GSCF User Guide
Contents
1. L cf 7 Homo sapiens Lei 8 Homo sapiens x 9 Homo sapiens Le 11 Homo sapiens Lei e prev Cm next Copyright 2008 2012 NuGO NMC and NBIC All rights reserved v Hovering over question marks will show additional information on required fields o v Use the upper left icon to select all rows in a table Name 201 202 EI 203 v Select multiple rows by click and dragging over multiple rows Human template Species Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens Homo sapiens EI 9 Homo sapiens 1 Getting started simple import and wizard Using the menu on top of the application you can either create view or import studies and study data Generally there are two ways to get your data into the database 1 Start the study wizard which will guide you step by step This will allow you to describe the study design all events and sampling events that take place and on what time Also into what event groups your subjects are organized Based on subjects event groups and events GSCF will create samples Samples are the links between GSCF and the assay modules where you can store specific data such as metabolomics or clinical chemistry values Go to ch2. prev quick save next Copyright 2008 2011 NuGO NMC and NE lormation go to http dbnp org After you have added an event or sampling event it will appear in a list below and you can modify this event if necessary Here you also need to create any event groups that occur in your study Make sure that each event is linked to a group Only then subjects can be added into this group see next step gt Important each event should be added separately gt Important a combination of sampling events subjects and groups will automatically create samples Choose The Type Of Event treatment challenge etc Sampling Event Template e Eis Blood sampling even EL mme Gun K Gou K K Start Time Duration Sample Template Control o 7 Ts Bod F Dood F e Bood prev quicksave next Subjects into event groups Click next this in between step allows you to select subjects and indicate to which event group they belong F Subjects Group 2 E E E lt E E E E E lt a E S Subject 7 E E Subject 8 E E Subject 9 gt Note event groups are created in Step 3 You can fill these groups with subjects between Step 3 and 4 Step 4 Samples 1 Start 2 Subjects 3 Events 5 Assays 6 Confirmation 7 Done This step gives a table with all the samples that were created Note that a combination of sampling events subjects and groups au
3. modify Copyright 2008 2012 NuGO NMC and NBIC All rights reserved For more information go to http dbnp org The result is one event in which all subjects take part Show Study Study Information Subjects Events timeline Events table Assays Samples Persons Pu Name Events Subjects diet event start time Diet_0s Os 187 Homo sapiens 28 Click on Browse gt My studies and use the pencil on the left to edit a certain study Samples are created as a combination of a sampling event a subject and an event group Change any of these to your needs and this will create more samples For example if you miss a certain subject add this subject in Step 2 Then navigate by clicking next and this subject can be selected into a certain eventgroup By clicking next GSCF now creates new samples based on the new subject that was added to an eventgroup See previous question how to add more samples into your study Then go to Step 5 and click next Now you reach the in between step where you can add samples to an assay Each sample name created in GSCF is composed of several fields For example the name 11 UrineAfterFasting AllPersons 1d has been created from Subject name 11 Event group All Persons Sampling event Urine After Fasting Starttime Sampling event 1 day If there are more samples with the same content then sample names get the addition 1 2 3 Yes you can change the names that are automatic
4. between reduction of the inflammatory status and glucose metabolism in healthy 60 overweight men Diclofenac 18 144 Blood Placebo S Relation between reduction of the inflammatory status and glucose metabolism in healthy 60 overweight men Diclofenac 18 144 _Blood_Placebo_ _4 Relation between reduction of the inflammatory status and glucose metabolism in healthy 60 overweight men Diclofenac 18 144 Blood_Placebo_ _8 Relation between reduction of the inflammatory status and glucose metabolism in healthy 60 overweight men Diclofenac i ei A Ce t ch ry C f J e Wns ynnaonr r n EL e Wwf A T A Z La en e eH L A en ZA My samples do not appear in the module What can I do LE EL kack A For samples to appear in a module attached to GSCF make sure you have selected the right module for this assay For example make sure you selected module Simple Assay Module when you trying to view samples in this module SAM Second make sure the right samples are actually in this assay You can check this by clicking next in Step 5 Here you can see a list of which samples are in what assay If the right samples do not exist for this assay and module add more samples Samples are created as a combination of a sampling event a subject and an event group Change any of these to your needs and this will create more samples For example if you miss a certain subject add this subject in Step 2 Then navigate by clicking next
