Interfacing a LabVIEW-driven DAQ instrument with LabWare LIMS
Contents
1. Test Analysis Result Name Result Entry Result Entry Table 1 File headers for each of the three cases LabWare LIMS LabWare LIMS version 5 0 is used to store the results from LabVIEW The data is imported using the CSV data file from LabVIEW The user can perform major functions using one file Also results can be entered automatically in one instance As mentioned before some field values are pre defined in LabWare LIMS and the same field values are used in LabVIEW so that the data can be integrated The following table shows the field names that are pre defined in LabWare LIMS Table 2 Importing Files to LabWare LIMS The files can be imported in two ways into LIMS either by manually selecting the file path each time we want to import the data or automating this process To import the files manually select the desired file The import files must have an extension of CSV The selected file will be parsed and the data will be displayed in the Import File Dialog If an error occurs during parsing it will be displayed in the Error Message field If the operation finishes successfully the CSV file is renamed with an extension of ARK and located in the same directory as the CSV file If an error occurs on any record in the file the entire operation fails and no data is imported 24 Peo eee LV driven DAQ inst Parsing Scripts MY _SCRIPT Sample Login Template LV_DATA TRY Sample ID Configuration Sampl2. Therefore the parsed output file from 35 LabStation should be similar to the parsed output file generated by LabVIEW for proper validation File based instrument integration is used with LabWare LIMS The instrument is added to the instrument table in LIMS Figure 20 shows the screenshot for the instruments defined in LIMS Instruments DAQ_INST LABVIEW LV LIMS are already added to the LIMS instrument table Instrument Group LABVIEW was defined for each instrument defined in LIMS The Instrument Group is used to tag the information with LabStation to configure the instrument 2 Instruments Edit Approval Audit Utilities Help SE ick Edit Mode C Report Mode Instrument Template A ipti DAQ_INST LABVIEW Inventory Filters LABVIEW LABVIEW Instrument using with LabVIEW LIMS Project Inventory Location LYV LIMS LABVIEW Instrument used with LabVIEW Lab W are LIMS Project Investigation ID Configuration Investigation Template Label Printer Laboratory Notebooks LabStation Lists Locations Lot Id Configuration Lot Template A a Parsing Script Formula Parsing Scripts Product Filter Product Specifications Project Filter Proiect Id Cantiquration ce Figure 20 Screen Shot for the Instruments added to LabWare LIMS Instrument Group was defined for each instrument defined in LIMS The Instrument Group is used to tag the information wit
3. Diagram of the VI calculating random path and displacement of a particle Since this data is to be used and stored in a LIMS system it has to be formatted in a way such that it can be parsed and read by LabWare LIMS Therefore in the second part of the VI the data is made compatible with LabWare LIMS system The data calculated in the first part of the VI is parsed and written on a comma separated value 18 CSV file usually depicted as CSV file The details of parsing the data in LabVIEW are discussed later in the chapter Following three different cases are defined in the second part of the VI The data is parsed depending on the case selected by the user Case 1 Result Entry Case 2 Modify Sample Case 3 Login Samples to Result Entry The details of each case are discussed below Case 1 Result Entry This case is selected if the user wants to assign tests and enter results for a range of defined sample numbers In this case the samples should be logged in manually by the user in LabWare LIMS Before executing the VI the user needs to define few field values which will be used by the program to parse the raw data so that it is ready to store in LIMS The user needs to define the sample beginning and the ending number for the result entry select the test analysis from the list on the front panel and define the file path where the formatted data file will be saved The test analysis LABV_ DATA and DATA are predef
4. Sitio 47 ALLENDE AI AA A 48 LIST OF FIGURES Figure 1 Screen shot of the block diagram of Y Lassie 9 Figure 2 Screen shot of the front panel Of VI eeeesesessseeesrsssesresseserssresseserssressessresressesee 9 Figure 3 Function palette in front Pal At 10 Figure 4 Function palette in block diagram A dt 12 Figure 5 Screen shot of LabWare LIMS with Integrated LabStation 0 eee 14 Figure 6 Pr ject UM a e Da bla ie ht E de 17 Figure 7 Block Diagram of the VI calculating random path and displacement of a o gatas ate EE EET E E TE gy tats E eso Ga sate E E 18 Figure 8 Screen shot of the block diagram for Case 1 Result Entry eee eeeeeeee 20 Figure 9 Screen shot of the block diagram for Case 2 Modify Sample eeee 21 Figure 10 Screen shot of the block diagram for Case 3 Login Samples Result Entry 22 Figure 11 Front panel of the LabVIEW LIMS Vi oooooocccnnncncoccconononcnonnnconncooncnnncnonnnonnncnns 23 Figure 12 Flow chart representing logic behind importing results using Sample Sample_Number Test Analysis Result Name Result Entry 28 Figure 13 Flow chart representing the logic behind importing results using Sample Text_Id Sample Template Test Analysis Result Name Result Entry 30 Figure 14 CSV data file for Case 1 Result Pntiy ud tdt 31 Figure 15 File Import Grid for Case 1 Result Entry oooooonnccnocococaconancnoncnoncnannnonn nono nonns 32 Figure 16 CSV da
5. block diagram it is there to act as a subroutine A VI within another VI is called a subVI and is considered a lower level call A subVI connects with a top level VI by means of a connector that passes data to outputs indicators in the block diagram and receives data from inputs controls in the front panel of the lower call terminal The icon is the graphical representation of the subVI and may be likened to constraints of a subroutine in written code To function as a subtask in a top level call there must be an icon and a connector 11 The LabVIEW graphical program is both hierarchical and modular Top level and low level calls such as routines within a subroutine are examples of this program s hierarchical nature Each subroutine or subVI can execute independently of the top level VI A subVI can be built upon other subVIs Functions v Programming ba a Structures Cluster amp Vari m amp Ji v f D M ma 2 T lu 2 e E ao fa o 3 By Synchronization Graphics amp So Report Gener Measurement I O Instrument I O vision and Motion Mathematics Signal Processing Data Communication Connectivity Express Favorites Select a VI Yv vv VO YV YV YV vY Y Figure 4 Function palette in block diagram Laboratory Information Management Systems Laboratory Information Management Systems LIMS are computer software that is used in the labora
