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iCollect - Information Systems Laboratory

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1. Collection Code ze Material Type v Collection Description Data Columns Choose Excel File Choose Work Sheet iCollect Templete Select Column Name Description Is Code C Select All Columns Delete Selected Column s Add Column Create Collection Figure 2 1 1 Collection Settings 2 1 2 Collection Data Structure This part involves how to define the data structure of a new collection You can perform one of the following options 2 1 2 1 Import from an MS Excel file You can add a new collection by importing the collection data and structure from an Excel file Click to browse a file containing the collection data and select which worksheet you want to import from the file In the installed folder you can find for example files in subfolder ExFile Go to step 2 1 3 formation eod DO 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 2 1 2 2 Use Template Several templates are included as examples of collection data structure You can choose which one appears in iCollect Template that would suit your needs and go to step 2 1 3 2 1 2 3 Specify column names and constraints In this option you can add a column to a collection data structure by clicking oncom J After all required columns have been added you ne
2. Connect Username Password Figure 11 4 1 2 Select source option Step 2 Go to select column s amp criteria as shown in Figure 11 4 1 3 to include whether columns to be sent with sample data If you choose to browse file or connect to DB server please select table first Select Column s amp Set Criteria Select All pad 22 ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Data for Submit to BRC Web Site Select IEEE E E v v 11 Step 3 Set column criteria Step 4 Set column name for catalogue Step 5 Check set as code checkbox at the column that used to stored sample code Step 6 Click Su Step 7 Specify the samples that you want to submit See figure 11 4 1 4 for the example IM Select All OriginalCode _ M O0001 MyYoo002 MYOO0003 MyYooo04 MY O0005 MY OO006 MYOO007 MyYoo008 MYO0009 MyYO0010 BCCCode_ Authority Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Fr Link 1 Koval 198 Koval 198 Genus _ Cordyceps Cordyceps Cordyceps Cordyceps Cordyceps Cordyceps Cordyceps 8 8 8 8 8 8 8 5 Cordyceps Cordyceps Cordyceps Hirsutella Hirsutella j 8 MyYO0011 j Figu
3. Parameter name Input parameter UserName Sting Userl Password String pss CollectionN ame String BCC Data ThaiD Created dataset Dataset Name Type Remark D ataName1 ThaiD Web service result lt xml version 1 0 encodingz utt 15 lt ArrayOfThaiDarwinCorePlus xmins xsi htto Awww w3 org 2001 xMLScheme instance xmins xsd http Awww w3 org 2001 MLSchema gt lt ThaiDarwinCorePlus gt i Kingdom xmlns http tempuri org ScientificName xmins http tempuri org gt Acetobacter lovaniensis ScientificName Synonym xmlns http tempuri org Family xmins http tempuri org gt Acetobacteraceae lt _Family gt Genus xmins http empuri org gt Acetobacter lt _Genus gt SpecificEpithet i xmins http tempuri org gt lovaniensis lt _SpecificEpithet gt Applications xmins http empuri org gt Application ApplicationsData lt Application gt Applications lt ThaiDarwinCorePlus gt lt ThaiDarwinCorePlus gt Kingdom xmins http tempuri org ScientificName xmlns http tempuri arg Acetobacter sp ScientificName l Synonym xmins http tempuri org Family xmlins http tempuri org Acetobacteraceae Family Genus xmlns http tempuri org Acetobacter Genus SpecificEpithet Figure 11 2 2 8 Invoke a web service function Figure 11 2 2 9 demonstrates h
4. Step 2 Click if you want to add a new type of quality control result Step 3 In the table Result Set click the row you want to modify make change on the result type and click Save Click De to remove the result type 8 2 Quality Control Records Two main functions are allowed in the menu Quality Control Records as below 8 2 1 Search Sample Specimen in Quality Control Records You can specify search criteria and click Search Search results will display in the List of Quality Checking Samples 8 2 2 Update the Quality Check Results In the List of Quality Checking Samples you can o Update the result for each row by specifying the result values for Result type and Check Date and click See J and o Click os to remove the quality check record 9 Services e Service New Deposit Service Data Remove Samples for Services Renewal Termination Service Configuration Figure 9 1 Services Menu 9 1 Service Configuration Under the Service Configuration menu iCollect allows user to create custom types of services 9 1 1 Service Types In Service types menu you can add edit and delete a type of services A list of default service types has been included in the iCollect system as shown in Figure 9 1 1 o To add a new type of services enter the service type and description and then cickL 9 J o To edit a type of services click on the row corresponding to the service type you want
5. iCollect 1 1 50 Sub Container Relation Box Box 81 perder Mame Cabinet LG150 Cabinet Cabinet L150 Cabinet Cabinet_S anyo 80 i Room Coolroorn Coolant Liquid Nitrogen Iw Tube 1 Tank 5 emperature 150 C Rack Rack_10Box rcm Hack Rack 1lUtwP j Volume 100 Unit Liter Hack Rack bBax Hack Rack BBax Freezer Details Single Position Multiple Positions Sub Container Details hd asinum Sub Container 12 Assign Position Position Details Humber of Columns B Number of Rows Label T ype New Sub Cotainer Edit Container Cabinet_LG150 Figure 6 1 2 Container Configuration Settings 6 2 Storage Configuration Select Storage Management from the menu Storage Container to create storage configurations that use the predefined container configurations into storage structure hierarchy There are four main tabs to support the storage management create Storage Tab This tab allows user to create a new storage facility into the database o Storage Organization Tab Storages created in will be defined their storage structure hierarchy in this tab e Copy Storage Tab The structure of existing storages can be copied to a new storage that has the same model Move Container Tab Sometime the existing storage facility might be failed it is necessary to transfer specimens samples and their data to another storage This part allows user to move the co
6. 7 Browse File Connect DB Select dataset Type DataSet String aray String Integer array Integer Int32 Decimal array Decimalf Bitmap array Btmap Other Export file List of Datasets Dataset Name Type Remark Create data Get Data i Select At GlearSetection AddRow AdiCoum seeded 2 of 198 rows Select column V set_VerbatimCoordinate System IV set GeoreferenceProtocol J set FootprintSpatialFit set CollectingMethod V set Sex Dataset Name Select FileExport Exportfile Figure 11 2 1 4 Mapping Data J formation T yos inb 62011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 43 iCollect 1 1 50 Step 6 Mapped and retrieved data will appear in the Create data as shown in Figure 11 2 1 4 click Select All to select all rows to be exported or click only the rows you want to export to the file Step 7 You can filter the number of columns by selecting column displayed in Select column s Step 8 Specify the file format for data export and click Step 9 Type filename and clickL See The progress bar will display during export process When the export finished a message appears saying Export completed 11 2 2 Data Exchang
7. Automatic Backup Setting Under the Administration menu select Backup Configuration to do the following tasks Schedule the backup to automatically run daily weekly monthly or at certain times Specify the location where the backup database will be saved Change and turn off the backup schedule The scheduled backup files will be maintained in the user defined folder However you can manually copy the backup files to other folders to maintain several backups 2 5 Storage Container Setting Under the menu Storage Container users can define container type and storage structure See detail in Section 6 2 6 Quality Control Profiles Setting Under the menu Quality Control you can click on Profiles to add a new profile See detail in Section 8 2 7 Service Configuration Settings Under the menu Services you can define a new service type and its profile See detail in Section 9 M radon POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 3 Specimen This part allows user to enter basic specimen information in a collection as defined in collection settings record by record through the menu specimen management or Import Export Specimens 3 1 Management When you open the Specimen Management window you will find three tabs including Add New Record
8. e tican Type Cu iw Select Code Service Code Been Deposit date ae Mame RAD SER d DOMOOQU3 530022 BIOTEC 21 4 2553 a 4 2554 Deposit ype wj 1 bomooooa 530022 BIOTEC 21 4 2553 214 255 Service Code DOMUODOODS 530022 BIOTEC 21 4 2553 21 4 2554 DOMDODU 530022 BIOTEC 21 4 2553 Maintenance period hat expired iL boMoooog 530022 21 4 2553 530023 21 4 2553 21 4 2554 S323 21 4 2553 el A 2554 Month 530023 21 4 2553 S3 0023 21 4 2553 COM OA 930023 21 4 2553 Mainterisrice period haz nol expired Hemairnind maimtenance panad Specimen Management Destroy Ccomoooos 530023 21 4 2553 eet coMoooo 530023 21 4 2553 21 4 2854 enewa 5 n eR COMOOO08 530023 BIOTEC 21 4 2553 214 255 Shipped Back ce Renewal Deposit Select deposit data Speciment List uns Details Options Reasons Exchange Service Profile ISIS iae fe ESL vj Account BIOTEC 53020 v Order Date 22 44 2 2553 v x j Service Date 22 u s 2553 E x Deposition length pear im n Total Specimen s Price 300 without discount Total Price Total Yearly Charge Discount Figure 9 3 3 3 Make a renewal deposit 6 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 CN ten Termi
9. 2 1 3 History of actions performed on the selected sample 4 2 Create Samples From previous section some specimens samples has already been selected and displayed in Create samples data grid Each row in Create samples can be used to increase a number of samples aliquots from the selected specimens samples within the following steps y nN Saas Create samples B A Specimen Lot Sample Select Reason 40M00005 AOMOOD02 04 Quality Checkin AOMODOO2 04 1 2 o TEE E i se 3 AOMOODO2 04 1 3 Select i select C Disappear C Loss L Discard Input by barcode scanner Option Print Preview barcode v Select for all Select samples Go to Storage Map Create Samples Figure 4 2 2 Steps to increase the number of samples At each row as shown in Figure 4 2 2 specify the specimen sample container and quantity of samples you want to create Check Keep to keep the source specimen sample The quantity of samples specified will be generated into the data grid on the right as shown in Figure 4 2 2 You can click to create samples for preservation otherwise click to open the Select reason frame to choose reasons for each sample After that click i30 fo Storage Ma to store and preserve the created samples into storage in Select Reason frame select a reason for creation of the samples wi
10. 4 Storage Monitoring Records 24 Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 7 Barcode This part allows user to easily find a sample s position in the storage and add a sample to a selected storage position using the barcode assigned by iCollect Users can also print barcode labels in any compatible printers and paste label on each sample container The barcode number found on the sample container can be read from the barcode scanner or entered directly into iCollect system to search for sample information In the Barcode module there are three following menus TH Storage Map Print Barcode Figure 7 1 Barcode Menu 7 1 Storage Map Using Barcode Scanner You can use the barcode scanner to read the barcode number from the sample container in order to move sample to and from the storage Collection Storage Map Select Mod Selected Container c1 B ct A New Container Predefined gctc J Create New Container Container Config Labe Create Container List of New Container s Send to Storage cower TET DLL UTE 5265 Acshsoacter quer ersiz Figure 7 1 1 Storage Map using Barcode Number e Add sample to storage After reading the barcode iCollect will retrieve and display a row of sample information in the table in List of unallocated samples You can click
