 63 Creating storage item templateS ssssseeesssseeeesssseseesssssseeessseseeessseseeesssssseeessssseress 63 Modifying and removing storag
124. ield ID1 PID ID2 ID2 ID3 ID3 Visit OPID Clinic Draw Time Received Time LDMS USRMANOO3 Required Required Optional Optional Optional Optional Optional Optional Optional Page 139 LDMS User Manual Preset projects WITSRepos The WITSRepos preset project must meet these requirements Data entry requirements Field Required Note ID1 Subject ID Required ID2 Study ID Optional ID3 Optional Visit Optional OPID Optional Clinic Optional Draw Time Optional Received Time Optional oe ZEBS The ZEBS preset project has these requirements Data entry requirements Field Required Note ID1 STUDYID Required S ID2 ID2 Optional ID3 ID3 Optional Visit Optional OPID Optional Clinic Optional ss Draw Time Optional s Received Time Optional LDMS USRMANOO3 Page 140 LDMS User Manual Codes units and abbreviations Codes units and abbreviations This section lists the codes units and abbreviations that are used in LDMS for various entry fields such as visits and specimen types These codes are used by both LDMS for the web and LDMS for Windows Specimen type codes Primary codes This section lists all of the available primary codes in LDMS LDMS USRMANOO3 Code AMN ANL APP ARB ARL ART BAL BHR BLD BMA BMC BMK BML BMR BRB BRN BRS BUC CER CRD CSC CSF CVB CVF CVL CXC Description Amniotic Fluid Anal Air Pollution Particles
125. ilters Type Der Type Conditio Visit Value HEQOO67G 01 v PL1 N A SAT feat E HEQOO67G 02 v PL1 N A SAT Eatv visit Unit HEQ0067G 03 v PL1 N A SAT Edit gt Clinic HEQOO67G 04 v PLL N A SAT Euit gt H ID3 1 The LDMS menu bar 2 The action menu 3 An applied filter 4 Currently viewed participant 5 Specimens 6 Sign out or switch laboratories LDMS menu bar The menu bar is used to navigate between different tasks in LDMS Hover the mouse pointer over a page to see its sub pages LDMS USRMANOO3 Page 13 LDMS User Manual Getting started filters Filters are available on most pages and will Limit the information that is displayed in the working area on the page For example if you are on the Specimen Management page and apply a filter with the value FRONTIER to the Project field only participants enrolled in the FRONTIER project will be displayed The filters that are available will vary depending on the current page To remove a filter after it has been applied click on it action menu The action menu is used in various areas of LDMS to perform a major task For example on the Specimen Management page the action menu is used to create a new participant signing out To sign out of LDMS as the current user click the Logout button in the upper right corner This button is available on every page change databases To change to a different laboratory database click the Change link in the upper right corne
126. imens that were entered or migrated from LDMS Specimens created using LDMS will not be assigned a specimen ID Specimen is available i E Specimen is assigned a storage location lt Specimen has been shipped to another laboratory amp Specimen has an additional enrollment Page 44 LDMS User Manual Specimen Management Field Usage Example Notes Stored Whether the Yes or no specimen currently has a storage location assigned sub additive If the specimen does not have a sub derivative additive derivative select NON Thaw count The number 3 of times the specimen has been frozen and thawed Total cell count Total number of 10 When entered it will be multiplied cells in millions by 1 million For example to indicate 10 million cells enter 10 to indicate 500 000 cells enter 5 visit value The protocol 1 Wk This comprises of two boxes a visit defined identifier number and visit type A visit value is for a visit typically a number or Letter The visit unit is selected from a pre defined list Hover the mouse pointer over a visit unit for a brief description Related sections Terms used in LDMS on page 16 Specimen records are stored as a hierarchy of related participant enrollment and information All of this information for a participant project combination comprise a record in LDMS Specimen conditions A specimen condition is a 3 letter code that indicates the status of a specimen Eve
127. in advance When receiving a shipping file it is possible to take shipping and storage items in the shipment and automatically asign them to your laboratory s storage The option to do this is provided when receiving a shipping file The items on the shipment will be placed in your storage based on what it is Item Where it will go in storage Storage unit Added as a new Storage unit In the SHIPPING IMPORT FREEZER on a level with the shipment number Level or container If the item was a storage item at the sending laboratory it will retain its original name in your storage If the item was a storage contain created for the shipment it will be LDMS USRMANOO3 Page 82 LDMS User Manual Shipping placed in the SHIPPING IMPORT FREEZER on a level with the shipment number These containers will generally have names like Auto generated box 76 1 in your storage Once the items are added to your storage you are not restricted to how you use them You can retain containers move them to different storage units and so forth Related sections Receiving shipments on page 81 Receiving a shipment is the process of importing a shipping file received from another laboratory to add the specimen s information into your laboratory s database Handling non LDMS shipping files Shipping files that did not originate from LDMS may not contain the global specimen ID needed by LDMS Such specimens will receive special handling when th
128. in order to use LDMS Frontier Science cannot provide user support for web browsers that are not listed although they may be able to use LDMS without any issues Other software LDMS can generate reports and other types of files in several different formats Most of these files can be opened by commonly used programs that are already on our computer PDF viewer Needed to view and print reports Many web browsers have a built in PDF viewer You can also download many PDF viewers for free such as Adobe Reader and Evince LDMS USRMANOO3 Page 10 LDMS User Manual Getting started Spreadsheet viewer Needed to view exportable reports Microsoft Excel or LibreOffice Calc can open these files Recommendations e Screens resolution at least 1024 pixels wide if you use a smaller screen size you will need to scroll right and left to see the full contents of most pages e Firefox or Chrome Internet Explorer may not be suited for complex web applications such as LDMS e A 2D barcode scanner can be used to scan barcode labels to get a specimen s global specimen ID e A printer for specimen labels Related sections LibreOffice website Adobe Reader website Evince PDF viewer website Firefox web browser Google Chrome web browser Signing in to LDMS Sign in to LDMS by using your user name and password and selecting a laboratory database Before you begin You must have a user account before you can sign in to LDMS Procedure 1
129. iner in the order that they are selected This will be important later if you utilize the auto fill feature Once all specimens to be stored have been selected click Continue at the bottom of the window The Select position for specimen window will open Select the position where the first specimen will be stored from either the Position box or the Preview image The global specimen ID for the specimen will be displayed in the window Positions that are gray are not available because a specimen already occupies that location A position that is black is an excluded position in the container s configuration Optional To place the remaining specimens to be stored automatically based on the container s fill order setting select the Auto fill from selected position option Page 61 LDMS User Manual Storage 9 Click Continue If there are more specimens to be stored and you did not select the Auto fill from selected position option you will be prompted to select a position for those specimens otherwise the window will close Results The specimens are now stored If you look at the storage tree you will see that they are now listed under the specified container What to do next Generate the Storage Details and Container reports These will help you know where the specimens need to physically be stored Related sections Generating a printable list of what is in storage on page 62 The Storage Details and Container reports can be u
130. infected with NDVW and treated with TSST TNN TSST with NDVNS1 TNV TSST with NDVB1 TOC Tocopherol Vit E TRI TriReagent TRX Triton X TRZ Trizol TSC Myeloid dendritic cell infect w Sendai Cantell and treat w TSST TSS TSST Toxic Shock Syndrome Toxin TTX Tetanus Toxoid treated UCT Urine cartridge UNK Unknown Sub A D UNT Untreated Unstimulated VCS Cervicovaginal secretions VIB Veal Infusion Broth VIR Virus VPS VP Stimulator VPT VP Target VTM Viral Transport Media ZLN Ziehl Neelsen Condition codes This section lists the specimen condition codes available in LDMS Code Description ANM Sample Anonymized ANP Aliquot not prepared LDMS USRMANOO3 Page 154 LDMS User Manual LDMS USRMANOO3 Code BKV CDT CLT coc CTM DIM DMG DSH DSR EQF EXP FRO HEM HUM ICT INT INV LBE LIP LKD LSH LYS NQA OPR osw OTH PST ONS REF SAT SHV SNC SNP SNR TNO TWD UNK VRU VPL Codes units and abbreviations Description Broken or cracked vial Consumed During Testing Clotted Combination of Conditions Explain Contaminated Dry Ice Melted Damaged container Delayed Shipment Destroyed Equipment Failure Expired Frozen Hemolyzed Exposed to high humidity Icteric Excess Bilirubin Incorrect Tube Invalid Specimen Lab Error Lipemic Leaked Lost Shipment Lysed Real time QA for viability and viable recovery not performed due to low volume of specimen collected Sample drawn outside
131. information on this report is identical to the hover text that appears throughout LDMS e Measurement codes e Visit unit codes e Time unit codes e Specimen condition codes Related sections Specimen conditions on page 45 A specimen condition is a 3 letter code that indicates the status of a specimen Terms used in LDMS on page 16 Specimen records are stored as a hierarchy of related participant enrollment and information All of this information for a participant project combination comprise a record in LDMS LDMS USRMANOO3 Page 97 LDMS User Manual Reports LDMS primary additive derivative sub additive derivative codes report Provides a list of LDMS primary additive derivative and sub additive derivative codes throughout LDMS Information displayed on report I I Note The information on this report is identical to the hover text that appears throughout LDMS e Primary codes e Additive codes e Derivative codes e Sub additive derivative codes Participant reports Participant identifiers report Provides a list of participants in your database by project Sorting Filter criteria Information displayed on report This report is sorted by project ACTG PID e Project and then by ID1 ACTG protocol e ID1 ACTG protocol type e ID2 Non ACTG PID ID1 e ID3 Non ACTG Prot ID2 e OPID OPID e Clinic Project SID ID3 Quick Add Templates Quick Add Template List Report This report provides a list of Quick
132. ing a visit that 10 mL tube is the primary specimen It may be processed then into smaller 1 mL tubes of double spun plasma These 1 mL specimens are the aliquots in LDMS Adding aliquots to a primary specimen An aliquot specimen is added to a primary specimen on the Specimen Management page Background An aliquot is added to an existing primary LDMS USRMANOO3 Page 35 LDMS User Manual Specimen Management Procedure 1 Inthe menu bar click Specimen Management 2 Find the participant by using filters on the left side of the screen 3 Click the arrow next to the Edit button to the right of the primary to which the aliquots will be added and then click Add New Specimen Figure 18 Adding a new aliquot to a primary specimen Add New Specimen Manage Enrollments ty Print Aliquot Labels for Coenrallments Delete The Create Specimen window will open 4 Enter the number of aliquots that were created into the Number of Aliquots box When entering more than one aliquot together all aliquots should have the same basic properties such as the same volume If you want to add multiple aliquots with different information you can still do so but you must edit the aliquots later For example if you have 3 aliquots that are identical but one has a different specimen condition you can add all three together and then change the condition of the one aliquot when you are finished 5 If the primary is co enrolled S
133. ional Note 11 digits of any combination of letters and numbers Selected from pre populated list Once selected the LDMS will check that the PID is associated with the selected protocol This field is not used by Aeras Select from pre defined List of visit units This field is not used by AERAS AERAS clinics are in the format ARSXX where XX are the 5th and 6th digits from the PID The AIEDRP preset project has these requirements Data entry requirements Field ID1 PID ID2 Protocol ID3 SID Visit OPID Clinic LDMS USRMANOO3 Required Required Required Required Required Optional Optional Note Must either pass the ACTG IMPAACT or HPTN ID1 validation check depending on the protocol Will determine what ID1 format should be used Must be NOSID or pass the ID1 validation Page 120 LDMS User Manual Preset projects Field Required Note Draw Time Optional a Received Time Optional Protocol and ID1 check used Protocol 103005 103006 103007 103008 103010 103011 COREO1 AIN501 AIN502 AIN503 AIN504 AMC ID1 validation used ACTG IMPAACT ACTG IMPAACT ACTG IMPAACT ACTG IMPAACT Either Either Either Either Either Either Either The AMC preset project has these requirements Data entry requirements Field ID1 ID1 ID2 PROTOCOL ID3 ID3 Visit OPID Clinic Draw Time LDMS USRMANOO3 Required Required Optional
134. ipant For other types of work such as quality control testing ID1 could also be something else like a testing panel number 6 Enter the name that you want to use for D2 into the ID2 Name box and a brief description into the ID2 Description box ID2 is typically used for a study or protocol identifying number 7 Enter the name that you want to use for D3 into the ID3 Name box and a brief description into the ID3 Description box ID3 is typically used as a sub study or sub protocol identifying number 8 Click the Save button Results The new group will be added to the list of groups that you specified Modifying and removing a project Local project can be modified or removed after they are created Before you begin A local project can only be removed if it is not currently in use Government projects cannot be modified or removed Background This might be needed if there was a mistake with the way the project was initially entered or if you need to update the descriptions for the participant fields Changes made to a project will automatically update existing participant records in LDMS Procedure 1 Click Administration gt Projects from the LDMS menu bar 2 Locate the project to be modified or removed from the list of projects 3 Doone of the following e To modify the group click the Edit button to the right of the project The Edit Project window will open where you can make your changes When you are done c