6. moy aa 2 Ed Search Samples GO CopyTo lt 13 gt lt 10 gt Samples Copy3tring Sample Sample Number Test Analysis Result Name Result Entry header Counterset cont 1 CopyString C Documents and Settings slakhanp Desktop Limsdata raw file FileWrite file header FileWrite file lt 13 gt lt 10 gt Search wi LBL1 LBL2 CopyTo lt 13 gt lt 10 gt DATA ConcatString DATA DISPLACEMENT DATA DATA ToString cont linenumber FileWrite file linenumber FileWrite file DATA FileWrite file lt 13 gt lt 10 gt Counter Inc cont Goto LBL a e woo Inn WYN HR BRR HO RR 0M gt o00N 19 23 12 22 Search Searches for string matching arg1 if found goto optional arg2 otherwise goto optional arg3 Figure 26 Screen Shot of the Parser Interface with the Parsing Script used with raw data 41 sed for LabVIEW LIMS Project Ea lx Kd 44 16 459374 45 20 646396 46 20 107355 47 22 647958 48 25 367597 49 29 128907 50 26 07015 gt IKII Parsing Information gt Samples 50 header Sample Sample Number Test Analysis Result Name Result Entry cont 51 file C Documents and Settings slakhanp Desktop Limsdata raw DATA DATA DISPLACEMENT 26 07015 linenumber 50 lt al arg2 otherwise goto optional arg3 YN Figure 27 Screen Shot of the Parsing Information from the Parser Interface The final form of the parsed raw dat
7. required field values The field values like sample beginning and ending number sample number for modification test analysis sample customer sample location etc can be entered in the front panel 22 LabVIEW LIMS VI Front Panel f Log in Samples Result Entry f LV_DATA DISPLACEMENT Figure 11 Front panel of the LabVIEW LIMS VI Details of the Data file As mentioned before the raw data is parsed such that it can be read and imported to LabWare LIMS The procedure and approach used to import the results file is discussed in the next section The data file is formatted the headers are added to the CSV file and saved by the VI in the directory from where it can be imported to LabWare LIMS The first line of the file contains the table and field names separated by commas For example Sample Sample_Number is used to indicate the sample number field in the sample table The lines following the first line contain the data corresponding to the table and field names where data is separated by commas 23 Three different headers are used for the three cases and therefore there is a different file format for each case Refer Table 1 Cases File Headers Case 1 Result Entry Sample Sample_Number Test Analysis Result Name Result Entry Case 2 Modify Sample Sample Sample_Number Sample Location Sample Assigned _ Operator Case 3 Log in Sample Text_ID Sample Template Sample Customer Samples to
8. ACEMENT 285 3333 141 DATA DISPLACEMENT 302 1206 142 DATA DISPLACEMENT 297 6969 143 DATA DISPLACEMENT 307 7230 144 DATA DISPLACEMENT 275 8251 145 DATA DISPLACEMENT 289 4273 146 DATA DISPLACEMENT 257 6602 147 DATA DISPLACEMENT 237 0047 148 DATA DISPLACEMENT 236 8317 149 DATA DISPLACEMENT 235 2798 Figure 14 CSV data file for Case 1 Result Entry 31 The following field values were entered in the front panel Sample Beginning Number 137 Sample Ending Number 149 Test Analysis DATA Result Name Displacement it is set to default Import File Dialog C Documents and Settings slakhanpWesktop Result Entry CSV _Sample Sample Number TestAnalysis ResultName ResultEntry Displacement 241 8492 Displacement 255 9301 Displacement 255 4211 Displacement 285 3333 Displacement 302 1206 Displacement 297 6969 Displacement 307 7230 Displacement 275 8251 Displacement 289 4273 Displacement 257 6602 Displacement 237 0047 Displacement 236 8317 Error Message Cancel Figure 15 File Import Grid for Case 1 Result Entry The data file shown in figure 14 is imported to LabWare LIMS Figure 15 shows the Import grid of LabWare LIMS for Case 1 There is no Error Message therefore the results are ready to be stored in the LIMS Figure 16 shows the results of the CSV data file for Case 2 Modify Sample The information entered in the front panel like Sample number for modificat
9. Indianapolis February 2005 Design of a green house for off season growth Department of Chemical Engineering and Technology Panjab University March 2003 Expanded Foam Molding Department of Chemical Engineering and Technology Panjab University November 2002 SKILLS LabWare LabVantage Sapphire eLab Notebook Waters eLab Notebook LabTrack CyberLab Molecular Modelling Spartan SYBYL Software Spotfire ChemDraw Total Chrom Computer Languages LabVIEW MEMBERSHIPS Member of Indian Institute of Chemical Engineers Member of Indian Society of Plastics REFERENCES Available on request 49
10. Interfacing a LabVIEW driven DAQ instrument with LabWare LIMS Swati Lakhanpal Submitted to the faculty of the School of Informatics in partial fulfillment of the requirements for the degree Master of Science in Laboratory Informatics Indiana University May 2007 Master s Thesis Committee Mahesh Merchant Ph D Chair Douglas Perry Ph D Silpa Wairatpanij MS Accepted by the Faculty of Indiana University in partial fulfillment of the requirements for the degree of Master of Science in Chemical Informatics Laboratory Informatics Specialization ACKNOWLEDGEMENTS I would like to thank everyone who has been a help at Indiana University Purdue University Indianapolis IUPUI throughout my two years at the School of Informatics I would like to thank Dr Douglas Perry for his efforts in creating the Laboratory Informatics program at IUPUI I am grateful to Dr Mahesh Merchant for the support and encouragement that I received from him throughout this project I am indebted to Silpa Wairatpanij for his invaluable guidance and support right from the beginning of my work Many thanks go to the staff at School of Informatics especially Ms Mary O Neill and Ms Elisabeth Hinshaw Osgood Special thanks are due to LabWare for awarding me with the LabWare Fellowship I would like to mention a special thanks to my parents sister and Sumit for their whole hearted support and encouragement throughout my program and I would li
11. LIMS CHAPTER 1 INTRODUCTION LabVIEW LabVIEW is an acronym for Laboratory Virtual Instrument Engineering Workbench It is a computer software development application created by National Instruments Austin Texas that aims to aid scientists and researchers in gathering and understanding data using computer programs LabVIEW is graphical G programming software that utilizes graphical objects to symbolize lines of code instead of text based languages In the source code of this graphical program data execution depends on the flow of data What may take days in C or Java written code is cut down to hours in G programming Moreover LabVIEW has built a general purpose library of functions and subroutines for most programming tasks The time saved allows the user to fully focus on and understand the data Even though some type of programming experience is useful a novice in text based programming language s can grasp the mechanics of LabVIEW because it is a graphical programming language utilizing iconic symbols to illustrate program action Operating LabVIEW The building blocks of the LabVIEW program are called Virtual Instruments VD The name comes from the fact that the program emulates the appearance and tasks of physical instruments while still operating in the same capability as a text based program There are three key components to any VI the front panel the block diagram and the icon and connector pane The figures 1 amp 2 b
