AUTOMATION OF DT LAB WORKFLOWS

By Avetis Ghukasyan (Avo)

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

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

BACKGROUND - DATA CHART

Category

Program/Script

Description Technologies Used

NMR GLUE Software Integration and automation of fragment screening

C#

NMR GLUE Overlord Integration and automation of fragment screening – overlord workflow

C#, Overlord, Automap, Tecan

CM Solubilise Method

One of the steps in the DMSO stock solution creation procedure

Tecan, VBScript

CM Matrix Rack Merger

Detection and calculation of remaining volumes of DMSO stock solutions in barcoded Matrix rack tubes

C#, Overlord, Automap, Tecan

CM Project Aliquoter Dispensing and dilution of DMSO liquid samples

C#, Overlord, Automap, Tecan

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.

GLUE SOFTWARE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)

Problem Solution Lines

• Manually create sample tracking sheets, run files• Pool and analyze data in a very limited way• Process data in Excel

• Automatically create sample tracking sheets, run files• Automatically pool and allow for data analysis• Process data in an SDF file

7893 C#

Benefit

• Click a button which automatically cuts down accidental user errors. Days of work becomes 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 specified folders

GLUE SOFTWARE - WORKFLOW(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)

GLUE SOFTWARE - USER INTERFACE(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)

Problem Solution Lines

• Perform pooling manually based on CSV files

• Design a set of scripts and a workflow within the Overlord to be able to automate the pooling process

1909 C# in OSC

GLUE OVERLORD(INTEGRATION AND AUTOMATION OF FRAGMENT SCREENING)

Benefit

• Instead of pipetting manually set up the workflow, run it and then walk away until it is finished

List of Features

• Barcodes/no barcodes• Lays out destinations on deck and gets source plates one at a time

SOLUBILISE METHOD

Problem Solution Lines

• Converting Mosaic output file into Tecan worklist manually

• Designing a script that automatically converts a Mosaic output file into a Tecan worklist

294 of VBS in GSC

Addition of DMSO to compound powders; one of the steps in the DMSO stock solution creation procedure.

Benefit

• Automatically generates worklist from Mosaic file• Error check on rack barcodes• Reduce human error

Gemini Script Component (GSC)

MATRIX RACK MERGER

Problem Solution Lines

• Merge CSV files• Update fields based on a formula• Detect errors manually

• Design a set of scripts that update fields based on a formula• Detect any errors based on the positioning of the tubes in the matrix rack• Be able to handle 12 racks

258 C# in OSC

Detection and calculation of remaining volumes of DMSO stock solutions in barcoded Matrix rack tubes.

Benefit

• 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)

PROJECT ALIQUOTERDispensing and dilution of DMSO liquid samples.

Problem Solution Lines

• Each plate had to be dispensed/diluted manually or by operating Tecan separately• Each plate is run separately

• Design a set of scripts and multiple workflows within to automate the process for multiple plates.• Defrost• Cap/de-cap/seal• Scan 2D barcodes, scan 1D barcodes• Check/handle errors• Show virtual graphs of plate maps• Make it flexible so it handles all kinds of plates

9875 C# in OSC

Benefit

• Biggest advantage is that one could actually walk away from the run after setting everything up which only takes a couple of minutes• What could have been done manually in 2 hours could be achieved automatically in 30 minutes (person does not need to be there only for setup)

PROJECT ALIQUOTER WORKFLOW - 3000 FEET VIEW

Inputs

Validate Source Plates

Validate Dest Plates

Choose Method

Solution Case 1 Solution Case 2

Required InputsValidate Source Plates

Validate Destination PlatesDecide on SolutionSolution Case 2Solution Case 1

PROJECT ALIQUOTER – 30 FEET VIEW

PROJECT ALIQUOTER – 30 FEET VIEW

• Browsing for a Mosaic control file• Deciding/Selecting if defrosting is needed

• Loading required plates onto hotels

Inputs

• Validating source barcodes against barcodes listed in Mosaic control file

• Recording positions of source plates

PROJECT ALIQUOTER – 30 FEET VIEW

Validate Source Plates

PROJECT ALIQUOTER – 30 FEET VIEW

• 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

Validate Destination Plates

Required InputsValidate Source Plates

Validate Destination PlatesDecide on SolutionSolution Case 2Solution Case 1

PROJECT ALIQUOTER – 30 FEET VIEW

PROJECT ALIQUOTER – 30 FEET VIEW

• 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

Choose Method/Decide on Solution

PROJECT ALIQUOTER – 30 FEET VIEW

Solution Case 1

• Puts all source plates on Tecan deck (sources do not need capping/decapping)

• Iterates through destination plates and process them one by one

Required InputsValidate Source Plates

Validate Destination PlatesDecide on SolutionSolution Case 2Solution Case 1

PROJECT ALIQUOTER – 30 FEET VIEW

PROJECT ALIQUOTER – 30 FEET VIEW

Solution Case 2

• Puts one source plate and one destination plate on Tecan deck (source plate needs capping/decapping)• Processes them individually

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 to communicate with

scientists Learned about the limitations of hardware Making workflow/scripts flexible

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

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

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

THANK YOU!

Do you have any questions?Are there any comments?