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User Manual For Sequencing Service Management

1. Tube Naming Convention Order ID C Sample ID Sample Name Tube Name Tube Type Or C Default Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done gt Internet 100 Fig No 3 34 Tube Naming Convention This screen displays the following details Order ID A unique identification number provided for an order Sample ID A unique identification number provided for the sample Sample Name The name of the sample Tube name The plate name Tube Type The plate type Default A check box provided for selecting the default naming convention Save Button provided to save the changes Cancel Button provided to cancel the operation By hitting on the save button the admin can save the new naming convention to the database 4 SEARCH AgileBio SARL Page 46 of 51 AGILEBIO Team Sofutons The application provides the facility to search for a sample from the existing list based on the id order plate or using a keyword any character of the sample name This is a common functionality provided for both the type of users which includes the Admin and the User respectively Search screen for the Admin The search screen for the admin will appear as follows fig no 4 1 ve a LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service
2. Sequencing Service Management Search by ID Order lor by keyword Application Order Operation Other Operation Plate Manager Plate ID Plate Name Type Order ID Plate Full Status Sample Position Print Delete Edit Upload 1 2 Plate 96 3 No iew Print Edit Upload Download Association 2 3 tplate 96 4 No iew Print Edit Upload Download Association 3 4 plates 96 5 No iew Print Edit Upload Download Association 4 5 platetest 96 6 8 No iew Print Edit Upload Download Association 5 6 Plate 96 test4 96 7 No iew Print Edit Upload Download Association Display Select Copyright AgileBio 2007 AII Rights Reserved SSM w 1 0 Powered by LabCollector v 4 21 AgileBio v a internet 100 Fig no 3 25 Plate Manager The screen displays the following details Plate id The unique identification number provided by the system A link is provided with the Plate Id admin can sort the list of the plate by clicking on the link Plate Name The name of the plate Type The type of the plate Order ID The order ids associated with the plate Plate Full Status The status of the plate either it is full or not Sample position Application provides a link under this column to view the order sample position in the plate refer below for details Print This is used to print the sample details with plate tube and well information of an individual plate Refer below
3. Order Operation menu then View Order Status and on selecting the Current option which will display the following screen fig no 3 5 L Customize Links LabCotlector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order wal or by keyword Application Order Operations Other Operation From Date To Date C3 Order Manager Order ID UserName No Of Sample Date Status Print iew Cancel 1 1 demoi23 4 2009 01 09 In progress Print iew Samples Cancel 2 2 demoi23 3 2009 01 09 Assigned Print iew Samples Cancel 3 4 demoi23 3 2009 01 09 Assigned Print iew Samples Cancel 4 5 demoi23 1 2009 01 09 Assigned Print iew Samples Cancel Display Select Copyright AgileBio 2007 All Rights Reserved SSM w 1 0 Powered by LabCollector v 4 21 AgileBio Done Fig No 3 5 Order manager This screen will display the following information Order Id The order ID number it is auto incremented AgileBio SARL Page 18 of 51 SAGILEBIO Team Sofutons User Name The name of user who submitted the order Number of samples The number samples inside the order Order date Date on which the order was submitted Print This is used to print the sample details with plate tube and well information of an individual order Refer below for the details View To view the details of samples Refer below
4. save button admin can save the information to the database To view the tubes the admin can access the Tube Manager by hovering over the Other Operation menu select the Tubes option and on selecting the View option will display the following screen fig no 3 30 This screen displays the list of the tube added by the admin AgileBio SARL Page 41 of 51 PAGILEBIO Team Sofutons w abe abcollector B a amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword ti e Application Order Operation Other Operation Tube Manager Tube Name Tube Type Order ID Print Delete Edit 1 test 0 5 ml 3 Print x Edit 2 tube 1 5ml 0 2 ml 11 Print x Edit Display Select m Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio a Internet 100 Fig no 3 30 Tube Manager The screen displays the following details Tube Name The name of the tube Tube Type The description of the tube Order ID The id of the order associated with the individual tube Print This is used to print the sample details with the tube information Refer below for the details Delete To delete the individual tube information from the list if it not associated with any order Edit To modify the previous information of indivi
5. If the user does not enter the To Date by default the application will search for all the archived order from the From Date provided by the user till the current date AgileBio SARL Page 25 of 51 JAGILEBIO Team Solutions 3 4 RESULT To view the results the admin can access the Result Order Manager by hovering over the Order Operation menu and on selecting the Result option will display the following screen fig no 3 13 All the completed result will be listed in this screen Customize Links LabColtlector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Search Application Order Operation Other Operation Result Order Manager Order UserName Number of Date Status Completed By Result Yiew ID Sample 1 9 demoi23 3 2009 01 14 Completed sadmin Download iew Samples Display Select Copyright AgileBio 2007 All Rights Reserved SSM w 1 0 Powered by LabCollector v 4 21 AgileBio Done Fo Fig No 3 13 Result Manager This screen displays the following information Order ID An auto incremented id for order numbering User name The name of user who has placed the order Number of Samples The total number of samples in an individual order Date The date on which the order was submitted Status The status of the order Comple
6. LabCollector amp Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Primer Name Primert Primer Sequence AAT ACG ACT CAC TA Temperature c 32 0 save Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done Ca internet 100 Fig no 2 10 Edit primer By hitting on the save button the user can update the data with the modifications The user can cancel the task by clicking on the cancel button AgileBio SARL Page 13 of 51 PAGILEBIO Team Sofutoans After logging into the application with the admin credentials the application will display the following home page fig no 3 1 we dhe Gone B A LabCollector amp Logout logged as Super Administrator Sequencing Service Management e E Application Order Operation Other Operation The Home Page Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a internet Q100 Fig No 3 1 Admin Home Page The admin can perform the following operations gt Application o User Management gt Order operation o View Order status Current Archived o Results gt Other Operation o Primer o Standard Services o Sample Type o Plate o Tubes O Naming Conven