11. B TOMO0001 Service Date 21 a u 2553 x Accept v TOMO0002 Service Lenght 1 Accept v TOM00002 03 Accept v TOM00002 04 Accept TOM00003 Accept v TOM00004 Accept TOMOOO05 Import Sample Select Excel File D iCollect ExFile E xample1 xls Select Work Sheet Sheet i Scientific name Type strain Order Family Identified by Isolated by Isolate date Substrate EIE D loolola Save amp Reject Figure 9 3 1 1 New Deposit Interface Normale TDD yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 noe Deposit To make a deposit transaction of specimens samples user can process a deposit via the New Deposit Menu as described below O O O O O 9 3 2 Open Detail tab as illustrated in Figure 9 3 1 1 Select Collection Service Profile Account for the deposit transaction Specify Order date and Service Date Import the specimens samples from the Excel file and click Imported data will appear in the List of Specimen s You can select the container type quantity and deposit decision for all or each specimen sample Switch to Options tab select a pricing option as shown in Figure 9 3 1 2 Back to Detail tab click service Data Details Options R
12. Specimen s samples part Figure 6 3 3 in Storage Map window specify the search criteria for each column and click EE Search to get all the samples in You can leave all criteria blank and click the selected collection o Search results will appear on the right Samples stored in storage facilities will display with its location in the Pos column o You can also export the search result to a file in a particular format such as CSV EXCEL Select a file format enter the filename and click Export 6 4 Storage Monitoring This part provides users to manually keep history of storage status for monitoring and alarm needs Users can regularly record liquid nitrogen level and temperature of freezers If the recording liquid level and temperature are under over the specified threshold values the storage name with warning message will display in red In Figure 6 4 open Liquid level tab to make a record of liquid level for a specific storage and switch to Temperature tab to update the temperature of storage w formation x FDA 2011 ISL BIOTEC All Rights reserved a Storage Monitor Liquid level Temperature Storage is freezer list History AddCabinetlD0L Temperature Date User Delete anne AddCoolroom200L 18 3 2553 22 57 59 toot AddT ank100L 16 3 2553 23 14 16 root C AddCabinet250L er 200 16 3 2553 23 14 02 root C T2002 1200 3 T200 24 Update Temperature 5 Figure 6
13. T able Tha arwinCorePlus List of Datasets Dataset Name Create data E Select sample image 7 Select From Catalogue Profile Select sample application Select sequence data Select Collection 7 Browse Fie Connect DB Select Table v Fiters Select From Catalogue Profile y hformation appa ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand S F9 S S S S S S S naa ReciD BCC Code Genus Name Species epithet SciNm BER Other Collection Nu Country Province IdenBy IdenDate Reference type Selected 0 of 0 rows Export file 4 iCollect 1 1 50 Figure 11 2 1 1 Upload Schema in Create Data Tab Step 1 Click to load the schema file Step 2 Select Table from the following choices Data Source v Select sample data Select sample application Select sample reference Select sequence data Select sample image Select From Catalogue Profile Select Collection Browse File I Connect DB Select Table Columns Criteria Figure 11 2 1 2 Specifying the Data Source e Select Collection select a data set that has been stored by iCollect itself e Browse File import a dataset from ms excel file xls
14. hsa00010 Int32 217 Sting blue pathway_id element list fg color list bq color list Figure 11 2 2 9 Accessing web services at KEGG alor pethway 127121207110 Jae Go kg B http fy genome jpn picolor pathway 127121 20711 17 35 hsaO0D010 htm v Bl s ad UCET ek Fie Edit View Favorites Tools Help Ww Favorites 33 suggested Sites ree Hotmail WebSlice Gallery v fe B B KEGG PATHWAY Glycolysis Gluconeagenesis Homo E y Pager Safety Tools e 4 Glycolysis Gluconeogenesis Homo sapiens human Pathway menu Pathway entry Hide description Glycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP energy and NADH reducing power It is a central pathway that produces important precursor metabolites six carbon compounds of glucose 6P and fructose 6P and three carbon compounds of glycerone P glyceraldehyde 3P glycerate 3P phosphoenolpyruvate and pyruvate MD M00001 Acetyl CoA another important precursor metabolite is produced by oxidative decarboxylation of pyruvate MD M00679 When the enzyme genes of this pathway are examined in completely sequenced genomes the reaction steps of three carbon compounds from glycerone P to pyruvate form a conserved core module MD M00002 which is found in almost all organisms and which often corresponds to operon structur
15. in Figure 9 3 3 4 Select a created service profile for termination of maintenance and click Save After the termination request has been processed iCollect will remove all the samples of selected specimens strains from storage destroyed and terminate the deposit Alternatively materials will be shipped back to the depositor for additional shipping and handling fee if depositors send their request As shown in Figure 9 3 3 1b click StippedBack tg open the service windows for processing the termination service with shipping and handling fee Search Search Select Collection American Type Cult Select Collection American Type Cult Deposit type Deposit type Service Code Service Code Lu Maintenance period has expired Maintenance period has expired C3 Maintenance period has not expired Maintenance period has not expired Remaining maintenance period Remaining maintenance period Month Month Specimen Management Specimen Management Shipped Back a Search for expired deposits b Search for non expired deposits Figure 9 3 3 1 Search deposits by the maintenance period conditions pinformation M 37 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 EE Check Expired Date Baw Search Specimen Select Collection American T e Cult EEn qum
16. on a row corresponding to the sample specimen you want to store into storage At the Storage pape ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Map treeview click on the storage you want to keep the specimen sample and click Add to Container e Remove sample from storage The sample stored in the storage facilities can be searched using barcode number Search result will appear in Search Specimen s Sample The container position where sample is stored will display in Storage Map or Storage Table so that you can remove the sample T F Selected Sampl from the storage by clicking 7 2 Scan Barcode To retrieve basic information of a sample you can use barcode scanner to read the barcode number labeled on the container If no barcode scanners are available you can type the barcode number found on the label to search for sample information In Figure 7 2 1 enter the barcode number and click 9 EB Scan Barcode Input by barcode scanner or enter barcode number l Search 5888 Acetobacter lovania Here is an example af a barcode Search Result allection Specimen Code Lot Ho Sample Ma Preserve Date Location Reason Figure 7 2 1 Scan Barcode Enter Barcode Number 7 3 Print Barcode Under the menu Print barcode three
17. or ms access file mdb e Connect DB retrieve dataset from MySQL or MS SQL database server Step 3 Determine what data you want to retrieve from database in Data Source by clicking on the checkboxes and choose a collection from the list shown in Select Collection When you change the Data Source selection you need to refresh Data Source by reselecting the collection in Select Collection f nformation N 42 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Columns Mapping C Select all Refer to columns defined in a web service Select Souce Destination HeclD BEC Code BER de Genus Name Genus Name Species epithet SeiMm Other Collection Nu Iv C L1 Province Application Country Reference type Figure 11 2 1 3 Customized Column Mapping Step 4 Go to Column Mapping specify the destination column from loaded schema that will be mapped with the source column Step 5 Click to select the column on that row or Click Select all to select all columns and click Create data Data Source Columns Mapping Select sample data 7 Select sample application Select all Refer to columns defined in a web service 7 Select sample reference Select sequence data Select sample image E Select From Catalogue Profile Select Collection
18. password he or she can change the password by going to Change Password menu as described above In case you forget password you can ask any users with administrative security level to set your new password To reset a user s password select a user name from List of Users shown in Figure 2 2 2 Type new password and click cw 1 2 2 4 Grant Privileges iCollect provides privileges that apply in different contexts and different level of operations Administrative privilege enables users to manage and customize iCollect configurations under the Administration menu Privilege for collections within iCollect system can be granted to users in Collection Privilege tab This privilege provides user permission to read and write access on a specific collection fl hformation M 5 AUN an 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 ES User Management Create User Edit Drop User Collection Privileges List of Users ya vel Collection Grant Permission userT est4 Read Test3 Read Test4 Write Test5 Write Test6 BCC test1 Naol Test Read OOO ST D3 LIST IST IST ST n d dM HH dM dud Figure 2 2 3 Grant Privileges on Collections to User In Figure 2 2 3 open Collection Privilege tab and select a user name you want to grant or revoke collection privilege from List of Use
19. samples registered within the collections 10 2 Storage Summary In the menu Storage Summary you can find the summary and charts of storage usages by storage types and storage configurations Total number of storages included in iCollect Total number and Percentage of occupied positions for each storage Total number and Percentage of empty available positions for specimens in each storage formation 39 mil DED X ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Comparison charts of storage usages 10 3 User Summary iCollect provides the summary of collections and specimens samples created by each user When you open User Summary window you will find the following Total number of user accounts registered within iCollect Average number of collections created by a user Number of collections and samples per user account Charts of collection distribution Click on Refresh to reload the update summary 10 4 Data Log In addition to usage statistics the full audit trail history of any individual user within iCollect is provided Under the Administration menu open the Data Log as show in Figure 10 4 to search and view who acted what to which data from which terminal and when Step 1 Specify the search criteria and Click to retrieve the history logs Step 2 The foll
20. the screen as shown in Figure 1 2 It contains from top to bottom Specimen Menu Sample Menu Storage Container Menu Barcode Menu Quality Control menu Catalogue Menu Services Menu Other Menu Statistics Menu Administration Menu Current User Menu Help Menu and Logout Menu The Administration menu will not appear for user without administrative rights To open or navigate menus drag mouse over the menu bar title then left click or just click with a single button mouse on the item you want 1 5 At the bottom left corner of the menu panel you can see current logon user name The current logon user can click on Change password to edit the account profile such as Password Address and E mail and click on the Logout when want to exit from the system pinformation M 1 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 MENU iid Specimen b 4 Sample E XX Administration Current User d root a Logout Figure 1 2 Menu panel 2 iCollect Configuration Settings Before you can start using iCollect the necessary settings in several menus described in Section 2 1 to Section 2 8 need to be done by the root user or user with administrative privilege Xx Administration Collection Setting Current User root Material Type ig Logout User Management Data Lo
21. 11 ISL BIOTEC All Rights reserved User Name Type user name Password Type user s password Administrator Checkbox Specify user security level with administrative rights Allow access to from other servers Specify user permission to access the database remotely Full Name This part includes First name Middle name and Last name E mail Fill out user s email address Contact Information Fill out user s contact information Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Q Create User Button Click to add a new user in the database 2 2 2 Edit and Drop User To edit user information select a user name from List of Users in Edit Drop User tab The information of selected user name including Full Name Email and Contact will appear You can edit information and click to record your modification In case of dropping a user name click on a user name from List of Users and click on Beier t to remove user from the system GE User Management Create User Edit Drop User Collection Privileges List of Users userTestl Change Password userT est Change userT est6 maximum characters 15 User s Details Administrator C Allow access to from other servers Full Name Email Contact Description Figure 2 2 2 Edit Drop User 2 2 3 Reset Password In general user already knows the