135. irectly matched to shipments between laboratories Instead you would need to use the shipment setup date and other information to match a shipment that you sent to the same shipment received at another laboratory New shipments New shipments are created on the Pending Shipments page The Pending Shipments page shows all data shipments that have been created but not yet sent This page serves the following purposes 1 Create new shipments 2 View or modify shipments that have been created but not yet sent 3 Ship a shipment Figure 31 The Pending Shipments page Batch Shippment Destination Shipment Setup Date Ship Date QA Qc Number Format Lab Temperature 119 LDMS 300 Dry Ice 08 5ep 2015 08 5ep 2015 Not Performed Edit Ship 118 LDMS 1 Dry Ice 02 Sep 2015 02 Sep 2015 Not Performed Eivhip 117 LDMS 350 Ambient 02 5ep 2015 02 5ep 2015 Not Performed Edit Ship m 116 LDMS 350 Ambient 02 Sep 2015 02 Sep 2015 Not Performed Edit Ship F 115 LDMS 350 Cold Packs 02 Sep 2015 02 Sep 2015 Not Performed Edit Ship gt 113 499 13 Aug 2012 Not Performed Edit Ship v 108 999001 01 Sep 2011 Not Performed EditShip 102 17 Dry Ice 11 3u1 2011 Complete With EditShip ha Errors E 66 999001 Cold Packs 05 Apr 2010 Not Performed Edit Ship gt 55 300 Cold Packs 25 Mar 2010 Not Performed EditiShip v The term ship in LDMS means that all of the specimens you want added to a shipment have been added and it is ready
136. is image shows how a primary specimen without aliquots created in LDMS for the web is converted to an aliquot if shipped to an LDMS for Windows laboratory In this situation if the new aliquot is shipped to a laboratory that users LDMS for the web it will recognize that the global specimen ID belongs to a primary specimen and not an aliquot and will turn it back into a primary specimen Related sections Specimen identifiers on page 29 All specimens in LDMS are assigned a unique specimen identifier Adding a primary specimen to a visit A new primary specimen is added to a visit on the Specimen Management page LDMS USRMANOO3 Page 31 LDMS User Manual Specimen Management Background A primary specimen is added to an existing visit The primary specimen can be added in LDMS even if it has not yet been processed into any aliquots Procedure Locate and select the visit 1 2 Click Specimen Management from the LDMS menu Find the participant to which the primary specimen will be added Use filters from the left side of the screen to narrow down the participants that are displayed Select the ID2 associated with the visit from the ID2 box The label for the ID2 box will depend on the project Common labels are study and protocol Add the new primary specimen 4 Click the down arrow next to the Edit button to the right of the visit to which the LDMS USRMANOO3 primary will be added and then click Add
137. is indicated within the shipping file The laboratory that generated the shipping file The shipment temperature that was indicated in the shipping file The date the shipping file was created The date that the shipping file was generated The date that your laboratory loaded the shipping file in LDMS only applicable to shipments that you received This indicates whether or not QA QC was performed on the shipping file If a shipping file was received and loaded into LDMS in error it may need to be removed Because multiple laboratories may be affected and the quality of specimen data affected the ability to unload a shipping file that was received requires you to contact LDMS User Support Procedure 1 Contact LDMS User Support This should be done first because if your session is idle for too long and you are logged out a new challenge code will be generated 2 Inthe menu bar click Shipping gt Shipment History 3 On the View button to the right of the shipment click the arrow and select Unimport 4 Provide LDMS User Support with the Challenge Code 5 In the Response Code box enter the code provided LDMS User Support 6 Click Unimport Related sections Challenge codes on page 15 A challenge code is password that you must give to LDMS User Support to perform certain actions in LDMS Un sending shipments After a shipping file has been generated and a shipment changed to sent in LDMS it is possible to ch
138. ition box or on the Preview e lt If you are adding more than one item you can select the Auto fill all from selected position This option will place the remaining storage items based on the fill order of the storage item containing it If you do not select this option you will be prompted to manually position each storage item Page 64 LDMS User Manual Storage f Click the Continue button The storage item s will now appear in the Default Levels List You can add sub levels and containers to the default levels that you ve added as needed 11 Click the Save template button Modifying and removing storage templates Storage templates can be modified or removed after they have been created Background Changes to templates will only affect new storage items based on the template Existing storage items that were based on the template will not be updated Procedure 1 Hover the mouse pointer over Storage from the LDMS menu bar and then click either Storage unit templates Level templates or Container templates depending on the type of template you want to modify 2 Select the template to modify from the Saved Templates box I 14 Note If you want to clear the screen so that you can create a new E template instead of modifying the selected template click the Add new button The settings for that template will be displayed 3 Modify the template as needed If you want to remove the template click the Delete
139. ive e Primary Derivative e Additive Non ACTG PID ID1 e Derivative Non ACTG Prot ID2 e Sub Additive Derivative Primary e Volume Project e Volume Unit Sub Add Der e Count Visit Unit Visit Value Primary specimen database dump report Provides a list of specimen ID numbers for primaries along with draw dates and received dates Sorting Filter criteria Information displayed on report This report is sorted by None e Specimen ID specimen ID e Other specimen ID e Draw date e Received date Sample counts for specified group report Shows how many specimens for a given derivative type are available for each group locally LDMS USRMANOO3 Page 95 LDMS User Manual Reports Sorting Filter criteria Information displayed on report This report is organized by Derivative e Derivative type project Project e Description of derivative Received date type Specimen date e Count number of specimens Specimen export report Designed for pulling information for local groups that have been shipped Sorting Filter criteria Information displayed on report This report is sorted by project e Shipped batch number e Protocol then by participant identifier e Project ID1 and then by specimen ID e Primary type e Derivative type e Additive e Sub additive derivative type e Draw date e Visit value e Visit unit e Global specimen ID e Original volume e Original volume unit e Available volume e Available volum
140. l errors such as receiving the wrong shipping file 6 Click Receive Shipment Results LDMS will assign the next available shipment number to the shipment What to do next Go to the Shipment History page to view the newly received shipment and perform additional actions such as QA QC Related sections Shipment QA QC on page 83 Shipment QA QC is the process of comparing actual specimens in a shipping container to the specimen that is expected in that container position by LDMS This should be done for shipments before they are sent and after they are received Related sections Import as is on page 82 When receiving a shipping file it is possible to take shipping and storage items in the shipment and automatically asign them to your laboratory s storage The option to do this is provided when receiving a shipping file Shipping and projects Import as is In order to receive a shipment a laboratory must already have the projects in the shipment defined For example if a laboratory sends you a shipping file that contains specimens in the FRONTIER project you must create the FRONTIER project at your laboratory before you can receive the shipping file If you do not create the project first you will receive an error message when attempting to receive the shipping file For this reason it is good practice to communicate with a laboratory before you send a shipping file to ensure that they have created the necessary projects
141. lected from a pre defined List For some protocols a temporary value such as NOSID may be used until the exact value is assigned to the participant For other protocols this field may not be used or may be optional These comments will not be included if the specimen data is shipped to another laboratory Availability means that the specimen exists and can be shipped stored and so forth Reasons that a specimen might not exist include being destroyed or being shipped to another laboratory For primary specimens that have not been processed into aliquots this is the enrollment that owns the specimen There are no rules or validation for this field it can be used to assign a special identifier if needed by your laboratory Selected from a pre defined List of codified values Hover the mouse pointer over a type for a more detailed description Page 43 LDMS User Manual Field Processing date Processing tech initials Processing time Reason specimen not collected Received date Received time Shipped Specimen condition Specimen ID Status LDMS USRMANOO3 Usage Example Date a primary 15 Oct 2012 specimen was processed into aliquot specimens The initials of JD the person who processed a primary specimen into aliquot specimens Time a primary 16 15 specimen was processed into aliquot specimens Explanation of Specimen why an expected potentially specimen was no
142. lick the Save button e To remove the project select Delete from the Edit menu to the right of the project Government projects Government projects are those that are defined by Frontier Science LDMS USRMANOO3 Page 116 LDMS User Manual Administration Frontier Science works with government funded projects to define the rules and specifications for their project These projects cannot be modified or removed by users Even though they cannot be modified they will still be visible on the Projects page User management User accounts are managed by Frontier Science Accounts for individual users are created and maintained by LDMS User Support To perform the following tasks you would need to contact LDMS User Support for assistance e Create a new user e Reset a users password e Manage what features in LDMS a user can access Users can modify their own passwords from within LDMS Changing your password Users can modify their own passwords from within LDMS Background While the creation and management of user accounts is handled outside of LDMS users can change their passwords on their own without contacting LDMS User Support Procedure 1 From the logout menu in the upper right corner of the page select Change Password Figure 45 The Logout menu Logout x Change Password The Change password window will open Enter your current password into the Password box Enter your new password into the New Passwor
143. ll automatically modify a specimen s availability There are other places where you can manually change availability e You can manually change the availability of both primary and aliquot specimens unless the specimen has been shipped e Specimens will automatically become unavailable if they are shipped e Ifaspecimen s volume changes to zero it is automatically made unavailable e A primary specimen will automatically become unavailable after aliquots have been derived from it and you cannot change it back to available unless the aliquots are deleted e Certain condition codes such as DSR destroyed will automatically change a specimen to unavailable LDMS USRMANOO3 Page 41 LDMS User Manual Specimen Management Table 2 Specimen conditions that modify availability Code Description QNS Quantity Not Sufficient SNC Sample Not Collected SNP Sample Not Processed ANP Aliquot Not Prepared LSH Lost Shipment DSR Destroyed Related sections Specimen conditions on page 45 A specimen condition is a 3 letter code that indicates the status of a specimen Specimen record details This section describes each specimen record entry box that appears on the Specimen Management page Field Usage Example Notes Used to indicate information such as the amount of time a participant was fasting Typically used for pharmacology specimens to indicate the amount of time after the last dosage was taken Additional time Avalue andauni
144. m Bronchus Wash Nasal Nasopharyngeal Nasopharyngeal Wash Naso oropharyngeal Codes units and abbreviations Page 142 LDMS User Manual LDMS USRMANOO3 Code NSB OPW ORH ORL OTH PAN PEN PFL PHR PHX PLC PLQ PRT REC RSC SAL SCR SEM SHR SIN SIS SKN SLU SPI SPL SPS SPT SSN SSS STL TBD TCA TER THR THW THY TIL TON TVC UNK Description Nasal brush Oropharyngeal Wash Oropharyngeal Oral Other Perianal Penis Pleural Fluid Hair Pubic Pharynx Placental Tissue Plaque Prostate Tissue Biopsy Rectal Rectosigmoid Colon Saliva Scrotum Semen Hair Scalp Sputum Induced Non Select Sputum Induced Select Skin Skin Lesion Sputum Induced Spleen Sputum Spontaneous Sputum Sputum Spontaneous Non Select Sputum Spontaneous Select Stool Specimen type to be defined Tracheal Aspirate Tears Throat Swab Throat Wash Thymus Terminal Ileum Tonsillar Biopsy Aspirate Transverse Colon Unknown Primary Codes units and abbreviations Page 143 LDMS User Manual Additive codes Code URN UTH VAG VCS VGL VSC VUL WAR Description Urine Urethra Vaginal Swab Cervicovaginal Secretions Vaginal Vaginal Secretions Vulva Warts Codes units and abbreviations This section lists all of the additive codes available in LDMS LDMS USRMANOO3 Code ACD AG1 AG2 AHP BBL BFM BOR BTM CPD CPH CPS CTK DFA DHP DPE DSE EDT END ETH FFN FMD
145. mpatibility with LDMS for Windows certain data entry fields are now automatically converted to upper case characters R 20255 A dialog window showing the version of assemblies is now available in LDMS in debug builds R 20432 The session timeout for debug builds has been disabled R 20523 Transactions will now have their exportable flag set and will be associated with one or more project IDs R 20647 ASP NET MVC has been removed as a deployable dependency Issues fixed R 20121 When receiving a shipping file that contains specimens collected for a project that does not exist at the receiving laboratory the project will now automatically be created as expected R 20173 Fixed issue where storage locations were sometimes corrupted during shipping file import R 20325 Fixed issue where aliquots could not be seen under certain circumstances when removing an enrollment R 20400 Fixed issue where a primary specimen s availability would be inappropriately changed to available even if it had aliquots when it was received in a shipping file R 20412 Fixed issue where the positions of specimens were not correctly displayed for received CSV shipping files R 20504 Changed language on sign in page to refer to WebLDMS instead of LDMS R 20514 Fixed issue where the application version number was no longer displayed after an unsuccessful sign in attempt R 20572 Fixed issue where draw date was erroneously not marked as required when cr