5. quire within jy data the s especially wear dncinne Application information You will enter a search page but if you search without any given character for username you get a full list of all known users and administrators Username Enabled Account Expired Account Locked Password Expired admin user NTC Renger roberthorlings martiencaspers bartkeijser bioclaims thomaskelder test123 2 3 Next True False Enabled Account Expired Account Locked True False False True False False True False False True False False True False False True False False True False False True False False True False False False False False Either o Password Expired False False False False False False False False False False To see the role for a certain user name click on that name and go to the tab Roles Here you can see if this user has admin rights 22 Edit User User info Roles E ROLE_ADMIN Copyright 2008 2011 Nu 5 2 Readers and writers When a new study is created other users can become Reader or Writer of that study Readers are able to see the study but cannot edit it Writers can also edit the study Before you assign Readers and Writers make sure your study is published first How to publish a created study Before a study is actual visible to study readers and writers make sure that the box Published is checked This can be done in the first page of
6. since only minimal necessary information is imported Disadvantage comparing two studies is more difficult if users only fill in minimal study meta data gt Use the content list on page 2 to navigate through this guide gt For any questions that could not be answered through this guide please email support thehyve nl 1 1 Create a new study wizard For creating a new study you have to have a login See chapter 7 Access control on how to become a user Click on Create gt Create a new study using the menu on top This will start the 6 step study wizard Step 1 Start 2 Subjects 3 Events 4 Samples 5 Assays 6 Confirmation T Done Define basic properties of your study Fields indicated by an arrow are required You can choose an appropriate template or create a new template This will allow you to add and modify fields Template add modify el 9 Title gt Mass Sequencing Study Description gt Test study DI mice intervention stud Code add modify Start Date Published Ce Publications No publications selected Add Publication Contacts No contacts selected In some browsers Firefox 4 Safari and Chrome fields can be enlarged by dragging the indicated lower right corner of the text field Step 2 Subjects 1 Start 3 Events 4 Samples 5 Assays 6 Confirmation T Done Use this step to manually add a number of subjects report the number of subjects in your study and choose the
7. with straightforward design A gt A part of the study design j troduction Quicksearch A list of studies choose eneric Study Capture Study n that can store any ological study It co akes it possible to ustomize h 1 order to allow flexibility to capture all information you require within Quick Start study and to make it possible to compare studies or study data the ystem uses customizable templates and ontologies It is especially esianed to store complex studv desians including cross over desians Through the studies menu you lt studies or study data Create Step 1 Import file Select your excel file The excel sheet should have this format every study subject sample or event has its own row gt Itdoes not matter in what column which information is stored as you can map the field in the template on the columns in your excel sheet gt Itdoes not matter how many headers are included in your excel sheet as you can define in which row the first subject sample or event can be found A B C D E 1 mouse Weight Cage number Number of mice in cage 2 200 25 1 2 3 201 25 3 1 2 4 202 26 4 2 2 5 203 24 4 2 2 D 204 24 2 3 3 Make sure to select the correct data template e g a mouse subject template for a mouse study The importer will show a preview of your uploaded excel file Choose type of data template PPS Mouse e Select data template Show 5 EN entries Column Column l Maan
8. GSCF User Guide Version 1 5 Date 02 03 2012 Written by Janneke van der Ploeg Introduction GSCF GSCF Generic Study Capture Framework is a web application that is designed to store the design of biological studies in a database GSCF serves as a linking hub for other modules it links to the data in the various assay modules So before data in modules can be entered the study design needs to be in GSCF The following image headers illustrates what type of information can be stored in GSCF Show Study Study Information Subjects Events timeline Events table Assays Samples Persons Publications title description code startDate Introduction assay modules Users can create samples by their study design in GSCF and indicate where PPS3 Excessive intake of dietary fat is known to be a contributing factor in the development of obesity In this study we determined the dose dependent effects of dietary fat on the development of this metabolic condition with a focus on changes in gene expression in the small intestine C57BL 6 mice were fed diets with either 10 20 30 or 45 energy E derived from fat for four weeks n 10 mice diet We found a significant higher weight gain in mice fed the 30E and 45E fat diet compared to mice on the control diet These data indicate that the main shift towards an obese phenotype lies between a 20E and 30E dietary fat intake Analysis of differential gene expression in
9. able at all steps of the create study wizard For example to indicate the type of study design choose an existing Study template or add modify templates This will show a popup where you can define the fields you want to appear next to default fields for study details Choose Add Modify to add or edit templates Start page 1 of 7 2 Subjects 3 Events 4 Samples i Define the basic properties of your study In this step of the step by step study capturing tool all the basic information the more specific the information that is filled out the more valuable the syst the study template of choice currently a fixed set and define your study val Template gt Title gt Human intervention Description Mice intervention Mice intervention NNC Code add dify Start Date gt add modify Published Te Publications SEN No publications selected Add Publication Now you can see a list of existing templates add modify Select template Showing templates for Study compare Please select a template to edit or create a new template Microbial population Bes Re Mice Intervention Ta E Ba Human Intervention 2 e Mice intervention NNC Ta Ee Create new template By clicking the first icon you can change the name and description For each template you can also describe additional fields Click on the second icon to modify template fields 26 In this screen you can create new fields in