22. 7 BIOTEC natee 521 89 root insert add new sample Sample 3 11 2010 11 47 BIOTEC natee 1521 83 root insert add new sample Sample 13 11 2010 11 47 BIOTEC natee 521 89 root insert add sample s rea Sample 3 11 2010 11 47 BIOTEC natee 521 83 root insert add new specime Specimen 3 11 2010 3 32 BIOTEC natee 521 89 root insert add new sample Sample 3 11 2010 5 20 BIOTEC natee 521 89 root insert add new sample Sample 3 11 2010 5 20 BIOTEC natee 1521 89 root insert add new sample Sample 13 11 2010 520 BIOTEC natee 521 89 root l insert add new sample Sample 3 11 2010 5 20 DINTE A RK31 oa rack i dd mM REA C aramla 721 NNN E n User name Action Action detail Data Group Date Figure 10 4 Data Log f nformation M 40 PDE 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 11 Other 11 1 Import Export This part allows you to import export specimen data from to data file e The Import tab provides users to import the data from an MS excel file in three steps Step 1 Choose a collection you want to import the data Step 2 Click LE that contains the data Step 3 You need to map the column from the excel file with the collection data column At each row in the mapping table c
23. Billing amp ddress Home Address 123 aaa Office Address Shipping Address Home Address ae Office Address Description Figure 9 2 1 Customer Registration 9 2 1 Customer Registration To register a new customer open the Customer Data window as shown in Figure 9 2 1 o Click New to start the registration for a new customer o Enter the following information of the customer Name Type the customer name Profit Checked if is affiliated with a profit organization Home Address Specify the customer s home address O Email Type an email address Office Address Specify the customer s office address Q Billing Address and or Shipping Address Specify if it is the same as customers Home Address or Office Address o Click The registered customer will appear in the bottom left table you can click on the row containing the customer name you want to edit or delete o If you want to delete the customer click o If you make changes on the customer click to record your changes 9 2 2 Account Registration To open an account for a registered customer open Account window as shown in Figure 9 2 2 o Click New Account to open a new account for a customer o Enter the following information of the account Customer Name Select the registered customer name Q Account Name Specify the account name Billing Address and or Shipping Address Specify if it is the same as customers Home Office Billing
24. Edit a Single Record and Edit Delete Record Sheet view 3 1 1 Add New Record In this tab you first choose a collection the collection data structure of a single record will appear You can then enter information on a specimen for the selected collection and click Save 3 1 2 Edit a Single Record There are three steps in updating the specimen information Step 1 Choose a collection you want the list of specimens of that collection will display Step 2 Locate a specimen from the list to edit the data presented in the Specimen s Detail frame Step 3 Other types of specimen information including images references and applications can be added to each specimen as well e Click to add update information about specimen s utilizations e Click to add update a list of references toa specimen record See detail in Section 3 4 e Click Specimen s Images to add update images into specimen records e Click to add update files into specimen records In addition iCollect provides you to view the deposit and quality check records for each specimen e Click to view the quality checking records e Click Deposition Log Jto view the deposit history for the selected specimen 3 1 3 Edit Delete Record Sheet View This tab allows user to search view and update multiple specimen records 3 2 Geographic Coordinates If the specimen contains the information of location in latitude and longitude
25. L National Center for Genetic Engineering and Biotechnology BIOTEC Thailand Genus Cir iceps Cordyceps Cordyceps Cordier Cordyceps Cordyceps Cordyceps Cordyceps Cordyceps Cordyceps Hirsutella Hirsuitella Unidentified Ophiocordyceps Akanthomyee Unidentified CONF Hirsutella Unidentified Orl scaridyrepi a Cordyceps 56 iCollect 1 1 50 Figure 11 4 5 2 Map columns Step 9 click Step 10 select sample to be deposited See figure 11 4 5 3 for an example ld Jf i m 1 SIEIEIEIE vi QI sigidi8 8 8 18 18 18 18 8 B B m n en iii AE i BERE ardente 3d en I s 8 8i518 Hi i Ji T B i Figure 11 4 5 3 Select sample to submit ami il Sd Js yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Step 11 click 12 Backup and Restore Backup and restore operations are available to users with administrative rights Under the Administration menu select Backup Restore to backup the database to any folder specified by users and restore the backup file to database The backup restore process will start if no other users still logged in iCollect system p s E Backup amp Restore Seles Backup Restore Backup Database Backup locatio
26. Make your changes to the service type and description Click to record your changes o Click on the row corresponding to the service type you want click to delete that type f nformation M 28 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Service Types Save Delete Service Type Description Identification of different organisma and cultures Loan Samples Patent Deposit Provides storage and quality control of materials for patent purposes Public Deposit Provides storage and quality control of material for public access Safe Deposit Offers secure confidential storage and quality control of proprietary material Supply of Materials Distribute the materials deposited in the public collection to the third parties Termination of Maintenance Termination of Maintenance Add New Service Type Description Figure 9 1 1 Service Type Definitions 9 1 2 Documents for services This part allows user to register the generic types of required documents that must be submitted by the customers in the service process In Documents for services menu you can add edit and delete a document type A list of default document types has been included in the iCollect system as shown in Figure 9 1 2 o To add a new type of documents enter the Document Name and Description and t
27. Substrate Figure 5 2 Catalog Format M radon mi NDX yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 16 iCollect 1 1 50 6 Storage Container Management The Storage Container management module allows user to configure and customize the physical layout of the storage capacity at the laboratory Container and Storage are two generic terms used in this module e Container There are two types of containers as below o Containers that are used to store aliquots or samples of biological materials Containers for instance boxes tubes plates cane and bags can be with both single position and multiple positions o Containers that will be stored inside the storage for holding sub containers Shelves drawers and racks are considered this type o Storage Storages include storage cabinets compartments and rooms Most often this will be freezers and refrigerators which used to preserve the aliquots or samples at a very low temperature ui Storage Container Wu Container Type Container Configuration Storage Management Em Storage Map DE Storage Monitoring Figure 6 Storage Container menu 6 1 Container Settings The two main steps involved in the configuration process are Step 1 Open Container Type from the menu Storage Container to create generic container and storage typ
28. Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 a Reference s t3 Search Add New Reference Title Reference Title Year E m ISBN Code Generate Ref Auto Number Show All Add Import BibTex Format Search Result s List of Reference s Select Code Title Type Author s x save oot DB Atfective CoonitiveLearingandD ecisio Inproceedings Hyunail amp hnandRosalindw x save 0t 07 R sparss toloimaneReviewotAff ctis Article Rosalindw Picard 00109 FieviewotAifentiveComputing Article AaronSloman x save Bl 00112 TheY ankeeY ears Book J JoeToreandT omVerducci x Save 00113 DesignofaCarbonFiberCompositeGridSt Book vonHicks III Michael x Lsee O 0014 m x save 00117 iari nce ste siano mmelne Ls inproceedings LeCun Y x save 00118 Athoorlicahianemorkiaback Pripag ica LeCun Y lt y Set Specimen s Reference s Collection List of Specimens List of Specimen s Reference Code Biotec culture collection 1 C 00107 dc 1 ADMIDD001 A0M00002 amp DM OODO2 03 AOM OOOO2 04 ADMOOD03 AOMOO004 AOMOO005 ADMODODO bd Figure 3 4 2 Set Specimen s references Step 1 Select a collection and click a specimen in the List of Specimens from Reference s window Figure 3 4 2 to select a specimen you want to add references Step 2 In Search Result
29. a 11 4 2 View submit log 11 4 3 New Order From BRC 11 4 4 New Deposit From BRC 11 4 5 Deposit to BRC 12 Backup and Restore 13 Help f nformation pad tab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 f nformation E pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 1 Getting started with iCollect 1 1 After the installation of iCollect on your machine The iCollect icon will be placed on your desktop Now you can start iCollect by Double click on the icon to open the Log In page Figure 1 1 of the system 1 2 Select DB Server you want to connect The default DB Server is localhost If you want to connect to other iCollect s DB server type the IP address or server name at the DB Server box 1 3 Type your username and password Click Login to connect to iCollect Note A MySQL root account is required for initially setup the iCollect system The root user has all privileges within the iCollect system F I Collect E DB Server localhost v Microbe Edition User Name root gt gt gt 303 Password Figure 1 1 Login Screen 1 4 Once you sign in you can begin using iCollect The menu panel appears at the left of
30. ame test Type strain Order Gene Type Beta tubulin p Sequence Type DNA Sequence Sequence Validated format Gene Type atitccccgggaaaag J Sequence Type Search Result AOMOO005 test Figure 3 3 2 Search and Update Sequence Data 3 4 References The Reference menu provides user to manage information on references of a specimen sample The References information includes journal articles books book chapters proceeding articles and reports In this part users can perform two following tasks 3 4 1 Add Import the references e Enter directly a single record of reference to the system Enter a reference title into Reference Title and Click iCollect will add and display a row containing the reference title from previous step into the Search Result s List of Reference s table o Update the data for each row of reference and set the reference code Click Ere o Click to delete the reference on that row e Import the references from the BibTex file o Click on to browse and select for a file containing the references data in BibTex format o iCollect will upload the file into Search Result s List of Reference s table o Update the data for each row of reference and click o Click to delete the reference on that row 3 4 2 Set Remove references to a specimen sample f nformation M 10 pad 2011 ISL BIOTEC All Rights reserved Information
31. amples Detail Select collection v Code i Show on Catalogue Online Show Column name Criteria cis I Name Browse Gene Type v Sequence Type v Sequence Sequence Validated format Gene Type vi Sequence Type v Search Result Note Add New Delete Save Blast Figure 3 3 1 Molecular Sequence Interface e o modify or delete a sequence Step 1 Select a collection from Search collection in Search Samples frame Step 2 Specify the criteria to retrieve the record you want to modify or delete For example specify the strain code column as AOMO005 and click Search The results will be shown in the Search Result tree view Step 3 Select a sequence you want to update delete For example click on test in the tree iCollect will display the sequence information of test in the Detail frame a If you want to update the data modify any information as you want and click to record your changes b If you want to delete the data click Delete MH naton 9 POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 a Sequence Search Samples Detail Select collection Biotec culture collection v Code ADMO0005 Show Column name Criteria Strain code 40M00005 Scientific name N