7. Management Search by ID Order or by keyword Application Order Operation Other Operation Order Sample Manager OrderID Sample Name Sample Type Primer Name Amount Tube Plate Well Status Result View Edit Cancel 1 2 samplel Plasmid M13 Forward 1 000 Plate 69 Test 2 Al Completed File1 File2 View Edit Cancel 2 2 sample2 Plasmid M13 Forward 2 000 Plate 69 Test 2 Bi Completed File File2 View Edit Cancel 3 2 sample3 Plasmid M13 Forward 22 000 Plate 69 Test 2 Ci In progress View Edit Cancel 4 2 sample4 Plasmid M13 Forward 34 000 Plate 69 Test 2 Di In progress View Edit Cancel Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio a Internet R 100 Fig no 4 1 Search by ID Search by order id To search for a sample using the Order Id enter the order id of the sample to be searched in the search field and select the Order option from the drop down list and click on the search button The application will display the searched result on the screen In case of an invalid search the application will generate the message No Record Found Search by plate id To search for a sample using the Plate Id enter the plate id of the sample to be searched in the search field and select the Plate option from the drop down list and click on the search button The application will display the searched
8. Order Operation Other Operation Edit Standard Services Service Code Primer extension seque Service Type Type 1 Price 100 00 Primer extension Description sequencing service Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Internet R 100 Fig no 3 20 Edit Service Admin can make changes to the previous information of the standard service By hitting on the Save button modifications will be stored in the database 3 7 SAMPLE TYPE To add the sample type the admin can access the Add Sample Type by hovering over the Other Operation menu select the option Sample type and on selecting the Add option will display the following screen fig no 3 21 These sample types will be visible to all the users AgileBio SARL Page 33 of 51 PAG LEB O Team Solutions ve te LabCollector LabColtlector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order x or by keyword Application Order Operation Other Operation Add Sample Type Sample Type Description x save cance Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done Internet R 100 Fig no 3 21 Add Sample type This screen display following
9. address of the user Delivery Address The delivery address of the user Billing Address The billing address of the user Profession User s profession Institution The name of the institution Phone Phone number of the user Mobile Mobile number of the user Fax Fax number of the user User Type The type of the user Admin User AgileBio SARL Page 16 of 51 AGILEBIO Team Sofutons User Block Options provided for blocking a user By default the status of an user is not blocked Save User Button provided to store the modified data into the database Cancel Button provided to discard the changes done By hitting on the Save User button modifications done to the user details will be stored in the database To add a new user the admin can access the Add User by hovering over the Application menu select the User management option and selecting the option Add User will display the following screen fig no 3 4 _ LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order Y or by keyword OO Application Order Operation Other Operation v Add User Name fe E mail Billing Address Username Profession Password Designation
10. cancel the sample if status is Assigned Back Link is provided to go back to Order Manager screen User will be able to view the result files in the Result column only if the order is completed and the admin has uploaded the result files two result files for each sample which comprises of a sequence file and chromatogram file User can download the result file by clicking on the links provided in the Result column On clicking the Edit link will open the following screen The user can make the modifications to the required field and on hitting the Save button will save the changes made to the database we a LabCollector LabCollector amp Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Edit Sample Sample Name sample2 Size bp 0 Concentration ng pl 0 000 Purification Method Impurity Ratio Amount Of Sample pl 10 Sample Type Plasmid v Primer Name SP6 k Services Primer extension sequencing service Primer Site save Corer eh AeitnDin DNN T All Diehte One nmrod CCM ese AM s Done a internet R 100 Fig No 2 4 Edit Sample e View By clicking on the view link given under the View column opens a popup and enables the user to view all the information of
11. for the details Cancel Button provided for canceling the order This is functional only if the order status is assigned Print By clicking on the Print link will display a screen which contains the sample details with plate tube and well information of an individual order fig no 3 6 This screen has the following details e User Name The name of the user who has placed the particular order e Order ID Order ID e Order Date The date on which the order was submitted e Phone No The phone number e Sample Name The name of the sample e Sample Type The sample type name e Primer Name The primer name e Amount The amount of the sample e Service name The name of the service for a particular sample e Tube Plate The name of plate or tube e Well The well position if the plate is used e Status Status of the sample e Print Print button provided to print the details present on the screen AgileBio SARL Page 19 of 51 SAGILEBIO Team Sofutons sequencing Service Manager User Mame demol25 Order Date 2009 01 09 Order ID 3 Phone Ho 025 242 542542 Ha Name hia Type Name ay cia wen Name F 2 2 samples Plasmid F 10 j Flate 1 Completed extension Sequencing 3 A E fo dt A E Fig No 3 6 Print View By clicking on the View Samples link under View column the application will display the Order Sample manager screen from this scree
12. information Sample Type The name of the sample type Sample Description The description of the Sample type Save Button provided to save the information Cancel Button provided to cancel the operation By hitting on the save button the admin can save the information to the database To view the sample type the admin can access the Sample Type Manager by hovering over the Other Operation menu select the Sample Type option and on selecting the View option will display the following screen fig no 3 22 This screen displays the list of Sample type added by admin AgileBio SARL Page 34 of 51 PAGILEBIO Team Sofutons We apr abcollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID or by keyword Application Order Operation Other Operation Sample Type Manager Sample Type Sample Description Delete Edit 1 PCR fragment PCR Product x Edit 2 Plasmid Plasmid x Edit 3 Cosmid Cosmid x Edit 4 Bac Bac x Edit 5 Phage Phage x Edit Display Select _GoPage Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio gt Internet 100 Fig no 3 22 Sample Type Manager The screen displays the following details Sample Type The name of the sample Sample Description The d
13. sample Tube Plate The name of the plate or tube Well The position of the well if plate is selected Status The status of the sample Result The name of the result file if they are uploaded by the admin View A link is provided to view the detailed information about the sample Edit A link is provided to edit the previously entered details Cancel A link is provided to cancel the sample if status of the sample is Assigned Search screen for the User The search screen for the user will appear as follows fig no 4 3 w abe LabCollector B LabCollector R Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Order Sample Manager OrderID Sample Name Purification Method Sample Type Primer Name Amount Size Status Result View Edit Cancel 1 1 samplel Plasmid M13 Forward 2 000 0 Completed Fileil File2 View Edit Cancel 2 1 sample2 Plasmid M13 Forward 2 000 0 Completed Fileil File2 View Edit Cancel 3 1 sample3 Plasmid M13 Forward 2 000 0 Completed File1 File2 View Edit Cancel 4 1 sample4 Plasmid M13 Forward 2 000 0 Completed File1 File2 View Edit Cancel Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Internet 100 Fig no 4 3 Search by ID Search by order id To search for a sample