10. ally created by GSCF However especially when you have a long list of samples this has to be done all manually Go to the Study Edit gt Samples Another option is to import samples and thereby use your own samplenames During the import you can attach samples to corresponding subjects that you have in GSCF See chapter 1 page 13 for more details on sample import Click on Search gt Advanced Search Select your GSCF fields and values you want to search for Then select type of output based on Studies Samples or Assays For example show me all samples from subjects that are at least 62 years of age Search database 1 Select criteria N B Comparing numerical values is done without taking into accou Field Operator Value EH e Age RELTIME Subject Age years Subject 2 Cage no Subject Cage no before exp Subject 3 No mice in cage Subject Age child at sampling Sample Storage condition SamplingEvent 29 This will result in the following output Query results Sample search 7 38 samples found with subject age years gt 60 Ia Name gt Study gt Subject Ag years Di 18 144 Blood Placebo L w Relation between reduction of the inflammatory status and glucose metabolism in healthy 60 ge overweight men Diclofenac 18 144 Blood Placebo Relation between reduction of the inflammatory status and glucose metabolism in healthy 60 _ overweight men Diclofenac F 18 144_Blood_Placebo_0s Relation
11. and this subject can be selected into a certain eventgroup By clicking next GSCF now creates new samples based on the new subject that was added to an eventgroup 30
12. and you will get a list of all the samples that match to the specified criteria Results of this search can be exported for example as CSV file Query results Sample search 1 2801 samples found with samplingevent sampletemplate contains blood and subject age reltime gt 30 Ia Name gt Study SamplingEvent Subject sampleTemplate Age RELTIME F 1029 49_Blood_2b_0sTailBlood PPS1 Tail blood 12w Ia 1029 49 Blood 2b iw PPS1 Tail blood 12w ry 1029 49 _Blood_2b_1wiSmTailBlood PPS1 Tail blood 12w F 1029 49 Blood_2b_iwtihTailBlood PPS1 Tail blood 12w F 1029 49_Blood_2b_iwis PPS1 Tail blood 12w 1029 49 Blood_2b_iw2hTailBlood PPS1 Tail blood 12w a 1029 49 _ Blood_2b_ 1w30mTailBlood PPS1 Tail blood 12w F 1029 49_Blood_2b_iw3dBloodSacrifice PPS1 Blood sacrifice 12w F 1029 49_Blood_2b_1w45m PPS1 Tail blood 12w F 1029 49_Blood_All_ 2w3d10hTailBlood PPS1 Tail blood 12w Showing 1 to 10 of 2 801 entries r eviot 1 2 3 4 5 Next Last b Search within results SI Export as CSV 4 Refine by classification Metagenomics Export as fasta Metagenomics r Search again SI Export metadata Metagenomics 2 Za Discard results Previous searches gt Note especially when you choose sample as the output format this search can take several minutes since the number of samples can be very high 15 3 Visualize The visualization tool GSCF allows you to visualize any data that is entered into the database This can be subjec
13. apter 1 1 for a more detailed description Advantage full description of your study design and easy to compare with other GSCF created studies that are fully described Disadvantage because a lot of information can be stored to describe your study it takes some time before you can start using the modules Especially when your study contains a lot of samples gt 1000 the wizard can become a bit slow 2 a lf you have a sample list of all samples in your study you can use the short way to get data into the system Since samples samplenames are the link between GSCF and the assay modules you can simply create a study and describe study metadata A Home Create Import Browse Analyze Export Introduction d gt A complete study with p straightforward design Phenotype Database is store any biological study It contains templa e part of the study e to customize esign In order to allow flexibili n you require within a study and to make it g A list of studies or study data the system uses customiza bsi NET UA ies It is especially designed to store comp i A cross over designs and challenges b Then use the importer Import gt A part of study design to import your Excel sheet and thereby import your own sample names These names can then be used in the various assay modules to add metabolomics data Go to chapter 1 3 for a more detailed description Advantage you can quickly enter data into the module
14. dicate what is required for these fields and you can organize all fields add modify Human intervention switch Available fields Currently this template contains the following fields These fields are available for adding to the template Drag fields to reorder Drag fields to the list of Drag a field to the template to add it available fields to remove the field from the template title Short text Type Dropdown selection of a epes terms description Long text code Short text Create new field startDate Date published True false t Institute Short text a t Consortium Short text a t Objectives Long text a t Study protocol File La t Central conclusion Long text ia e t objective related inclusion criteria A Other parts within the GSCF study design that apply the template system are Subjects Species template Events Sampling Events Samples and Assays 27 FAQs 1 4 YY JIC i Click on Browse gt My studies to view your studies It is possible that other users indicate you are reader of a study These studies also appear in this list UULCEC OLM Click on Browse gt My studies and use the pencil on the left to edit a certain study Just as creating a new study this will start the study wizard Using next and previous you can navigate through your study and update any information from this study Events or sampling events can be imported using a short wizard the same way yo