12. LIMS To integrate LIMS with LabVIEW same fields are defined in the VI For better data flow the VI can be configured such that it can pull the data from LIMS database and can update the required fields in LabVIEW VI The other important issue in interfacing LabVIEW with LabWare LIMS is the use of data file results in a regulatory environment In this project the data file is stored in a drive on the system therefore it can be easily changed or edited by anyone using the system In a regulatory environment the Universal Naming Convention UNC should be used In a network the UNC is a way to identify a shared file in a computer without having to specify or know the storage device it is on In Windows operating systems and possibly other operating systems the UNC can be used instead of the local naming system such as the DOS naming system in Windows UNC specifies a common syntax to describe the actual location on a network resource such as a shared file folder or printer In the second part of the VI where the raw data is parsed the date and time when the data is generated is not recorded In this project only the date and time when the data is stored in LIMS is recorded When working in a regulatory environment it is essential to record when the data was generated and when it was stored Therefore the VI needs some configuration so that it can be used in a regulatory environment 46 REFERENCES 1 Bishop Robert National Inst
13. Log in Samples Result Entry csv Sample Template Result Entr Lw 12 20 2006 253 LY DATA Displacement Lw 12 20 2006 254 LY DATA Displacement L w 12 20 2006 255 LY DATA Displacement Lw 12 20 2006 256 Ly DATA Displacement LW 12 20 2006 257 LV DATA Displacement Lw 12 20 2006 258 LY DATA Displacement Lw 12 20 2006 259 LY DATA Displacement Lw 12 20 2006 260 LY DATA Displacement L w 12 20 2006 261 Ly DATA Displacement LWw 12 20 2006 262 LY DATA Displacement Lw 12 20 2006 263 Ly DATA Displacement i Error Message Cancel Figure 19 File Import Grid for Case 3 Login Samples Result Entry If an error occurs during parsing it will be displayed in the Error Message field If the operation finishes successfully the CSV file is renamed with an extension of ARK and located in the same directory as the CSV file If an error occurs on any record in the file the entire operation fails and no data is imported The CSV file is renamed with an extension of ERR and another file is created with an extension of LOG which contains the error message LabStation The main purpose of using LabStation is to validate the results from LabVIEW The raw data generated by LabVIEW LIMS VI is used with LabStation and the standard procedure as explained below is followed to parse the raw data in LabStation LabStation has a huge library of parsing commands that can be used to parse the data collected from various instruments connected to LabWare LIMS
14. V_DATA WK316 DATA DISPLACEMENT 3242 3 LV_DATA WK316 DATA DISPLACEMENT 0 2541 4 LV_DATA WK316 DATA DISPLACEMENT 0 2013 5 LV_DATA WK316 DATA DISPLACEMENT 1 6152 6 LV_DATA WK316 DATA DISPLACEMENT 1 3635 7 LV_DATA WK316 DATA DISPLACEMENT 1 1397 8 LV_DATA WK316 DATA DISPLACEMENT 0 2435 9 LV_DATA WK316 DATA DISPLACEMENT 0 9340 10 LV_DATA WK316 DATA DISPLACEMENT 2 8533 11 LV_DATA WK316 DATA DISPLACEMENT 4 5030 12 LV_DATA WK316 DATA DISPLACEMENT 4 0047 13 LV_DATA WK316 DATA DISPLACEMENT 1 5586 14 LV_DATA WK316 DATA DISPLACEMENT 0 1399 15 LV_DATA WK316 DATA DISPLACEMENT 1 4268 16 LV_DATA WK316 DATA DISPLACEMENT 2 4231 17 LV_DATA WK316 DATA DISPLACEMENT 0 4301 18 LV_DATA WK316 DATA DISPLACEMENT 1 2906 19 LV_DATA WK316 DATA DISPLACEMENT 1 9518 20 LV_DATA WK316 DATA DISPLACEMENT 2 2350 21 LV_DATA WK316 DATA DISPLACEMENT 0 6459 22 LV_DATA WK316 DATA DISPLACEMENT 3 1266 23 LV_DATA WK316 DATA DISPLACEMENT 1 3341 24 LV_DATA WK316 DATA DISPLACEMENT 0 0503 25 LV_DATA WK316 DATA DISPLACEMENT 0 1325 Figure 18 CSV data file for Case 3 Login Samples Result Entry The data file shown in figure 18 is imported to LabWare LIMS and the Import Grid is shown in figure 19 There is no Error Message therefore the results are ready to be stored in the LIMS 34 Import File Dialog C Documents and Settings slakhanpWesktop
15. a file is shown in figure 28 which is similar to the output file from LabVIEW for Case 1 and therefore completes the validation 42 P Limsdata raw Notepad File Edit Format view Help Sample Sample_Number Test Analysis Result Name Result Entry a 1 DATA DISPLACEMENT 1 046164 A 2 DATA DISPLACEMENT 0 063221 3 DATA DISPLACEMENT 1 088534 4 DATA DISPLACEMENT 0 450563 5 DATA DISPLACEMENT 0 739451 6 DATA DISPLACEMENT 2 620418 7 DATA DISPLACEMENT 1 225149 8 DATA DISPLACEMENT 3 849606 9 DATA DISPLACEMENT 7 316901 10 DATA DISPLACEMENT 2 704882 11 DATA DISPLACEMENT 3 098681 12 DATA DISPLACEMENT 3 122131 13 DATA DISPLACEMENT 1 82982 14 DATA DISPLACEMENT 0 404812 15 DATA DISPLACEMENT 0 345485 16 DATA DISPLACEMENT 0 712846 17 DATA DISPLACEMENT 2 556662 18 DATA DISPLACEMENT 2 966996 19 DATA DISPLACEMENT 0 553234 20 DATA DISPLACEMENT 0 440851 21 DATA DISPLACEMENT 0 8961 22 DATA DISPLACEMENT 0 746447 23 DATA DISPLACEMENT 0 08046 24 DATA DISPLACEMENT 0 832457 25 DATA DISPLACEMENT 3 594865 26 DATA DISPLACEMENT 3 204937 27 DATA DISPLACEMENT 6 480622 Figure 28 Parsed raw data file from LabStation for Case 1 Result Entry 43 CHAPTER 5 CONCLUSION This project interfaces LabWare LIMS with LabVIEW The different type of data is integrated using LabVIEW and the results are validated using LabStation The LabVIEW LIMS VI is an easy t
16. ata such that it is ready to be stored in LIMS The screen shot of the block diagram for this case is shown in figure 10 The final form of the data file is shown in figure 18 File Edit View Project Operate Tools Window Help gt al ajn e es bal lot 13pt Application Font 1 tor Tar gt 1 Belect Low Log in Samples Result Entry bad A Select Test Analysis 28 2 RingText Text 5 mr SAMPLE SAMPLE NUMBER gt Sample Text_ID La LEC TEST ANALYSIS b ile with LIMS Headers REUME Sample Template 12 RESULT NAME Build Text2 text_id Select Sample Location e template Sample Customer Ex A E EJ EJ gt test analysis HH abe RingText Text b result name pem b displacement A a H esult Name EN mota Result H abe a tj b sample customer mH El a No For Modification p Select Assigned Operator o E ie RingText Text gt Select Sample Customer ES Test Analysis ES Sample Template HLE i D RingText Text Select Sample Customer Select Sample Template elect Sample Location elect Assigned Operator 28 es 7 IRingText Text v lt v Figure 10 Screen shot of the block diagram for Case 3 Login Samples Result Entry Figure 11 shows the screenshot of the front panel of LabVIEW LIMS VI It can be seen from the screen shot that the user can select the case from the front panel and fill the
