2016_May Dotmatics UGM Bob Coner
Transcript of 2016_May Dotmatics UGM Bob Coner
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4 Years In – How A Biotechnology Company Has Grown In Its Use Of
Dotmatics
Robert ConerMay 2016
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May 20162NOT CONFIDENTIAL
Agenda
• Where we started• How we use Dotmatics now
– Design– Synthesis & Purification– Sample Logistics– Screening/Testing
• Extending Dotmatics Example
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A Drug Discovery and Development CompanyOncology focused
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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
• Commenced operation in August 2011• Based at the BioCenter in UTSW Dallas• More information at
http://pelotontherapeutics.com
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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 BoardMichael S. Brown, M.D. 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 DirectorsJohn CreecyDavid V. Goeddel, Ph.D.Leo Guthart, Ph.D.Tim Kutzkey, Ph.D.Frank McCormick, Ph.D.Brett 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, PMPNaseem Zojwalla, M.D.Tai Wong, Ph.D.
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Where we started
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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Transitioning to Dotmatics
• Convert existing Excel file to SD file and Load with Register
• Start using ChemELN and Register compounds from there
• Setup assay data analysis protocols and start using Studies. Use BioELN to capture experiments.
• Use Browser to query and analyze data
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Growth over time
• Use Nucleus to load HTS data and Vortex to analyze
• Added new projects• Added new assay data analysis protocols• “Side loaded” DMPK data• Barcode all reagent and sample containers
and use Inventory to manage location• Add custom extensions
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Design Synthesis/Purification
Materials/Sample logisticsScreening/Testing
• Procure materials
• Synthesize
• Purify/characterize
• Prepare Sample
• Dissolve
• Dilute
• Distribute to screen
• Reduce raw data• Execute screen
• Develop the assay
• Select compounds to make
• Mine, search and invent analogs
• Analyze patternsProject Workflow & Tracking and
Decision making
• Assess design ideas
• Load data to dbs
• Procure reagents
Discovery Cycle
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Initial load of HTS data
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Initial load of HTS data
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Initial load of HTS data
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Initial load of HTS data
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Initial load of HTS data
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Analyze HTS data in Vortex
Next step: Resynthesize & test the hits…
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Synthesis - ChemELN
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Synthesis - ChemELN
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Compound Registration – from ChemELN
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Sample Logistics
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Materials Management
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Assay Data Processing and Publishing
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Assay Data Processing and Publishing
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Assay Data Processing and Publishing
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Assay Data Processing and Publishing
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Design – Analyze Data
Multiple tabs – all data in one place
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Design – Analyze PK data (from Winnonlin)
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Design – Analyze Stability Data
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Behind the Scenes
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Dotmatics Pivoter
Instead of trying to use Oracle’s PIVOT statement, you point and click
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Example Pivot
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Dotmatics Pivoter converts PK data from this
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To this
Data here is output of Dotmatics Pivoter
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Extending Dotmatics Example
• Several of our chemists came from other companies that had a method for automatically adding analytical data to their notebooks
• Requirements: - Take no longer than 24 hours to add spectra to Dotmatics after creation- Exclude certain spectra from being added- Indicate which spectra goes with which notebook and page- Work for both LC and NMR instruments- Never add spectra to a closed notebook page- Never add a spectra that has been removed manually from a page
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Analytical instrumentation setup
Agilent LCMS
Agilent LC
Agilent NMR
Replication scripts
run twice daily
Windows File Share
Backup at Offsite Data
Center
Dotmatics Server
DotmaticsELN
Analytical attachment script runs once per day
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May 201634NOT CONFIDENTIAL
Extending Dotmatics Example
• Several of our chemists came from other companies that had a method for automatically adding analytical data to their notebooks
• Requirements: ✓ Take no longer than 24 hours to add spectra to Dotmatics after
creation- Exclude certain spectra from being added- Indicate which spectra goes with which notebook and page- Work for both LC and NMR instruments- Never add spectra to a closed notebook page- Never add a spectra that has been removed manually from a page
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Agilent NMR
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Agilent LC
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Extending Dotmatics Sample
• Several of our chemists came from other companies that had a method for automatically adding analytical data to their notebooks
• Requirements: ✓ Take no longer than 24 hours to add spectra to Dotmatics after creation ✓ Exclude certain spectra from being added
✓ Indicate which spectra goes with which notebook and page ✓ Work for both LC and NMR instruments
- Never add spectra to a closed notebook page - Never add a spectra that has been removed manually from a page
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Processing Algorithm
• Python script runs periodically (using cron) on our Dotmatics server
• It walks the directory tree of the shared folder that contains all of our analytical data
• For each analytical pdf:– A SHA512 hash is calculated for the pdf and checked vs. the database, if found,
pdf is skipped. If not found, hash added to database.– Filename of pdf is analyzed to look for a notebook-page pattern. If not found,
skipped.– Using notebook and page, experiment is located in TM_EXPERIMENTS table
and EXPERIMENT ID extracted. If experiment is closed or not found, skip.– PDF is added to ELN_QCDATA table with EXPERIMENT ID– Studies ChemELN will read the PDF from the ELN_QCDATA table when the
experiment is opened
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Table to record hashes of analytical pdfs
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ELN_QCDATA table
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CHEMELN page example
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Overview
• Several of our chemists came from other companies that had a method for automatically adding analytical data to their notebooks
• Requirements: ✓ Take no longer than 24 hours to add spectra to Dotmatics after creation ✓ Exclude certain spectra from being added
✓ Indicate which spectra goes with which notebook and page ✓ Work for both LC and NMR instruments ✓ Never add spectra to a closed notebook page ✓ Never add a spectra that has been removed manually from a page
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Summary of Dotmatics
• Grows with us• Supports the Discovery Cycle• Can be extended
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Acknowledgments
Peloton Therapeutics, Inc. DotmaticsZhaodan CaoTzuling ChengRobert CzerwinskiXinlin DuBarry GogginJonas GrinaGuangzhou HanHeli HuangJohn Josey
James RizziStephen SchlachterHuiling TanBin WangKeshi WangPaul WehnShanhai XieRui XuHanbiao Yang
Alister CampbellPhil MounteneyDan Ormsby
Jason CastanadaTheresa Smith
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Q & A
• Contact Information:– Robert Coner– Peloton Therapeutics– Manager, R&D Informatics– 2330 Inwood Drive, Suite 226, Dallas, TX 75235– [email protected]– Phone: +1-469-271-7811– https://www.linkedin.com/in/bobconer– Skypeid: conerbob