15. e This will allow you to export measurements from SAM for example Select the study and assay for export and Submit Select the assay you want to export data from With this exporter you can export meta data about samples from an assay to a file First select a study from the first list and then select an assay from that study from the second list Human PPS an intervention study EN antigen panel Le haematological l l l l clinical chemist m Copyright 2008 2011 NuGO NMC and NBIC All rights reserved For more information go to http dbnp org EET LC NMR GC clinical chemistry urine In the next screen you can specify in more detail which fields you want to export If you want to export SAM Assay data make sure that Measurements is checked Select the columns that you want to be included in the resulting file In this step you can make a selection from the available fields stored in the database a module if available v Subject Data name species Gender Age RELTIME Body Weight g Cage no mice in cage Cage no ampling Event Data startTime duration sampleTemplate Control ample Data name lig kik ss an naan ki i name Measurements Cholesterol 19 Finally select the file type All types can be opened in Excel 20 Select type of resu
16. ectID DataFile HybName SampleNa ArrayType Label StudyTitle Array ID Species name species Body WeicC 2 Subject 6 Subject6 WholeBody control PPS3 Mus musc Subject 6 Mus musculus 3 Subject 8 Subject8_ WholeBody control PPS3 Mus musc Subject 8 Mus musculus t Subject 5 Subject5 WholeBody control DG Mus musc Subject 5 Mus musculus 5 Subject 7 Subject7_WholeBody control PPS3 Mus musc Subject 7 Mus musculus 5 Subject 10 Subjecti0_WholeBod control PPS3 Mus musc Subject 10 Mus musculus 7 Subject 3 Subject3_WholeBody Minocyclin PPS3 Mus musc Subject 3 Mus musculus 3 Subject 9 Subject9_WholeBody Minocyclin PPS3 Mus musc Subject 9 Mus musculus 3 Subject 1 Subject1_WholeBody control PPS3 Mus musc Subject 1 Mus musculus 0 Subject 4 Subject4_WholeBody Minocyclin PPS3 Mus musc Subject 4 Mus musculus 1 Subject 2 Subject2_WholeBody control PPS3 Mus musc Subject 2 Mus musculus 2 Subject 16 Subjecti6 WholeBodHF AL PPS3 Mus musc Subject 16 Mus musculus 3 Subject 12 Subject12_WholeBod cHF PPS3 Mus musc Subject 12 Mus musculus 4 Subject 17 Subject17_WholeBod cHF PPS3 Mus musc Subject 17 Mus musculus 5 Subject 14 Subjecti4_ WholeBodHF AL PPS3 Mus musc Subject 14 Mus musculus 6 Subject 13 Subject13_WholeBod HF AL PPS3 Mus musc Subject 13 Mus musculus T Subject 20 Subject20_WholeBod Chow PPS3 Mus musc Subject 20 Mus musculus 4 2 Export Assay data If you want to export a study but also the data from the assays that belong to this study use Export gt Export Assay data to fil
17. i ZAIT Factory 201 25 3 Mouse 202 26 4 add mo dify u Bo a A A ES 10 Step 2 Assign properties Map the information in your excel sheet on the columns using the dropdowns If a certain field is missing go to back to Step 1 where you can modify or add fields for a certain template mouse Weight name IDENTIFIER Body Weight g Le Don t impart 200 name IDENTIFIERS 201 no mice in cage 202 Cage no Body Weight oi 203 te De 304 24 2 Showing 1 to 5 of 102 entries Step 3 Add information Add information to the table when necessary Multiple rows can be selected by click and dragging Species Step 4 Confirmation Check whether the information is correctly mapped and click gt Next Click on the study title to view your imported study data Show Study Study Information Subjects Events timeline Events table Assays Samples name species Body Weight g Cage no 200 Mus musculus 25 7 1 201 Mus musculus 253 1 202 Mus musculus 26 4 2 203 Mus musculus 24 4 2 How to import my own samples and samplenames This chapter will show you how to import your own samples and sample names Start with Import gt A complete study with straightforward design This will start a short wizard Home Create Import wse Analyze at can store any em akes it possible to A complete study with straightforward design Introduction gt NMC Data Support Plat biological study It coni gauea
18. inclusion criteria objective Taking aspirin or aspirin containing drugs other anti inflammatory drugs or any drugs or herbal medicines known to alter platelet function or related the haemostatic system in general exclusion criteria Events Fasting Food intake Sampling Blood Saliva Urine after fasting events Public Owner user Readers jsaito metabolomics Writers z 24 How to make a study publicly available If you want to make a study publicly readable so even for non DSP users you can indicate this also in the first step Make sure that Public is checked Template human intervention study x Title PPSH Description The human PPS Q enrolled ten healthy Z Code NuGO_PPSH Q Start Date 01 09 2007 Q Published Q Goals gt 1 assess the UI Study Performed At Rowett Institute of Nutrition and P Subjects Exclusion Criteria Taking aspirin or D aspirin containing A Subjects Inclusion Criteria e Ascertained as D healthy by a general Data Produced At Publications No publications selected Add Publication Contacts Roos Baukje de Principal Investigator Add Contact Add User Writers mmwbhendriks Jildau Add User 25 6 Templates In order to allow flexibility to capture all information you require within a study and to make it possible to compare studies or study data the system uses customizable templates and ontologies Templates are avail