17. ate Laboratory Robot LabVIEW was used to develop joystick code for complete control of 4 axis of the Zymate robot AWARDS Inaugural Recipient of the LabWare Fellowship for Innovation in Laboratory Informatics 2005 2006 PRESENTATIONS Scientific Data Management amp Analysis National Cancer Institute School of Informatics Indiana University Purdue University Indianapolis December 2005 Programmatically Controlling the Zymate Laboratory Robot School of Informatics Indiana University Purdue University Indianapolis December 2005 48 Information Architecture of the Web As It Relates To Chemical Informatics School of Informatics Indiana University Purdue University Indianapolis May 2005 Pre Hospital Patient Data from the Marion County Patient Database Database design HIPAA Security Products in Market Problems and Future Work School of Informatics Indiana University Purdue University Indianapolis May 2005 FTC and the Internet Advertising and Marketing on the Internet School of Informatics Indiana University Purdue University Indianapolis April 2005 Website Analysis NIST Chemistry Workbook School of Informatics Indiana University Purdue University Indianapolis April 2005 URL Spoofing School of Informatics Indiana University Purdue University Indianapolis February 2005 Next Generation Search Tools School of Informatics Indiana University Purdue University
18. e Number Table 2 Pre defined fields in LabWare LIMS The CSV file is renamed with an extension of ERR and another file is created with an extension of LOG which contains the error message The importing of files can be set as an automatic process on any LIMS client PC To set a client PC for automatic importing the following steps were followed 1 Select System from the Configure menu then Select Client 2 Set the File Import Directory to the drive and path where the CSV files will be located in this project C LW LIMS V5 LW LIMS_LAKHANPAL 3 Set Import files to Yes for automatic operation 4 Click on OK to confirm the settings 25 LIMS client PC will now poll for CSV files in the background and process them without user prompting or interaction The activity is indicated by the status pane of the main menu Again the completion of any importing can be verified by the CSV file being renamed with an ARK extension or ERR and LOG extensions File Import Logics Results can be imported by using different logics and result values In this project the results are imported using three different file formats Now we discuss the logic behind setting result values using three different the import file structures Case 1 Result Entry The following flow chart represents the logic behind importing results using Sample Sample_Number Test Analysis Result Name Result Entry Figure 12 The impor
19. e named Limsdata raw File Instrument Setup Full File Pathname for the Data Files Wildcards accepted El CADocuments and Settingsislakhanp Desktop Polling Time in seconds vr TF IncludeSubdirectories when Polling Post Archive Actions Leave Raw Data File unchanged C Delete Raw Data File Change Raw Data File Extension to f Cancel Figure 22 File Instrument Setup in LabStation 38 Parsing Script for Result Entry par Notepad DAR Fie Edit Format View Help Search Samples GO copyTo lt 13 gt lt 10 gt Samples copystring Sample Ssample_Number Test Analysis Result Name Result Entry header Ccounterset cont 1 Copystring C Documents and sSettings slakhanp Desktop Limsdata raw file Filewrite file header Filewrite file lt 13 gt lt 10 gt search 5 LBL1 LBL2 copyTo lt 13 gt lt 10 gt DATA concatstring DATA DISPLACEMENT DATA DATA Tostring cont linenumber Filewrite file linenumber Filewrite file DATA Filewrite file lt 13 gt lt 10 gt CounterInc cont Goto LBL End instance variables name Parsing Script for Result Entry fileextension par Figure 23 Parsing Script used to parse the raw data for Case 1 Result Entry Select a Data File to Parse from C Documents and Settings slakhan SEE Raw data from Instrumentraw 12 22 2006 05 49 52 PM Samples 50 1 1 046164 2 0 063221 Delete Number of Files Cancel Figure 24 Assigning a raw data
20. ec L3LEC gt SAMPLE LOCATION Build Text sample number SAMPLE ASSIGNED_OPERATOR gt sample location Result b assigned operator aber Sample No for Modification 124 Select Assigned Operator 2 Ts 22 RingText Text gt Select Sample Customer ES Test Analysis ES Sample Template e e 71 i D RingText Text Select Sample Customer Select Sample Template elect Sample Location elect Assigned Operator Form a 31 RingText Text Figure 9 Screen shot of the block diagram for Case 2 Modify Sample Case 3 Login Samples to Result Entry By selecting this case the user can perform major functions with one CSV extension file The user can log a sample assign tests and enter results using one data file The user needs to define the sample text_Id select the sample template sample customer test analysis from the list on the front panel and define the file path where the formatted data file will be saved before executing the VI Since the sample does not yet exist proxy identification of the text id for the sample is required in order to specify which records belong to same sample The Sample 21 Customer WK316 and LAB Sample Template LV_DATA TRY Test Analysis DATA is predefined in LabWare LIMS The result name DISPLACEMENT is set to default and the Result Entry is the actual data The information entered before executing the VI is used to parse the raw d
21. elow show the block diagram and the front panel of a typical VI E swati data vi Block Diagram File Edit View Project Operate Tools Window Help a Ol F Sa hal os 13pt Application Font 20 555 5 swati data vi Front Panel File Edit View Project Operate Tools Window Help D E O n 13pt Application Font lo gt Random Path ts 1 1 1 I 1 1 J 1 1 1 1 1 1 1 CONS L0 1520 25 30 35 40 4S O AAA Time Figure 2 Screen shot of the front panel of VI Front Panel The front panel is the VI s interactive interface built with controls inputs and indicators outputs that replicate conventional instruments like thermometer etc It can also represent the output in the form of graphs charts boolean digital waveforms and other controls that may be found in the real world The LabVIEW programmer can simply drag and drop the input data to the panels using the mouse wire them and get the results on the front panel Figure 3 illustrates the Function palette in the front panel Controls 3 gt abe j 123 do Path Numeric Boolean String amp Path m 2 Ea ER x Array Matrix List amp Table Graph 3 1 b b oO a 4 Enum cai Ring amp Enum Containers 10 E BS Refnum Variant Decorations System Classic Express NET amp Activex Select a Control v YV vY v Figure 3 Function palette in front panel Block diagram The bloc