32. ct 1 1 50 11 4 3 New Order From BRC This menu is used to retrieve order that has been sent from BIOTEC BRC See figure 11 4 3 1 for more details List of Order s Service Code Order By Order Date Quantity TotalPrice Service Type Se Refresh TERT ICONE NE NEN NN 2011 5 34 4 206 samnao noksiri 16 nanman 2554 5 Select a service profile 4 TT H Save List of sample s Mo Specimen Code Collection Quantity Match Collection in Stock Accept Reject 10 Plant natee 1 x E E 2 100 Plant_natee i F F Figure 11 4 3 1 New Order from BRC Interface e To manage order Step 1 Select new order from BRC tab Step 2 The login window will appears on the screen as shown in Figure 11 4 3 2 login using your BRC account Please enter user name and password User Name Password OK Cancel Figure 11 4 3 2 Login to BIOTEC BRC window Step 3 iCollect will retrieve and list orders from BRC automatically Step 4 Click on certain order to view sample list Step 5 Map the ordered sample with your collection in iCollect Step 6 To accept order check accept Otherwise check reject Save Step 7 Select service profile then click See M radon N 5 4 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 11 4 4 New Deposit From BRC This menu is used to retriev
33. ct system as shown in Figure 9 2 3 o To add a new type of material enter the nationality name and description and then click 5 o To edit a nationality click on the row corresponding to the nationality you want Make your changes to the nationality name and description Click to record your changes o Click on the row corresponding to the nationality you want click to delete the nationality M radon 32 POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 G 2 Nationality E3 List of Nations Mame Description Save Delete amp fghanistan Albania m Sms sme dx Sa been Wem Sme ste wwe sa tt hme sacjtbsei aa a mw C8 crs kem E omes sie umm Sa bene Emm ome Lost Seas O o Sam bna Bam a Gt fap A a Description Figure 9 2 3 Nationality Data Settings 9 3 Service Operations This part allows users to manage the service process using the predefined service profiles S Service New Deposit Service Data List of speciment s Details Options Reasons Exchange Select container for all AgarPlate Select quantity for al 2 Service Profle Depost Microorger 2L Accept Reject for all Accept Account BIOTEC 53020 Order Date 213 2553 m E Accept
34. cted Samples Remove All Samples Search Specimen s samples ji Y List of unallocated samples wd Select Specimen Lot Sample Preserve Date Container AOMODOD1 7 Well AOMOO001 box3x4 40M00001 box3x4 AOMODDD1 box3x4 AOMODOO1 Ti j Box3x4 40M00001 AgarPlate 40mM00001 AgarPlate AOMODDO1 AgarPlate AOMODOD1 Ti AgarPlate AOMODOD1 AgarPlate select All Add to Container Add to Container auto Set Preserve Date SF ololololalololo Figure 6 3 1 Add Samples to Storage formation TDD yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 22 iCollect 1 1 50 6 3 1 Moving samples into storage In Storage Map menu as shown in Figure 6 3 1 you can move sample to and from storage within the following steps o Select a container containing the sample you want or you can search for location of the samples o When the container is selected the samples stored inside will appear Click on the sample you want to move and click Remove Selected Samples If you want to move all samples in the containers click Remove All S amples o All removed samples from previous steps will display in the List of unallocated samples Select the samples you want to move and locate the target container in the tree l Add to Contai o Select th
35. d Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Move o Click to move the source container into the target destination container 5 2 Storage Management Create Storage Storage Organization Copy Storage Move Container Select a source container Select a destination container Eesti rack1 A rack1 B rack1 4 rack1 C rack1 B rack1 D rack1 C rack1 E rack1 D rack1 F rack1 E test1 4 rack1 F Figure 6 2 4 Move Storage Tab 6 3 Storage Operations In the Storage Map menu the in and out movement of samples in the storage are recorded and tracked for audit trail Moreover the graphical tree view of the samples can be used to trace the aliquot sample back to its original parent 5 Storage Map Collection Biotec culture collection v Storage Map Select Mode Selected Container test E test Cabinet LG150 Specimen rackl Rack 10Box rack1 B Rack 1 Box BINDS rackl C Rack l Box ADMODOO1 Biotec culture collection Container Contig P m gU rackl F Rack OB ox AOMO0004 Biotec culture collection Label testl 4 Cabinet LG150 reate Container testl B Cabinet LG150 New Container 9 Predefined Create New Containel A40mMo0004 Biotec culture collection List of New Containers Name Container Config Del SS SS Remove Selected Container Remove Sele
36. d the web service defined type and perform the data mapping See detail in Section 11 2 2 2 M radon 44 POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 o After all required input parameters are ready you can input the parameter and click o Results will return and appear in the Web service results 11 2 2 1 Data Preparation for DataSet and Array Type To prepare the DataSet or Array type you can perform the following steps Step 1 In Create Data tab open Select dataset type tab Step 2 Select the data type you want to create Figure 11 2 2 1 Click DataSet to select the DataSet type Click String Array for an array of string values Click Integer Array to prepare an array of integer values Click Decimal Array to prepare an array of decimal values Click Bitmap Array to prepare an array of bitmaps O O O O O Select dataset Type Load Schema DataSet String aray String Q Integer array Integer Int32 Decimal array Decimal Bitmap array Bitrnapt Other Esport file Figure 11 2 2 1 Select a type of dataset Step 3 Determine what data you want to retrieve from database for the preparation At the Source Data in Figure 11 2 2 2 a click to select the data source and choose acollection from th
37. e criteria for data selection in creating their own personalized collection of specimens samples Figure 5 Catalogue Menu 5 1 Catalog profiles Users are able to create the catalog profiles in order to select a set of specimens samples to be public available f hformation An CPi Nil DIN yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 14 iCollect 1 1 50 EE Catalog Profile Preview Collection Profile Detail Select Collection American Type Culture Collection v Name test List of Profile Display name test Type Public v Create By Create Date Update By Last Update In Use Add New Cancel Save Profile Figure 5 1 1 Profile Detail In Profile Tab a catalog profile can be created within five steps Step 1 Select a collection and enter the following items in the Profile Detail Figure 5 1 1 Name Type catalog profile name O Display Name Type the catalog name used for display Type Select a type of catalogs Private and Public In Use Specify the description of collection Step 2 Click to add the new profile Step 3 Add Set the criteria for selection of the specimen sample the catalog profile in the Profile s criteria as illustrated in Figure 5 1 2 Step 4 Click to record the profile s criteria and update th
38. e list of specimens strains that will be included in the catalog Step 5 Click to open the preview tab to view the data that will be shown in the catalog Notice that specimens from safe and patent deposits will not included in the catalog Profile s Criteria Column Operator Filter AND Operator Filter OR Operator Filter OR Strain code Scientific name e Type strain v Isolated by Isolate from Isolate date Location Medium Temperature L WWuduldd Lu du dududdd1 v v v v v v v v v v Hazardous st ce F amp S S ST ST IS S S S S Save Catalog Preview Catalog Figure 5 1 2 Profile s criteria settings Step 6 In Preview tab the data that matches the profile criteria will be shown in a table You can select specimens by clicking on the checkbox and click to remove them from the catalog Click to save the catalog list After saving the catalog list you can perform the following tasks e Click to open the catalog format window to view the catalog e Click to export the data into an XML file f nformation M 15 TUN 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 e Click to export the data into an Excel file Profile Preview Pre
39. e list shown in Select Collection Or you can import data from a file and database server which use the same procedure as described in section 9 2 1 SciNm SciNm Data Source v Select sample data Select sample application Columns Mappin 2 eines Qi Sa aga din Select B n Refer to columns defined in a web service pm M Select Source Destination Select From Catalogue Profile ReclD a Select Collection BOC BCC Code BCC Code v C Browse File Connect DB Genus Name Genus Name v Select Table X Species epithet Species epithet v v v Family Family Other Collection Nu Country Province IdenBy IdenDate Application OOO BI ETI ET IE EST EST ST IST 8 ST Reference type a Data Source b Column Mapping Figure 11 2 2 2 Data Source and Data Mapping Step 4 Go to Column Mapping as shown in Figure 11 2 2 2 b specify the destination column that will be mapped with the source column Click to select the column on that row or Click Select all to select all columns Step 5 click M radon POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 45 iCollect 1 1 50 Step 6 Mapped and retrieved data will appear in the Create data as shown in Figure 11 2 2 3 click Select All to select all rows to be exported or click only the rows
40. e sample that has been deposited to you from BIOTEC BRC See figure 11 4 4 1 for the screen example List of Order s Service Code Deposit By Deposit Date Quantity Total Price Service Type Servic Refresh l To Collection 2011 5 43 1 67 18 ugue 2554 3 0 00 Safe Deposit BCC Safe Y 2011 5 43 1 68 18 nataran 2554 4 0 00 Safe Deposit BCC Safe z z Select a service profile 2011 5 43 1 72 19 nataran 2554 7 0 00 Safe Deposit BCC Safe Sent To Service New Deposit 4 TI p List of Sample s Figure 11 4 4 1 New Deposit Interface e To manage deposit order Step 1 Click on New Deposit from BRC tab The login window will appears on the screen login using your BIOTEC BRC account Step 2 iCollect will retrieve and list orders from BIOTEC BRC automatically Step 4 Click on certain order to view sample list Step 4 Select collection to save sample Step 5 Select a service profile sent To Service New Depasi Step 6 Click M radon N 55 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 11 4 5 Deposit to BRC This menu is used to deposit sample to the specified user as shown in Figure 11 4 5 1 Service Data Deposit To samnao noksiri Select Collection BCC Deposit Demo Deposit Type Safe Depository x Order Date 18 wa 2554 Service Length 1 Remar
41. e target container click Adata Container 6 3 2 Viewing samples or containers in storage Storage Map Selected Container cabinet 4 test Cabinet L15 testl amp Cabinet_LG150 testl B Cabinet_LG150 cabinet Cabinet Sanyo 80 A Tray22e26 Al 42 485 Ad 425 Be AT Ae OSS AIO Ad 512 AIS 814 A15 Bi B2 BS B4 B5 Be B7 BS B3 BIO Bil Bli2 E13 Bid BIS Ci C2 C3 C4 C3 Ce C7 C8 C3 C10 C11 C2 C13 C14 C15 D DS D3 BI 011 Bl D13 B14 D15 Ei E E3 EA ES EB E7 E8 ES E10 E11 Elz E13 Elid E15 Fi F8 FS F4 F5 FB F OFS F3 FIO F11 Fiz F13 Fi 4 Fis a1 G2 G3 G4 G3 GE G7 G8 G3 G10 G11 Gl2 Gis G14 G15 Tia m o A a p m m ho m ca m Ta cn iwl m Hi He H3 H4 H3 HE H H8 HS AIO H11 Hi HIS Hid H15 ro a E zn m zo Ia H H1 Ne 1H3 14 H5 Ji J2 J3 J4 J5 JE J7 J8 J8 TO Jiz 414 J15 E1 HB Ka K4 Ka HB E7 ES ES RIO ET KI2 EIS KT ES LF L3 10 i LAT L12 L13 Lig L13 me fi al a Fo t T tn m bd biz eS hdd S BAS 17 i3 TO Ali eT biia bilg he hl hla h h hla ne hn h 172 hin bir bla kld bld bld bld 4 blic Remove Selected Container Remove Selected Samples Remove All Samples Figure 6 3 2 Storage Tree and Map There are two main parts in v
42. e via Web Services This part allows user to select and submit a dataset to a destination via SOAP protocol In Web Service Management tab as shown in Figure 11 2 2 you can specify URL or a web service location and click to load the WSDL or Web Service Definitions for parsing and analyzing what services are available what are needed for input parameters and what will be returned The available services will appear in Web service function list When you double click on a service in Web service function list its required input parameters will be listed and displayed in the bottom left table View web service method D IR L WAL http localhost BAC Sr SubmitD ata asms kra 180000 wv eb xervice nction II SumitD ata getAttnbute 1 GetShowett l MienCalecin SEEMS SumilDataANDImage LoadN ewOrder Hecorcded rder LoadO rderstatus UpD ateOrderD ata Parameter name E ppe CE String DataSet a Input parameter String E String Figure 11 2 2 Accessing to the web service APIs o If the types of required parameters are Generic and single such as String you can directly enter the data value into the Input parameter DataSet and Array type you need to construct a set of multiple data values for this parameter See detail in Section 11 2 2 1 Web services Defined Type you must loa
