1. Building an End-to-End Informatics System
for a Biotech Startup using Dotmatics
Robert Coner
June 27, 2013

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Agenda
• Company Overview
• Existing “System”
• Replacement with Dotmatics
• Future Directions
• Q & A
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A Drug Discovery and Development Company
Oncology 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 Board
Ralph 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 Directors
Michael S. Brown, M.D.
David V. Goeddel, Ph.D.
Tim Kutzkey, Ph.D.
John Creecy
Brett Ringle, J.D.
Scientific Collaborators
Sally Comerford, Ph.D.
Rick Bruick, Ph.D.
Kevin Gardner, Ph.D.
Robert Hammer, Ph.D.
Ben Tu, Ph.D.
Management
John 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 in
Graphpad
Data Shared in
PowerPoint 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.

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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