146. nce items AND OR and numbers corresponding to the grid rows above 1 OR 2 AND 3 AND 4 File Type C Por cpap Generate Report In this example the report that will be generated will contain all BLD or ART specimens that also have a volume greater than 10 mL 1 Report categories 2 Add criteria to table below 3 Logic for generating report 4 File format for the report Procedure 1 On the LDMS menu bar click Reports gt Standard Reports 2 In the Report categories box select a broad category for the report you want to generate 3 Inthe Report box select a report Optional Add one or more filter to narrow down the information displayed on the report a Select a data item to filter by from the box below Filter Criteria Additional boxes will appear to specify the details for the filter b Select an operator from the middle box EI Note The lt gt operator means not equal to c Select a value for the filter from the third box The values available will be dependent on the filter For example if you are filtering by Additive only valid additives in LDMS will be displayed d Click the Add button Your criteria will be added to the list of filters If you want to remove it after it has been added click the Delete button to its right Page 91 LDMS User Manual Reports 5 Optional Specify logic for the report in the box below the filter criteria The logic is formed by using
147. nd the world to manage specimen tracking inventory storage specimen shipment and much more This manual is the authoritative resource for learning to use LDMS for users It explains many concepts important for using LDMS and provides instructions for using most features I 14 Note This manual covers for LDMS for the web If you are Looking for E information about LDMS for Windows it has a separate user manual Both user manuals can be found on the LDMS web page Getting started Getting started LDMS is a web based laboratory data management solution used to manage collections of biological specimens This manual describes how to use LDMS and is intended for users at laboratories About LDMS LDMS is a web based data management solution for laboratories managing biological medical specimens It is specifically designed for the needs of small and medium sized research laboratories It runs in web browser and does not need to be installed on a computer This means that LDMS can be accessed around the world from many web enabled devices such as laptops tablets and traditional desktop computers LDMS can perform many tasks including e cataloging specimen information such as its volume additive and current condition e managing the transfer of specimen information between laboratories e generating labels for specimens e keeping track of where specimens are located in storage units Frontier Science manages data for labor
148. ng specimen information Overview on page 20 Records are added to LDMS from the top down starting with the creation of a new participant Quick add on page 37 The quick add feature allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS Entering cryopreservation information on page 37 Crypreservation information can be entered for aliquot specimens with the CEL derivative type PBMC Cells Viable Entering cryopreservation information Quick add Crypreservation information can be entered for aliquot specimens with the CEL derivative type PBMC Cells Viable Procedure 1 On the Specimen Management page location the specimen for which you are entering Cryopreservation information 2 From the Edit button to the right of the specimen click the down arrow and then click Cryopreservation This option will only be available for specimens with the derivative type CEL 3 Doone of the following e If results were obtained select Results Obtained e If results were not obtained select the reason there are no results from the Reason list 4 f results were obtained complete the information in the HIV Status Primary Specimen Details Aliquot Details and Technician Details sections 5 Inthe Processing Tech Initials box enter the processing technicians initials Inthe Data Entered By box enter your initials 7 Click Save The quick add feat
149. nnot be linked across projects enrollment The protocol or study in which the participant is enrolled visit A specific event at which a primary specimen was collected from a participant primary specimen The specimen that was collected from the participant such as an unprocessed tube of blood aliquot A specimen that was created by processing a primary specimen into a smaller specimen Each part of a specimen record is selected in sequence For example you must specify a project before enter participant information Likewise you must create the information for a visit event before you can add specimens that were drawn at that visit Related sections Participant identifiers on page 21 LDMS USRMANOO3 Page 17 LDMS User Manual Specimen Management A participant identifier is a series of numbers and Letters that uniquely identifies a participant within a specific project Visit identifiers on page 27 A visit identifier defines the type of visit Specimen identifiers on page 29 All specimens in LDMS are assigned a unique specimen identifier Specimen record details on page 42 This section describes each specimen record entry box that appears on the Specimen Management page Navigation on the Specimen Management page The Specimen Management page shows all of the visits for a specific participant and protocol combination Important The labels for certain buttons and menus in LDMS vary based on the project For one particip
150. ntitative Culture Placenta Placenta Slice Periopaper Strip QFT TB Ag Red Cap QFT Mitogen Purple Cap QTF Nil Grey Cap Red Blood Cells Rectal Resting CD4 T cells Saliva Supernatant Dermis Inner Supernatant Dermis Outer Secretions Supernatant Epidermis Inner Semen Supernatant Epidermis Outer Serum Hair Scalp Skin Slide from a primary sample Smear SNO Strip Sponge Unfractioned Sputum Induced Supernatant from a Quantitative Culture Unfractioned Sputum Serum High Speed Spun Quantitative Culture Held beyond 14 Days Stool Culture Supernatant Swab Specimen type to be defined Codes units and abbreviations Page 149 LDMS User Manual Code TD4 TFS THW THY TIS TON TRC UMB UNK URN VAG VCP VTM Ww WBP WEK WFC WFS WPK XDA XFL XPA XPD XPR XTN Description Resting CD4 T cells Tear Flo Strips Throat Wash Thymus Tissue Tonsillar Biopsy Aspirate Trucount Placenta Cord Slice Unknown Derivative Urine Vaginal Vaginal cup Viral Transport Media D Wet Dry Whole Blood Pellet Specify Methodology Wick Wek Cell Sponge Codes units and abbreviations Unstimulated whole blood cell lysed fixed frozen with DMSO for flow Stimulated whole blood cells lysed fixed frozen with DMSO for flow Whole Blood Packed Extracted DNA Extracted Fluid from RNA RT PCR for Sequencing Extracted RNA Extracted Pellet from DNA PCR for Sequencing Extracted Pellet from RNA
151. nual Labels There may be times where you need to generate labels from a variety of sources For example you may want to print labels for all specimens received on a specific day The Labels page allows more complex logic for selecting the labels to print Figure 42 The label generation page Project FRONTIER Frontier Science Internal Study Format Frontier Label i Create Format Modify Format Delete Format Barcode LDMS Standard Label Fields Specimen ID Global Spec ID ID 2 Protocol VID Value VID Unit ID 1 PID Primary Additive Derivative Sub Add Der Volume Vol Units Time Time Unit Spec Date Spec Time Other Specimen ID Label Barcode Label 2 1 x 1 75 Zebra printer Notch on Left 8 rows Label Manufacturer Manufacturer Unknown Specimen Criteria Received Batch No 15 add Field Operator Value ne Batch o 15 Delete Skip Generate Labels Procedure 1 Select the project for which you are generating labels from the Project box 2 Select a type of label from the Format box The Label Fields section will show a preview of the labels 3 Select a label paper type and size from the Label box Add search criteria to determine which specimens should have labels printed For example to print labels for blood specimens that your laboratory received on 04 Mar 2014 you would apply the filter Received date 04 Mar 2014 and Primary BLD a Select the information to filter from the first box such as
152. ny places throughout LDMS not just the Labels page R 20836 Added support for the REPRIEVE project General improvements LDMS USRMANOO3 R 19891 If JavaScript is not enabled or available you will now see a warning message prior to signing in to LDMS R 20213 Shipping files are now named with simply the shipment number This improves compatibility with LDMS for Windows R 20710 Added navigation links to improve LDMS s compliance with the Section 508 Amendment to the Rehabilitation Act of 1973 R 20908 Added new label format for the REPRIEVE project Page 166 LDMS User Manua LDMS USRMANOO3 l Release notes R 20864 Added check to prevent the creation of shipping files that contain no specimens R 20943 Improved ability to import primary specimens from LDMS for Windows A feature added to LDMS for Windows version 10 0 allows it to import shipments that contain primary specimens without aliquots by converting the primary into an aliquot If such a specimen is shipped back to a laboratory using LDMS the aliquot will now be converted back into a primary R 21091 Changed the way LDMS receives shipping files to ensure compatibility with updated shipping files in the future R 21096 Changed connection timeout time This helps prevent unnecessary timeouts when using LDMS on a slow Internet connection R 21189 Labels will no longer be generated for unavailable specimens R 21255 Updated LDMS s logo R 21257 To help ensure co
153. ocessing or freezing time such as the time the specimen was collected since the patient s last medication does or the number of hours that the patient was fasting The substance that is mixed in with a specimen that was collected from a patient such as an anticoagulant represented in WebLDMS by a 3 letter code aliquot specimen availability A specimen that was created by processing a primary specimen such as creating double spun plasma aliquots from a blood primary specimen Also known as sub specimen A property of a specimen that indicates whether or not the specimen is available at your laboratory for shipping storage and testing LDMS USRMANOO3 Page 169 LDMS User Manual Terms Also known as not available never store available volume The amount of a specimen that is in a state that it can be used such as the remnants of a primary after it has been processed into aliquots barcode A 2D image that contains a specimen s global specimen ID and can be ready by a 2D barcode reader batch A shipment to another laboratory challenge code A randomized code generated when you attempt to access certain restricted features in WebLDMS used by LDMS User Support to determine the response code needed to access the feature Also known as challenge password lock code clinic The site where the visit occurred at which a primary specimen was collected co enrolled A primary specimen that is associated with more than one patient visit
154. ocol ACTG protocol type Additive Condition Derivative Import date Laboratory ID Non ACTG Prot ID2 Other specimen ID Primary Project Shipment number Specimen date Specimen ID Specimen time Sub additive derivative Time Time unit Visit unit Visit value Volume Volume unit Information displayed on report e Import batch no the shipment number e Import date e Sending laboratory e Specimen ID e Project Prot e Primary e Additive e Derivative e Sub additive derivative e PID ID1 e VID e Condition e Volume e Specimen date e Specimen time e Other specimen ID e Time Time unit Page 99 LDMS User Manual Imported specimen report summary Reports Shows the number of a specific type of specimen received as part of a shipment from another laboratory Sorting Filter criteria This report is sorted by ACTG protocol ACTG protocol type Additive Derivative shipment number Import date Non ACTG prod ID2 Primary Project Sending laboratory ID Shipment number Sub additive derivative Shipped specimen report detail report Information displayed on report e Sending laboratory e Batch number shipment number e Project protocol combination e Import date e Primary e Additive e Derivative e Sub additive derivative e Count Lists the specimens within a shipment organized by shipment number Sorting Filter criteria This report is sorted by ACTG Protocol
155. of specimen records and related information for participant enrollments In LDMS a participant an enrollment and specimens drawn from a participant including the specimens derived from them form a specimen record Specimen records are added and displayed on the Specimen Management page Terms used in LDMS Specimen records are stored as a hierarchy of related participant enrollment and information ALl of this information for a participant project combination comprise a record in LDMS LDMS USRMANOO3 Page 16 LDMS User Manual Specimen Management A specimen record in LDMS is the collection of specimen study and visit information for a specific participant Figure 4 Contents of a specimen record Participant ID1 FRONTIER WK4 Visit J 56C FU Enrollment ID2 30 4 B L 4 4 09 Sep 2015 Primary specimen 05000 001PHE00 000 0500 001PHE00 003 Aliquot specimens D 0500 001PHE00 003 0500 001PHE00 003 The top of a specimen record represents the largest part such as a clinical trials network the right side of this image is an example of each item project The organization that sponsors or conducts the study in which the participant is enrolled participant The person or specimen source if the project doesn t work with human samples that is participating in a given project If a person is participating in more than one project they will be considered two different participants in each project Participants ca
156. oject ID2 ID1 Visit Draw date Draw time Primary Additive Derivative Sub additive derivative Volume Storage location Related sections Creating new shipments on page 72 Creating a shipment means defining which specimens will be sent and where they are going to be sent Receiving shipments Receiving a shipment is the process of importing a shipping file received from another laboratory to add the specimen s information into your laboratory s database Background Once you have the shipping file from the laboratory sending you the specimens you can import the specimen information into LDMS Procedure 1 From the menu bar click Shipping gt Receive Shipments 2 Click Select File A window will open to select the shipping file The shipping file will generally be named ship your Laboratory ID number xml for LDMS shipping files or Lab your Laboratory ID number csv for CSV files 3 Optional If you want specimens to automatically be assigned storage Locations select Import directly into storage 4 Click Preview Shipment 5 Review the shipment to ensure it is correct LDMS USRMANOO3 It is a good idea to check that the shipping destination is your laboratory and that the specimens are what you were expecting Click the View button next to Page 81 LDMS User Manual Shipping shipment containers to see what specimens are in the shipment By checking the shipment at this stage you can avoid potentia