43. eReferences Family Country Province IdenBy 4 IdenD ate Application S S ES S ST ST ST EST S ST ST SC IS Reference type Figure 11 2 2 5 Reference Objects and Methods defined by Web Services Step 5 click Step 6 Mapped and retrieved data will appear in the Create data as shown in Figure 11 2 2 5 click Select All to select all rows to be exported or click to select only the rows you want to include in the dataset Step 7 You can filter the number of columns by selecting column displayed in Select column s Step 8 Type the dataset name and click The dataset created will appear in the List of Datasets 11 2 2 3 Data Preparation for a single record of Web Service Defined Type To prepare a single record of Web Service Defined type you can perform the following steps Step 1 Double click on the row containing the web service defined type Figure and open the create new data type from web service tab VIEW WED service method WAL Ato localhost BRCAW ebS ervice asm L2 SentD ataz Parameter name Type Input parameter Figure 11 2 2 6 Double click on the web service defined type Normale endi M yos inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 47 iCollect 1 1 50 Step 2 Inpu
44. each branch of the tree Within List of Samples treeview users can use to do following Click on the H checkbox to select the specimen sample Click to expand the tree branch to view the list of samples Click to collapse all levels within that branch Right click on the tree node to view the history log of the specimen sample within that branch or edit the reason in creating removing the sample on that node O O O O Search Samples List of Samples Right click to view log Select collection biotec animal celline v w 7 KOMO0002 w KOM00002 03 Show Column name Criteria w C KOMO0002 04 d E C KOMO0003 N T Sample 1 gt Service 5b30051 L Species A LES Type of cell w v KOMO0004 eedem w C KOMO0005 Edit Reason Source of cell line C KOMO0007 Characteristics F C KaMD0008 Life expectancy Brief history since Culture medium Lot Sample Create Remove View Log O Subcultivation pr f Name of originating C Show all gum Search Search Figure 4 2 1 1 Search and Select Specimens Samples within three steps Step 3 The selected specimens samples will display in Selected sample s Users can click on o Click to select and submit samples from the selected specimens samples to be appear in Create samples See detail in Section Create samples o Click Remove to submit samples to Remove sampl
45. easons Exchange Select Options Yearly Profit Mon Prafit Charge Price Price Nea 0 500 100 ation O 1000 300 On Select ptnMm Sew Figure 9 3 1 2 Selection on Pricing Options Make a Service order To make a service order open the Service Data menu O O O O a formation POG 2011 ISL BIOTEC All Rights reserved Locate the Detail tab as illustrated in Figure 9 3 2 1 Select Service Profile Account for the deposit transaction Specify Order date Click to open Select Sample s for Service window as shown in Figure 9 3 2 2 Select a collection and its catalogue you want to retrieve specimens and samples for services Click on a specimen the list of samples will appear Click on a sample and click b to send the sample into Selected Sample s To remove a sample from the selected list click on the sample and click LJ In case of deposit service the specimens samples for deposit must be previously imported through the Import export Specimens menu Click to finish samples selection and close Select Sample s for Service window The selected samples will appear in List of Specimen s in Detail tab Switch to Options tab select a pricing option as shown in Figure 9 3 2 3 Back to Detail tab update status accept or reject for each row and click sae Total price will be calculated and shown Click to receive the order The order status bar will disp
46. ed to determine which column is a key of the collection A key column is one that uniquely identifies a particular record in the collection o Click on the isCode checkbox at the row corresponding to the column you want to select as a key column o Click on the Select checkbox at the row corresponding to the column you want to include in the collection or click Select All Columns checkbox if you want to select all columns and go to step 2 1 3 2 1 3 Click to create a new collection The description and structure of collections created from previous step can be modified in Edit Collection tab and deleted in Delete Collection tab 2 2 User Account Settings Under the Administration menu you can click on User Management to add new user accounts edit drop existing users and grant permission to access and use collection data GS User Manageme nt Create User Edit Drop User Collection Privileges Host Name Login Information UserName F maximum characters 15 Password maximum characters 15 Administrator Allow access to from other servers Additional Information Full Name Email Contact Information Description Figure 2 2 1 Create a new user account 2 2 1 New User Accounts Open the Create User tab as shown in Figure 2 2 1 to add a new user account and enter the following user information o o e o e FUN E pad 20
47. es datagrid as shown in Figure 4 2 1 2 to be further removed see detail in Section Remove samples Create samples y Remove samples Qo Specimen Lot Sample Position Cancel Select reason Reason 11 299 9 e e Input by barcode scanner Add New Reason Go to Storage Map Remove Sample Figure 4 2 1 2 A Selected sample appear in Remove samples datagrid o Click in to view the history log of the selected specimens samples as illustrated in Figure 4 2 1 3 MH naton Th i fff M pi yos inb 62011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 12 iCollect 1 1 50 ad Sample Log m mj X Search Code Sample Action By Update date ADM0000203 1 Create Sample root 20 3 2553 11 35 ADMO0002 03 1 Remove Sample root 27 3 2553 11 35 AOMO0002 03 1 Quality Checking root 27 3 2553 11 35 ADMDODO2 03 2 Create S ample root 27 2 2553 11 35 Sample No 40M00002 03 2 Remove Sample root 27 3 2553 11 35 ADM OOO02 03 2 Quality Checking root 27 3 2553 11 35 3 3 Select collection Biotec culture collection v Sample Code AOMO00002 03 A0OMO0002 03 Create Sample root 27 3 2553 11 35 AOMO00002 03 Remove Sample root 2773 2553 11 35 AOMO0002 03 Quality Checking root 27 3 2553 11 35 Figure 4
48. es as shown in Figure 6 To adda new type of containers enter the container name and set the container properties as below and C ckL 9 If both Is Freezer and Is Storage are not checked the container will be used to store the samples of biological materials f both Is Freezer and Is Storage are checked the container is considered Freezer For example the refrigerated cabinets where biomaterials can be preserved at a very low temperature could be specified as freezers f Is Storage is checked the container is considered Storage or what containers can be stored inside O To edit a container type click on the row corresponding to the container you want Make your changes to the container name and properties Click seve to record your changes To delete the container click on the row corresponding to the container you want click Delete f ffnformation M 17 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 a Container Type ls Strorage ls Freezer Save Delete Cabinet Cane Canister CoolRoorn Plate Hack Room Shelf Tank e Joa Tray Tube Well HOO SILET IST ETI ET EST ET ET LES ETIE HOO ISI ET ELE E STILE ET SH ET LE Create Mew Container Type Mame C Is Storage Is Freezer Figure 6 1 1 Container Type Settings Step 2 Selec
49. es in bacterial genomes Gluconeogenesis is a synthesis pathway of glucose from noncarbohydrate precursors It is essentially a reversal of glycolysis with minor variations of alternative paths MD M00003 v b 0 Jj Homo sapiens human GLYCOLYSIS GLUCONEOGENESIS Starch and sucrose B Y Qo D Glucose 1P 5 D Glucose extracellular Os D Gl cose 6P 5319 Pentose o Internet a Figure 11 2 2 10 View the returned HTML via a web browser 11 3 Taxonomical Data Checking Hel Ml v Rio In several cases the collection data will include taxonomic data which need validation and update of taxonomical classification iCollect provides this feature to enable user to check the taxonomic data with the Global Check list at www sp2000 org and the fungal database at www indexfungorun org 11 3 4 illustrates a part of the Check Taxonomy window 6 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand Figure 50 iCollect 1 1 50 ES Check Taxonomy Sees Search Samples Check Select collection Biotec culture collection Reference To www sp2000 org Show Column name Criteria Check Spelling Check Taxonomy Strain code Column name Column Maping Fi Scientific name Strain code C Type strain Order Order_Name Order Family Family Name Family Identified b
50. ew Order From Web Site Figure 9 3 2 4 Received Order 9 3 3 Renewal and Termination of Maintenance This part allows user to handle requests from depositors to renew or terminate their deposit After the deposition period has expired the depositors may request to renew or terminate their deposit To make a renewal deposit you may search Normale TDD yos inb 62011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 36 iCollect 1 1 50 for specimens strains that their maintenance period has expired Figure 9 3 3 1a A list of specimen will appear for your selection Click Renews 0 to open Renewal window to renew the deposit of selected specimens Figure 9 3 3 3 Click to remove all the samples of selected specimens strains from storage destroyed and terminate the deposit if depositors not responding to your requests for renewal of maintenance However depositors may request termination of their deposit at any time Figure 9 3 3 1b illustrates how to search for specimens strains for termination request before the end of maintenance period Select a collection and click Maintenance period has not expired or specify the Remaining maintenance period Click search and select the required specimens as illustrated in Figure 9 3 3 2 Click to open Termination of Maintenance service windows as shown
51. file For example pricing depends on the costs of different sample preparations Step 4 Click to record the profile ES Service Profiles List af Service Profile s Service Prafile Data Type Safe Deposit se Mame Supply Microorganism Filter by Type Type Supply of Materials Derosit Microorganisms Details Service s Condtion Request Document S Criteria J Document Listed prices are for single s Lx l Exclude packaging and shi x Order Form MAT will be charged i Options Option Name Freeze died culture Active culture on agar Culture extract Figure 9 1 3 Service Profile Settings 9 2 Customers amp Accounts Registration To request the services customers need to register an account within the following steps M formation 30 POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 33 Customer Data E3 Search Customer Customer s Details Column name Criteria j Name aaa Password Customer Name i C Profit Gender Male v 3 Office Name Home Address 123 aaa Customer Address Office Address Home Tel Home Fax Email aaa mail com Nationality Thai Foreign Select Nationality Telephone Office Name aaa Office Address 999 xyz Office Tel Office Fax Office Email
52. files Dating PE irj Erkt Dadaba accord set view 1 1 2 Imparz mssort Speer 113 Moclculr Sequence 1 1 4 Check TaxsricmM 147 Gabs chee uring ii Specific hama l4 1 Cats charga via Wee Lernia 14 2 1 Dnia Preparation for Dabszat amd Array Typa 14 2 1 Dris Mepaston Par an Array of Wab lerrion Dafi ad Type 3 4 2 2 Deia Preparatizn jar amp ngia record of Wart Lardrs Defined Type 34 2 4 Casing Wut Service 1 5 Rafpranca 3 5 3 Addrirmport Ta rabeen 3 5 2 Dees prine tn a padme gm pas rwrimbTero WAR TUMIMETCHEDE A1 nier aga 4 2 Wiesing amphi or corseira m boag 4 31 Zamching rama in ricrea Dun WI PELULUDD AE Sigh means Hara Lanier ir Gerai I ngnewwtu and Boy CTI Cw Figure 13 1 User manual window formation POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand Stee eC ee ee m RR An um de de de Reach cem eer en 59
