Building an End-to-End Informatics System for a Biotech Startup using

Dotmatics

Robert ConerJune 27, 2013

June 27, 20132NOT CONFIDENTIAL

Agenda

• Company Overview• Existing “System”• Replacement with Dotmatics• Future Directions• Q & A

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A Drug Discovery and Development CompanyOncology focused

• Funding• CPRIT: $11M

Company Recruitment, Formation and Relocation Grant

• Venture Capital: $18M

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• World class scientific founder and experienced drug discovery team

• Novel oncology project pipeline based on innovative science

• Strong funding and venture capital support

• CPRIT investment in fundamental biomedical and clinical science

• Commenced operation in August 2011

• Based at the BioCenter in UTSW Dallas

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Experienced Scientific and Business Team

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Multidisciplinary Drug Discovery Team

• 33 employees, 17 Ph.D. level scientists, >100 years drug discovery experience

• Scientific team members have delivered over 20 new chemical entities into human clinical trials

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Experienced Scientific and Business Team

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Multidisciplinary Drug Discovery Team

• 33 employees, 17 Ph.D. level scientists, >100 years drug discovery experience

• Scientific team members have delivered over 20 new chemical entities into human clinical trials

Scientific Advisory BoardRalph J. DeBerardinis, M.D., Ph.D.William G. Kaelin, Jr., M.D. Thomas J. Kelly, M.D., Ph.D.David H. Johnson, M.D., F.A.C.P. Steven L. McKnight, Ph.D.

Board of DirectorsMichael S. Brown, M.D. David V. Goeddel, Ph.D.Tim Kutzkey, Ph.D.John CreecyBrett Ringle, J.D.

Scientific CollaboratorsSally Comerford, Ph.D.Rick Bruick, Ph.D.Kevin Gardner, Ph.D.Robert Hammer, Ph.D.Ben Tu, Ph.D.

ManagementJohn Josey, Ph.D.James Rizzi, Ph.D.Eli Wallace, Ph.D.Michael Bakes, PMP

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Existing “System”

Registry & Materials Inventory in Excel

Data Analysis inGraphpad

Data Shared inPowerPoint and stored on File Share

Paper notebooks for IP capture

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Limitations of Existing System

• Requires chemists to maintain Excel based Registry and Materials Inventory.

• Cannot query data. Have to dig around on the file share for Powerpoints and Excel sheets.

• Paper notebooks need manual countersigning and are required to be scanned to PDF for electronic filing. Cannot easily search and share reaction sketches between experiments.

• Data analysis for biologists is labor intensive. Would spend an entire afternoon analyzing data for a single experiment run.

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Transitioning Registry to Dotmatics

• Convert existing Excel file to SD file– Many structures were embedded as Chemdraw– Some needed to be redrawn by Chemists

• Setup Single Compound Registration form in Dotmatics Register

• Setup Registry Search Form in Browser• Load the initial registry data• Chemists enter new compounds into Register

& Excel sheet is retired

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Single Compound Registration

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Registry Search form in Browser

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Transitioning Data Analysis to Dotmatics

• Setup data analysis protocols in Studies with:– plate formats– data readers– calculations (common ones are built in, e.g. IC50)

• Load legacy data kept in an Excel spreadsheet• Some assays (< 20%) have special processing

requirements. We load these with python scripts into separate database tables.

• Setup Browser forms to query data regardless of source. Browser is very flexible in its configuration options.

June 27, 201312NOT CONFIDENTIAL

Transitioning Data Analysis to Dotmatics

Reduced biology data analysis time from an afternoon to < 30 minutes

1) Enter sample information and select plate format

2) Pick reader and load data file. Verify data mapped OK.

3) Calculate curves and publish data

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Transitioning Data Analysis to Dotmatics

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Transitioning to Chemistry eNotebook

• Decision to not load legacy PDF notebooks. Started with a clean slate in Dotmatics.

• Load SD file of commercial reagents and list of solvents commonly used in the lab

• Configure pre-existing ChemELN Browser project to allow searches of countersigned PDFs. ChemELN will generate these automatically when pages are eSigned.

• Setup separate ChemELN project for chemistry collaborator in China and expose to them via https link. Limits their access to only data that they enter into the system.

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Transitioning to Chemistry eNotebook

• Has very nice convenience features:– Load in previously used reaction schemes, reagents, and

products– Clone pages for new experiments– Reagents and Products sections are automatically populated

from reaction scheme (includes IUPAC names)– Compound registration uses structures from the products of the

reaction sketch– Write up includes macros that refer to IUPAC names. If you

change your structures, then the write up changes automatically to match.

– Easy to switch between eNotebook and Browser– Incorporates analytical attachments into countersigned PDF

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Transitioning to Chemistry eNotebook

Reaction

Reagents

Solvents

Products

Write Up

File Attachments (usually analytical data)

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Summary of Dotmatics Advantages

• One stop shop– One vendor that provides all informatics tools that we need

• Easy deployment– Just need to install Java and a web browser to utilize all functionality

• Thin client– Collaborators in China with low bandwidth can use the system

• Multiplatform– Works on Mac OS and Chrome (and Windows with IE)

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Future Directions

• Materials Inventory & Sample Tracking– Dotmatics is making some requested changes for us

• Biology ELN– Dotmatics is making this work better with Chrome and Mac OS

• Gateway– Use instead of the file share

• Vortex– Some one off use of this (e.g. HTS data analysis), would like to use it

more

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Q & A