2015_May Dotmatics UGM Bob Coner
Transcript of 2015_May Dotmatics UGM Bob Coner
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Extending Dotmatics Functionality With Exe Runner and Studies
Robert ConerMay 2015
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May 20152NOT CONFIDENTIAL
Agenda
• Company Overview• Extending Dotmatics Overview• Examples
– Docking– MS Word Patent Tables– Data Loading
• Implementation Details• Q & A
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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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May 20155NOT CONFIDENTIAL
How can dotmatics be extended?
Studies Forms
Database Trigger
Exe Runner starts
Job Controller
Execute JobInsert Results into Database(Data Loading)
Dotmatics Pivoter
(Data Loading)
Email Job Status and Results to
User
Results available in
Browser(Data Loading)
Dotmatics Custom (Python)Legend:
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Example: Docking with Schrodinger’s Glide
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May 20157NOT CONFIDENTIAL
Example: Docking with Schrodinger’s Glide
Link to results (Pymol .mae file) delivered in email
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Example: Docking with Schrodinger’s Glide
Open mae file in PyMol
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Example: Generating Tables for Patents
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Example: Generating Tables for Patents
Link to generated MS word documents arrives in email
Example output
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Example: Loading Data
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Example: Loading Data
View uploaded results in Browser
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May 201513NOT CONFIDENTIAL
What is Exe Runner?
For Linux,you need a shellscript to wrap thecall to python
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How are the studies forms setup?
TRIGGER "DS3_USERDATA"."PTX_DOCKING_TRIGG" AFTER INSERT OR UPDATE ON PTX_DOCKING_TRIGGER FOR EACH ROWDECLARE EID VARCHAR(20) := :NEW.EXPERIMENT_ID; JOBNUM INTEGER;BEGIN SELECT PTX_EXE_RUNNER_JOB_ID_SEQ.nextval into JOBNUM FROM DUAL; --GET NEW JOB NUMBER INSERT INTO DS3_USERDATA.PTX_EXE_RUNNER_JOB(EXPERIMENT_ID,JOBID,TYPE) VALUES (EID,JOBNUM,'DOCKING'); -- CREATE JOB INSERT INTO DS3_APPDATA.EVENT_TRIGGER(EVENT) VALUES ('COMMANDER'); -- START DOT EXE RUNNER TO EXECUTE JOBEND;
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Configuring Pulldowns
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How are jobs managed?
Jobs are created by the trigger and then picked up and executed by the Exe Runner
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Pivoting data
(SELECT PTNUMBER, RESULT_NUMERIC, ASSAYNAMETYPE, RESULT_ALPHA, ITC_N, CREATION_DATE FROM PTX_BIODATA_HIF2_VW ) PIVOT ( MAX(result_alpha) AS ALPHA, AVG(result_numeric) AS NUMERIC, stddev(result_numeric) AS STDDEV, listagg(ITC_N,' ') WITHIN GROUP (ORDER BY ITC_N) AS ITC_N, COUNT(result_numeric) AS COUNT, MAX(CREATION_DATE) AS MAXDATE FOR ASSAYNAMETYPE IN ('786-O Cell VEGF Elisa 10uM' AS ELISA_10, '786-O Cell VEGF Elisa 2.5uM' AS ELISA_2p5, 'ITC ' AS ITC, 'VEGF ELISA 786-O' AS VEGF_ELISA,'ALPHASCREEN ' AS ALPHASCREEN,'Luciferase ' AS LUCIFERASE, 'SPA ' AS SPA ) )
Some datasets are loaded into unpivoted tables and need to be pivoted for Browser.
Don’t use Oracle Pivots (example below). Use the Dotmatics Pivot Engine...
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Dotmatics Pivoter
Instead of trying to write SQL, point and click
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May 201519NOT CONFIDENTIAL
Example Pivot
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Dotmatics Pivoter converts from this
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To this
Data here is output of Dotmatics Pivoter
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Summary
• DotExeRunner – Can execute custom code for you• Oracle Triggers – Can be used to insert data into database and
force ExeRunner (and Dotmatics Pivoters) to run as you need• Studies Forms – Provide a user interface to pass information
to your custom code• Dotmatics Pivot Engine – If you have unpivoted data tables,
this is much better than using Oracle Pivots.
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Acknowledgments
Peloton Therapeutics, Inc. DotmaticsZhaodan CaoTzuling ChengRobert CzerwinskiDarryl DixonXilin DuBarry GogginJonas GrinaMegan HalfmannGuangzhou HanHeli HuangJohn Josey
Melissa MaddieSarah OliveJames RizziStephen SchlachterHuiling TanBin WangKeshi WangPaul WehnShanhai XieRui XuHanbiao Yang
Alister CampbellPhil MounteneyDan Ormsby
Jason CastanadaShikha O’BrienTheresa 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: robertdconer