19. ling Ldlr 9whf_9wLiver LDLR_9WHF C57BL 6 NLDLr Male 76 Ow Ow ei DZ 1 77 Cheese eegenen dle Ohad had nine IMM faalt Ce7oi me hiMeft Aiala 7 ns Ms Describe your subjects samples and events by using existing templates Excel file to import gt Uploaded dbnp link array2 events xls Subject template Human subjects kel BEES no event template EN Sampling event template Blood sampling P ers 8 Previous Next Hi Skip The important step during import is to map your columns with GSCF terms to indicate how your excel sheet is structured Any data you want to skip can be indicated by selecting Don t import For example choose subject name where your subject IDs and sample name identifier where your samplenames are Imported file step 2 of 4 Assign columns to template fields You uploaded dbnp link array2 events vs This list shows the first 5 rows of the uploaded file for reference the excel file with the fields in the database Excel columns SubjectID SampleName Label Example data L 022 L 22 OrganSampling Ldlr Swhf LDLR SwHF L 041 L 41 OrganSamopling Ldlr 9whf LDLR 9wHF L 050 L 50 OrganSamopling Ldlr 9whf LDLR 9wHF L 076 L 76 OrganSampling Ldlr Swhf LDLR 9wHF L 077 L 77 OrganSamplina Ldir 9whf LDLR 9wHF Template field name identifier a name identifier E m Don t import sa 7 Don t import Subject name identifier Edit data after species Gender Samp
20. lingEvent startTime duration sampleTemplate connected event name Previous Next Copyright 2008 2012 NuGO NMC and For more information go to http db material 12 Fill in missing values and select assays if you wish The wizard will then give a study summary After Save you can view your study Show Study Study Information Subjects Events timeline Events table Assays Samples Persons Publications Parent Subject Parent Sampling Event Parent Event Group name L_103 Blood sampling at 0 seconds L_103_OrganSampling_Ldlr_9whf_9wLiver L_120 Blood sampling at 0 seconds L_120_OrganSampling_Ldlr_Swhf_9wLiver L_201 Blood sampling at 0 seconds L_201_OrganSampling_Ldlr_16whf_16wLiver L_202 Blood sampling at 0 seconds L_202_OrganSampling_Ldlr_16whf_16wLiver L_203 Blood sampling at 0 seconds L_203_OrganSampling_Ldlr_16whf_16wLiver L_204 Blood sampling at 0 seconds L_204_OrganSampling_Ldlr_16whf_16wLiver L_205 Blood sampling at 0 seconds L_205_OrganSampling_Ldlr_16whf_16wLiver L_206 Blood sampling at 0 seconds L_206_OrganSampling_Ldlr_16whf_16wLiver L_207 Blood sampling at 0 seconds L_207_OrganSampling_Ldlr_16whf_16wLiver L_208 Blood sampling at 0 seconds L_208_OrganSampling_Ldlr_16whf_16wLiver L_209 Blood sampling at 0 seconds L_209_OrganSampling_Ldlr_16whf_16wLiver L_210 Blood sampling at 0 seconds L_210_OrganSampling_Ldlr_16whf_16wLiver 13 2 Advanced search Data from GCSF and the assay modules ca
21. lting file Tab delimited txt J Comma Separated USA UK csv Semicolon Separated European csv 5 Access control 5 1 Admin and users GSCF makes a distinction between administrators and users When a new users registers he or she will automatically become a normal user When a new user is added by the administrator he can give this user either normal user rights or an administrator role How to create a new user or admin Go to Admin gt Create User List Users Create User Manage Modules Setup wizard Application information All three username password and email address are required fields To finish this user make sure User confirmed and Admin confirmed are checked and click Save Create User Username Password Email address User confirmed Admin confirmed Account expired Account locked Password expired Save Copvriaht 2008 2011 NuGO NMC and NBIC All riahts reserved For more information aa How to give a user administrator rights Only after a user has been created the option of giving administrator rights is enabled This can be found in the Roles tab while editing a user Edit User User info Roles E ROLE_ADMIN Copyrig 21 How to see all users and their access rights Go to Admin gt List Users Search Modules Admin gt List Users Create User Manage Modules iy biological jtomize e l Setup wizard
22. n customize design In order to allow flexibili gt A list of studies n you require within Qui a study and to make it Oe Tee s or study data the Thro stud seve mark system uses customizab e Ir is especially designed to store complex study designs including cross over designs and challenges 11 Define basic information of your study and click next Arrows indicate required fields New study step 1 of 4 O Define the basic properties of your study Enter all the basic information of your study Keep m mind that the more specific the information that is filled out the more valuable the system will be Template demo ei NM Publications demo No publications selected Title demostudy Add Publication Description description H Fass Code kd null do Demoman ei Start Date 7 01 03 2012 Thursday 1 March 2012 Add Contact Blob Upload Authorization Public Vi Published t Readers Add User Writers Add User gt Next D Open Save Choose the excel file with appropriate subject and sample data for example A B C D E F G H 1 SubjectID SampleName Label Strain genotype Gender name old starttime endtir 2 L 022 L_22 OrganSampling_Ldir_9whf_9wLiver LDLR_9wHF C57BL 6 NLDLr Male 22 0w Ow 3 L_041 L_41_OrganSampling_Ldlr_ 9whf_9wLiver LDLR_SWHF C57BL 6 NLDLr Male A Ow Ow 4 L_050 L_50_OrganSampling_Ldir 9whf_9wLiver LDLR_SWHF C57BL 6 NLDLr Male 60 Ow Ow 5 L076 L_76_OrganSamp