22. file to parse in LabStation 39 Since the parser interface is not very user friendly in LabStation only one parsing script is defined and that is for Case 1 Result Entry Therefore LabStation can be used to enter the results for the samples that are already logged in LIMS whereas LabVIEW is used to parse the data for each case Figure 25 shows the screen shot of the raw data generated by LabVIEW that will be parsed in LabStation This raw data file will be parsed and put in a CSV extension file so that the results can be imported and stored in LabWare LIMS Figure 26 shows the screen shot of a portion of the parser interface in LabStation Figure 27 shows the screen shot of a portion of the parser interface that includes the test file and the parsing information interface Raw data from Instrument raw Notepad File Edit Format View Help LabVIEW Measurement writer_version 0 92 Relative slakhanp 2006 12 24 20 09 55 319999 wwwend_of_Header 1 1 046164 063221 088534 450563 739451 620418 225149 849606 316901 704882 098681 2122131 82982 404812 345485 712846 556662 966996 553234 2 3 4 5 6 7 8 9 Be 1 1 0 ani 20 0 ide Le 53 57 0 1 2 1832457 Figure 25 Screen shot of the raw data file used with LabStation 40 BE Generic Parser Interface MY_SCRIPT Parsing script used for LabVIEW LIMS Project File Edit Test Options Audit
23. h LabStation to configure the instrument This Instrument is now configured in LabStation Select Instrument 36 Configuration and add the instrument Figure 21 Instrument Type is defined as LABVIEW the source is selected as FILE the instrument holds Jobs parsing script MY_SCRIPT is selected Since the source is defined as File the user also needs to further define the File Instrument Setup In the file instrument setup the full path name for the data file is defined and the polling time is set to 0 Figure 22 Define Instrument al Instrument Type Source FILE Holds Jobs C Samples Setup Parsing Script QiMv_scriPt Filter Script Y Figure 21 Instrument Configuration in LabStation A job is created manually that requests for data These requests are passed along to the instrument queue to await data from the instrument Samples are added to the Job First job samples are assigned to an instrument queue in order to acquire data then the 37 job sample is selected and Assign Raw Data File is selected from the Edit menu Figure 24 This will open a file selection dialog Select the appropriate file and the data is assigned to the selected Job Sample s Now the data is parsed and the status of the Job Sample changes from incomplete to complete The screenshot of the parsing script used is shown in Figure 23 The parsed data is saved in a new fil
24. ined in LabWare LIMS The test analysis DATA is used by default The sample beginning and ending numbers and the file path can be defined on the front panel The result name is also needed to import the results in LIMS In this case the result name is set to default DISPLACEMENT because the calculation is not changing in any case and it s known that displacement results are imported The final form of the data file is shown in Figure 14 The screen shot of the block diagram for this case is shown in Figure 8 19 LabVIEW LIMS VI Block Diagram File Edit View cas Operate Tools Window Help gt a om F gs bal off 13pt Application Font 1 tor Tar ES the case al Result Entry for already logged in samples Default _v P Select Test Analysis EE RingText Text M oe is Baer sane E Pee SAMPLE NUMBER LILET A ANALYSIS RESULT ENTRY Bul Tex tt gt J File with LIMS Headers ll sul a a error out I a RESULT NAME ATT i i displacement a Select Sample Location coco test analysis result name Sample No for Modification E Select Assigned Operator m 72 RingText Text gt Select Sample Customer Belect Test Analysis Select Sample Template EE 1 re Lok Loy pngText Text Select Sample Customer Sample Location z Assigned Operator KDE Select Sample Template RingText Text M Figure 8 Screen shot of the block diagra
25. ion Sample Location Assigned Operator is used to parse the raw data The following field values were entered in the front panel Sample Number for Modification 155 Sample Location Laboratory Assigned Operator System 32 E Modify Sample CSV Notepad File Edit Format view Help SAMPLE SAMPLE_NUMBER SAMPLE LOCATION SAMPLE ASSIGNED_OPERATOR 155 Laboratory System Figure 16 CSV data file for Case 2 Modify Sample The data file shown in figure 16 is imported to LabWare LIMS and the Import Grid is shown in figure 17 There is no Error Message therefore the results are ready to be stored in the LIMS Import File Dialog C Documents and SettingsislakhanpWesktopWModify Sample CSV Sample Sample Number Sample Location Sample Assigned Operator Laboratory Error Message Cancel Figure 17 File Import Grid for Case 2 Modify Sample Figure 18 shows the CSV data file for Case 3 Login Samples Result Entry The following field values were entered in the front panel and where used to parse the raw data 33 Sample Beginning Number 1 Sample Ending Number 25 Sample Template LV_DATA Sample Customer WK316 Test Analysis DATA Result Name Displacement P Log in Samples Result Entry csv Notepad File Edit Format Yiew Help Sample Text_ID Sample Template Sample Customer TEST ANALYSIS RESULT NAME RESULT ENTRY 1 LV_DATA WK316 DATA DISPLACEMENT 0 0000 2 L
26. k diagram is the source code location for executing programs in LabVIEW and is equivalent to text based programming such as C The block diagram has three central parts to its source code nodes wires and terminals This is the site 10 where the wiring of graphical objects or terminals is connected to the functional nodes Terminals are the controls inputs and indicators outputs of the block diagram When compared with written source code nodes are equal to statements functions and subroutines An example of a node may be an addition function or a while loop The addition function is considered a lower level VI It is part of the general purpose LabVIEW library of functions and subroutines for programming tasks Execution of the program with all three nodes terminals and wires can occur when wiring between the terminals and nodes has been connected to designate the flow of data The terminals in the front panel have parallel terminals on the block diagram thereby data continuously flows from the interface in the front panel to the source code in the block diagram and back to the interface Figure 4 illustrates the Function palette in the block diagram Some subpalettes like Instrument I O Structures Numeric Array Boolean etc are subVIs which are used to perform subroutines like opening closing or inserting a database Icon Connector An icon symbolizes a VI in another block diagram When an icon is placed in a foreign
