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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
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.
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).
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
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;
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.
Browse and navigate the entire database via the web
Chemical list query & manipulationCreate & Filter chemical lists
Extensible Chemical List Viewer• Column list is a collection of classes
with same interface• Allows great flexibility in column
format and sorting tools.
Extensible Chemical List Viewer• User can configure displayed columns
Extensible Chemical List Viewer• Allows for sorting by column• Sort order is property of list
Extensible Chemical List Viewer
• Export Functions for Presentations:• Export to Excel with structures (Thanks Alberto!)
• Export to TDT for Merlin
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.
Task Oriented Reporting Tools:
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.
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.
Acknowledgments
Joseph Cohen
Maya Binun
Kun Wang
TJ O’Donnell
Hanghui Liu
Klaus Gubernator
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