23. n also type the assay name to see what features are possible Y Axis clear simple assay module antigen panel Wi Adiponectin ug mL Alpha 1 Antitrypsin mg mL Alpha 2 Macroglobulin mg mL Al pha Fetoprotein ng mL Apolipoprotein Al mg mL Apolipoprotein CIIN ug ml Apolipoprotein H ug mL Beta 2 Microglobulin ug mL Brain Derived Neurotrophic Factor mg dml Several aggregation options are possible By default Average is selected however you can choose any of the options that are enabled The graph will reload when you choose another type of calculation of your data The tool enables you to visualize your data in different kinds Depending on the type of data you selected the types are functional For example if you choose to have categorical data on the X axis e g event group name or subject number you cannot choose for a scatterplot VISUALIZATION TYPES X AXIS Y AXIS TYPE Numerical Numerical Scatterplot Linechart Numerical Categorical Horizontal Barchart Categorical Numerical Barchart Linechart Categorical Categorical Table 18 4 Export data Both GSCF as well as Assay data can be exported 4 1 Export GSCF data A whole study with GSCF data can be exported as a SimpleTox Excel file To do this navigate to Export gt Export studies as SimpleTox Excel file Select which studies you want to export and click Export The output will look like this A B C D E F G H J K L 1 Subj
24. n be queried by using the Advanced search Use the menu on top of the page and click on Search gt Advanced search Modules Advanced search On this page you can search for any of the parameters fields used in GSCF and the modules This can be Age Subject Name Cholesterol or other feature names used in Simple Assay module or Classification or other fieldnames used in Metagenomics module Search example Let s assume you want to have a list of all blood samples where subjects are of age 30 or higher among all your studies First you have to specify parameters Note that while you type for a fieldname you will get a list of possible fieldnames that exist in the database Search database 1 Select criteria N B Comparing numerical values is done without taking into account the units E g a weight of 1 kg equals 1 grams Field Operator Value SamplingEvent sampleTemplate contains blood EI Age RELTIME Equals Le EI Age RELTIME Subject ib Age years Subject Cage Subject ria Cage no Subject m Cage no before exp Subject 2 No mice in cage Subject i Age child at sampling Sample Storage condition SamplingEvent sequences Me tagenomics 3 Forward primer Metagenomics Mid name Metagenics Choose your output format results can be shown on either study sample or assay level 2 Output type Choose the type of output Samples gt Studies 3 EFES 14 Click Search
25. plot Table Boxplot VISUALIZE 3 advanced settings 1 message Below the Visualize button there are links for advanced settings and messages If your data is invalid to be visualized or cannot be found a message will appear Click on the link to read the full message Click on advanced settings for more interface options Especially with studies that have a lot of data the first item is important by default the tool will show a graph as soon as enough parameters is known To visualize a graph manually deselect this item x Visualize the data as soon as enough parameters are known FJ Visualization type Always show values in the graph if this box is unchecked value s are only shown when you hover over a datapoint Note that hover on a barchart with value O isn t possible Horizontal Barchart O barchart Linechart Scatterplot Table Boxplot Angle labels on the x axis if this box is checked labels are shown at a VISUALIZE 45 angle W gt Place legend outside the graph 3 legend is only shown when the group by 492 advanced settings leq S ys group by message option is used Ok 17 3 2 How to get module data visualized Instead of GSCF fields you can also select fields from the modules that you have entered data into For instance you can select a feature from SAM simple assay module by selecting this on the Y axis All features are grouped together by assay name You ca
26. ss spectrometry for protein identification Alterations in the PBMC transcriptome are being analyzed by employing the Affymetrix microarrays specifically designed for NuGO and plasma and urine sample metabolite profiling is achieved based on NMR GC MS GC MS MS and LC MS MS platforms comprising non targeted and targeted approaches Moreover a panel of 89 hormones cytokines and chemokines and metabolic factors was analyzed on a commercial targeted profiling platform RulesBasedMedicine www rulesbasedmedicine com In this unique combination of nutrigenomics tools this study should provide the most comprehensive metabolic phenotyping possible in human volunteers with minimal invasive methods for obtaining appropriate biosamples code NuGO_PPSH startDate 2007 09 01 00 00 00 0 published true Objectives 1 assess the biological intra and inter individual variance of a huge spectrum of molecular metabolic and clinical parameters employing the different omics technologies at baseline and after a 36 h fasting period 2 identify common and unique changes in these parameters in response to fasting 3 determine the most comprehensive and sensitive omics approaches to detect and quantify the effects of a nutritional fasting challenge in humans Institute Rowett Institute of Nutrition and Health University of Aberdeen Aberdeen Consortium NuGO objective Ascertained as healthy by a general medical examination including an haemotinic assessment related
27. strates how GSCF and assay modules are related Preprocessing pipelines Queryable data Content WS A BIS o E E E A ANES E E EA E A AA 3 1 Getting started simple import and wizard ssssnesseensssersssersssersssersssersssrrsssrrssserosserossrressresssrrsssresssersssrressreesseree 4 1 1 Create a new study Wizard EE 5 LEIET ET E 9 1 3 Import part of study TEE 10 P EE E e EE 14 DEE 16 3 1 HOW toget GSCF Catal VISUGIIZEG KEE 17 3 2 How to get module data visualized nossnennesseensssereesssreresssreresssreressererosssrersssrrresssrerossererossrereosseeressereresseeee 18 AEO A E 19 4L Export GSCF OATI svssisacvaicsaessusaevaensscsenneagaeneetndesossynns ay E E eee 19 AD EDONA SAY a WE 19 BCC OSS COO a A E E E A E EA 21 5 41 AVC ERC 21 S2 FACS eS ANAWE Scares rece cates cect zap ev cedn ce E T ou wana vw eee 23 e EE 26 Ee 28 Tips and tricks General v Use import study data to import large datasets for example many subjects from an excel sheet into your study see also Chapter 1 3 Import part of study design v When you want to use Advanced search and choose sample as the output format note that this search can take several minutes since the number of samples could be very high Study wizard v Use next and previous at the bottom of the page to navigate or use quick save at any time during the wizard to complete it at another point in time