14. the admin AgileBio SARL Page 31 of 51 PAGILEBIO Team Sofutons Ww abe LabCollector R Logout logged as Super Administrator Sequencing Service Management om O Application Order Operation Other Operation Service Manager Service Name Service Type Service Price Delete Edit Primer extension sequencing service Type 1 100 00 x Edit Single standard DNA sequencing a 2 eee Type 2 150 00 x Edit 3 Direct PCR prod Type 3 25 00 x Edit Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done Internet 100 Fig no 3 19 Service Manager The screen displays the following details Service name The name of the standard service Service type The name of the service type Service price The price of the standard service Delete Icon to remove the individual service detail from the list Edit Link provided to edit the previous information of service detail is given below Edit By clicking on the Edit link the admin will be able to navigate to the Edit Standard Service fig no 3 20 AgileBio SARL Page 32 of 51 AGILE BIO Team Sofutans we de LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword O e Application
15. 3 45 000 222 Completed Filei File2 View Edit Cancel 3 sample Bac ptTriplEx 3 45 000 o Completed File1 File2 View Edit Cancel 3 sample Bac ptTriplEx 3 25 000 0 Completed Filei File2 View Edit Cancel 3 sample Bac pTriplEx 3 44 000 0 Assigned View Edit Cancel 3 sample Bac pTriplEx 3 33 000 0 Assigned View Edit Cancel 3 sample Phagel ptTriplEx 3 99 000 0 Assigned View Edit Cancel Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio internet 100 Fig No 2 3 Order Sample Manager The screen will display the following details of the sample Order Id An Order Id is a system generated identification number generated for every individual order Sample name The name of the samples in the order Purification method The name of the purification method used for the sample Sample type Type of the sample like PCR Product BAC etc Primer name Name of the primer sequence Amount The Amount of the sample Size The size of sample Status The status of the sample Result The link of result file will display here if status is completed Edit A link is provided to edit the sample information if it is in progress More details are given below View Link to view the details of sample including details added by admin More detail given below AgileBio SARL Page 6 of 51 SAGILEBIO Team Solutions Cancel To
16. Confirm Password a Institution Ph Address one Mobile Fax Delivery Address User Type Select J Save User Copyright AgileBio 2007 All Rights Reserved SSM w 1 0 vi Done Fig 3 4 Add user The following information will be entered in the Add User screen Certain fields are mandatory and they are marked by red asterisk Name The name of the user E mail The email address of the user Username Account name of the user Password Password of the user Confirm Password Confirmation of the password Address The address of the user Delivery Address The delivery address of the user AgileBio SARL Page 17 of 51 PAGILEBIO Team Solutions Billing Address The billing address of the user Profession User s profession Institution The name of the institution Phone Phone number of the user Mobile Mobile number of the user Fax Fax number of the user User Type The type of the user Admin User User Block Options provided for blocking a user By default the status of an user is not blocked Save User Button provided to store the data into the database Cancel Button provided to discard the changes done Hitting the Save User button will save the data into the database 3 2 VIEW ORDER STATUS CURRENT To view the current order status the admin can access the Order manager by hovering over the
17. Operation Other Operation Plate Naming Convention C Order ID F Sample ID Sample Name C Plate Name Plate Type Well Or C Default Ea Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a internet 100 Fig No 3 33 Plate Naming Convention This screen displays the following details Order ID A unique identification number provided for an order Sample ID A unique identification number provided for the sample Sample Name The name of the sample Plate name The plate name Plate Type The plate type Well The well position in the plate Default A check box provided for selecting the default naming convention Save Button provided to save the changes Cancel Button provided to cancel the operation By hitting on the save button admin can save the new naming convention to the database AgileBio SARL Page 45 of 51 ePAGILEBIO To change the naming convention for Tube the admin can access the Tube Naming Convention Name prefix will be reflected in result files by hovering over the Other Operation menu select the Naming Convention option and on selecting the Tube option will display the following screen fig no 3 34 we te LabCollector m S LabCollector amp Logout logged as Super Administrator Sequencing Service Management Application Order Operation Other Operation
18. Service Management SSM module has been developed as one such add ons using PHP MySQL AJAX and JavaScript It is completely independent of the existing Lab Collector except that the application uses the security features of Lab Collector This application can be accessed by two types of users the Admin and the User respectively User can place submit the orders and track the status of the orders User can search edit and cancel the order An order may contain one or more samples User will get the result result files when the order is completed and the user can download the result files Admin can check the submitted order cancel the order and create jobs Admin can assign the plate or tube to the order and also manage the plate or tube Admin will be able to assign and change the status of order and also upload the result files Each sample has two result files and the name of the result files follow a specific naming convention These naming conventions depend on the location where the sample is processed in the plate or tube we ahe Home mn LabCollector S of bt Sequencing Service Management Login Please enter your login l is f a internet R 100 Fig No 1 1 Login page AgileBio SARL Page 3 of 51 PAGILEBIO BIO After logging in with the User credentials the user will get the following screen Fig No 2 1
19. User Manual For Sequencing Service Management Add on for LabCollector La bC ollector By AgileBio www AgileBio com www LabCollector com AGILEBIO Team Solutions support agilebio com The information in this document shall not be disclosed outside your organization and shall not be duplicated used or disclosed in whole or in part for any purpose other than to evaluate the proposal provided that if a contract is awarded to AGILEBIO as a result of or in connection with the result of this document you the evaluator shall have the right to duplicate use or disclose the information to the extent provided by the contract This restriction does not limit your right to use the information contained in the proposal if it is obtained from another source without restriction SAGILEBIO Team Solutions Table of Contents 1 INTRODUCTION 2 USER 2 1 VIEW ORDER STATUS 2 2 PLACE ORDER 2 3 RESULT 2 4 PRIMER 3 ADMIN 3 1 USER MANAGEMENT 3 2 VIEW ORDER STATUS CURRENT 3 3 VIEW ORDER STATUS ARCHIVED 3 4 RESULT 3 5 PRIMER 3 6 STANDARD SERVICES 3 7 SAMPLE TYPE 3 8 PLATE 3 9 TUBE 3 10 NAMING CONVENTION 4 SEARCH AgileBio SARL 10 11 14 15 18 25 26 28 30 33 36 40 44 46 Page 2 of 51 SAGILEBIO Team Sofutons 1 INTRODUCTION This is the add ons module provided for the LabCollector application Using this module the user can track the sequencing service flow Sequencing
