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Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

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Page 1: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Software Architecture to Support The Compound Discovery

Process

Mike Richards

Senomyx, Inc.

MUG 2003

Page 2: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

We track all aspects of the compound discovery process

• Virtual library creation

• Chemical Synthesis

• Chemical Transfer

• Chemical Storage

• Chemical Availability

• Ordering/Purchasing

• Literature Information

• Analytical Results

• ALL Screening Results

• DNA Sequence

• Vectors/Constructs

• Transfections

• Cell Culture Media (lot#)

• Cell line history/lineage

• Cell Passage/Transfer

• Cell Storage

• Freeze Thaw cycles

• ALL Screening Results

Page 3: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Tracking and running the discovery process leads to a large

amount of complex data.

Tracking and running the discovery process leads to a large

amount of complex data.

Page 4: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

How to give users web access to all the data:

• Browse and navigate the entire database via the web• Chemical list query & manipulation tools• Extensible Chemical list viewer • Integrated Spotfire Data Viewing• Task oriented reporting tools (to be phased out).

Page 5: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Browse and navigate the entire database via the web

• All items are given a number (barcode) from the same numeric sequence

• Barcodes used as Primary Key in database

Page 6: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Browse and navigate the entire database via the web

• Single Lookup table (Senobase.WhatIsIt) can identify an item.

• Lookup Table maintained by Triggers on item tables

• Lookup table references table name and URL for describing an item

• Item ID passed in URL through query string

• One central web application directs requests to correct location based on information in WhatIsIt.

CREATE OR REPLACE TRIGGER TU_PROJECTS AFTER UPDATE OR INSERT ON SENOBASE.PROJECTS FOR EACH ROW

DECLARE CT NUMBER;BEGIN

/*test for existence */SELECT COUNT(PC_SEQ_ALL) INTO CT FROM SENOBASE.WHATISIT WHERE PC_SEQ_ALL = :new.P_PROJECT_ID;

IF CT > 0 THENUPDATE SENOBASE.WHATISIT SET PC_INFORMATION_ID = 26, PC_REQUESTOR_ID = 28, PC_DATE = SYSDATE,

PC_APP_NAME = 'TU_PROJECTS'WHERE PC_SEQ_ALL = :new.P_PROJECT_ID;

ELSE INSERT INTO SENOBASE.WHATISIT(PC_SEQ_ALL,

PC_INFORMATION_ID, PC_REQUESTOR_ID, PC_DATE, PC_APP_NAME)

VALUES (:new.P_PROJECT_ID, 27, 28, SYSDATE, 'TU_PROJECTS'); END IF;END TU_PROJECTS;

Page 7: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Browse and navigate the entire database via the web

• All Links redirect through the lookup application using WhatIsIt

• Tables Without defined interfaces are represented in table form

• A web tool can be changed or inserted by updating one URL in the database.

Page 8: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Browse and navigate the entire database via the web

Page 9: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Chemical list query & manipulationCreate & Filter chemical lists

Page 10: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Extensible Chemical List Viewer• Column list is a collection of classes

with same interface• Allows great flexibility in column

format and sorting tools.

Page 11: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Extensible Chemical List Viewer• User can configure displayed columns

Page 12: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Extensible Chemical List Viewer• Allows for sorting by column• Sort order is property of list

Page 13: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Extensible Chemical List Viewer

• Export Functions for Presentations:• Export to Excel with structures (Thanks Alberto!)

• Export to TDT for Merlin

Page 14: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Spotfire Integration• Web Install• Server-Side Website writes pages with

Client JS that controls spotfire (Decision Site Navigator).

• Custom Templates for each data View.• Imbedded HTML in Template makes

“Details-on-Demand” show Daylight chemical structures and raw data images.

Page 15: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003
Page 16: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Task Oriented Reporting Tools:

Page 17: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Task-Oriented Reporting tools:

• Adopted for quick solutions.• Too inflexible, only serve 1 need.• Continual revision, upgrade, change becomes a

maintenance nightmare.• Tools do not leverage other display options like

ListViewer, Excel Export, Spotfire Viewing.• Plan to replace many tools with one query

reporting application.

Page 18: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Summary:Generic system-wide viewing tools have allowed the users to display the data THEY needed, not the data WE guessed they wanted.

Because the users could get to the data (somehow) we reduced the number of “emergency” projects to display data for an immediate need.

Canned query & display tools lead grow towards a specific need, reducing their utility in other applications.

Page 19: Software Architecture to Support The Compound Discovery Process Mike Richards Senomyx, Inc. MUG 2003

Acknowledgments

Joseph Cohen

Maya Binun

Kun Wang

TJ O’Donnell

Hanghui Liu

Klaus Gubernator