AUTOMATION OF DT LAB    WORKFLOWS  By Avetis Ghukasyan (Avo)
OUTLINE   Background       Myself       Project       Data Chart   Projects       NMR           GLUE Software      ...
BACKGROUND   Myself     Junior studying Computer Science at Wentworth      Institute of Technology     Interested in bi...
BACKGROUND - DATA CHARTCatego   Program/Script                Description               Technologies  ry                  ...
GLUE SOFTWARE - BACKGROUND(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)   fragment screening: a process of mixing va...
GLUE SOFTWARE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)Problem                                       Solution     ...
GLUE SOFTWARE - WORKFLOW(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)
GLUE SOFTWARE - USER INTERFACE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)
GLUE OVERLORD(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)Problem                         Solution                   ...
SOLUBILISE METHODAddition of DMSO to compound powders; one of the steps in the DMSOstock solution creation procedure.     ...
MATRIX RACK MERGERDetection and calculation of remaining volumes of DMSO stocksolutions in barcoded Matrix rack tubes.Prob...
PROJECT ALIQUOTERDispensing and dilution of DMSO liquid samples.Problem                      Solution                     ...
PROJECT ALIQUOTER WORKFLOW - 3000 FEET VIEW                InputsValidate Source Plates  Validate Dest Plates       Choose...
PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs          Validate Destination Plates Validate Source Plates   Decide on S...
PROJECT ALIQUOTER – 30 FEET VIEWInputs                       • Browsing for a Mosaic control file                       • ...
PROJECT ALIQUOTER – 30 FEET VIEWValidateSourcePlates                        • Validating source barcodes against          ...
PROJECT ALIQUOTER – 30 FEET VIEWValidateDestinationPlates                          • If defrosting is selected then valida...
PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs          Validate Destination Plates Validate Source Plates   Decide on S...
PROJECT ALIQUOTER – 30 FEET VIEW                   Choose Method/Decide on Solution                   • If source plates d...
PROJECT ALIQUOTER – 30 FEET VIEW                     • Puts all source plates on Tecan deck                       (sources...
PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs          Validate Destination Plates Validate Source Plates   Decide on S...
PROJECT ALIQUOTER – 30 FEET VIEW                           • Puts one source plate and one destination                    ...
PROJECT ALIQUOTER – 1 FOOT VIEWLow Level View – Workflow – Destination Plate Check
CHALLENGES Getting used to new programming environment and  its rules Adapting scripts to changes Adapting/learning how...
CHALLENGES (CONTINUE)   Making workflow/scripts flexible       Problem         Code is nothing but a translation of an ...
CHALLENGES (CONTINUE)   Making workflow/scripts flexible       Example         One of the examples is the predefined la...
LESSONS Schools do not teach C# so I am glad I got to write  almost 20000 lines of code in MV C# 2008 Express Working wi...
THANK YOU!Do you have any questions?Are there any comments?
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Automation of Discovery Technology Lab Workflows

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This presentation is a quick overview of all of my projects for Cubist Pharmaceuticals while I was working as an intern. I have worked on 5 projects for automating discovery technologies lab workflows and all of them are described in full detail in this presentation.

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Automation of Discovery Technology Lab Workflows