20. be assign to the sample AgileBio SARL Page 23 of 51 SAGILEBIO Team Sofutons By clicking on the view link the admin will be able to view the details of the sample fig 3 11 http localhost LabCollector Mozilla Firefox Sample Information User Name demoil23 Order Date 7009 01 09 Sample Name asdasd Primer Site Size bp 0 Plate Plated Concentrationftngfyuly 0 000 Tube Purification Method Order Status Assigned Impurity Ratio Dye Terminator Amount of Samplefpl 50 Sequence Text File Sample Type Phage Chromatogram File Primer Name M13 Forward Comment Services Direct PCR prod Fig 3 11 Sample Information Admin will be able to view all the information associated with a sample Following are the information added by the admin Plate The name of the plate Tube The name of the tube Order Status The order status Dye terminator The name of the dye terminator Sequence Text file The name of the sequence result file Chromatogram file The name of the chromatogram file Comment Comment AgileBio SARL Page 24 of 51 JAGILEBIO Team Solutions 3 3 VIEW ORDER STATUS ARCHIVED The orders which are older than 6 month and have the status as completed will be archived To view the archived order the user can access the Order Manager by hovering over the Order Operation menu select the View Order Status option and on selecting the Archi
21. ccount only enabled users will be permitted to login to the application Edit A link is provided to edit the previous information refer below for the details AgileBio SARL Page 15 of 51 AGILEBIO Team Sofutons Edit By clicking on the Edit link the application will display the Edit User screen This screen facilitates the admin in modifying the previously added user information _ LabCollector G3 _ Home m LabCollector amp Logout logged as Super Administrator j Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation v Edit User Name Demo User demoi23 Adress E mail demol23 qmail cam Sing Anaras Username demo123 Profession Prefession Password Designation Designation Confirm Password Institution Instituition demol23 Adress Per anen Phone 025 242342342 Mobile demoiz3 Adress Fax Delivery Address User Type User Block Oves No Save User Cancel Copyright AgileBio 2007 All Rights Reserwed SSM w 1 0 Done Mig Fig No 3 3 Edit User Edit User screen display following fields Name The name of the user E mail The email address of the user Username Account name of user Password Password of the user Confirm Password Confirmation of the password Address The
22. dard DNA sequencing ba 2009 01 14 Completed sequencing service Fig no 3 27 Print This screen contains the sample details with plate tube and well information of an individual plate By clicking on the print button the admin will be able to print the information present on the screen By clicking on the Association link application provides following screen fig no 3 28 This screen facilitates the admin to associate the result files with the respective sample and the order id AgileBio SARL Page 39 of 51 PAGILEBIO Team Solutions we tk Ea Collector Pe B LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation Sample Result Files Associtiation Manager Please ensure the file name will be identical Order ID Sample Name Sequence File Name Chromatogram File Name Select v v Seqi seq Seqi Bi Select v vy Seq2 seq Seq2 4B1 Select v v Seq3 seq Seq3 4B1 Select v w Seq4 seq Seq4 4B1 save Done a Internet 100 Fig no 3 28 Association This screen displays following information Order ID Admin can select the order id from the drop down Sample name Admin can select the sample name from the drop down list Sequence file Name The list of the name of the sequence files pr
23. de amp Brome LabCollector amp Logout logged as User Sequencing Service Management Search by ID or by keyword fe O Order Operation Other Operation The Home Page Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio a Internet Q100 Fig No 2 1 User page User can perform the following operations gt Order operation o View Order status o Place order o Results gt Other operation o Primer 2 1 VIEW ORDER STATUS To view the order status the user can access the Order Manager by hovering over the Order Operation menu and selecting the View Order Status option will display the following screen fig no 2 2 AgileBio SARL Page 4 of 51 AGILEBIO Team Sofutons ww LabCollector oe LabCollector amp Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Order Manager Order ID Number Of Sample Date Status View Cancel 4 1 2009 01 07 In progress View Samples Cancel 2 8 3 2009 01 08 Assigned View Samples Cancel 3 9 4 2009 01 09 In progress View Samples Cancel Display Select Coage Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Internet R 100 Fig No 2 2 Order Manager This screen displays th
24. dual if it not associated with any order detail is given below AgileBio SARL Page 42 of 51 PAGILEBIO Team Sofutans Edit By clicking on the Edit link admin will able to navigate to the Edit Tube fig 3 31 screen he che labcollector se IE LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword ee Application Order Operation Other Operation Edit Tube Tube Name Tubel Ea Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a Internet K 100 v Fig no 3 31 Edit Tube This screen displays the following fields Tube Name Name of the culture tube Tube Type The type of culture tube Save Button provided to save the changes Cancel Button provided to cancel the operation Admin can do the modifications and by hitting on the save button and can save the modification to the database AgileBio SARL Page 43 of 51 SAGILEBIO Team Sofutons Print By clicking on the Print link the application displays the following screen 3 32 Sequencing Service Manager Details User Name demol23 Order Date 2009 01 14 Order ID 2 Phone No 020 25657821 Sample Name Sample Type Primer Name Amount Service Tuhe Plate Well Status Name Done Ca Internet 100 Fig no 3 32 P
25. e and on selecting the Add option will display the following screen fig no 3 24 These plates will be visible to all the admin we te LabCollector 5 z LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation Add Plate Plate Name Plate Type Select Ea Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a internet A 100 Fig no 3 24 Add plate The screen displays the following details Plate Name The name of the plate Plate Type The type of the plate admin can select the type from the drop down list Save Button is provided to save the information Cancel Button is provided to cancel the information Hitting on the save button the information will be store in the database To view the plates the admin can access the Plate Manager by hovering over the Other Operation menu select the Plate option and on selecting the View option will display the following screen fig no 3 25 This screen displays the list of plate added by admin AgileBio SARL Page 37 of 51 Paci LEBIO Team Solutions we Bd G labcollector E 3 LabCollector R Logout logged as Super Administrator
26. e list of the orders Assigned and in progress submitted by individual user Application will display the following details Order Id An Order Id is a system generated identification number generated for every individual order Number of samples The number of samples associated with every individual order Date The date on which the order was placed Status The current status of the order View A link provided to view the details of the samples associated with the order For the details please refer below Cancel To cancel the order if status is Assigned If the status of the order is Assigned then the user can Cancel that order otherwise the application will restrict the user from canceling an order AgileBio SARL Page 5 of 51 AGILEBIO View Team Sofutons By clicking on the View Samples link under view column user will be able to go to the Order Sample Manager here the user will be able to view all the samples as well as the details of sample s of the individual order fig no 2 3 we tk LabCollector amp LabCollector R Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Order Sample Manager au fF UUNPe OrderID Sample Name Purification Method Sample Type Primer Name Amount Size Status Result View Edit Cancel 3 sample Cosmid pTriplEx