27. ke to dedicate my thesis to them ABSTRACT The main purpose of this project is to automate information management and analysis as well as to integrate different types of data We intend to interface data acquisition DAQ instruments with LIMS by using LabVIEW LabVIEW Laboratory Virtual Instrument Engineering Workbench is graphical programming software from National Instruments NI LabVIEW is the tool of choice due to its unparalleled connectivity to instruments powerful data acquisition capabilities natural dataflow based graphical programming interface scalability and overall function completeness and designed specially for data acquisition NI has many kinds of DAQ instruments that can be used with LabVIEW DAQ VI s LabVIEW programs LabVIEW plug in data acquisition DAQ boards will help perform single point and continuous measurements LabWare LIMS is able to interface to a variety of instruments using LabWare LabStation module Integrated LabStation is used to validate the results The data used and generated by the instruments using LabVIEW will be maintained by a LIMS TABLE OF CONTENTS ACKNOWLEDGEMENTS usina ais 3 ABSTRACT 2 ds AA i 4 TABLE OF CONTENTS 0 AAA tn A A At id 5 TTS ECO FIGURES in ie 6 LIST OF TABLES dadas 7 INTRODUCTION sist 8 BACKGROUND iira pan aia 16 METHODS nailon iaa 18 RESULT PS A aaa 31 CONCLUSION oia AA a AE AA E 44 DISCUSSION iia E gedise iad eoapaasnsaaotadenad nay A at 45 REFERENC O
28. lity The rise of Informatics coupled with the increasing speed and complexity of the analytical instruments is driving more sophisticated data manipulation and warehousing tools that work hand in glove with LIMS to manage and report laboratory data with ever greater accuracy and efficiency Data collection from various instruments is a routine for most of the laboratories The purpose of this thesis project is to create an interface between LabVIEW and LabWare LIMS LabVIEW program will be used to simulate the data from the 16 instrument The raw data will be parsed and thus getting meaningful information that can be stored in LIMS LabStation is also used to parse the same raw data file generated by LabVIEW and therefore validating the results coming from LabVIEW Figure 6 z Dasa Data CSV data file Used with LabStation Stored in Data parsed amp results ee compared Figure 6 Project Outline 17 CHAPTER 3 METHODS LabVIEW Laboratory Virtual Instrument Engineering Workbench LabVIEW version 8 0 was used to build the LabVIEW LIMS VL A LabVIEW program virtual instrument VI is written to produce random data that can be used with LabWare LIMS The VI has two significant parts The first part of the VI creates an example to acquire data from an instrument In the first part the VI calculates the random path and the displacement followed by a particle Figure 7 Figure 7 Block
29. lity studies method development and integration studies Graduate Research Assistant Indiana University August 2005 till present Interfacing LabVIEW driven DAQ instrument with LabWare LIMS Graduate Teaching Assistant Indiana University January 2005 May 2005 Held weekly study sessions grading quizzes in Chemistry Tutor Math Assistance Centre Indiana University January 2005 July 2005 Graduate Engineer Trainee Gurdarshan Leathers Limited India August 2003 June 2004 Design of an effluent treatment plant and the removal of toxics from industrial wastewater Summer Intern Rallis India Ltd India May June 2003 Industrial waste water management system setup of the new waste water recycle system and a brief study of the effects of pesticides pollution in the environment Practical Surveying Training Jagatjit Distilleries Hamira India Jun 2002 Educational Training India International Trade Fair ITF New Delhi India Dec 2002 LABORATORY INFORMATICS PROJECTS Scientific Data Management amp Analysis National Cancer Institute Dataset Database was populated by parsing the records of interest from the files in the dataset the data was then analyzed and visualized using Spotfire LabTrack CyberLab and Waters NuGenesis eLab Notebook was also used LIMS for Gel Electrophoresis of DNA Application of LabWare and LabVantage Sapphire for developing the Gel Electrophoresis LIMS system Programmatically Controlling the Zym
30. lt is added to that test and selected for update The new ad hoc result added to the test will not be reportable It can be made reportable by adding the Result Reportable field to the import file and setting its value to T Case 2 Modify Sample The import parser must distinguish between records that are intended to update information on a sample If the Sample Number is valid then the fields Sample Location Assigned Operator will be updated on the specified sample If the Sample Number is not valid an error will be generated 27 ERROR Analysis in Database Valid for Sample Figure 12 Flow chart representing logic behind importing results using Sample Sample_Number Test Analysis Result Name Result Entry Case 3 Login Samples to Result Entry The flow chart in figure 13 represents the logic behind importing results using Sample Text_Id Sample Template Test Analysis Result Name Result Entry Since in this case the sample does not yet exists proxy identification of the text id for the sample is required in order to specify which records belong to the sample Either its Sample Number or Text ID must identify each sample If the Text ID is valid then all remaining 28 fields will update information on the specified sample These fields can be sample test or result fields If a sample template has been specified then the record will log a new sample If a sample is being logged and a Text ID wa
31. m for Case 1 Result Entry Case 2 Modify Sample This case is selected if the user wants to modify any sample that has already been logged in LabWare LIMS In this case the sample location and or the assigned operator can be modified by defining the sample number Before executing the VI the user needs to define few field values which will be used by the program to parse the raw data so that it is ready to store in LIMS The user needs to define the sample number that is to be modified select the sample location the assigned operator from the list on the front panel and define the file path where the formatted data file will be saved The Sample Locations WK316 and Laboratory Assigned Operator System Swati Lab User are predefined in LabWare LIMS There can be a case where the user wants to modify only the sample location and not the assigned operator In this case the user can select the new 20 sample location from the front panel and keep the assigned operator unchanged No field value can be left blank The screen shot of the block diagram for this case is shown in figure 9 The final form of the data file is shown in figure 16 LabVIEW LIMS VI Block Diagram DER File Edit View Project Operate Tools Window Help gt al OAE bal of 13pt Application Font w Jori 5 i Modify Samples Select Test Analysis m ingText Text gt SAMPLE SAMPLE NUMBER ile with LIMS Headers b 13 L