  1. 1. AUTOMATION OF DT LAB WORKFLOWS By Avetis Ghukasyan (Avo)
  2. 2. OUTLINE Background  Myself  Project  Data Chart Projects  NMR  GLUE Software  GLUE Overlord Workflow  Compound Management  Solubilise Method  Matrix Rack Merger  Project Aliquoter Challenges Lessons Questions/Comments
  3. 3. BACKGROUND Myself  Junior studying Computer Science at Wentworth Institute of Technology  Interested in bioinformatcis, cheminformatics, and medical informatics  Worked at MAVERIC for almost a year designing scripts for data mining software Project  Automating processes that were being done manually  Making programs/workflows user friendly and flexible  Reducing human error and making processes more efficient
  4. 4. BACKGROUND - DATA CHARTCatego Program/Script Description Technologies ry UsedNMR GLUE Software Integration and automation of C# fragment screeningNMR GLUE Overlord Integration and automation of C#, Overlord, fragment screening – overlord Automap, Tecan workflow CM Solubilise Method One of the steps in the DMSO Tecan, VBScript stock solution creation procedure CM Matrix Rack Detection and calculation of C#, Overlord, Merger remaining volumes of DMSO Automap, Tecan stock solutions in barcoded Matrix rack tubes CM Project Aliquoter Dispensing and dilution of DMSO C#, Overlord, liquid samples Automap, Tecan
  5. 5. GLUE SOFTWARE - BACKGROUND(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING) fragment screening: a process of mixing various compounds with an enzyme and recording the compounds that stick to it (recording the hits). Since the compounds being mixed with the enzyme are very small a sensitive method is needed to detect the hits. One of the most common fragment screening methods employs NMR . This method is very effective but the downfall is that it can be slow. One way to go around it is with the process of pooling (pool size 4-24). The bigger the pool size the fewer times one has to run the NMR, however the bigger the pool size the more time one has to spend deconvoluting the sample made from all the compounds. The whole process of fragment screening can approximately take up to 10 days or more. It includes a lot of manual labor mainly when preparing the samples.
  6. 6. GLUE SOFTWARE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)Problem Solution Lines• Manually create sample tracking • Automatically create sample 7893sheets, run files tracking sheets, run files C#• Pool and analyze data in a very limited • Automatically pool and allowway for data analysis• Process data in Excel • Process data in an SDF fileBenefit• Click a button which automatically cuts down accidental user errors. Days of workbecomes minutes of automation• Uses/manipulates SDF files instead of Excel files which adds a lot more flexibility• Has a built-in project manager which organizes SDF files, sample tracking sheets,runs files in a very easily accessible manner• All of the data analysis, sample tracking files, follow-up files are saved in the specifiedfolders
  7. 7. GLUE SOFTWARE - WORKFLOW(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)
  8. 8. GLUE SOFTWARE - USER INTERFACE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)
  9. 9. GLUE OVERLORD(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)Problem Solution Lines• Perform pooling manually • Design a set of scripts and a workflow 1909 C# inbased on CSV files within the Overlord to be able to OSC automate the pooling processBenefit• Instead of pipetting manually set up the workflow, run it and then walk away until it isfinished List of Features • Barcodes/no barcodes • Lays out destinations on deck and gets source plates one at a time
  10. 10. SOLUBILISE METHODAddition of DMSO to compound powders; one of the steps in the DMSOstock solution creation procedure. Problem Solution Lines• Converting Mosaic output • Designing a script that automatically converts 294 offile into Tecan worklist a Mosaic output file into a Tecan worklist VBS inmanually GSCBenefit• Automatically generates worklist from Mosaic file• Error check on rack barcodes• Reduce human error Gemini Script Component (GSC)
  11. 11. MATRIX RACK MERGERDetection and calculation of remaining volumes of DMSO stocksolutions in barcoded Matrix rack tubes.Problem Solution Lines• Merge CSV files • Design a set of scripts that update fields 258 C#• Update fields based on a based on a formula in OSCformula • Detect any errors based on the positioning• Detect errors manually of the tubes in the matrix rack • Be able to handle 12 racksBenefit• MRMerger Method can handle processing up to 12 racks on the Automap in one run.• Allows the user to walk away during processing• Adds efficiency and removes user error by doing the file processing automatically. Overlord Script Component (OSC)
  12. 12. PROJECT ALIQUOTERDispensing and dilution of DMSO liquid samples.Problem Solution Lines• Each plate had to be • Design a set of scripts and multiple 9875 C# indispensed/diluted manually workflows within to automate the OSCor by operating Tecan process for multiple plates.separately • Defrost• Each plate is run • Cap/de-cap/sealseparately • Scan 2D barcodes, scan 1D barcodes • Check/handle errors • Show virtual graphs of plate maps • Make it flexible so it handles all kinds of platesBenefit• Biggest advantage is that one could actually walk away from the run after settingeverything up which only takes a couple of minutes• What could have been done manually in 2 hours could be achieved automatically in30 minutes (person does not need to be there only for setup)
  13. 13. PROJECT ALIQUOTER WORKFLOW - 3000 FEET VIEW InputsValidate Source Plates Validate Dest Plates Choose Method Solution Case 1 Solution Case 2
  14. 14. PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs Validate Destination Plates Validate Source Plates Decide on Solution Solution Case 1 Solution Case 2
  15. 15. PROJECT ALIQUOTER – 30 FEET VIEWInputs • Browsing for a Mosaic control file • Deciding/Selecting if defrosting is needed • Loading required plates onto hotels
  16. 16. PROJECT ALIQUOTER – 30 FEET VIEWValidateSourcePlates • Validating source barcodes against barcodes listed in Mosaic control file • Recording positions of source plates
  17. 17. PROJECT ALIQUOTER – 30 FEET VIEWValidateDestinationPlates • If defrosting is selected then validate destination plate barcodes and defrost source plates simultaneously • If defrosting is not selected then only validate destination plate barcodes
  18. 18. PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs Validate Destination Plates Validate Source Plates Decide on Solution Solution Case 1 Solution Case 2
  19. 19. PROJECT ALIQUOTER – 30 FEET VIEW Choose Method/Decide on Solution • If source plates do not need to be capped/decapped go to Case 1 • If source plates need to be capped/decapped go to Case 2 • Flexible in a way so that if more solutions are needed one can easily do so
  20. 20. PROJECT ALIQUOTER – 30 FEET VIEW • Puts all source plates on Tecan deck (sources do not need capping/decapping) • Iterates through destination plates and process them one by oneSolution Case 1
  21. 21. PROJECT ALIQUOTER – 30 FEET VIEW Required Inputs Validate Destination Plates Validate Source Plates Decide on Solution Solution Case 1 Solution Case 2
  22. 22. PROJECT ALIQUOTER – 30 FEET VIEW • Puts one source plate and one destination plate on Tecan deck (source plate needs capping/decapping) • Processes them individually Solution Case 2
  23. 23. PROJECT ALIQUOTER – 1 FOOT VIEWLow Level View – Workflow – Destination Plate Check
  24. 24. CHALLENGES Getting used to new programming environment and its rules Adapting scripts to changes Adapting/learning how to communicate with scientists Learned about the limitations of hardware Making workflow/scripts flexible
  25. 25. CHALLENGES (CONTINUE) Making workflow/scripts flexible  Problem  Code is nothing but a translation of an algorithm. With any outside change algorithm changes as well  Update codes to new hardware  Average computer users can not change the code so one always needs a programmer around  Solution  Use external files which reflect the outside change then feed the files into the algorithm/code  Any person can change the file because no programming knowledge is required  Files reflect the change and algorithm will recognize the change from the files
  26. 26. CHALLENGES (CONTINUE) Making workflow/scripts flexible  Example  One of the examples is the predefined labware type file which includes all of the labware type + information about them  When a new labware is added there is no need for a programmer to change the code – file reflects the change and is fed into the algorithm
  27. 27. LESSONS Schools do not teach C# so I am glad I got to write almost 20000 lines of code in MV C# 2008 Express Working with million dollar equipment raised my confidence Learned about Overlord and Gemini software environments which are widely used Never before have I tackled a project on which I worked for over 3 months in real world Making code flexible so that changes do not require a lot of effort
  28. 28. THANK YOU!Do you have any questions?Are there any comments?

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