53. format user can view the location on map via this menu e To view map Step 1 Select a collection from select collection combo box Step 2 Specify criteria and choose column to display data in filters box optional Step 3 Click LSet Step 4 Select sample to display on the map Step 5 Click View Map 3 3 Molecular Sequences Users can add update delete and search the molecular sequences When you click Molecular Sequences from the menu panel the Sequence window will be display The Sequence window is vertically separated into two main parts On the left hand side you can search the molecular sequences of the specimens samples in a collection On the right hand side you can add a new pinformation M 8 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 sequence file update and remove the existing sequence file to a specimen sample e To add a sequence Step 1 Select a collection from Search collection in Search Samples frame Step 2 Choose a specimen sample from the list in Code Step 3 Browse for a sequence file or enter a sequence directly in the Sequence tab Step 4 Type Name select Gene Type and Sequence Type Step 5 If the input sequence contain invalid character Step 6 Click to add the sequence information into database Search S
54. g Backup Restore Backup Configuration Figure 2 1 Administration Menu M formation POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 2 1 Collection Settings Under the Administration menu shown in Figure 2 1 you can click on Collection Settings to define and create the data structure of each collection There are three options in creating a new collection including import from CSV file use templates and interactively specify field names and constraints Figure 2 1 1 illustrates three tabs for creating editing and deleting the collection settings In Create Collection tab you can configure a new collection in three steps described in Section 2 1 1 to Section 2 1 3 2 1 1 Collection Description This section contains three following items Collection Name Type collection name For example BIOTEC CULTURE COLLECTION O Collection Code Type Collection Code For example BCC is the code of BIOTEC Culture Collection Material Type Select a type of biological materials from the list O Collection Description Specify the description of collection Notice An asterisk symbol in Figure 2 1 1 specifies the field need to be completed Ge Collection Settings Create Collection Edit Collection Delete Collection Collection Description Collection Name
55. hen cickL 5 o To edit a type of documents click on the row corresponding to the document type you want Make your changes to the Document Name and Description Click to record your changes o Click on the row corresponding to the document type you want click to delete the document type S Document for Service List of Document s lu Document Name Description Save Delete Deposit Form MTA Material Transfer Agreement Order Form Identification Form Add New Document Document N ame Description Figure 9 1 2 Documents used in service process M radon e t tons inb 2011 ISLIBIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 20 iCollect 1 1 50 9 1 3 Service Profiles This part gives user to define each profile for services After specifying the service and document types open the Service Profiles window as shown in Figure 9 1 3 to define the service profile in following steps Step 1 Enter the profile name of service and determine the service type For example the profile name supply bacteria is in supply of materials service type In Details textbox users can optionally add the more detailed description of service profile Step 2 Specify the conditions of service and the required documents for service requests Step 3 Define pricing options for each service pro
56. hoose the value under Source Column that you want to import into the column in Destination Column When you finish the column mapping click Import e he Export tab allows users to export the specimen data from iCollect into a file in particular format including Excel CSV TXT and XML First choose a collection and its columns you want to export the data and click View Next choose the file format Select Fileexport and click Export to open the specimen data file and choose the worksheet 11 2 Data Exchange In Data Exchange menu there are two options provided for schema mapping data mapping and exchanging the data with other organizations Standard Schema and Web Services 11 2 1 Data Exchange using a Specific Schema This part allows user to upload the target Data Schema from the specified schema file e g Excel XML File formats to use in data mapping In Create data tab as shown in Figure 11 2 1 1 select Load Schema tab to create the dataset by mapping data columns of source schema iCollect and target schema within following steps Data Exchange Web service management Create data Create new data type from web service Create data Data Source pu 2 Select dataset Type Load Schema 7 Select sample data E Select sample reference Columns Mapping v Select all Refer to columns defined in a web service File Palh Source C Numi xml Browse Select
57. iCollect 1 1 50 iCollect User s Guide Copyright 2011 x formation E pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Table of Contents 1 Getting started with iCollect 2 iCollect Configuration Settings 2 1 Collection Settings 2 1 1 Collection Description 2 1 2 Collection Data Structure 2 1 2 1 Import from an MS Excel file 2 1 2 2 Use Template 2 1 2 3 Specify column names and constraints 2 2 User Account Settings 2 2 1 New User Accounts 2 2 2 Edit and Drop User 2 2 3 Reset Password 2 2 4 Grant Privileges 2 3 Material Type Settings 2 4 Automatic Backup Setting 2 5 Storage Container Setting 2 6 Quality Control Profiles Setting 2 7 Service Configuration Settings 3 Specimen 3 1 Management 3 1 1 Add New Record 3 1 2 Edit a Single Record 3 1 3 Edit Delete Record 3 2 Geographic Coordinates 3 3 Molecular Sequences 3 4 References 3 4 1 Add Import the references 3 4 2 Set Remove references to a specimen sample 4 Sample Management 4 1 Search Specimen Samples 4 2 Create Samples 4 3 Remove Samples 5 Catalog 5 1 Catalog profiles 5 2 Catalog formats 6 Storage Container Management 6 1 Container Settings 6 2 Storage Configuration 6 2 1 Create Storage Tab 6 2 2 Storage Organization Tab 6 2 3 Copy Storage Tab 6 2 4 Move Container Tab 6 3 Storage Operations 6 3 1 Moving samples into storage 6 3 2 V
58. ican Type Culture Col Select Specimen ADMDDDO ADMDDDOS 2 3 AOMOOON 2 Select Sample 3133 Lot Samplett COM DOT L OMOOOU 03 COMO 04 COM DOES COMOOO04 COM OUS COM OO COM DOCS Lot 5 Service Order Selected Sample s 3138 COMOOO02 Lottt Sample Figure 9 3 2 2 Select Samples for Services W formation eod yos inb 62011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory ISL 35 National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Service Data Details Options Reasons Exchange AOMONS Lot 5 Change Samples Figure 9 3 2 3 Select a pricing option Find Services Service Data Service Profile Es Details Options Reasons Exchange Account Service Profile Ecc Sel Customer fy Account samnao noksin 45002 Order date Tie Order Date 189 0 2554 Bo Service Date iv Status Heceive Status Total S ample s B Total Specimen s BH Remark Hen Price a without discount esult s Code Date iic xai niia Total Price 0 Total Yearly Charge D 1 16 wn 2554 i ye B SUT Ilo W n LII Discount U Calculate 540001 Search List of Specimen s Collection Code Sample Status Reject Reason MYOUDOS MYO0D7 BCC MYOUDOB Change Samples Delete Get N
59. iewing samples and containers in storage facilities as shown in Figure 6 3 2 o Storage Tree On the left a list of defined storages is display in a visual presentation of hierarchical storage structure o The icon indicates the container can be expanded to view the next level or the list of samples You can click to expand the branches of the tree o Click to collapse all levels within that branch o Storage Map and Table On the right a list of samples in the containers will display in the map or table o If the container is assigned the exact position dimension the samples will be presented in a map o Ifthe container is not assigned the exact positions the samples in the container will be presented in a table f nformation M 23 Lg is fab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 6 3 3 Searching samples in storage Search 5pecimen s samples Filters Search Result Column Criteria Specimen Sample Lot Pas Strain code ACMOO001L Scientific name Bex moonu1 Type strain AOMOO001 Order Family Identified by aom T Isolated by AOMOO001 Isolate date AOMOOO01 Substrate AOMOOO01 testi testi f APO aocMOnno1 bestl frack1 Ay testd fracki Ay bestl fracki Ay 1 d B 6 T a g Figure 6 3 3 Search Samples in Storage To search samples in storage o Open Search
60. iewing samples or containers in storage 6 3 3 Searching samples in storage 6 4 Storage Monitoring 7 Barcode 7 1 Storage Map Using Barcode Scanner 7 2 Scan Barcode 7 3 Print Barcode 8 Quality Control 8 1 Quality Control Profiles 8 2 Quality Control Records f nformation pad tab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand COCTOCOCOCOMONNNNOUUOOBRA A HRWWWWD iCollect 1 1 50 8 2 1 Search Sample Specimen in Quality Control Records 8 2 2 Update the Quality Check Results 9 Services 9 1 Service Configuration 9 1 1 Service Types 9 1 2 Documents for services 9 1 3 Service Profiles 9 2 Customers amp Accounts Registration 9 2 1 Customer Registration 9 2 2 Account Registration 9 2 3 Nationality 9 3 Service Operations 9 3 1 Deposit 9 3 2 Make a Service order 9 3 3 Renewal and Termination of Maintenance 10 Statistics amp Log 10 1 Collection Summary 10 2 Storage Summary 10 3 User Summary 10 4 Data Log 11 Other 11 1 Import Export 11 2 Data Exchange 11 2 1 Data Exchange using a Specific Schema 11 2 2 Data Exchange via Web Services 11 2 2 1 Data Preparation for DataSet and Array Type 11 2 2 2 Data Preparation for an Array of Web Service Defined Type 11 2 2 3 Data Preparation for a single record of Web Service Defined Type 11 2 2 4 Calling Web Service 11 3 Taxonomical Data Checking 11 4 Link to BIOTEC BRC 11 4 1 Submit Dat
61. k Select OriginalCode MYOOOO1 x Year s Source Collection IBS BCE Deposit Demo Column MacroHabitat Subsite Site District feo country Latitude NorthSouth Lunglitude Fastest Elewation GPSStatus Reference Step 1 Select recipient from deposit to combo box BCE Column MacroHabitat subsite_ I site District Z Province Country Latitide z NorthSouth Longtitude Esstwest E Elevation esses 7 Reference GetData MYOO008 MYOO010 MYOO017 MYOO018 MYO0019 IMYOO020 MY00021 El MY00022 M1 v Select All MYOOD0Z2 MYO0003 MYOOO04 MYOOO05 MYOO006 MY00007 MYOD008 MYOO011 MY00012 MYO0013 MYOO014 MYO0015 MYOO016 BCCCode 16757 BBHCnde 98973 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010 10011 10012 10013 14479 10015 i0015 10017 10018 10019 10020 Figure 11 4 5 1 Deposit to BRC Interface Step 2 Select collection Step 3 Select deposit type Step 4 Set order date Step 5 Set service length Step 6 Add remark optional Step 7 Select source collection Step 8 Map source collection s columns with BIOTEC BRC collection s columns Figure 11 4 5 2 illustrates the example of column mapping w formation E Ce iso 2011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory IS
62. lay at the bottom of the window The received order will be display as in Figure 9 3 2 4 34 Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 iCollect will display a confirmation dialog box asking user to save changes that have been made Click to confirm otherwise click Cance changes in the previous step Click click Cance Find Services Service Data Details Options Reasons Service Profile For Bcc Sell The confirm receive order dialog box will appear after user has saved Yes to receive order otherwise Exchange Account Service Profile For Bcc Sell v iv v Customer Account AccountDemo 54100 Order date Ivi Order Date 20 wn 2554 vit SemiceDate x Status Order Iv Status Total Sample s 1 Price Price 0 Clear Search Result s Code Date Total Price 0 40003 20 w a 2554 540002 20 win 2554 Di 10 540001 16 w a 2554 Discount List of Specimen s Collection Code Total Specimens 4 Remark without discount Total Yearly Charge 0 Sample Status Reject Reason BCC For Test DPOOD0 Status Order Figure 9 3 2 1 Make a a ar Lill Select Sample s for Service Select Collection Select Catalogue Profile Amer
63. llowing tasks Profiles 5 Records Figure 8 1 Quality Control Menu 8 1 Quality Control Profiles This part allows users to create and edit the quality control profiles e Adda new profile Step 1 Click a dialog box as shown in Figure 8 1 1 will appear Type the profile name and Click Lok J The new profile will be found in the table List of Quality Control Profiles iCollect Please specify a new profile name Figure 8 1 1 Add a New Profile Name Step 2 Click at the row containing the new profile name and click to add a type of quality control result A dialog box in Figure 8 1 2 will appear so you can enter the result type and click Lok The added result type will be displayed in the table Result Set You can add more than one result type for each profile iCollect Please specify a result type Cancel Figure 8 1 2 Add a Result Type e Edit a profile You can click to retrieve all quality control profiles from the database Search results will display in the table List of Quality Control Profiles Step 1 In the List of Quality Control Profiles click at the row containing the profile name you want to edit The result types of that profile will appear in the table Result Set f nformation M 21 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50