157. olume Volume unit Specimen date Received date Primary Additive Specimen condition Volume Other specimen ID Comments from the Specimen Management page Should the number of aliquots entered stored and shipped by your laboratory by project protocol combination as well as the total across all projects and protocols Sorting Filter criteria Information displayed on report This report is sorted by project ACTG protocol Project protocol protocok combination ACTG protocol type combination Clinic ID e Number of aliquots entered Derivative into LDMS Project e Number of currently stored aliquots Specimen date i e Number of shipped aliquots Specimen log report Provides detailed information about every primary and aliquot within a laboratory s database Sorting Filter criteria Information displayed on report This report is sorted by project ACTGPID e PID ID1 protocol combination then by ACTG protocol Project prot draw date ane Shen grouper ACTG protocol type SID ID3 by primary aa Additive VID Clinic ID Clinic Condition OPID Derivative Primary specimen ID LDMS USRMANOO3 Global specimen ID Import date Non ACTG PID ID1 Global specimen ID Specimen time Specimen date Page 102 LDMS User Manual Sorting Specimen processing report Filter criteria Non ACTG Prot ID2 OPID Other specimen ID Primary Project Received date SID ID3 Shipped Specimen date Specimen ID Specimen
158. omatically assigned by LDMS and cannot be assigned manually More than one condition code applies the comments field in LDMS can be used to list the applicable codes The specimen has been destroyed There is something noteworthy or unusual about the specimen but no other available condition code applies Page 49 LDMS User Manua Storage Storage L Code Description SAT Satisfactory UNK Unknown YST Did consent to storage NST Did not consent to storage Storage Usage The default condition code for new specimens indicating that the specimen was collected processed and handled as expected Indicates that there is a significant gap in knowledge in the specimen s history For example if the specimen was collected by another laboratory that was not using LDMS and is several years old and it may have been stored or treated improperly this code may be appropriate The participant has provided consent to storage of the specimen The participant did not provide consent to storage of the specimen The Storage page is used to define how your real world storage is set up and where individual specimens are stored The Storage page is organized into four sections Stored specimens This is where you will actually perform storage work such as creating a new storage unit or assigning a storage location to specimens Storage unit This is where you can define templates for commonly used templates storage
159. ontact Contact Phone Phone 410 114 6767 Fax Fax 410 114 0430 E mail E mail lab300 fstrf org Number of Specimens 4 Comments Shipping Manifest Box Name a Batch Number 119 Setup Date 08 Sep 2015 Shipped No Ship Date 08 Sep 2015 Spec Date or Spec Sub Spec ID Global Spec ID Project Prot PID ID1 VID Clinic Harvest Date Time Prim Add Der A D Volume Pos 500V05001596 BEQO03ZN 05 VQA 009RSMA O009RSM 01A8 Wk _ 8000 01 Mar 2005 12 34 BLD EDT CEL N A 1ML H E 500V05001596 BEQ003ZN 03 VQA 009RSMA 009RSM 01A8 Wi 000 01 Mar 2005 12 34 BLD EDT CEL N A 1ML H F 500V05001596 BEQ003ZN 01 VQA 009RSMA O009RSM 01A8 Wk 8000 01 Mar 2005 12 34 BLD EDT CEL N A 1ML H G 500V05001591 HEQ003X5 01 VQA 007RSMB 007RSM 05B 19 Apr 2005 BLD EDT CEL N A 1ML H H 1 The shipment number 2 The date that the shipment was initially created 3 Sending laboratory s contact information 4 Receiving laboratory s contact information 5 Name of shipping container 6 Specimens in the shipping container Procedure 1 Do one of the following e For pending shipments click Shipping gt Pending Shipments from the menu bar e For sent shipments click Shipping gt Shipment History from the menu bar 2 Locate the shipment for which you want to generate a manifest 3 Click the arrow next to the View button to the right of the shipment and then click Generate Manifest 4 Select PDF from the File type box Because manifests are intende
160. or study specimen condition A codified three letter property assigned to all specimens in WebLDMS that indicates the current condition of the specimen derivative type The type of aliquot that was created from a primary specimen such as a plasma aliquot derived from a blood primary Data Management Center DMC The branch of Frontier Science that manages clinical and laboratory data for clinical trials and also develops and maintains laboratory software such as WebLDMS Acronyms DMC draw date That date that a primary specimen was collected from a patient enrollment A combination of a patient and a protocol excluded position A location within a storage item that is intentional left empty for the purpose of helping people determine which end of the storage item is the front fill order The logic used to add specimens or other storage units to a storage or shipping container when they are automatically added frozen date Indicates when a specimen was frozen typically used to document the moment that the freezing process began global specimen ID A unique identifier assigned to all primary specimens and aliquot specimens aliquot specimens derived from a primary specimen will share the primary s ID however will have a unique sequence number such as 01 for the first aliquot 02 for the section aliquot and so forth LDMS USRMANOO3 Page 170 LDMS User Manual Terms ID1 A unique identifier for a patient on a spe
161. orage FEPOMta cesecsecsssesssssesesssesseseesessessesssseeseseseseeseeees 105 SPECIMENS remaining in storage repOft ssssssessssssssesssssssersssssseesssssreessssssressse 106 Specimens in storage per PID report sesse eessseseeessssseeesssseseesssssseeesnesseerssssseeesss 106 Storage container location repOrt essesseeesssssseeessseseeessssseeesssssseesssosseerssseseeesssss 107 Storage count report by freeZef sssssseesssssseeessssseeessssseeesssesseesssssseeessssreeessssssees 107 Storage detail re POrtesssesccscssstasuerssseciscsutscstecdecl cutevceceuertetuesueswssdsenssssiuabesbaascebesueeectte 107 Cabels niisiis ioes t osoo a eae Se aa E EE EREE aain 108 PAD ONS wcetonasts rta na a aa aa aa ea a aie a Ret Mego ah Ee eMac cats oe 108 Understanding label formats c cssesssssssssssessessessessesscsessesssscsscescsssssessessesseseeseseeseeseeseeees 108 kabel formatsion ae aretea deka data aati E A T 108 BalCOUSSyrscisescsisttvsen cndceddcteettadvaavabusdeassed ooselus susdundeidsteetveresasstevacdaved savuad e as 109 PAB EAE A A A vesisescatsiiotoenes 109 How to use a barcode reader With LDMS sssssssssssssssssssressssssssssssessesssssess 109 Printing labels ANYWHETE c ccssssssssssssessssssssssssssccsssscsssascascassassessssssssssssssessesssssscescesceseases 109 Generating labels from the Labels Ppage cesessesssssccsssssssessessessesessessesscseesteseescescenees 110 Defining new label form
162. orage item such as a storage unit or storage level the specimens in all sub levels and containers will be modified as well From the edit menu to the right of the storage item click Set condition code Figure 29 The Edit container menu Edit gt Store Specimens Set Condition Code Print labels Delete The Set Condition Code window will open Contact LDMS User Support and obtain the response code You must provide LDMS User Support with the challenge code displayed in the window They will use this to generate the response code Warning Do not close the Set Condition Code window or a new challenge A code will be generated Select the condition code to apply from the Specimen condition box Enter additional information about the specimens into the Comments box Information that is typically included here includes details for specimens that were not collected an explanation of a condition or an explanation of why a specimen is not available Enter additional information about the specimens into the Internal only comments box Comments entered here are for your laboratory s use only These comments will not be included if the specimen s information is shipped to another laboratory Click the Save button Page 68 LDMS User Manual Shipping Results The condition code comments and internal only comments for all of the specimens in the storage location will be updated as you specified Related sections
163. osoft Excel or 97 2003 Data only header row LibreOffice Calc Microsoft Excel XLSX A workbook that will work in Excel 2007 or Microsoft Excel Workbook Data only later preferred for exportable reports 2007 or later or LibreOffice Calc Microsoft Word doc A Word document with formatting such Microsoft Word or 97 2003 as tables and headers can be difficult to LibreOffice Writer modify depending on the report Microsoft Word rtf A rich text file that can be edited by many Microsoft Wordpad 97 2003 Editable word processors uses less formatting which makes it easier to modify Rich Text Format rtf Same as Microsoft Word 97 2003 format Microsoft Wordpad but compatible with RTF word processors XML xml A Crystal Reports XML file The scheme for An advanced text this format is available editor such as Notepad Tab separated Text ttx A text file with information separated by A text editor such tab characters as Notepad LDMS USRMANOO3 Page 92 LDMS User Manual Administrative reports User permissions report Reports Shows each user account associated with your LDMS laboratory and the user s access to specific pages in LDMS Example Figure 39 The User Permission Report User Permissions Report aoe m vw Specimen CE d O Daere y S Res o S Administration E S Account O labels E ses o fa o C SX dT System Administrator 1 The user s name 2 The user s permissions by pag
164. ote For specimens this option will be called Remove instead of Delete The Delete Item window will open 4 Optional If you want to change the specimens that are stored at the Location being removed to unavailable select the check box This means that the specimens will not be available to add to storage again They will also not appear as available to ship when shipping specimen data to another laboratory You will still be able to find the specimens however on the Specimen Management page If you do select this option you will also be prompted to select a condition for the specimens and enter a comment This comment will be applied to each specimen 5 Click the Delete or Remove button LDMS USRMANOO3 Page 67 LDMS User Manua L Storage Modifying the condition of stored specimens LDMS USRMANOO3 The condition of all specimens in a specific storage location can be modified at once Before you begin The storage location must not contain any specimens that are part of a pending shipment Background There will be occasions when you need to update the condition of all the specimens in a storage location at once This might happen for example if there was an equipment failure and all of the specimens in a storage unit were thawed Procedure 1 2 Click Storage gt Stored Specimens from the LDMS menu bar Locate the storage item that contains the specimens you want to modify If you select a higher level st
165. ow you are going to put them in a shipping container 2 You can assign the specimens to a container on the Storage page then ship the container Both of these methods can be used together within the same shipment Sending a container from LDMS storage is generally preferred over creating ad hoc shipping containers By using a container that has already been organized and checked you will save time and reduce the possibility of sending the wrong specimens LDMS USRMANOO3 Page 70 LDMS User Manual Shipping Shipment numbers Shipment numbers are assigned to sent and received shipments to identify it at your laboratory When a new shipment is created or received it is assigned the next available shipment number by LDMS For example if the last shipment that you received had the shipment number 152 the next shipment whether you receive it from another laboratory or create it to send will be assigned the shipment number of 153 Shipment numbers are not unique between laboratories nor will they be the same at the laboratory that sent and shipment and the laboratory that received it For example if you create a shipping file it may be assigned the number 153 at your Laboratory When the receiving laboratory receives the shipping data file it will be assigned the next available shipment number at their laboratory which will probably be different from the shipment number at your laboratory For this reason shipment numbers cannot be d
166. pant can be created two ways e If you want to create a new participant without any enrollments or visits use the Specimen Management page e If you want to create a new participant allow with an associated visit and specimens use the Quick Add feature The Quick Add feature requires you to enter at least one visit date with the participant If the participant has not yet had a visit you must use the Specimen Management page LDMS USRMANOO3 Page 21 LDMS User Manual Specimen Management Procedure 1 From the LDMS menu bar click Specimen Management 2 From the action menu in the top left of the page click Add Participant Figure 6 The action menu with Add Participant selected Add Participant hn 3 From the Project box select a project Figure 7 The Create Participant page Create Participant Project Example Project D4 0111111 OPIDs Add OPID OPID Action 1693951990 Delete Save Cancel The ID1 box will change to appropriate name for the selected project 4 Inthe ID1 box enter the participants identifier The label for the ID1 box will vary by project In the example above ID1 is PID 5 Optional In the OPIDs box enter an other participant identifier and then click Add OPID More than one OPID can be added for the same participant To removed an OPD that was added click the Delete button to the right of it 6 Click Save If the project has validation checks for
167. pply a template a message with further instructions will appear Warning Applying a template will clear any information you already A entered on the Quick Add screen In addition once the template is applied you cannot change projects unless you apply a different template or click Clear Template 3 Optional Complete the Participant Information a Select the project from the Project box b Select the ID1 for the participant or enter a new ID1 if you are adding a new participant 4 Complete the Enrollment Information by selecting an ID2 or by entering a new ID2 5 Complete the Visit Information section Optional Add a primary specimen a In the Primary Information section click Add New b In the row that appeared enter the information for the primary specimen to be created c Optional To view and modify all of the information for the primary click Edit in the right column 7 Optional Add an aliquot specimen a Highlight the primary specimen for the aliquot b In the Aliquot Information section click Add New c In the row that appeared enter the information for the aliquot specimen to be created 8 At the bottom of the page click Add LDMS USRMANOO3 Page 38 LDMS User Manual Specimen Management TBD in quick add templates The TBD code can be used in quick add templates for certain sections that might need to be completed when the template is used For example you may need create a template for a visit where the