27. e sample type Amount of sample The amount of sample Primer name The name of the primer Primer site The primer site information Service type The name of the service type used for the individual sample Comment Comment if any Add This button is used to add rows in the form Remove This button is used to remove rows from the form Only one line can be removed at a given instance Save By hitting on this button data will go to server side and stores in side the database AgileBio SARL Page 9 of 51 PAGILEBIO Team Solutions The sample name sample type amount of sample and primer name are the mandatory fields Checkboxes are given with the sample type primer name and service type to set the selected value for other none selected values User can add any number of rows to add more than one sample for one order using Add button User can also remove the added rows from the order form Default row in the form is one 2 3 RESULT To view the results of the completed orders the user can access the Result Order Manager by hovering over the Order Operation menu and selecting the Result option which will display the following screen fig no 2 6 Result order manager contains the list of all the completed orders with the results my aby Pabcollector n a Ba _LabCollector E Logout logged as User Sequencing Service Managem
28. e will be displayed if the admin has uploaded the sequence result file Chromatogram File The name of the chromatogram file will be displayed if the admin has uploaded the chromatogram result file User can download these result files by clicking on the names of the required result file displayed in the Sample Information screen 2 2 PLACE ORDER To place an order the user can access the Sequencing Service Order Form by hovering over the Order Operation menu and selecting the Place Order option which will display the following screen fig no 2 5 AgileBio SARL Page 8 of 51 SAGILEBIO Team Sofutons Ww dhe Grew Document EE LabCollector k Logout logged as User Sequencing Service Management Order Operation Other Operation Sequencing Service Order Form Sample name Size Concentration Purification Impurity Sample Type Amount of Primer Name Primer Service Type Comment ng pl Method Ratio Sample pl Site me es lt ii B A Done La Internet 100 Fig No 2 5 Sequencing service order Form The details of the fields on the Sequencing order form are as follows Sample name The name of the sample Size Sample size or length Concentration ng pl The concentration of the sample Purification method The name of the method used for purification Impurity ratio The impurity ratio for the sample Sample type The name of th
29. ector BF LabCollector R Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Order Sample Manager Order ID Sample Name Purification Method Sample Type Primer Name Amount Size Status Result View Edit Cancel 1 1 samplel Plasmid M13 Forward 2 000 0 Completed File1 File2 View Edit Cancel 2 1 sample2 Plasmid M13 Forward 2 000 a Completed Filei File2 View Edit Cancel 3 1 sample3 Plasmid M13 Forward 2 000 0 Completed File1 File2 View Edit Cancel 4 1 sample4 Plasmid M13 Forward 2 000 8 Completed File File2 View Edit Cancel 5 2 samplel Plasmid M13 Forward 1 000 0 Completed File1 File2 View Edit Cancel 6 2 sample2 Plasmid M13 Forward 2 000 0 Completed Filei File2 View Edit Cancel 7 2 sample3 Plasmid M13 Forward 22 000 0 Completed File1 File2 View Edit Cancel 8 2 sample4 Plasmid M13 Forward 34 000 0 Completed File1 File2 View Edit Cancel z 5 asdsad Cosmid M13 Forward 25 000 0 In progress View Edit Cancel Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered bv LabCollector v 4 21 AaileBio Done Internet A 100 cl Fig no 4 3 Search by keyword AgileBio SARL Page 50 of 51 BAGILEBIO Jean Solutions Note Application provides the facility to change the number of the records displayed on the screen This can be achieved by selecting the required
30. ector amp Logout logged as User Sequencing Service Management Search by ID or by keyword Order Operation Other Operation Primer Manager Primer Name Primer Sequence Temperature c Size Delete Edit 1 Primeri AAT ACG ACT CAC TAT AG 32 0 22 A Edit Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done internet R 100 Fig No 2 9 Primer Manager Primer manager displays the following fields Primer name The name of the primer Primer Sequence The sequence of the primer Temperature The melting temperature of the primer Size Size length of the primer sequence Delete Icon provided to delete the details of the primers Edit Link provided to edit the previous information of the primer Details are given below Edit Clicking on the Edit link displays the Edit Primer screen fig no 2 10 the user can edit the previously added information of the primer from this screen This screen displays the following details Primer Name The name of the primer AgileBio SARL Page 12 of 51 AAGILEBIO Team Sofutons Primer sequence The name of the primer sequence Temperature The melting temperature of the primer Save To save the changes Cancel To cancel the operation we we Labcollector T A
31. ed Edit Link provided to details AgileBio SARL of the generic the primer sequence to delete the generic primer from the list database edit the previously entered information refer below for the Page 29 of 51 PAGILEBIO Team Solutions Edit By clicking on the edit link admin will go to the Edit Primer screen fig no 3 17 we a LabCollector eA LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation Primer Name M13 Forward Primer Sequence GTA AAA CGA CGG C Temperature c 723 SI Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a Internet A 100 Fig no 3 17 Edit Primer The screen displays the following details Primer Name The name of the generic primer Primer Sequence The sequence of the generic primer Temperature The temperature of the generic primer Save Button provided to save the modifications Cancel Button provide to discard the changes By hitting on save button the admin can save the modifications tothe database 3 6 STANDARD SERVICES To add a standard service the admin can access the Add Standard Service by hovering over the Other Operation menu select the Standard Services option and on se
32. ent Order Operation Other Operation Result Order Manager Order ID Number Of Sample Date Status Result Wiew 1 3 3 2009 01 09 Completed Download View Samples Copyright AgileBie 2007 All Rights Reserved 55M w 1 0 Powered by LabCollector w 4 21 AgileBio Log Internet 100 Fig No 2 6 Results Order Manager The Result screen displays the following details Order Id The auto incremented number for order id Number of Samples The number of samples in an individual order Date The date on which the order was submitted Status The status of the order AgileBio SARL Page 10 of 51 JSAGILEBIO Team Sofutons Result Link provided under this column to download the result file in the zip format View View the sample details Details are given below Search User can search according to date Download All User can download all the completed result in zip format through this link User can download all the result files of an individual order in a zip format by clicking on the Download link The Download All option enables the user to download the result files of all the completed orders in zip format User can also search the result of a particular date range View By clicking on the View samples under view column will display the Order Sample Manager fig no 2 3 similar to the Order Manager the only difference is all the samp