64. main steps are involved in printing the barcode labels e Step 1 Sample Selection Select a collection you want to print the barcode label specify the search condition and click _ Search results will appear as a list of samples specimens presented in the Tree view tab e Step 2 Label and Printer setting In this step you can create the customized barcode label with including sample information with the barcode image At the top right frame of Print Barcode window you can also setup a custom printing layout according to number of barcode labels within a single page page margins label width amp height barcode image size font size and horizontal amp vertical pitch so the labels can Preview be printed in compatible printer Click to open Show Barcode tab and you can preview a page of barcode labels before printing e Step 3 Barcode Labels Printing Print To print all the labels you can click or click on the toolbar in Show Barcode tab f nformation M 26 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 8 Quality Control This part allows user to create definable quality control profiles Each profile allows test methods to be defined and data to be recorded for each sample Under the menu Quality Control which illustrated by figure 8 1 you can perform the fo
65. n D scollect ExFile BAK TSK GS Backup amp Restore Backup Restore Restore Database Figure 12 1 Backup and restore As shown in Figure 12 1 you are allowed to perform the following tasks Click on Backup tab to backup the database e Default Backup location will appear Click to change to other folders e Click Bake tg start the backup process Click on Restore tab to restore the backup files to database e Browse to locate the backup folder e Click to restore the backup data into database 13 Help Help menu provides a user manual for new user to getting start with the program 13 1 View Manual To view user manual please click on view menu The user manual will be displayed as shown in Figure 13 1 f nformation M 58 PDE 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Emet 1 1 45 Microbe Gatton iCollect User s Guide Copseiget ib 2018 irm WIDE LEUT B Page amenrad Inkyemior Gees Labcesier TE hio Carme hr mme Loge eer a Daday EO Thieme Elect 3 1 45 Microbe Edition Table of Contents L Cabin bi bae Sih olhs li Bedlect Configuration Sache 1 1 Colhection Stig ELI Colleton Daeriptcn LI Collection Gate structura A Bast amisi l4 amp Crank Friilegen 1 2 Material T Taten 1 1 duoc Bact tebang 21 4 Secr ga FLactminer Sing 2 5 Ceimlege Cocired Pro
66. nation of Maintenance Select deposit data Speciment List ae Details Options Reasons Exchange TOMOOD07 Service Profile termination Account BIOTEC 3020 Order Date 22 n s 2553 x ji Service Date 22 vai si 2553 v x Deposition length year uml Remark Total Specimen s Price without discount Total Price Total Yearly Charge Discount Calculat Figure 9 3 3 4 Termination of specimens samples maintenance 10 Statistics amp Log iCollect provides feature for BRC administrators and collection managers to summarize and analyze trends of collection data and usages of storages Under the menu Statistics you can find three types of summary statistics Storage Summary User Summary Figure 10 1 Statistics Menu 10 1 Collection Summary When you open the menu Collection Summary iCollect will give you a summary on all specimen collections including Total number of collections registered Total number of specimens and samples Maximum Average and Minimum number of specimens and samples per collection and storage Maximum Average and Minimum number of samples per specimen In the Collection Summary tab choose a collection to see the summary of number of specimens and samples Two in built comparison charts of collections are included to give you see the different number of specimen
67. ntainer between storages 6 2 1 Create Storage Tab i New Storage To create a new storage click and enter the storage information as below o Select a type of storage from the list of Storage Configuration previously defined in the Container Type setting o Enter the storage facility name in Storage Label o Specify the warning condition for storage monitoring the minimum liquid volume and maximum temperatures o Click M formation _ aa NY 1 9 ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 2 Storage Management Create Storage Storage Organization Copy Storage Move Container List of Storages Storage Detail testi Cabinet LG150 testi A Cabinet LG150 Storage Configuration Cabinet LG150 v Storage Label test Set Warning Conditions Minimum Volume 19 lt 100 Liter Maximum Temperature 1 gt 150C more than one storage Remove Storage New Storage Figure 6 2 1 Create Storage Tab 6 2 2 Storage Organization Tab aJ Storage Management Create Storage Storage Organization Copy Storage Move Container Storage Organization amp testi Cabinet LG150 Add Container to Storage Rack 10Box B Rack 10Box Container Configuration C Rack 10Box D Rack 10Box E Rack 10Box F Rack 10Box rack1 4 Rack 10Box
68. o Gee if the data is correct spelling or containing the valid taxonomic classification o Yellow if the data is not found from the Global Check list or the selected reference website o BB if the data contains the invalid taxonomical classification Step3 For the invalid taxonomic data or Red record you can click to update the data as specified in the Check List 11 4 Link to BIOTEC BRC This menu provides a convenient way to send and receive data to BIOTEC BRC web service In this menu user can submit deposit and order samples or collections through BRC 11 4 1 Submit Data This part allows user to submit samples to BIOTEC BRC as shown in Figure 11 4 1 1 f nformation M 51 TUN 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Data for Submit to BRC Web Site Select All Submit Data E i Figure 11 4 1 1 Submit data form Step 1 select source as shown in Figure 11 4 1 2 i Select data choose samples data from collections that has been stored in iCollect ii Brose file import samples from ms excel file xls or ms access file mdb iii Connect to DB Server retrieve samples from MySQL or MS SQL Database server Select Source Select a Collection mi Browse File Browse Connect to DB Server Host Port Schema
69. ollowing steps Step 1 In Create Data tab open Select dataset type tab Step 2 Click Other Figure 11 2 2 4 to select a web service defined type Select dataset Type Load Schema DataSet String aray String Integer array Integer Int32 Decimal array Decimal Bitmap array Bitrnapt Figure 11 2 2 4 Web service Defined Data type Step 3 Determine what data you want to retrieve from database for the preparation At the Source Data click on the checkboxes to select the data source and choose a collection from the list shown in Select Collection Step 4 Go to Column Mapping as shown in Figure 11 2 2 5 Click Refer to columns defined in a web service to be checked Specify the Reference object and its Method that will be used in mapping with the source column o Click on to select the column on that row or Click Select all to select all columns x formation E pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand 46 iCollect 1 1 50 Columns Mapping Select all Refer to columns defined in a web service Select Source Reference object Method ReclD BEC Code ThaDaminC v Genus Name set Kingdom set ScientificName Species epithet SciNm set SpecificE pithet Lj set_ Applications Other Collection Nu set Fil
70. or Shipping Address You can enter other address by clicking Other checkbox to enable typing other address Active Account Click if the account is active 3l Jf formation zm TADA ystems lab 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Discount Enter the discount rate for this account o Click The opened account will appear in the bottom left table you can click on the row containing the account name you want to edit or delete o If you want to delete the account click o f you make changes on the account Click to record your changes 3 Account Joe Search Account Details Customer name iv Code Customer Name aaa AccountCode Account name Account Name aaa3 Billing Address Customer Office Customer Home Customer Billing Address Customer Shipping Address Other List of amp ccount s Customer Account aaal aaa 999 xyzff aaa3 ana tl ZI Shipping Address Customer Office Customer Home Customer Billing Address Customer Shipping Address Other 999 xyz Active Account Discount 100 Total Order Delete Account Figure 9 2 2 Account Registration 9 2 3 Nationality Under the Nationality menu you can add edit and delete a nationality A list of default nationality has been included in the iColle
71. ow to access KEGG database through web services Accessing the URL http soap genome jp KEGG wsdl available web services will be listed In Figure 11 2 2 9 a web service get html of colored pathway by elements was selected and invoked to get the html page of a color pathway map for a specified pathway hsa00010 You can get the html page at http www genome jp tmp color pathway 127121207110735 hsa00010 html from result in Web service result You can use a web browser to access the html result to view the pathway map as shown in Figure 11 2 2 10 W formation mappa yos inb 2011 ISLIBIOTEC Al Rights reserved Information Systems Laboratory ISL 49 National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 sh Data Exchange Web service management Create data View web service method Created dataset URL http soap genome jp KEGG wsdl Dataset Name Type Remark Web service function list get_elements_by_pathway get_element_relations_by_pathway color pathway by elements mark pathway by objects color pathway by objects get html of marked pathway by objects get html of colored pathway by objects ISB RS Mica ISS Uk get_genes_by_pathway encoding utf l 5 ix SE nome Jt PALES Pst get enzymes by pathway get reactions by pathway Parameter name Type Input parameter Sting
72. owing items in Search Result will be displayed in Data Log table User Domain Name Display the Network Domain name where the computer used by user is located Computer Name Display the Computer Name where the user logon to the system User Name Display the User name of who made the action Action Display the type of actions that users acted to the data including insert update and delete Action Detail Display the detail on data attributes that were changed Data Group Display the data group that was affected by the action Date Display the date when the action was done Step 3 Check or Uncheck Show checkbox to select the column from search result You can also export the data log to a specified file by selecting a file format and clicking New ES Data Log ooo 00 OG Search data Show Columns Export data Username Column Select file type to export Action iet 5 User domain name v Esport file Date Computer name Export status User name Data group i T ction S S S S Action detail Data log User domain Computer name name BIOTEC natee 521 89 root insert add new service Service 3 11 2010 10 03 BIDTEC natee 1521 89 root l insert add sample s rea Sample 3 11 2010 10 42 BIOTEC natee 1521 89 root linser add new sample Sample 13 11 2010 11 47 BIOTEC natee 1521 83 root l insert add new sample Sample 3 11 2010 11 4
73. racki B Rack 10Box rackl C Rack 10Box rack1 D Rack 10Box racki E Rack 10Box racki F Rack 10Box Label Specified more than one container OOOOOOOOOOOO amp testi A Cabinet LG150 Add to Selected Storage Remove Selected Container Clear Selection Figure 6 2 2 Storage Organization Tab As illustrated in Figure 6 2 2 to define the storage structure o click on the node containing storage name you want from the Storage organization treeview o Select a container type to be stored inside the storage from the list of Container Configuration M formation 20 POG 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 o If you want to store only one container inside the storage just enter the Add to Selected 5 name at Label Specified and click to finish the process o If you want to store more than one container click more than one containers checkbox to enable the Label Running part o Choose the label type to be alphabetic or numeric o Specify the letter or number used in running the container label name o Specify the quantity of containers you want to store inside the selected storage Add to Selected Storage ve o Click to finish the process 6 2 3 Copy Storage Tab ad Storage Management ES Create Storage Storage Organization Cop