168. protocol requirements Specimen drawn outside of protocol defined visit window Other Explain Processed after Specified Time Quantity Not Sufficient Refrigerated Satisfactory Short volume Sample not collected Specimen not processed Sample Not Received CRF Received Shipping storage temperature not optimal warmed Thawed Unknown condition Viable recovery may be outside expected parameters higher or lower Viability percent may be less than the expected parameter Page 155 LDMS User Manual Unit codes Measurement codes Codes units and abbreviations This section lists the measurement codes available for specimen units available in LDMS Code CEL CM CRD CTN EA GR MG ML MM N A PG UG UL UNK Time unit codes This section lists the time unit codes available in LDMS Code Day Fst Hrs Min Nft Pol Prd Pre Psd Pst Ran RPD Sec Tr UNK LDMS USRMANOO3 Description Cells Centimeters Cards Container Each Grams Milligrams Milliliters Millimeter Not Applicable Picograms Micrograms Microliters Unknown Units Description Day Fasting Hours Minutes Non Fasting Pooled Predialyzer Pre Dose Postdialyzer Post Fasting Random Random Post Dose Seconds Trough Unknown time unit Page 156 LDMS User Manual Visit codes This section lists the visit unit codes available in LDMS Code A Aut B L Bth Cb CFM Ch Day EDV Ent EOR Eos EOX EPH Exp Ext FCF FUP
169. r Row Column or Col umn Row from the Coordinate order box If Row Column is selected each level or container position will be identified in the format row column b Select how columns and rows are to be labeled from the Column labeling and Row labeling boxes To use letters to identify rows or columns select Alphabetic to use numbers select numeric Select the fill order for storage items based on this template from the Fill order box Fill order can be used when adding a new level or container to storage items based on this template While you must specify a fill order you can override it when add storage items Optional Select a position s in storage items based on this template to be excluded from the Excluded positions box Excluded positions are used to help identify the orientation of the container meaning which side is the front and which is the back Review the Preview for storage items based on this template Optional For storage units only Add default levels for new storage units based on this template a Click the Add level button The Add Level window will open b Select a template from the Saved Templates box The information for the template will be displayed however you will not be able to modify it c Specify how many levels to add in the Number to add box d Click the Continue button The Select Position for Level page will open Select a position for the first storage item you are adding from either the Pos
170. r next to the laboratory name Applying filters to a page Filters are available on several pages and are used to narrow down the information that is displayed so that you can find something Background On many pages in LDMS all information for a particular task will be displayed together For example if you are on the Specimen Management page all participants in your laboratory s database will be displayed If your laboratory has information for 200 participants all 200 will be displayed by default and you would need to page through each one to find what you are looking for Filters can be used to temporarily limit the amount of participants shown so that only records of interest are displayed This is the primary way to search for items in LDMS Procedure 1 Open a page with filters such as the Storage or Specimen Management pages Filters are displayed in the filters panel on the left side of the page below the action menu 2 Locate the desired filter LDMS USRMANOO3 Page 14 LDMS User Manual Getting started Filters are grouped into categories such as visit filters and specimen filters Some categories will be specific to the current page For example the storage container filters will only be available on the Storage page Figure 2 The filters panel Applied 1 filter Participant Filters Project FRONTIER X ID1 OPID In this example the FRONTIER filter has already been applied to Project
171. r on the report select the check box under Display e For items that you want to use to sort records on the report select the check box under Sort 3 In the Fields to display and Sort results by section use the Up and Down buttons to set the order of items Fields displayed on the report will be shown from left to right in the order you specify Results will be sorted in the order specified An item can be removed by clicking the X next to it or deselecting the check box LDMS USRMANOO3 Page 89 LDMS User Manual Reports If you sort by Destination Lab ID and Ship Date the records on the report will first be sorted by the destination laboratory and then by the shipment date 4 Optional To remove duplicate records under Fields to display select Distinct Any rows on the report that have the same values across all displayed fields will only appear on the report once 5 Optional Apply a filter to your report in the Selection criteria section If no selection criteria is specified all data from your laboratory will be included a In the All Fields section click an item to select it b In the Selection criteria section select an operator and value for your filter c Click Add d In the box below the filters enter logic for applying the filter using the numbers next to each item If you leave this box blank filters will be applied as 1 AND 2 AND etc For example if you want to apply filter 1 and either filter
172. rage unit as is into storage an unnecessary level will not be added to SHIPPING IMPORT FREEZER R 22332 When un shipping a storage unit unnecessary levels are no longer added to the UNSHIPPED FREEZER R 21989 Added restrictions to the SHIPPING IMPORT FREEZER to prevent unexpected uses of this storage unit R 21994 Fixed issue where shipping reports could not be generated for a pending shipment until the shipment window was saved closed and re opened R 22025 Updated shipping validation logic so that additional time and additional unit must both be set or both be empty R 22089 Fixed issue where duplicate specimen validation errors could be displayed for the same data entry issue R 22093 Collection date is now marked as a required field when modifying a primary specimen R 22103 Fixed field alignment on the log in page R 22141 Fixed issue where filter criteria warnings persisted even after the condition that caused the warning as been corrected Page 160 LDMS User Manual LDMS USRMANOO3 Release notes R 22145 After generating a validation error when adding a specimen using the Quick Add feature the Quick Add template will now remain selected as expected R 22146 When a validation error is generated using the Quick Add feature duplicative error messages for the same issue will no longer be generated R 22787 After generating a validation error when trying to save a specimen using the Quick Add feature certain fields will no
173. re the sequence number A sequence number of 000 indicates that the global specimen ID belongs to a primary specimen any other number indicates that it belongs to an aliquot specimen Figure 12 The global specimen ID of primary and aliquot specimens a f Primary 0500 0005JE00 000 Aliquot 0500 0005JE0O0 001 This image shows the relationship between a parent primary and aliquots derived from it Related sections Specimen identifiers in LDMS for Windows on page 30 LDMS for Windows handles specimen identifiers in a few ways that differ from LDMS Specimen identifiers in LDMS for Windows LDMS for Windows handles specimen identifiers in a few ways that differ from LDMS Understanding the differences between the way LDMS and LDMS for Windows assign specimen identifiers is important if your laboratory does work with other laboratories LDMS USRMANOO3 Page 30 LDMS User Manual Specimen Management LDMS will not assign a specimen ID to a specimen and will only assign a global specimen ID LDMS for Windows will assign both The format of the global specimen ID differs as well depending on which system assigned it Figure 13 Specimen ID and global specimen IDs interoperability WebLDMS LDMS For Windows Shipped Specimen ID None Specimen ID 5000V13000001 Global Specimen ID 0500 HEQ00676 001 Global Specimen ID 0500 HEQ00676 001 LDMS for Windows hipped WebLDMS Shippe Specimen
174. roject The rules for preset projects fall into two categories e Validation rules that can be enforced by LDMS such as requiring that ID1 be formatted a certain way e Requirements that cannot be enforced by LDMS such as requiring specimens to be entered within a certain period of time after they are received by your laboratory Important The information for individual projects provided here are for convenience only Always refer to guidance provided by the project for the must up to date instructions ACTG IMPAACT The ACTG IMPAACT preset project has these requirements LDMS USRMANOO3 Page 118 LDMS User Manual Data entry requirements Field ID1 PID ID2 Protocol ID3 SID Visit OPID Clinic Specimen Time Received Time Notes Required Required Required Required Required Available Required Depends Optional Preset projects Note 8 characters long 7 numbers and one letter between A and L if the PID does not have 7 numbers add leading zeros to the front of it Select from the pre defined list of protocols Study Identifier LDMS will remember previously entered SIDs and automatically populate ID3 when the same project PID protocol combination is entered If you do not Know the SID or a SID has not yet been assigned enter NOSID Select from pre defined List of visit units LDMS will automatically populate the clinic using one previously entered for the same PID
175. rride it when adding levels to the storage unit d Optional Select a position s in the unit to be excluded from the Excluded positions box Excluded positions are used to help identify the orientation of the container meaning which side is the front and which is the back 11 Review the Preview of the new unit If any empty levels will automatically be added the new unit they will be listed in the Default Levels section 12 Click the Save button Results The new unit will have been added to the storage tree The storage tree is in alphabetical order so you may need to change pages in the storage tree to find your new storage unit Related sections The storage tree on page 51 The storage system in LDMS is a hierarchy of storage items Storage templates on page 63 Templates allow you to add commonly used storage items quickly by defining them in advance Adding a new level in a storage unit A new level is added to an existing storage unit or storage level Before you begin You must have created the storage unit before you can add levels to storage in LDMS In other words you cannot create a level that is not associated with a storage unit Procedure 1 Click Storage gt Stored Specimens from the LDMS menu bar 2 Find the storage unit to which you are adding a level If you want to add a sub level to an existing level find that level instead You can used the filters on the left side of the page to help find the
176. ry primary specimen and aliquot specimen in LDMS has a condition assigned to it The detaul condition for new specimens is SAT satisfactory but there are many others The majority of conditions indicate a deviation from the expected handling for a specimen For example if a specimen was supposed to be collected in one type of tube but another was used the INT incorrect tube type condition code could be used to indicate this There are several places where the condition of specimens can be changed e onthe Specimen Management page by editing an individual specimen e when receiving specimen data from a shipping file e onthe storage page all specimens in a storage location can be modified A common use for specimen conditions is indicating when an expected primary specimen was not collected By setting the specimen s condition to an applicable code such as QNS if not enough sample could be collected and by entering descriptive comments you can explain the omission of the expected specimens LDMS USRMANOO3 Page 45 LDMS User Manual Specimen Management Related sections LDMS abbreviated codes report on page 97 Provides a list of LDMS unit visit time specimen condition codes used in LDMS and their meaning Destroying a specimen Specimen destruction is noted in LDMS by applying the DSR specimen condition Background When a specimen is destroyed it is important to document that destruction in LDMS Procedure 1 From the
177. s 2 or 3 enter 1 AND 2 OR 3 To apply a filter that excludes specimens that originated from laboratory 500 select Source Lab ID in the All Fields section the lt gt operator and enter 500 6 Inthe File Type list select the format for your report output 7 Optional If you do not want a header row with the name of each column to appear on your report deselect Include Headers 8 Do one of the follow e To save your report so that it can be run later enter a name for your report into the Saved Queries box at the top of the page and then click Save e To view the first 100 records of the report in your browser click Preview e To generate and save the report in the indicated file type click Generate Report Generating a report All reports are generated by following this procedures Background By default any report is generated using all available data in laboratory s database If you want to narrow down the records that will appear on a report you must apply LDMS USRMANOO3 Page 90 LDMS User Manual LDMS USRMANOO3 Reports filters If more than one filter is applied only records that met all of the filters will appear on the report Figure 38 The Reports page Report Categories Specimen Report Primary Specimens Received Filter Criteria Volume Unit ML Ada Field Operator Value 1 Primary BLD Delete 2 Primary ART Fase 3 gt 10 Delete 4 ML Delete Valid sente
178. s even when automatically signed out of an idle session Background You will automatically be signed out of LDMS if you leave a page idle for 15 minutes When this happens you will receive a notification that you have been signed out If you attempt to leave the current page you will be directed back to the sign in page If you had unsaved changes when you were automatically signed out those changes will be lost when you are redirected to the sign in page This is to prevent unauthorized users from saving changes from a session that is signed out It is possible to save unsaved changes on a page after being logged out by signing in using another tab in the same web browser Procedure 1 Without leaving the page with unsaved changes open a new tab in your web browser 2 In the new tab go to the LDMS sign in page Sign in as the user with the unsaved changes Close the new tab Results The original tab with the unsaved changes will now be considered signed in You will now be permitted to continue working and to save any changes made LDMS USRMANOO3 Page 12 LDMS User Manual Getting started Downloading files Different web browsers have different way of handling file downloads Many modern web browsers are configured by default to try to open certain types of files automatically or download them to a default location For example by default Firefox will attempt to open PDF files using a built in PDF viewer Likewise Chrome