28. t related data such as weight BMI or average age but also SAM data such as average leptin levels measured grouped by event group To enter the visualization tool go to Analyze gt Visualize and you will see the control panel for visualizations on the left Home Create Import Browse Analyze Export Modules Study clear Search 4 gt Visualize x AXIS clear Y Axis clear Group by clear Aggregation Sum Count Average Median No Aggregation Visualization type Horizontal Barchart W barchart Linechart Scatterplot Table Boxplot VISUALIZE de advanced settings ial O messages 16 3 1 How to get GSCF data visualized First select your study and choose parameters for the X and Y axis You can use the search bar and just type the field you want to use The Group by functionality is optional so you can leave this unchanged Step 5 will allow you to specify how to aggregate the data but average is selected by default If there are multiple visualization types possible you have to indicate how you want to view it If all parameters are set the graph will automatically be generated Study clear NuGO_PPSH Human PPS an intervention study EX X Axis clear name Y Axis clear GSCF subjects BMI kg m2 L Aggregation Sum Count Average Median No Aggregation 6 Visualization type Horizontal Barchart barchart Linechart Scatter
29. template Then add these subjects to your study and fill out the required information in the table Number Of Subjects To Add 11 o Of Species Homo sapiens Le HM With Template Human i Human template oO Name Species Individ 1d Gender Age Years years Ot hms fel Male E 2d Homosepins Cel Female cel 0 0 S Homosepins Gel Female _ E oL nengen NI mm Si If you have an excel file with subject list a separate importer can be used Especially when you have detailed subject information this importer can be used very efficiently See Topic 3 Import part of study design page 10 Step 3 Sampling Events 1 Start 2 Subjects 4 Samples 5 Assays 6 Confirmation 7 Done Any treatment challenge or occurrence in your study can be defined in the events step An event is defined as anything that happens to subject s in your study that is not resulting in a sample Whereas sampling events if the event results in extraction of samples where you want to store measurements upon First choose between treatment or sampling event Chepose The Type Of Event treatment challenge ete Then choose the appropriate sampling event template Choose The Type Of Event treatment challenge etc Sampling Event Template Blood after fasting e Si Blood after fasting Body Weight Fat biopt Feces Organ sampling Saliva Sampling human microbial flora Urine Urine after fasting
30. the small intestine showed a fat dose dependent gradient in differentially expressed genes with the highest numbers in mice fed the 45E fat diet The main shift in fat induced differential gene expression was found between the 30E and 45E fat diet Furthermore approximately 70 of the differentially expressed genes were regulated in a fat dose dependent manner Many of these genes were involved in lipid metabolism related processes and were already differentially expressed on a 30E fat diet Taken together we conclude that up to 20E of dietary fat the small intestine has an effective buffer capacity for fat handling From 30E of dietary fat a switch towards an obese phenotype is triggered We further speculate that especially fat dose dependently regulated lipid metabolism related genes are involved in development of obesity NuGO_PPS3 2008 04 01 00 00 00 0 Studies the assay data is stored In these assay modules users can easily import for example bulks of numerical data from Excel files The following modules are Subjects Events currently available for GSCF e Metagenomics Samples Groups e Clean transcriptomics CTD L e Metabolomics e Simple Assay Module SAM e Transcriptomics Vv Assay modules For example the Simple Assay Module SAM is used to store clinical data such as Rules Based Medicine assays but also physical measurements such as body Omics raw data weight of mice The image below illu
31. the study create Wizard This determines whether this study is published accessible for the study readers and if the study is public for anonymous users A study can only be published if it meets certain quality criteria which will be checked upon Save The option is maybe a bit hidden and easily skipped but can be found here Template human intervention study x Vom o PPSH Description S The human PPS enrolled ten healthy Code NuGO_PPSH Ai 09 2007 9 Date Published assess the SS d II p P Study Performed At Rowett Institute of Nutrition and Subjects Exclusion Criteria Taking aspirin or a aspirin containing F Subjects Inclusion Criteria Ascertained as D healthy by a general Data Produced At Publications No publications selected Add Publication Contacts D Roos Baukje de Principal Investigator Add Contact Public Iv Readers Add User Writers mmwbhendriks Jildau Add User 23 How to add users as readers or writer of a study In the first step of the study create wizard you can assign users as public Readers or as Writers of the study E Add User Writers mmwbhendriks Jildau Add User Click on Add User and select the user you want to become a Reader and click on Add to add this person as Reader Follow the same procedure for Writers to assign a user as Writer Add user x Select a user from the database admin keesvb prasad ewa d