33. er Operation Other Operation Order Sample Manager OrderID Sample Name Sample Type Primer Name Amount Tube Plate Well Status Result View Edit Cancel 1 1 samplel Plasmid M13 Forward 2 000 Plate 69 Test 1 Al Completed File1 File2 View Edit Cancel 2 1 sample2 Plasmid M13 Forward 2 000 Plate 69 Test 1 Bi Completed File1 File2 View Edit Cancel 3 1 sample3 Plasmid Mi3 Forward 2 000 Plate 69 Test 1 ci Completed File1 File2 View Edit Cancel 4 1 sample4 Plasmid M13 Forward 2 000 Plate 69 Test 1 D1 Completed Filei File2 View Edit Cancel Ss 2 samplel Plasmid M13 Forward 1 000 Plate 69 Test 2 Al Completed Filei File2 View Edit Cancel 6 2 sample2 Plasmid M13 Forward 2 000 Plate 69 Test 2 B1 Completed Filei File2 View Edit Cancel 7 2 sample3 Plasmid M13 Forward 22 000 Plate 69 Test 2 Ci In progress View Edit Cancel 8 2 sample4 Plasmid M13 Forward 34 000 Plate 69 Test 2 D1 In progress View Edit Cancel Display Select 7 Copyright AgileBio 2007 All Rights Reserve d SSM v 1 0 Powered by LabCollector v 4 21 AgileBio gt Internet R 100 Fig no 4 2 Search by keyword This screen displays the following details of the searched result Order ID A unique identification number provided for an order Sample Name The name of the sample Sample Type The name of the sample type AgileBio SARL Page 48 of 51 AGILEBIO Team Sofutons Primer name The name of the primer Amount The amount of the
34. er Operation menu select the Primer option and on selecting the View option will display the following screen fig no 3 16 This screen displays the list of generic primers added by admin AgileBio SARL Page 28 of 51 BAGILEBIO Tam Solutions we we LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation Primer Manager Primer Name Primer Sequence Temperature c Size Delete Edit M13 Forward GTA AAA CGA CGG CCA GT 72 3 17 x Edit 2 M13 Reverse AAC AGC TAT GAC CAT G 71 9 16 x Edit CCC AGT CAC GAC GTT 3 M13 pUC Forward GTA AAA C 55 0 23 x Edit 4 M13 pUC Reverse AGC GGA TAA CAA TTT CAC 54 23 x Edit ACA GG T3 ATT AAC CCT CAC TAA AG 70 0 17 x Edit 6 T7 AAT ACG ACT CAC TAT AG 69 0 17 x Edit 7 SP6 ATT TAG GTG ACA CTA TAG 45 0 18 x Edit Display Select Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a Internet R100 Fig no 3 16 Primer manager Primer manager displays following details of generic primers Primer name The name of the generic primer Primer Sequence The sequence of the generic primer Temperature The temperature of the generic primer Size The size length Delete Icon provid
35. escription of the sample Delete Icon provided to delete the individual sample type information from the list Edit Link provided to modify the previously added information of the individual service refer below for the details Edit AgileBio SARL Page 35 of 51 PAGILEBIO BIO By clicking on Edit link admin will able to go Edit Sample Type fig 3 23 we te abcollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by 1b Orie E orby keywot Application Order Operation Other Operation Edit Sample Type Sample Type PCR fragment PCR Product Description save cancer Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a Internet Q100 Fig no 3 23 Edit Sample type The screen displays the following fields Sample type Name of the sample type Description Description of the sample type Save Button provided to save the changes Cancel Button provided to cancel the operation Admin can make the modifications and on hitting the save button can save the modifications to the database 3 8 PLATE AgileBio SARL Page 36 of 51 JSAGILEB O Team Sofutons To add the plate the admin can access the Add Plate by hovering over the Other Operation menu select the option Plat
36. esent in side the zip uploaded by the admin Chromatogram File Name The list of the name of the chromatogram files present in side the zip uploaded by the admin Admin can select the order id and sample name against the files Hitting on the save button the information will store in the database If both the files sequence and chromatogram has been uploaded from this screen the status of the sample will be 3 9 TUBE To add the tube the admin can access the Add Tube by hovering over the Other Operation menu select the Tubes option and on selecting the Add option will display the following screen fig no 3 29 AgileBio SARL Page 40 of 51 JPAGILEBIO Team Solutions we te LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order _ or by keyword lt lt Application Order Operation Other Operation Add Tube Tube Name Tube test ESI La Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a Internet 100 Fig no 3 29 Add Tube This screen displays the following information Tube Name The name of the tube Tube Type The type of the tube Save Button provided to save the information Cancel Button provided to cancel the operation By hitting on
37. esult file will be displayed if a result file has been uploaded and by clicking on the link admin can download the result file View A link provided to view the details Refer below for the details Edit A link provided to edit the sample information Refer below for the details Cancel A link provided to cancel delete the sample provided the status is Assigned By clicking on the Edit link admin will be able to get the Sequencing Service Order Form for an individual sample fig no 3 8 AgileBio SARL Page 21 of 51 PAG LEB O Team Sofutons Customize Links LabCollector amp Logout logged as Super Administrator H Sequencing Service Management Search by ID Order or by keyword tt i Application Order Operation Other Operation Sequencing Service Order Form Details Provided By User Admin Sample Name Plate Assign Well gt Size bp Tube Concentration ng pl a Order Status Assigned v Purification Method Dye Terminator Impurity Ratio Sequence Text File Amount Of R Sample ul Chromatogram File Sample Type Primer Name 7 Comment Primer Site Services E Done BOK Fig 3 8 Edit Order The admin can fill the following information for the sample Plate Select Plate type Plate name and well p
38. for the details Delete Icon is provides to delete the plate from list if no order is associated with the plate Edit Link is provided to modify the plate information if no order is associated with the plate Upload An Upload link is provided under Upload column to upload a zip file of the results against the plate Download Link is provided to download the uploaded zip file Association A link is provided to associate the result files present in the uploaded zip with the sample present in the plate Refer below for detail AgileBio SARL Page 38 of 51 AGILEBIO Team Sofutons By clicking on the View link provided under the View column the application provides the following screen fig no 3 26 A feo A W irj demoi23 3 s2 Done La GB Internet 100 Fig no 3 26 well with sample information In this screen admin will be able to view all the wells of the plate with the information whether they are filled or not By hovering over any block of the well the admin will be able to see the user name order id and sample name separated by a colon By clicking on the Print link provided under the column Print the application provides a following screen fig no 3 27 Sequencing Service lanager Details Plate Name Platel Plate Type 96 Plate ID 1 UserName Order ID Order Date Sample ime Well Status Name T 2009 01 14 Plasmid wW Single Al stan
