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.

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 THEN UPDATE 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 & manipulation Create & 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