179. s next to the item s name such as 1 2 indicates that items position in its parent storage item To the right of each storage menu is the Edit menu for that item The options available from this menu will vary depending on the type of storage item ee The storage system in LDMS is a hierarchy of storage items There are several types of storage items in LDMS From biggest to smallest these are storage unit This is the main cooling unit used to store specimens such as a freezer or a refrigerator level This is an intermediate part of a storage system such as a shelf within a freezer You can add an additional level to another level For example you might have a shelf that contains racks of boxes where the rack is a level on the shelf which is a level in a freezer Page 51 LDMS User Manual Storage container This is the storage item that holds specimens such as a box Figure 20 The LDMS storage hierarchy Storage Unit Levels EE HE EE HE EE HE Sub levels EE EE EE EHE EE HE ain i ie wa wa Containers Ba a ye ae oe fe ia E oe ooe ee oo ee oo ee eo ee eo ee oo Specimens Se 3s Ss co co oo oo co oo oo oo ee oo eo oo ee oo Coe ee ee ee ee oo The storage hierarchy is visualized on the Storage page in LDMS as a tree Figure 21 The storage tree on the Storage page we s0rReezer re 01 ACTG SHELF 02 HPTNATN SHELF 2 HEE 01 SERUM RACK JEE 02 URINE RACK 01 HP
180. s part of a pending shipment could be assigned a storage location in a container that was part of a different pending shipment i e it was on 2 shipments at once R 22890 Fixed logic for handing moving storage items into other storage items that are part of pending shipments R 22912 Text of laser label 6 will no longer be cut off R 22918 It is now possible to un ship shipments that contain storage levels R 22933 Filters will now autopopulate correctly when there are more than 100 possible options R 23221 Received time is now correctly a required field for HPTN R 23190 Fixed issue with the Import Shipment Container Sample Position patch which failed with a divide by zero error on laboratory 573 s database Page 161 LDMS User Manua l Release notes R 21943 Djini will now merge data_dojo_props instead of overwriting the default properties R 20526 Shipping files now include Samples OwnerVisitId R 21612 Removed predefinedVaLueld from participants enrollments and visits R 21944 Added Label Defaults RecordOwnerLabId as a primary key to prevent potential primary key violations R 22246 When moving specimens into or out of a storage container that is part of a pending shipment PendingShipmentStorageSampLes will now be updated R 22315 Re factored DojoTemplatesControLers LDMS release 20 May 2015 version 2 0 These are the enhancements made to LDMS release 20 May 2015 version 2 0 LDMS USRMANOO3 New features R 17
181. s refer to the quality of a specimen For example if a blood specimen clotted this is a qualitative issue that could prevent processing If there was a qualitative or participant abnormality that would prevent processing but no other code is applicable the SNP condition code can be used Table 7 Qualitative conditions Code Description Usage BLD Bloody The specimen such as a throat swab contained blood CLT Clotted The specimen has clotted often because the additive did not mix correctly with the specimen CTM Contaminated The specimen is visibly contaminated DCG Discharge present A specimen such as a vagina swab that contains discharge material LDMS USRMANOO3 Page 48 LDMS User Manual Code HEM HUM ICT LIP LYS SNP Description Hemolyzed Humidity Icteric Lipemic Lysed Sample Not Processed Quantitative conditions These condition codes refer to the volume of specimen collected Table 8 Quantitative conditions Code DFB SHV SNC Other conditions Description Difficult bleed Quantity Not Sufficient Short Volume Sample Not Collected Specimen Management Usage A blood specimen that has hemolyzed The specimen has been exposed to high humidity There are excessive amounts of bilirubin in the specimen There is excessive fat content in the specimen There has been a breakdown of cells in the specimen other than hemolyzation A generic code for when there is a qualitative is
182. s that differ from LDMS LDMS USRMANOO3 Page 69 LDMS User Manual Shipping Shipments are data transfer Shipping in LDMS is the process of transferring specimen information from one laboratory to another This is a parallel process to physically packaging and shipping specimens to another laboratory As specimens are packaged you will specify in LDMS that they are to be shipped You will then generate a data file with the information for those specimens called a shipping file Once created you provide that file to the laboratory that will receive the specimens In this sense it is more accurate to think of shipping in LDMS as data transfer between two laboratories LDMS does not assist with the physical shipment of specimens LDMS does not create postal labels for shipping boxes track the progress of shipments of couriers and other logistical tasks Laboratories need to implement their own solutions for the actual shipping process Figure 30 Shipping vs data transfer Sending Laboratory Receiving Laboratory o r pa a Email data file Load data file Ship specimens Receive specimens This figure illustrates how creating a shipping data file in LDMS and transferring it to a laboratory is a separate process from physically boxing and shipping the specimens to the recipient There are two ways to ship specimens using LDMS 1 You can select individual specimens to be shipped and then tell LDMS h
183. sed to print a list of all the storage items or specimens in a specific location Container report on page 62 The Container report is a printable graphic representation of the specimens within a storage container Generating a printable list of what is in storage The Storage Details and Container reports can be used to print a list of all the storage items or specimens in a specific location Background In addition to assigned specimens to a storage location in LDMS you will need to actually put the real life specimens in storage The Storage Details and Container reports can assist you in putting storage items in the correct Location It is good practice to print them after making changes to storage in LDMS Procedure 1 Click Storage gt Stored Samples from the LDMS menu bar 2 In the storage tree locate the storage item for which you need to generate a report 3 To the right of the storage item click Edit Click the down arrow next to the Reports button and then click either Storage detail or Container 5 Inthe File Type box select PDF pdf and then click Generate Report Container report The Container report is a printable graphic representation of the specimens within a storage container This report is useful for reconciling the storage locations assigned to specimens in LDMS and the actual real life contents of a storage item For example if you initially LDMS USRMANOO3 Page 62 LDMS User Manual S
184. seeessssseeesssssreesssssse 99 Imported specimen report SUMMATY ssssssssessssesessssssssessssssseesssssseesssssreessssssress 100 Shipped specimen report detail repOft ssesssssssesssssssersssssseesssssrerssssssresss 100 Shipped specimen report SUMMALY repOft sss s sssssssssssssssesssssssersssssssesssssseees 100 Shipping laboratory contact report sssssssseesssssssssssssssesssssseersssssreesssssreessssssees 101 Specimen FE POMS anain a AEE EE EN E AE 101 Cell yield QA QC summary report sssseeessssseeesssseseesssseseeessssseeessssseeesssseseerssssseeesss 101 Primary specimens received report ssss esssssseesssssseerssesseeessseseeesssssseesssseseeesssesee 101 SPECIMEN COUNT FEPOMT cscsssssessessessssssesssssecsecsscsscsscsscsscsecseeseeseesssucsessuesucsscsscsecses 102 LDMS User Manual Contents Specimen log re portes un csancincaiastende e E E nibon 102 SPECIMEN processing repOrt sseseeeesssseeeessssesresssseseeessssseeesssseseesssssseeesssssreessssseeessss 103 Specimens for a given group report ssesseeesssseseeessssseeesssssseesssssseeessseseeessssseeesss 104 SPECIMENS FOF a GIVEN group Zimmermanni isni een e RNA 104 Time to freeze QA QC summary repoOft ssssssssssssssssesssssssessssssseesssssreessssssresssss 105 Time to process QA OC summary repOfrt ss sssssssssssessssssssessssssseesssssrersssssreesssss 105 SHIPPING repor nana EEEN ENNA NNN 105 SPECIMENS NOT IN st
185. select the project to set defaults 3 Inthe Format box select the applicable default label format 4 Inthe Label box select the applicable default label stock size 5 Click Add Default Administration Administration The Administration page is where you can manage various settings in LDMS Projects Projects are the collaborative group organization or network that conduct studies LDMS USRMANOO3 Page 114 LDMS User Manual Administration There are two types of projects local projects and government projects Figure 44 The Projects page Name Description oe 2 Export Local InUse PHIA Population Based HIV PTID Country HIVRT A A View Impact Assessments CONTROL CONTROL CONTROLNAME PROTOCOL ID3 e e View UNKNOWN Unknown Group ID1 ID2 ID3 View FRONTIER Frontier Science Internal PID Study oA GF Edit Study m cadmus cadmus pid prot sid oS Edit XLOCAL XLOCAL ID1 ID2 ID3 oS oS fE 1 Whether data is copied into Frontier Science s central database 2 Whether the project is a government or local project 3 Whether there are specimens currently using the projects Local projects LDMS USRMANOO3 Local projects are projects that only exist at your laboratory A local project is one that has been defined by your laboratory These are general used for internal studies that only your laboratory will utilize although they can be sent to other laboratories through shipments Defining a new loc
186. sit 5 Add aliquots that were processed from the primary specimen Participants A participant is the source for a specimen entered into LDMS The participant is typically a person enrolled in a study Similar terms that you may be familiar with include patient and source In LDMS a participant refers to all of these concepts This means that a participant does not necessarily need to be a person For example a participant may be a control sample from which a specimen was created In LDMS a participant will be the first thing that you create when adding a new specimen record Newly created participants must be associated with a project and an ID1 or participant identifier If a person is taking part in more than one project that person will be considered two different participants in LDMS Participant identifiers A participant identifier is a series of numbers and letters that uniquely identifies a participant within a specific project A participant identifier is called ID1 in LDMS until you select a project for the participant Each project will have a different name for ID1 For one project it may be called PID for another project it may be called PANEL Adding participants using the Specimen Management page A new participant can be created on the Specimen Management page or the Quick Add page This section explains how to add them on the Specimen Management page Background A new partici
187. ss seessesossesssseessssessssecssescssseccsneccsssectssecrssseresseressseresss 141 SPECIMEN pe tode S en ora r a NA AEA N A 141 Primary code Suinn a AE T A E 141 Additive COG OS success cssssecissi cd ec saecs sexs usta R AAEREN 144 Derivative COD GS inensis ea aeaniino ee aonet 146 Sub additive derivative COdeS sse sssesssssssssssssssssssssssssssssssssessssssssssesssssssesessseess 150 CONGITION CORES ANa RR AR IAE E EA AR 154 et eto o S mnte oo A TEAN a 156 Measurement COCES ccceccscessscsssccssccssssssesscseseesessesessesessccessceusssssssseseseeseesesesseseeseeees 156 Time nit COM OS erheen ena aana a n n a 156 Visit code Se aa a a a a a a e aea oe Tai 157 R lease Notes ssion oun ee soeia eieae niss ebeo ss 158 LDMS release 08 Oct 2015 version 5 0 essssseeesssesseesssssseeessseseeessssseeesssssseeessssseeessss 158 LDMS release 20 May 2015 Version 2 0 e essssseeesssssseesssssseeessssseeessssseeesssssseeessssseeesss 162 LDMS release 19 Mar 2015 Version 1 1 sssessesesssessssssssssscessecsscessssessessessesseseens 166 Accessibility information oosoosoosossossesseseeseeseesessessesceseesessescesoesossossescesoes 169 LDMS User Manual About this manual About this manual This manual explains how to use LDMS for the web LDMS is a web based specimen management tool developed by Frontier Science for small and medium sized research laboratories It is used by clinics and laboratories arou
188. st k lt 10 Do one of the following e To save the shipment so that it can be modified again before the shipping file is generated click the Save button LDMS USRMANOO3 Page 74 LDMS User Manual Shipping e To generate the shipping file now and change the shipment s status to shipped click the Ship button Results If the shipment was saved a new shipment will be added to the Pending Shipments page It will appear at the top of the list and will have been assigned the next available shipment number What to do next You should perform QA QC on the shipment after it has been created before sending it Related sections Supported shipping file formats on page 77 These are the file formats that are supported for sending and receiving shipping files Shipment QA QC on page 83 Shipment QA QC is the process of comparing actual specimens in a shipping container to the specimen that is expected in that container position by LDMS This should be done for shipments before they are sent and after they are received Sending a pending shipment LDMS USRMANOO3 Sending a shipment is the process of generating a shipping data file on the Pending Shipments page Background The shipping file can either be in LDMS format or CSV format The file that is created will need to be transferred to the laboratory to add the specimens to their database Procedure 1 Click Storage gt Pending Shipments from the LDMS menu bar 2 Loc