32. tomatically created your samples You can make any adjustments or fill out empty fields when necessary Step5 Assays 1 Start 2 Subjects 3 Events 4 Samples 6 Confirmation 7 Done In this step assays can be created Depending on the assay type and module you choose later on you can attach measurements or data files to a set of samples Make sure to select the template e g clinical chemistry fill in an assay name and select the module e g simple assay module you wish to use Template Clinical Chemistry el Bee blood clinchem Di simple assay module Clinical Chemistry Platform Metagenomics clean transcriptomics database metabolomics simple assay module Samples into Assays After you click next an in between step allows you to select which assays were performed on which samples Select multiple rows by click and dragging Use checkboxes to indicate to what assay these samples belong It is possible to attach multiple assay to one sample Sample Type Sample Name blood clinchem blood_transcr E Subjecti_Blood_Group1_OsBlood Subjecti0_Blood_Group _OsBlood Subject11_Blood_Group _OsBlood Subject _Blood_Group1_OsBlood m D DI a SGubuect Blood Group Oeblood 1 Start 2 Subjects 3 Events d Samples 5 Assays 6 Confirmation T Done Check your data Any corrections can be made by going back to the corresponding steps in the wizard You can view or edit the newly created s
33. tudy or create a new study 1 2 Edit a study To view or edit an already existing study go to Browse gt My studies J Home Create Import Export Browse Search gt All studies Modules Now you see a list of studies that you have created or studies where you have the role of reader Click on the magnifying glass on the left to view a certain study or click on the pencil in the middle to enter the wizard This will allow you to edit this study Study List Code Title Subjects mA Kkodex Diclofenac 19 Homo sapiens mS 8957 Effect of Nutritional Interventions on 35 Homo Inflammatory Status in Healthy Overweight Men sapiens Foodmix ei a ra Fd NuGO_PFSH Human PPS an intervention study 10 Homo sapiens Am A ZS amp 10 0AD Identification of biomarkers and disease 262 Mus Events Compound treatment Oral Glucose Tolerance Test OGTT high fat post prandial challenge Fasting Food intake Bodyweight Compound treatment Assays simple assay module simple assay module metabolomics simple assay module metabolomics simple assay module 1 3 Import part of study design Instead of walking through the wizard GSCF also allows users to import a part of the study design This can be a list of subjects samples or events This is an example of importing subjects Click on Import gt A part of the study design using the menu on top Home Create Import Export Browse Search Modules A complete study
34. u can import subjects or samples described in chapter 1 3 Use the following format if you want to import events Describe starttime endtime and a column for event description second Diet treatment ww KI r ke D Subjectname starttime endtime Diet treatment Diet treatment N 134 ADEM Os 12w ADEM 134 A Green tea N 010_ADMA Os 12w ADMA 10 B Placebo N 123 AHIF Os 12w AHIF 123 B Placebo N 158 ALAN Gs 12w ALAN 158 B Placebo Use Import gt Import part of study design choose your file and indicate where your data begins If your excel sheet contains subject names you can link these events to the subjects you have in GSCF Choose your Excel file to import eee pe ei Date format dd MM yyyy EU India South America North Africa Asia Australia Use data from sheet 1 D Column header is at 1 D Choose type of data Event D V Attach Events to Existing Subjects Choose your study 01 linea_study01 D Choose type of data template diet treatment e e Select data template Show 5 D entries Light exposure Search ColumnoO Column Erem Seen 3 Column4 Column5 Column6 Subjectname harvest Diet treatment Diet treatment ADEM 134 N_134_ADEM IW storage ADEM 134 A Green tea ADMA 010 N_010_ADMA compound treatment ADMA 10 B Placebo AHIF 123 N_123_AHIF d gier analysis AHIF 123 B Placebo ALAN 158 N_158_ALAN dia P ALAN 158 B Placebo Showing rows 1 to 5 out of a total of 188 in diet di next challenge add
35. uh tjeerd Renger keestest y tikunov etalo001 NTCuser PatrickKoks nmc djacob65 kees Jildau mmwbhendriks mhendriks Add Close How to see Readers and Writers of a study To see who are Readers or Writers of a study go to the study list Browse gt All Studies and view a study On the first tab Study Information you can see a list of the study owner and the assigned Readers and Writers Show Study Study information Subjects Events timeline Events table Assays Samples Persons Publications title Human PPS an intervention study description The human PPS enrolled ten healthy volunteers that were asked to come to the Human Nutrition Unit in Aberdeen on four different days of the week during four weeks after an overnight fast to provide a blood sample for the isolation of plasma platelets and PBMC and a saliva and a morning urine sample to assess intra and interindividual variations in baseline levels On the fourth sampling day volunteers were fasted for an additional 24 h total of 36 h and again plasma saliva and urine samples as well as circulating blood cells were collected for transcriptome proteome and metabolome analysis All samples are being submitted to comprehensive profiling employing all omics technologies Biological variability and fasting responses are being monitored in plasma platelets peripheral blood mononuclear cell PBMC urine and saliva by proteomics based on 2D gel based platforms coupled to ma
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