32. o use program that can login samples modify samples and enter results in LabWare LIMS using one comma separated value data file The user needs to select few field values from the front panel depending on the case selected and then LabVIEW parses the raw data and writes it to a file that is automatically imported and stored in LabWare LIMS Using LabVIEW created CSV data file the user can now continuously enter store results and or update any sample information in the LIMS system automatically By pre defining fields in LIMS viz sample template users customers and other relevant features that can be anchored with the sample information the user can skip all other steps and can directly review approve authorize or reject samples right after importing the results in LIMS The user does not have to follow the standard steps in LIMS and can login samples assign tests enter results modify samples automatically that leads to automated information management The first part of the VI can be replaced by any instrument and can be used in conjunction with the second part of the VI Future Work This project can be continued further by using different instrument integration types RS232 COM Ports in LabStation As mentioned in the discussion this project can be configured as per the requirements mandated by the regulatory agencies 44 CHAPTER 6 DISCUSSION The results demonstrate the utility of LabVIEW to make data files that are c
33. ompatible with LabWare LIMS and hence the results and other sample information can be stored automatically in LIMS system The integrated LabStation by LabWare LIMS is used for the validation of the results from LabVIEW LabStation is used for file based instrument integration to store results in LIMS The raw data generated by LabVIEW is parsed using a parsing script in LabStation and the results are stored in LabWare LIMS The main purpose of using LabStation is to validate the results generated by LabVIEW Also we discuss the user interface and functionalities of these two softwares It is observed that parsing the data in LabVIEW is easier compared to parsing the same data in LabStation The LabStation parser interface offers a huge number of parsing commands However they are not very direct to use and the parsing interface is not very user friendly LabStation is a product of LabWare still there is no command or pre defined parsing script that can be used for any standard instrument integration to make a raw data file into CSV file or ASCII text files and thus compatible with LabWare LIMS The advantage of using LabVIEW is that it is not limited to any number of RS232 connections and can acquire data from a number of instruments at the same time whereas LabStation can acquire data from one instrument at a time Also LabVIEW can interface with any instrument on a network 45 In this project the field values are pre defined in LabWare
34. ort file is added and an ad hoc result is added to that test and selected for update The new ad hoc result added to the test will not be reportable It can be made reportable by adding the Result Reportable field to the import file and setting its value to T It 29 should be made sure that the sample status must not be canceled authorized or rejected for any of the case because no change is permitted to these samples Sample Text Id Valid Template Specified No Yes Analysis Analysis is i No Analysis in Valid de Alias Database Sample Exists Yes Add Test to Sample No Add Ad Hoc Result Yes Result Name Valid Yes Set Result Entry Figure 13 Flow chart representing the logic behind importing results using Sample Text_Id Sample Template Test Analysis Result Name Result Entry No 30 CHAPTER 4 RESULTS LabVIEW amp LabWare LIMS Figure 14 shows the results of the CSV data file for Case 1 Result Entry The information entered in the front panel like Sample beginning number Sample ending number Test Analysis Result Name is used to parse the raw data generated by LabVIEW P Result Entry CSV Notepad File Edit Format View Help SAMPLE SAMPLE_NUMBER TEST ANALYSIS RESULT NAME RESULT ENTRY A 137 DATA DISPLACEMENT 241 8492 138 DATA DISPLACEMENT 255 9301 139 DATA DISPLACEMENT 255 4211 140 DATA DISPL
35. rary of parsing functions that allows users to use a parsing script for each type of instrument interface It also provides a number of pre built parsing scripts for many popular brands of instruments Once the result has been 14 acquired LabStation can apply a user defined set of parsing instructions to parse out the key result information that LIMS is expecting from the instrument 15 CHAPTER 2 BACKGROUND Laboratory Information Management Systems LIMS are information management systems designed specifically for the analytical laboratory This includes research and development R amp D labs in process testing labs quality assurance QA labs and more Originally LIMS were developed in house by organizations wishing to streamline their data acquisition and reporting processes In house developed LIMS take considerable time and resources to implement therefore the need for a more immediate solution helped drive LIMS to the next stage in the 1970s Custom built systems became available during this time and were designed by independent systems development companies to run in specific laboratories These commercial systems while typically developed for a particular industry such as the pharmaceutical industry still required considerable customization to meet a specific laboratory s needs In 1990s open systems emphasizing user configurability were launched Today s commercial LIMS offer a high degree of flexibility and functiona
36. ruments Learning with LabVIEW 7 Express Upper Saddle River NJ Pearson Education Inc 2004 2 An Introduction to LIMS Available http www limsource com intro html 3 LabWare LIMS Customer Support Available http www labware com LWCustomerHomePage NSF 4 LabWare LIMS Version 5 User Guide Available http www labware com LW CustomerHomePage NSF 5 LabStation Version 1 User Manual Available http www labware com LWCustomerHomePage NSF 6 Universal Naming Convention Available http searchwebservices techtarget com sDefinition 0 sid26_ ci214159 00 html 47 APPENDIX SWATI LAKHANPAL 835 Camp Street Phone 317 603 2860 Indianapolis IN 46202 Email slakh11 yahoo com OBJECTIVE To obtain a full time position in Laboratory Informatics EDUCATION Master of Science Chemical Informatics Specialization Laboratory Informatics Indiana University Indianapolis IN GPA 3 90 4 0 Expected graduation December 2006 Thesis Topic Task level programming of Zymate laboratory robot using LabVIEW Bachelor of Engineering Department of Chemical Engineering amp Technology Panjab University Chandigarh India GPA 3 40 4 0 First class Graduation May 2003 Undergraduate Project Removal of Toxics from Industrial Waste Water WORK EXPERIENCE Intern Lab Rat Software Systems Indianapolis September 2006 till present Potential duties include system testing user documentation development usabi