189. sting browserconfig xml which LDMS does not provide Page 159 LDMS User Manua LDMS USRMANOO3 l Release notes Fixes R 20112 Fixed issue where LDMS did not retain the storage location of specimens in shipments created using LDMS for Windows R 20993 The Shipping Container Report will now show the correct positions of specimens rather than sorting by position and using the container s fill order R 21471 Minor miscellaneous changes to the Quick Add feature R 21601 Changed patient to participant throughout the user interface and reports R 22463 Changed draw to collection i e collection date and time throughout the user interface and reports R 22683 Changed draw to collection i e collection date and time and group to project on several reports R 22254 Changed group to project on several reports R 21773 When a shipment disclaimer is specified it will now appear in all places that it is expected R 21859 Specimens with multi line comments will no Longer cause layout issues on the QA QC page R 21880 If a project that is currently set as a filter is deleted that filter will no longer be permanently set R 21881 Fixed issue where the preview of very large shipments would not be rendered correctly when the shipment was received R 21891 The Storage Container Report now correctly shows the specimen date for primary specimens R 21984 When importing a sto
190. sue that prevents an otherwise correctly collected primary from being processed into aliquots but no other code applies The Reason sample not collected field should be used in conjunction with SNP Usage There was problems trying to obtain a blood specimen from the participant typically resulting in a lower volume than was expected This code is more specific than SHV which does not indicate why the volume was low There was not enough specimen available to create the aliquot For example if specimen collected from the participant was supposed to be 10 mL but only 5 mL was collected the aliquots that could not be created due to the low volume would be considered QNS QNS means there is no volume at all for the aliquot even though there was some volume for the primary The primary or aliquot specimen has at least some volume but not the full expected volume The primary specimen was not collected from the participant at all This might happen if the participant declined to provide a specific sample These condition codes are either automatically assigned to specimens or indicate some combination of issues The default condition code that is assigned to all new specimens is SAT satisfactory Table 9 Other conditions Code ANM coc DSR OTH LDMS USRMANOO3 Description Anonymized Combination of Codes Destroyed Other Usage The specimen was created using the anonymization tool in LDMS This code is aut
191. t Unit for visit e g WK Clinical site where specimen was collected Date specimen was collected Time specimen was collected Date specimen was received by laboratory 24 hour time specimen was received by laboratory Specimen ID used for specimen entered in LDMS for Windows only Will be generated automatically during import if blank Other specimen ID Three letter primary specimen code Three letter specimen additive code Three letter derivative specimen code Three letter sub additive derivative specimen code default is N A Volume of specimen Units used for specimen volumn Three letter code representing specimen s current condition default is SAT Notes about the specimen Assays assigned to the specimen This report shows a visual map of each container s contents along with the details for each specimen being shipped Page 79 LDMS User Manual Shipping The shipping container report can be generate while you are creating a shipment or after a shipment has been sent The shipping container report can be found on either the Pending Shipments or Shipment History page To the right of the shipment click the down arrow next to the button and click Shipping Container Report There is a key in the top right corner of the report that shows what information is within each box Each box on the report corresponds to one location in the container Locations that
192. t 4Hrs The additive EDT in the primary collection tube Selected from a pre defined List of codified values If there was no additive in the tube use NON Hover the mouse pointer over an additive for a more detailed description Additive type Available volume clinic The clinical site 102 Select from a pre defined list For where a visit a description of a clinic such as its occurred name hover the mouse pointer over it Collection date The date that a 02 Apr 2014 This will typically be one day If a visit visit occurred occurred over multiple days each event will considered a separate visit and listed as separately in LDMS They will still however have the same visit value and visit unit Collection time The time that the 13 30 This time should be the local time specimen was for the clinical site and be in 24 hour collected format In LDMS collection time is known as specimen time Comments Additional Used to provide additional LDMS USRMANOO3 details about the specimen information such as an explanation of a specimen s current condition This comment will be included if the specimen data is shipped to another laboratory Page 42 LDMS User Manual LDMS USRMANOO3 Field Derivative type Enrollment Frozen date Frozen time Global specimen ID ID3 Internal only comments Is Available Owner Enrollment Original volume Other specimen ID Primary type Usage The type
193. t can be sent Procedure 1 Click Shipping gt Pending Shipments from the LDMS menu bar The Pending Shipments page will open 2 From the LDMS action menu click Create Shipment The Pending Shipment Preview window will open 3 Complete the information on the General tab All information on this tab is required shipment date This is the date that the physical shipment was if it was already shipped or will be shipped If you don t know when you will be shipping the specimens select an approximate date it can be changed before the shipping file is generated format This is the type of shipping file you are creating Unless the destination does not use LDMS select LDMS Page 72 LDMS User Manual LDMS USRMANOO3 Shipping temperature This will be the method of temperature control for the specimens during transport Complete the information on the Shipping Destination tab Existing laboratories that are using LDMS and LDMS are already available for selection The contact information for these laboratories is maintained by Frontier Science a Select either Contact Lab Number or Lab Name This is how you will select the laboratory Contact is the shipping contact person on file for the laboratory Lab Number is the laboratory s LDMS ID Lab Name will show each laboratory in alphabetical order b Select a laboratory from the drop down box below If you selected Contact or Lab Name the number in parenthesis ne
194. t compromised collected during a visit The date the specimen was received by your laboratory 12 Mar 2014 The time the 14 45 specimen was received by your laboratory Whether the Yes or no specimen has been shipped to another laboratory The current SAT condition of the specimen A legacy 500V10000110 specimen ID used only by LDMS Icons indicating various properties about a specimen Specimen Management Notes Use local time If present the value entered for the parent primary specimen will be used for aliquots derived from the primary If the processing tech initials are set for a primary aliquots derived from the primary will receive those initials as well You can change the initials for individual aliquots if needed Use local 24 hour time If present the value entered for the parent primary specimen will be used for aliquots derived from the primary Typically used in conjunction with a specimen condition code that indicates an issue with the specimen such as QNS quantity not sufficient If necessary use the Comments box for the specimen provide more details Times should be entered in 24 hour local time Selected from a pre defined List of codified values Hover the mouse pointer over a condition for a more detailed description The specimen ID is an identifier for the specimen that was used by older laboratory management software It will only be present for spec
195. t intended to be refrigerated TNO Temperature Not Optimal The specimen was stored or shipped at any temperature other than the temperature specified by the protocol TWD Thawed The specimen was frozen and has been warmed so that it is no longer frozen LDMS has a field to track a thaw count which can be used to keep track of how many times the specimen has been thawed This information can be found on the Details Window for the aliquot in Specimen Management Shipping conditions Qualitative co These condition codes apply to issues with a specimen shipment where the specimens are unaccounted for or were received Late If the shipping issue damaged the specimens a temperature related code such as DIM dry ice melted may be more appropriate Table 6 Shipping conditions Code Description Usage DSH Delayed Shipment A shipment did not occur on schedule but there is no obvious damage to the specimens If there was obvious damage a more descriptive temperature related code such as DIM or TNO may be more appropriate LSH Lost Shipment A shipment was created and sent but did not arrive at the receiving laboratory Neither the shipping or the receiving laboratory can locate it SNR Sample Not Received A data collection form such as a CRF was received but a specimen listed on the form was not received This differs from LSH in that only some specimens were not received compared to an entire shipment nditions These code
196. t to the DSR destroyed condition code can have very serious consequences LDMS does not provide undo functionality to reverse such an action A challenge code is a fail safe mechanism that can prevent accidental changes to specimen data LDMS USRMANOO3 Page 15 LDMS User Manual Specimen Management If you attempt to access a feature locked with a challenge code LDMS will prompt you for the response code Figure 3 Prompt for challenge password Set Condition Code Note The following values will be applied to all specimens within this storage unit Challenge Coe ill NETBUKNE Response code P Specimen Condition Comments Internal Only Comments Unavailable Save Cancel In this example you would provide LDMS User Support with the code BKPRMY and they will provide you with the Response Code to access this feature You must contact LDMS User Support and give them the Challenge Code If appropriate they will provide you with the response code which will then unlock the feature for your use The code will change each time the feature is accessed and will be needed even if the feature was previously unlocked Warning Do not close the challenge password window before you obtain the Response Code Doing so will cause a new Challenge Code to be generated which will require a different Response Code Specimen Management Specimen management The Specimen Management page is where you can manage the details
197. tainer E FRONTIER Box 1 Container 1 of 1 Position Row Column H G Global Specimen ID BEQ003ZN 01 Scanned Global Specimen ID Performed By Other Specimen ID Comments Processed at site JD Specimen ID 500V05001596 Primary BLD Additive EDT Derivative CEL Sub Add Der NIA Pass Specimen Alt P Project YOA Fail Specimen Alt F ps DUNNING Fill Order Right to Left Bottom ID2 3E to Top Collection Date 01 Mar2005 Container Type Storage Collection Time 12 34 Time Visit 8 Wk volume 10000000 CEL Save Cancel 1 Containers in the shipment 2 Currently selected specimen 3 Manually pass or fail selected specimen 4 Currently selected specimen s global specimen ID 5 Modifiable boxes If the shipment contains multiple containers you will need to change containers during QA QC since each container must be reviewed separately While performing QA QC you have the option to modify each specimen s other specimen ID and comments If you do so these changes will be reflected in the specimen information on the Specimen Management page Performing QA QC QA QC is performed by selecting the QA QC option for the shipment on either the Pending Shipments or Shipment History page Background QA QC should be performed after creating a pending shipment but before creating the shipping file It should also be performed on shipments from other laboratories after they have been received LDMS USRMA
198. the numbers in the column in the filter criteria along with the words AND OR or parenthesis 6 Select a format for the report from the File Type box 7 Click the Generate button Results The report will be generated in the format that you specified You may be asked to open or download the report depending on your web browser s default behavior Available report formats This section describes the file formats in which LDMS can generate reports e If you are generating a report from the Exportable reprts category the Microsoft Excel Workbook Data only file type should be used e Reports in any category other than Exportable are designed for PDF e Use other file types for reports may result an unexpected formatting depending on the report There may also be variations in the file type s format depending on the specific report Table 13 File types for LDMS reports File type Extension Description Opened by Crystal Reports pt Do not use N A PDF pdf A formatted report intended to be printed A PDF viewer such on letter size paper preferred as Adobe Reader Character separated csv A text file with all information separated A text editor such values by comma characters as Notepad Microsoft Excel XLs A workbook for versions of Excel prior to Microsoft Excel or 97 2003 Excel 2007 this version contains a header LibreOffice Calc row for each column Microsoft Excel xls Same as above but usually without a Micr
199. thiothreitol EDTA Ethanol Fetal Bovine Serum Formaldehyde Formalin Filter Paper First Spin Fungal Broth HIV GAG envelope peptide Page 151 LDMS User Manual LDMS USRMANOO3 Code GIT GLM GLT GLY GMS GRS H20 HBS HCL HPA HTC 118 I1b IAP IL2 IL6 ILA INK IgG LES LFT LPS LVT LYB M2V MA1 MAC MAF MAS MDB MET MFS MIF MIT MRN MT2 MUC N A NCL Codes units and abbreviations Description Guanidine Isothiocyanate GITC Glycerol Media Glutaraldehyde 20 Glycerol Giemsa Staining Gram Stain E hematoxylin and eosin stain Water Hank s Balanced Salt Solution Hydrochloric Acid Hep A Human Tumor Cell Line IL 18 IL 1b Iodoacetic Acid Phenanthrolene IL 2 Interleukin 2 Interleukin6 IL 12 IL 15 Interleukin 12 Interleukin 15 India Ink Immunoglobulin G Lesion Left Lipopolysaccaride L var Target Lysis Buffer M2V MAC 101 MAC Antigen MAC LR114F Culture Filtrate M Avium Sensitin Middlebrook broth Methanol Malaria Freezing Solution Merthoilate Formalin Merthiolate Iodine Formalin MF MIF Mitogen Control Messenger RNA MT2 Cell Line Mucins Not Applicable N acetyl L cysteine Page 152 LDMS User Manual LDMS USRMANOO3 Code NDN NDV NDW NIL NKC NOH NON NPI NSL NUC OCT OKT OTH P24 PAR PBS PCS PEI PFM PHA PIL PLD PMI PPA PRS PTI PTK PVA PWM RFW RGT RNL RNP RPM RTB S52 SCB SDS SEB Codes units and abbreviations
