1. Extending Dotmatics Functionality With
Exe Runner and Studies
Robert Coner
May 2015

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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 Company
Oncology 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 Board
Michael 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 Directors
John Creecy
David V. Goeddel, Ph.D.
Leo Guthart, Ph.D.
Tim Kutzkey, Ph.D.
Frank McCormick, Ph.D.
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
Naseem Zojwalla, M.D.
Tai Wong, Ph.D.

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How can dotmatics be extended?
Studies
Forms
Database
Trigger
Exe Runner
starts
Job Controller
Execute Job
Insert 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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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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What is Exe Runner?
For Linux,
you need a shell
script to wrap the
call 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 ROW
DECLARE
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 JOB
END;

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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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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. Dotmatics
Zhaodan Cao
Tzuling Cheng
Robert Czerwinski
Darryl Dixon
Xilin Du
Barry Goggin
Jonas Grina
Megan Halfmann
Guangzhou Han
Heli Huang
John Josey
Melissa Maddie
Sarah Olive
James Rizzi
Stephen Schlachter
Huiling Tan
Bin Wang
Keshi Wang
Paul Wehn
Shanhai Xie
Rui Xu
Hanbiao Yang
Alister Campbell
Phil Mounteney
Dan Ormsby
Jason Castanada
Shikha O’Brien
Theresa 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
– robert.coner@pelotontx.com
– Phone: +1-469-271-7811
– https://www.linkedin.com/in/bobconer
– Skypeid: robertdconer
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