37. s specified this Text ID will be used for the new sample if the sample template contains the Text ID field as a user entry field Otherwise the Text ID is treated as proxy identification for the records in the import file and is only used for that purpose In either case the import parser grid will display the actual Text ID for the new sample If neither Sample Number nor Text ID is specified and a sample template is not specified an error is generated Each test is identified by Test Analysis field In this case Test Analysis is used for the results entry therefore a match is first attempted on the Analysis Names on the sample then on the Alias Names of the Analyses on the Sample Also for the result entry data each result must be identified by the Result Name field Anytime the Result Name is specified a match is first attempted on the result names on the tests assigned to that sample then on the Alias Names of the results on the tests assigned to that sample If the Result Name is not found then the sample is searched for a result that has a result alias that matches the name in the import file If the Result Name does not match any of the existing results on the specified test it is added to the test as an ad hoc result if the matching test has a status of incomplete If the Result Name does not match any of the existing results on the specified test and all matching tests have status of complete then a new test matching the name in the imp
38. t parser must distinguish between records that are intended to update information on a sample If the Sample Number is valid then the fields will be updated on the specified sample If the Sample Number is not valid an error will be generated Similarly when importing the data in the above mentioned format it should be made sure that the test details exist and that the right tests are added to the right sample Each test is identified by Test Analysis field In this case Test Analysis is used for the results entry therefore a match is first attempted on the Analysis Names on the sample then on the Alias Names of the Analyses on the Sample Also for the result entry data each result must be identified by the Result Name field Anytime the Result Name is specified a match is first attempted on the result names on the tests assigned to that sample then on the Alias Names of the results on the tests assigned to that sample 26 If the Result Name is not found then the sample is searched for a result that has a result alias that matches the name in the import file If the Result Name does not match any of the existing results on the specified test it is added to the test as an ad hoc result if the matching test has a status of incomplete If the Result Name does not match any of the existing results on the specified test and all matching tests have status of complete then a new test matching the name in the import file is added and an ad hoc resu
39. ta file for Case 2 Modify Sample eee eeeeeceseeeceeeeeeeeeeeeeeeeeenaeees 33 Figure 17 File Import Grid for Case 2 Modify Sample oooonoconnncnnocanococonncnonocannnonanonanonos 33 Figure 18 CSV data file for Case 3 Login Samples Result Entry oooonoccccnoccccnocccinnnnnos 34 Figure 19 File Import Grid for Case 3 Login Samples Result Entry ooooonnoccccnoccccnnnnos 35 Figure 20 Screen Shot for the Instruments added to LabWare LIMS ieee eee 36 Figure 21 Instrument Configuration in LabStati0N ooooonononnncnonononnnonancnnncnoncnannnona nono ncnns 37 Figure 22 File Instrument Setup in LabStation esessseeseesesesssressersresressersresreeseeseeseresee 38 Figure 23 Parsing Script used to parse the raw data for Case 1 Result Entry 39 Figure 24 Assigning a raw data file to parse in LabStati0M oooccnnnccnnncnooccnonncannnonanonnnonns 39 Figure 25 Screen shot of the raw data file used with LabStation ooooconnccnnncnnnnnnocncnnncnn 40 Figure 26 Screen Shot of the Parser Interface with the Parsing Script used with raw data A cupsao ge anaemia geno tdaca tistiaslaten sees a a gadadeaas S EAN 41 Figure 27 Screen Shot of the Parsing Information from the Parser Interface 42 Figure 28 Parsed raw data file from LabStation for Case 1 Result Entry 43 LIST OF TABLES Table 1 File headers for each of the three cases Table 2 Pre defined fields in LabWare
40. tory for the management of samples standards laboratory users and other laboratory functions LIMS are generally targeted towards environmental research 12 or commercial use viz pharmaceutical or petrochemical The main goal of using LIMS is to create an organization where e Instruments used in the laboratories can be integrated with LIMS and can receive instructions return the results back to LIMS where they can be stored e Laboratory users can perform calculations document and review the results received from integrated instruments and other resources e Management can supervise the laboratory process to ensure the regulatory demands LabWare LIMS LabWare LIMS is a customer configurable LIMS with a variety of optional modules The use of modules allows the LIMS to integrate into any computing environment LabWare LIMS offers major capabilities for pharmaceutical companies that help automate the laboratories It is an object oriented application designed for Windows users It has a built in scripting language called LIMS Basic and therefore allowing the user to configure the extensions It also includes Database Management Utility that allows records to be imported exported to LIMS via CSV files Instrument interfacing is accomplished in LIMS using the built in LabStation module discussed next In this project the LabStation module is used with the LabWare LIMS LabStation The integrated LabStation by LabWare LIMS is used for ins
41. trument integration It is a general purpose instrument interfacing tool that can accept results from almost any type of instrument and enter those results into LIMS automatically or upon user s review and approval The built in instrument integration software assures regulatory compliance 13 issues like 21 CFR Part 11 Title 21 Code of Federal Regulations 21 CFR Part11 applies to records in electronic form that are created modified maintained archived retrieved or transmitted under any records requirements set forth in Agency regulations Part 11 also applies to electronic records submitted to the Agency under the Federal Food Drug and Cosmetic Act the Act and the Public Health Service Act the PHS Act even if such records are not specifically identified in Agency regulations LabStation offers various mechanisms to integrate various instruments to LIMS such as e Serial RS 232 Communications COM ports e File based Import e Reports stored in the NuGenesis Unify Vision Product Version 5 2 or higher Screenshot 12 LABWARE LabWare LIMS for Windows SYSTEM File Configure Run LabStation Utilities Search Help FL EA a Ka ee Figure 5 Screen shot of LabWare LIMS with Integrated LabStation There are fundamentally two types of instruments that can be used with LabWare LIMS LabStation RS232 and file generating instruments In this project file based instrument integration is used LabStation comes with a complete lib
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