200. tify specimens What to do next If the primary was collected for more than one protocol or project you must also co enroll the specimen so it is associated with each applicable visit Related sections Entering specimen information Overview on page 20 Records are added to LDMS from the top down starting with the creation of a new participant Quick add on page 37 The quick add feature allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS Co enrolling a primary specimen Co enrolling is the process of associating a primary specimen with more than once visit or protocol Background A participant may be participating in two different protocols at the same time and a single primary specimen might be collected to meet the needs of a visit from each protocol You can also co enroll a primary specimen to move it between visits This might happen for example if you selected the wrong visit for the primary specimen and you want to move it to the correct visit rather than deleting it Procedure 1 Inthe menu bar click Specimen Management 2 Local the specimen to be co enrolled Use filters from the left side of the screen to narrow down the participants that are displayed LDMS USRMANOO3 Page 33 LDMS User Manual LDMS USRMANOO3 oS wp Specimen Management Click the down arrow next to the Edit button to the right of the primary to be
201. to be sent When you ship a shipment you will be prompted to save a shipping data file this file is the shipment In addition to sending a physical package of specimens to the receiving laboratory you will need to provide the LDMS USRMANOO3 Page 71 LDMS User Manua L Shipping laboratory with the shipping data file This is most commonly done using email but you could also put the file on a disc or re writable USB drive and include it with the physical shipment Related sections Batch storage report on page 80 This report lists the specimens in a shipment and their assigned storage location Shipment numbers on page 71 Shipment numbers are assigned to sent and received shipments to identify it at your laboratory Icons and their meaning on page 54 The icons next to the items in the storage tree indicate the type of storage item and special properties such as its additive or whether the item is part of a pending shipment Creating new shipments LDMS USRMANOO3 Creating a shipment means defining which specimens will be sent and where they are going to be sent Before you begin e The specimens must have already been entered into LDMS e If you want to ship a storage container with specimens you must have already assigned the specimens to the container in LDMS Background I I Note You can save an incomplete shipment such as leaving the destination E blank however you will need to complete the shipment before i
202. torage assign specimens to a storage location in LDMS you can print the container report and use it as a guide when inserting the actual specimens in the container Figure 28 Container report Container Report 4 X 3 Box Legend Sobel Spec ID Prim LN TANK FS RACKIFS Box REGuotcd 0e IREO BLD REaooTC4 10 50005000477 500V 05000477 Ol 500V09000001 31 Jan 2005 El 31 Jan 2005 SER ff31 Jan 200 METABOLIC METABOLIC 403301 403301 1 00 Vst 1 00 Vst 1 Storage location of container 2 Dimensions of container 3 Legend showing how to interpret the information for a specimen 4 An excluded position 5 An empty location The top right corner of the container report contains a key that shows how to interpret the details of a specimen listed on the report Storage templates Templates allow you to add commonly used storage items quickly by defining them in advance Template allow you to setup commonly used storage items such as a box that your laboratory uses and re use the template as often as needed If you need to add a storage item that is a slight variation of an existing template you can modify the template while creating the new storage item For example if you need to create a storage container that has an excluded corner that is not in the template you can add it manually without needing to modify the template Creating storage item templates Storage item templates can be created for storage units levels an
203. torage tree 51 55 Index storage unit creating 55 moving 65 storage units removing 67 stored 18 42 stored specimens page 50 studies 24 sub add der type 35 sub additive derivative 42 system requirements 10 T tabs 12 templates for storage items 50 63 63 65 templates in storage 55 57 thaw count 31 35 42 TNO 47 total cell count 31 42 TWD 47 U undo 15 UNK 49 unshipping shipments 86 user interface 13 users changing 12 creating 117 manage permissions 117 reset password 117 V visit adding 27 visit value 42 volume 31 WwW web browser 10 12 13 workflow 20
204. ts Field Required Note ID1 PID Required ID2 CP Optional oa ID3 SID Optional Visit Optional on OPID Optional Clinic Optional Draw Time Optional Received Time Optional oe CIPRA The CIPRA preset project must meet these requirements Data entry requirements Field Required Note ID1 PID Required Must be 9 characters in the CIPRA ID1 format ID2 Protocol Required In the format P 0 10 ID3 ID3 Optional op Visit Required OPID Optional Clinic Optional ss Draw Time Optional Received Time Optional CIPRA ID1 format AABBCCCCD AA 01 to 99 LDMS USRMANOO3 Page 125 LDMS User Manual Preset projects BB 01 to 99 CcCcc 0001 to 9999 D Oto9 CONTROL The CONTROL preset project must meet these requirements Data entry requirements Field Required Note ID1 CONTROLNAME Required ID2 PROTOCOL Optional ID3 ID3 Optional Visit Optional OPID Optional os Clinic Optional oe Draw Time Optional Received Time Optional CPCRA The CPCRA preset project has these requirements Data entry requirements Field Required Note ID1 PID Required ID2 Study Optional ID3 Bth Sex Optional a Visit Optional Fs OPID Optional Clinic Optional Draw Time Optional Se Received Time Optional LDMS USRMANOO3 Page 126 LDMS User Manual CPQA Preset projects The CPQA preset project has these requirements Data entry requirements Field ID1 PanelID ID2
205. ttons and then select Print Labels This will print all labels associated with that item For example if you select Edit Participant gt Print labels you will print the labels for all specimens associated with that participant Likewise if you click Edit primary gt Print Labels you will print all labels associated with that primary e On the Storage page click the down arrow next to Edit button next to any storage item and then click Print Labels This will allow you to print labels for all specimens stored at that location e On the Pending Shipments page click the down arrow next to the Edit Ship button next to a shipment and then click Print Labels When creating labels specimens that are not available will not be included Related sections Generating labels from the Labels page on page 110 You can use the Labels page to print labels using more complex Logic than can be used in other places Generating labels from the Labels page You can use the Labels page to print labels using more complex Logic than can be used in other places Background If you want to generate labels you generally want to do so on either the Specimen Management Storage or Shipping page On these pages you can create labels for a specific participant a particular shipping or storage container or an individual shipment These are the most common scenarios for which you will need to generate labels LDMS USRMANOO3 Page 110 LDMS User Ma
206. tus of shipment Shipping E a a Meee Atay ae Stored x Ship Date Date batch was sent Shipping Ship temp Temperature of Shipping 7 Global Specimen ID x shipping batch xl F E Distinct Selection criteria tatu Not performed Add Name Operator Value 1 Additive EDT Remove 2 O Additive SST Remove Valid sentence items AND OR 0 and numbers corresponding to the grid rows above 1or2 File Type Text CSV Include Headers O Preview Generate Report Example custom report This is an example of a custom report for tracking specimens on shipments that have not been sent This report will find all specimens in your laboratory s database that are part of a shipment and are still available It filters by specimens that are available and have a shipment setup date all specimens with a shipment setup date will meet the before 30 Sep 2099 criteria since that date is in the future This report would be useful for identifying specimens that you are expected to ship but still have in your possession Fields to display e Global specimen ID e Batch number e QA QC status e Shipment setup date e Destination laboratory ID Sort results by e Destination laboratory ID e Batch number Selection criteria e Available Yes e Destination laboratory ID lt gt Your_Laboratory_ID e Shipment setup date lt 30 Sep 2099 LDMS USRMANOO3 Page 88 LDMS User Manual Reports Modifying or deleting a saved report
207. ure allow you to create all of the specimens from a participant visit at once and is the preferred method for entering new visits in LDMS If you add specimens to a participant on the Specimen Management page you would need to add each primary and set of aliquots individually The quick add feature allows you to select or create a participant and enrollment create a new visit and enter all of the specimens collected at that visit from one screen For new visits this significantly LDMS USRMANOO3 Page 37 LDMS User Manual Specimen Management reduces the amount of time it takes to enter a new visit in LDMS You can even create templates for common visits to save more time Once a template has been used any visits or specimens that were created are not associated with the template This means that if the template is later changed or removed visits that were entered using the template won t be changed Adding specimens using Quick Add Quick Add is used to enter information for a participant enrollments and multiple specimens all on one page Background This is useful when you want to enter a lot of information for a participant at once Templates if available can be used to fill in predefined information for you Procedure 1 From the LDMS menu bar select Specimen Management gt Quick Add 2 Optional From the Template list select a template to apply Use the Template Filters to narrow down the list of templates When you a
208. vasetuets AEE EEE EEE A a E EEEE EE EEES 125 LDMS User Manual Contents GON TARO Lerressces feo ii saechs Bence eee E ela cS GR Soh BE A ea 126 EPER Aaea rA AAE A E AA easton 126 CPO Anaa a a a aN a a a eee 127 FACTS EE A EEEE N EN ITE E AAA TI TE tare taste 127 FAN EAE EEES AE ANA ETE S A AIEA NAINEN ATE TAA 128 HPTN sasessastesstssvssesatvsestessesnestesaciadaassstesecsvesbeteadeacete sneasedeais duaaistent E aa aa 128 IP RE Ko a AAEE AAT AENA T Baths sett 129 DOA AAE AE T AOE T AS AOIR E it Gs E ET TA ATN 130 TR ETENE E EE AEA A EATEN NAS T E ENAT E EE 131 MACS TE NENEA SOE A NS V E E E E AE ate TE E ET E 131 DAAC BAITA E EEE AEN A AAA INANA AO AE EEIE AEII T E E lems teag 132 DAT C Taa A E AR 132 MT i PAEO EE EPEA O E EE E E EAE A 133 NIGHD WEStatisccsciccsetessessctiesscetessgebeasdeacctteadest sticstadivaiesseesben E A EER 133 PACS ER EE A TE TE U 134 REPRIEVE a E NENE AE NAN oak AI oe SOS N 134 SHIM e E EE haha A EA A EEE E E A E EAE EAE 134 SIN RP AEAN OEREN IEN A ENE EEE A A E E E AAA E E 135 VOR T TE E E E A A EA 136 MATIN es E E E E E AOA natch hse vaste 137 WEIN aasenso erika E SERE AEE A 137 MA S a a Sadana bain ase hehehehe 138 VIT S Poca re eee TN T ATAN EEA TOENE ROEA 139 WITSR EDOS irie EL EE OE N ENN RE O OA ENET ited 140 7A bse A ES E ASEE EAA EN E E E AT A I E E AEA A 140 Codes units and abbreviation scccscccssscessccessccsscccscccssccessecesscesseecees 141 Codes units and abbreviationS e
209. ve OPID e Aliquots remaining in Primary storage Project Specimen date Specimens in storage per PID report Shows the number for a given project participant combination that have a storage location assigned in a laboratory s database Filter criteria Sorting Information displayed on report This report is sorted by project ACTG PID ID1 e Project and then by participant e ACTG protocol e PID e ACTG protocol type e Count number of aliquots e Non ACTG PID ID1 e Non ACTG prot ID2 e OPID LDMS USRMANOO3 Page 106 LDMS User Manual Reports Sorting Information displayed on report Storage container location report Shows the storage location for all containers in a laboratory s database Sorting Filter criteria Information displayed on report This report is sorted by storage ACTG protocol e Storage location unit name and then by ACTG protocol type e Container name container position Freezer name Position Level name Non ACTG prot ID2 Project Sublevel name Storage count report by freezer Shows the number of specimens stored in a given storage unit for a given project protocol combination Sorting Filter criteria Information displayed on report This report is sorted by storage ACTG PID ID1 e Freezer unit and then by project ACTG protocol e Project protocol protocol combination and then ACTG protocol type e Primary by derivative a a os Derivative e Additive Non ACTG PID ID1 e Deriv
210. w time 31 42 DSH 48 DSR 41 46 49 DSS 10 E Edit Participant button 23 empty structure 55 enrollment adding 24 modifying 25 removing 25 Enrollments 23 EQF 46 Evince 10 excluded position 52 55 57 EXP 47 extended search 14 F filters applying 14 removing 14 Firefox 10 FISMA 9 FRO 47 Frontier Science 10 frozen date 31 35 42 LDMS User Manual G global specimen ID 29 30 42 109 109 H HEM 48 HUM 48 icons 54 ICT 48 ID1 validation 21 ID2 24 24 27 115 IDS 42 115 identifiers 29 INT 47 internal only comments 31 35 42 68 Internet Explorer 10 INV 46 L label size 109 labels 108 109 109 110 112 113 laboratory ID 29 laser labels 109 LBE 46 LDMS 10 51 63 LDMS User Support 15 117 level creating 57 moving 65 levels removing 67 LibreOffice Calc 10 LIP 48 LKD 47 local time 31 log on 11 logic 90 LSH 41 48 LYS 48 M manage enrollments 33 menu bar 13 50 Microsoft Excel 10 N navigation 18 NIST 9 not available 41 Index 0 Opera web browser 10 OPR 46 original volume 42 OSW 46 OTH 49 other specimen ID 29 31 42 P paper size 109 participant adding more than one 20 creating 21 21 modifying 23 multiple projects 21 OPID 21 project 21 search for 18 view different 18 participant identifier 23 password 117 passwords 117 118 PBMC 37 PDF files 13 PDF viewer 10 permissions 117 positioning in storage 55 57 59 positions only 52 primary spe
211. xt to each laboratory s name is the laboratory s LDMS ID number c Select or enter the person to receive the shipment at the receiving laboratory from the Contact Person box Laboratories can be added to LDMS These will only appear as available for selection by your laboratory Since all laboratories that use LDMS and LDMS are already listed the new laboratory is assumed to be using some other laboratory management system a Select New lab b Complete all the boxes in the Shipping Destination and Contact Information sections c Optional If you want to save this laboratory for future use select the Save address box Complete the information on the Contact at sending lab tab This is where you enter the information for the person at your laboratory who should be contacted if there is an issue with the shipment Optional Complete the information on the Shipment notes tab This information will appear on the shipping manifest and will be shown to the receiving laboratory when they load the shipping file These comments are in addition to comments that were entered for individual specimens Use the Comment box for general information about the shipment The Disclaimer box can be used to provide information about the restrictions placed on the specimens usage Add specimens to the shipment on the Shipment Contents tab e Add a container already setup on the Storage page to the shipment from the Storage Containers List e A

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