39. lecting the Add option will display the following screen fig no 3 18 These services will be visible to all the users AgileBio SARL Page 30 of 51 JSAGILEB O Team Sofutons we te LabCollector LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order vi or by keyword Application Order Operation Other Operation Add Standard Services Service Code Service Type Price Description Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Jone internet 100 Fig no 3 18 Add Standard Service This screen displays the following fields Service Code The name of the service code Service Type The type of service Price The price of the service Description The description of the service Save Button provided to save the service Cancel Button provided to cancel the operation By hitting on the save button the admin can save the details of the service to the database To view the standard services the admin can access the Service Manager by hovering over the Other Operation menu select the Standard Services option and on selecting the View option will display the following screen fig no 3 19 This screen displays the list of services added by
40. les will be displayed with their result files Sequence file and chromatogram file 2 4 PRIMER To add a new primer the user can access the Add Primer by hovering over the Other Operation menu and selecting the Primer and then Add option which will display the following screen fig no 2 8 CE Sr O A E T LabCollector amp Logout logged as User Sequencing Service Management a ey E or by keyword Search clear Order Operation Other Operation Add Primer Primer Name Primert Primer Sequence AAT AC GAS T CAC TA Temperature c 32 opyris tS AgileRica gt oO ANI Fe Reserved 5 Powrered by LabCollector w 4 21 Agile Bi Ca E Internet Sisco Fig no 2 8 Add Primer Add primer screen has the following fields Primer name The name of the primer Primer sequence The primer sequence Temperature The melting temperature of the primer Save Button provided to save the data Cancel Button provided to cancel the operation AgileBio SARL Page 11 of 51 JSAGILEB O Team Sofutons By hitting on the save button the data will be stored in the database By hovering on the Other Operation and Primer and then selecting the View user get the Primer Manager window and will be able to view the list of primers added by the user fig no 2 9 we wk Labcollector B z LabColl
41. n the admin will be able to view the list of the samples as well as the details of the sample s of an individual order fig no 3 7 AgileBio SARL Page 20 of 51 PAGILEBIO Team Sofutons L Customize Links LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Search Application Order Operation Other Operation Order Sample Manager Order Sample ID RO Sample Type Primer Name Amount Tube Plate Well Status Result Yiew Edit Cancel In 1 1 adsad Phage M13 Forward 25 Plate1 Pi progress iew Edit Cancel 2 1 sdasds Phage M13 Forward 50 Plate1 46 4ssigned iew Edit Cancel 3 1 asdasd Phage M13 Forward 50 Plate1 Assigned view Edit Cancel 4 1 asdasd Phage M13 Forward 50 Plate1 Assigned iew Edit Cancel Display Select 1 Copyright AgileBio 2007 All Rights Reserwed SSM w 1 0 Powered by LabCollector v 4 21 AgileBio Done Se s a Fig No 3 7 Order Sample Manager The screen provides the following details Order Id Order id Sample name The name of the sample Sample type The sample type Primer name The primer name Amount The amount of the sample Size The size length of the sample Tube or Plate Name of tube or plate Well The well position if well is selected Status The status of the sample Result The r
42. number of record from the drop down menu provided next to Display fig 4 3 There is also a facility to navigate to a specific page by entering the page number in the text box provided just before the Go page button and on clicking on the Go page button will reveal the entered page we we LabCollector B zi LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation From Date cs To Date cs Search Order Manager Order ID UserName No Of Sample Date Status Print view Cancel 1 2 demoi23 4 2009 01 22 In progress Print View Samples Cancel io 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done a internet R 100 Fig no 4 4 AgileBio SARL Page 51 of 51
43. osition for the sample Assign Link is provided to assign the well to the sample refer below for details Tube Tube name for the sample Order Status Admin will able to change the order status Dye Terminator Dye terminator provided by the admin Sequence Text file To upload sequence result file if result generated Chromatogram file To upload chromatogram if result generated Comment To put some comment Save To save the modification Cancel To discard the changes By hitting on the save button admin can save the changes to the data base If result files have been uploaded the status of the sample will changed to completed By clicking on the Assign link provided in the Sequencing Service Order Form application provides the following screen fig no 3 9 AgileBio SARL Page 22 of 51 AGILEBIO Team Sofutons xs ny amp amp amp p Lh GB Internet ioo Fig no 3 9 well in the plate This screen displays the entire well in side the plate By clicking on the edit button admin will get following screen fig no 3 10 1 t 4 4 5 T a 10 11 1t cod mt eo wp OoWOOOUO0d OOOOQOQOO0 OHOOOOUOOO DDATA AT m HOOOOUOOO OOOOOQOdO OHOOOOUOOO Ao ooo Ao ooo baee e e AA a ooo OOOOOQOdO Ca Internet E 100 Fig no 3 10 Assign well of Plate The admin can assign the well by selecting the check box Hitting the save button the well will
44. ple Manager AgileBio SARL Page 27 of 51 PAGILEBIO To add the generic primer the admin can access the Add Primer by hovering over the Other Operation menu select the Primer option and on selecting the Add option will display the following screen fig no 3 15 These generic primers will be visible to all the users we wt abcollector SS LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation Add Primer Primer Name Primer Sequence Temperature c Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio a Internet R 100 Fig No 3 15 Add Primer The details to be filled in the Add Primer screen are as follows Primer Name The name of the generic primer Primer Sequence The sequence of the generic primer Temperature The melting temperature of the generic primer Save Button provided to save the primer information Cancel Button provided to cancel the operation By hitting on the Save button the admin can save the generic primer information in the database Duplicate generic primers cannot be added To view the generic primer the admin can access the Primer Manager by hovering over the Oth
45. result on the screen In case of an invalid search the application will generate the message No Record Found This screen displays the following details of the search result Order ID A unique identification number provided for an order AgileBio SARL Page 47 of 51 AGILEBIO Team Sofutons Sample Name The name of the sample Sample Type The name of the sample type Primer name The name of the primer Amount The amount of the sample Tube Plate The name of the plate or tube Well The position of the well if plate is selected Status The status of the sample Result The name of the result file if they are uploaded by the admin View A link is provided to view the detailed information about the sample Edit A link is provided to edit the previously entered details Cancel A link is provided to cancel the sample if status of the sample is Assigned Search by Keyword To search for a sample using the keyword enter the keyword any character of the sample name to be searched in the search field and click on the search button The application will display the searched result on the screen In case of an invalid search the application will generate the massage No Record Found We de abcollector mm B LabColtlector amp Logout logged as Super Administrator Sequencing Service Management Application Ord