74. re 11 4 1 4 Select sample to submit Step 7 Choose submit data option Step 8 Select a collection on web that the samples will be stored on BIOTEC BRC Step 9 Set material type Step 10 Click stbit ata The program will open a confirm dialog ask you for a confirmation click Step 11 The login to BRC dialog will appear on the screen Specify username and password and then click Step 12 iCollect will display a submit result message on the screen 4 2 View submit log Submit log records the information of your collection that has been submitted to BIOTEC BRC See figure 11 4 2 1 for more details Submit Date Lisl Ul Specimen Code BRC Web Login iCollect s Collection BRC Web s Collection Submit Columns Number of iCollect Login Specimen 16 WA 2554 16 n n 2554 13m n 2554 13m n 2554 13 WA 2554 13 WA 2554 w formation x TUN 2011 ISL BIOTEC All Rights reserved uu samnao BCC 16052554 RE BA 5 MYO000 MYOQ root samnao BCC BCC16052554 OriginalCode B 5 MYQ0001 MYOO root samnao sponge testAddNewColu 20 MUS A 01 MUS root samnao sponge testAddNewColu 20 MUS A 01 MUS root samnao sponge testAddNewColu 10 MUS A 01 MUS root samnao sponge testAddNewCalu 10 MUS A 01 MUS Figure 11 4 2 1 Submit log window 53 Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iColle
75. rs On the right hand side in the table at the row corresponding to the collection you want check Grant checkbox to grant read or write access permission on the collection to selected user and uncheck the Grant checkbox to revoke the permission from the user When you finish click Save to update user s permissions 2 3 Material Type Settings Under the Administration menu open the Material type window Figure 2 3 to add edit and delete a type of biological materials A list of default material types has also been included in the iCollect system o To add a new type of material enter the material name and description and then cickl 59 o To edit a material type click on the row corresponding to the material you _ want Make your changes to the material name and description Click to record your changes o Click on the row corresponding to the material type you want click to delete the material type M radon x 6 TUN 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Material Type List af Materials g Description Save EN Algae au NN c NR m ey O See Jiosee ES 00 prem ba Se Jose fe PERS Wawca sme Jose Wuma sme oem Ba 00 0 sme Jose Beta ooo Sae Jose Pea oo Sn roues vos ne one C Se JLDste m BE Figure 2 3 Material Type Settings 2 4
76. s List of Reference s table click Select checkbox on the row corresponding to the reference you want Step 3 Click to set the selected references to the specimen The list of selected references of the active specimen will then appear in the List of Specimen s Reference Step 4 Click on the checkbox in front of the reference code appear in the List of Reference Specimen s Reference and click to remove the checked reference from the specimen 4 Sample Management Y Sample F Management Figure 4 1 Sample Menu In Sample Management Figure 4 1 this part allows users to search create and remove samples of biological materials 4 1 Search Specimen Samples Users can search for specimens samples in a particular collection and perform actions on the selected specimen samples in three steps as shown in Figure 4 2 1 1 Step 1 Choose a collection from the list shown in Select collection The columns of selected collection will appear Users can specify values of each column to search the specimen samples and Click Search M formation Y 1 1 pad 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Step 2 Search result will display in List of Samples treeview a visual presentation of hierarchical node data There are three types of icons displayed at
77. t Container Configuration from the menu Storage Container to create container configurations that represent actual containers used in the lab and where the container configurations will be stored In Container Configuration window as shown in Figure 6 1 2 click Nem Container to define a new container configuration within three steps 69 Choose a Container Type defined in Step 1 and enter the configuration name if the selected container type is Freezer the Freezer Details will be enabled otherwise will be disabled e In Freezer Detail users need to specify a type of coolant such as liquid nitrogen liquid carbondioxide temperature and volume Determine the Sample capacity of container single position and multiple positions a For single position container click single position and click Save J b If multiple positions checked there are two options as below Option I Specify Maximum sub containers to limit the number of Samples stored in the container but the storage position assignment is not required Option Il Select Assign Position if position assignment is required for c For both options at the Sub Container Relation section you can define what types of sub contianers can store inside the container M radon N 18 FDA 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand
78. t the values for each parameter in the Input Parameter Value column Figure 11 2 2 7 When finished specify the dataset name and click Create Dataset The created dataset will appear in a table List of Datasets Web service management Create data Create new data type from web service Find Parameter Member Detail List of Datasets Dataset name Type Remark dataset ThaiD arwinCorePlus Po Request Input parameter Member list parameter name Type value e a Dataset name dataset Create dataset Figure 11 2 2 7 Create a single record of a web service defined type 11 2 2 4 Calling Web Service After finishing data preparation the dataset created will appear in Created dataset table in Web Service Management tab You can select the created dataset from the list to specify for Input Parameter of the web service When you have already specified all input parameters for the service function click to invoke the web service function Return results will display in the Web service result as shown in Figure 11 2 2 8 M formation PDD ystems lab 48 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 Web service management Create data View web service method URL http localhos BRC w ebService asms i Meeke HelloWorld
79. thout storing into any storage facilities and click Click RENE 13 M radon mi DADIN DO 2011 ISL BIOTEC All Rights reserved Information Systems Laboratory ISL National Center for Genetic Engineering and Biotechnology BIOTEC Thailand iCollect 1 1 50 to select the selected reason for all samples you want to create Then click to create the samples 4 3 Remove Samples In Remove samples as shown in Figure 4 2 3 you can perform the following steps to remove the samples At the row corresponding to the specimen sample you want to remove click to choose reason in removing the sample The Select reason frame will appear on the right in select Reason frame select a reason in removing the sample and click ssec Click Select or allsamples to select reason for all samples you want to remove click to remove the samples The samples removed with quality checking reason will appear in the menu Quality Control Records Rzmove samples mm reason Specimen Sample Position Cancel Mass reason Reason mmo fmm Select Reason oO Quality Checking C Used Disappear Loss Discard Cancel Service Input by barcode scanner Select for all samples Add New Reason a Remove Sample Figure 4 2 3 Removing a sample 5 Catalog This part allows users to create custom catalog printing for distribution or report Users can determin
80. view 38 Sample s Select Strain code enki Type strain Isolated by Isolate from Isolate date Location lt M DOMO0002 04 Melanommataceae V COM0000203 Sirindhorn Resea E vi COM00002 04 Tsingi Resea v COMOD004 Siindhom Riese V CoMOD005 Sirindhom Resea comoo007 SirndhomResea COMODOO8 Sirindhom Resea POMODOD Xylariales v POMOD002 Pleosporales POMOO00203 Pleosporales POMO0002 04 Pleosporales POM ODOO3 Incertae sedis vi POMODDD4 Hypocreales POMOODDS ylariales POMODO0 Pleosporales Em POMODODS Incertae sedis Ilii v Check All Df the Collection Of the Preview catalog Terminated Specimen Specimen Specimen Total Specimens 52 38 10 Safe deposit and Patent T 5 View Report Export to XML Export to Excel Figure 5 1 3 Catalog Preview 5 2 Catalog formats This part allows user to view the catalog report generated from the specified catalog profile within the following steps o Select a collection and its catalog profile o You can change the column title if you want o Click to view the catalog report EI Cata log Format E zl t3 Catalog Format Search Select Collection Effaltcteme I EE ET De Catalog Profile xxx v Format E Column title Select Column Family Family Identified by Identified by Medium Medium Order Order Substrate
81. y L Isolated by mome www sp2000 collection 2009 Isolate date Data is col Substrate Invalid Taxonomic Relations Update Sample Search Result 10 S ample s Select Strain code AOMODDD1 ADMO0002 AOMOD002 03 AOMO0002 04 AOM00003 AOMODODA AOM00005 AOM00007 AOMOD008 IS ES ES S S ST ST ST ST E Select all Figure 11 3 4 Check taxonomy data There are two validation modes of taxonomic data Check Spelling and Check Taxonomy You can process the validation of taxonomic data within three steps Step 1 Choose a collection and its taxonomic columns such as Family Genus and Species and cick Seach Search Results will appear in the bottom sheet view and the selected columns will be shown in the table within the frame Check Step 2 Choose a data reference from Reference To There are two modes of data validation e Click Check Taxonomy if you want to validate the hierarchy of taxonomic relationship Otherwise click Check Spelling to verify only the spelling of the data e Specify the column from the reference in Column Mapping for each row You can select more columns by clicking the checkbox in the Search table on the top left of the screen In Check spelling mode you can select only one column at a time of validation e Click to start the validation Results from validation will display by coloring the sample data with different colors
82. y Storage Move Container Storage Configuration testi v Dimensions testi Cabinet LG150 Quantity v racki A Rack 10Box racki B Rack 10Box racki C Rack 10Box rack1 D Rack 10Box Mame Specified Storage Name racki E Rack 10Box im ium Cd Cd im 1d racki F Rack 10Box 4 Rack 10Box B Rack 10Box C Rack 10Box we D Rac ki OBox E Rack_10Box F Rack_10Box im iudi jL n NamefRunning Copy Storages Figure 6 2 3 Copy Storage Tab To copy a storage structure o Click to open Copy Storage tab as illustrated in Figure 6 2 3 o Select a storage configuration shown in the list of Storage Configuration o Enter the quantity of storages to be copied o Specify the name for new storages copied from the selected configuration in the following two alternatives o Name Specified you can manually specify the individual storage name o Name Running The storage name will be automatically running by user defined label type and start of the label o Click to generate copies of storage facilities 6 2 4 Move Container Tab To move container between storage facilities o Click to open Move Container tab as shown in Figure 6 2 4 o Select a container you want to move out from the left source container treeview o Locate and select a target container that you want to move the source container in M formation 2 1 Pid 2011 ISL BIOTEC All Rights reserve
83. you want to include in the dataset Create data Select All Clear Selection Add Row Add Column Selected 3 of 1088 rows Select columnis C Select all EIGENEN Acetobacter lova amp cetobacterace BCC Code ReclD BCC Code Genus Name 15888 Acetobacter Species epithet SciNm Family lovaniensis 15851 15833 15333 15338 15937 15936 15908 Acetobacter Acetobacter Acetobacter Acetobacter Acetobacter Acetobacter Acetobacter Acetobacter sp Acetobacter sp Acetobacter sp Acetobacter sp Acetobacter sp Acetobacter sp Acetobacter sp Acetobacterace Acetobacterace Acetobacterace Acetobacterace Acetobacterace Acetobacterace Acetobacterace Genus Name Species epithet SciNm Family Dataset Name cares ER ojc a0 ci 4 co n5 1EOn7 M ankar Create Dataset DataSel Select FileExpott Export file Remark Figure 11 2 2 3 Mapped Dataset Result Step 7 You can filter the number of columns by selecting column displayed in Select column s In case of Array data types String Array Integer Array Decimal Array and Bitmap Array you can choose only one column that its data type is not mismatch Step 8 Type the dataset name and click The dataset created will appear in the List of Datasets 11 2 2 2 Data Preparation for an Array of Web Service Defined Type To prepare an array of Web Service Defined type you can perform the f

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