46. rint This screen has the following details User name The name of the user who placed the order Order id The order id of the sample Sample name The name of the sample Sample type The sample type Service Name The service name Tube plate Tube or plate name Status The status of the sample Print By hitting the print button the admin will be able to print the details present on the screen 3 10 NAMING CONVENTION Admin can change the naming convention of the result files sequence and chromatogram The names of the result files follow a specific naming convention These naming conventions depend on the location where the sample is processed in the plate or tube This naming convention will be used as the prefix of the generated result files AgileBio SARL Page 44 of 51 SAGILEBIO Team Sofutons To change the naming convention for plate for the samples which are processed inside the plate the admin can access the Plate Naming Convention Name prefix will be reflected in result files screen by hovering over the Other Operation menu select the Naming Convention option and on selecting the Plate option will display the following screen fig no 3 33 w _abcollector EY LabCollector R Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order
47. ted By The name of admin who has completed the order Result By clicking on the link Download in the result column the admin can download the result in zip format View To view the details of the samples of an individual order Admin can download all the result file of an individual order in zip format by clicking on the Download link under the Result column View By clicking on View Samples link under the View column the admin user can navigate to the Order Sample Manager fig no 3 14 of an individual order The admin can view the list of samples as well as the details of the sample s which includes the result files of AgileBio SARL Page 26 of 51 AAGILEBIO Team Sofutons an individual sample The admin can also download the result files of an individual sample we apr LabCollector B H LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keywords Application Order Operation Other Operation Order Sample Manager Order ID Sample Name Sample Type Primer Name Amount Tube Plate Well Status Result View M13 puCc 1 1 test Phage Faad 11 000 plate p4 Completed Filei File2 View cisplay e Se U Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Internet 100 Fig no 3 14 Order Sam
48. the sample which also includes the information added by the Admin fig no 2 5 AgileBio SARL Page 7 of 51 PAGILEBIO Team Solutions ww labcollector ee LabCollector R Logout logged as User Sequencing Service Management Search by ID or by keyword Seah Sea gt LabCollector Windows Internet Explorer http 192 168 100 30 Lab_new_3 view_total_order ph Sample Information User Name demoi23 Order Date 2009 01 09 1 3 Samplel View Edit Cancel 2 3 sample2 prid 8 OrderID Sample Name View Edit Cancel iew Edit Cancel View Edit Cancel Sample Name Sample 1 Primer Site 3 3 sample3 Size bp 0 Plate Plate1 Concentration ng pl Purification Method Order Status Assigned 0 000 Tube Impurity Ratio Dye Terminator a of Sample 10 Sequence Text File p Sample Type Plasmid Chromatogram File y LabCollector v 4 21 AgileBio Primer Name T3 Comment Services r amp Internet 100 internet 100 Fig No 2 5 Sample information The details added by the admin in the Sample Information screen are as follows Plate The name of plate where the sample will be processed Tube The name of tube where the sample will be processed Dye Terminator Name of the dye terminator used for the sequencing Sequence Text File The name of the sequence result fil
49. tion AgileBio SARL Page 14 of 51 PAGILEBIO Team Solutions Admin can assign the plate tube to the samples The admin will be able to upload the result file for the individual sample when they are completed There are two result files one is sequence file and another is chromatogram file 3 1 USER MANAGEMENT To view all the users the admin can access the User Manager by hovering over the Application menu select the User Management option and then select the View User option which will display the following screen fig no 3 2 w abe abcolector S LabCollector Logout logged as Super Administrator Sequencing Service Management Search by ID orbykeyword Application Order Operation Other Operation User Manager Username Type Enabled Edit Delete 1 demo123 User v Edit x 2 admini23 Administrator v Edit Xx 3 tester User y Edit x 4 demotester User v Edit Xx 5 santgadada User y Edit x 6 nehatester User y Edit Xx 7 testneha User y Edit x 8 testersam User v Edit A Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio Done Local intranet 100 Fig No 3 2 User Manager The screen displays the following details Username The identification of the user account Type The type of the user account Enabled An icon is provided in this column to enable or disable the user a
50. using the Order Id enter the order id of the sample to be searched in the search field and click on the search button The application will display the searched result on the screen In case of an invalid search the application will generate the message No Record Found This screen displays the following details of the search result Order ID A unique identification number provided for an order AgileBio SARL Page 49 of 51 AGILEBIO Team Sofutons Sample Name The name of the sample Sample Type The name of the sample type Primer name The name of the primer Amount The amount of the sample Tube Plate The name of the plate or tube Well The position of the well if plate is selected Status The status of the sample Result The name of the result file if they are uploaded by the admin View A link is provided to view the detailed information about the sample Edit A link is provided to edit the previously entered details Cancel A link is provided to cancel the sample if status of the sample is Assigned Search by Keyword To search for a sample using the keyword enter the keyword any character of the sample name to be searched in the search field and click on the search button The application will display the searched result on the screen In case of an invalid search the application will generate the massage No Record Found w k LabColl
51. ved option will display the following screen fig no 3 12 we de Labcoliector B LabCollector amp Logout logged as Super Administrator Sequencing Service Management Search by ID Order or by keyword Application Order Operation Other Operation From Date ms To Date 73 Search Order Manager Order ID UserName Number of Sample Date Status view No Record Found Display Select 8 Copyright AgileBio 2007 All Rights Reserved SSM v 1 0 Powered by LabCollector v 4 21 AgileBio E internet 100 Fig 3 12 Archived order This screen has the following fields Order ID The id of an order it is an auto incremented number User Name The name of the user who has submitted the order Number of Samples The total number of samples inside the order Date The date on which the order was submitted Status The status of the order View By clicking on the link under this column admin will be able to navigate to the Order Sample Manager for the details of the samples Search To search for an order belonging to a specific date range Whenever the screen opens up for the first time it will display No Record Found when the user selects the required date range and clicks on the search button all the completed order of the given date range will be displayed

User Manual For Sequencing Service Management

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