Cost effective Cheminformatics for Small Chemistry Teams Integrated Within Larger Discovery Groups

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1 Cost effective Cheminformatics for Small Chemistry Teams Integrated Within Larger Discovery Groups John McNeil September 15, We make tools to help bench scientists be more productive, efficient, and creative. Invent solutions Integrate Technology Manage IT Bioinformatics 2

2 LabSynch Overview Objectives - Record better information with less work Share complete methods and data in context LabSynch is a fully integrated: - Electronic lab notebook Collaboration web service Sample tracking system Data capture and analysis tool LabSynch is Open Source (GPLv2) 3 What is LabSynch? 1 LabSynch LabSynch Page LabSynch Page LabSynch Page LabSynch Page LabSynch Page LabSynch Page Page Wiki Pages LabSynch Database Flexible LIMS Database 2 3 R Statistical Programming Language 4 External Database External Database 4

3 LabSynch at Ambrx, Inc. 5 Molecular Biology 6

4 Custom Request/Report System 7 Protein Analytics 8

5 Dose Response Fitting Plate Map (xls) Plate Data (.txt) From Hypothesis To Conclusion 9 Automated PK/PD Analysis Plate Layout Template Reader Data Reader Data Reader Data Study Design Wizard Plate Setup Plate Analysis Plate Analysis Plate Analysis sample labels PDF animals animals samples samples samples Re-Assay Plate Analysis Report 10

6 Problem Chemists want compound organization, batch tracking, sub-structure searching Biologists want complete history of lots, including small molecules and conjugates LabSynch s database is not structure-aware 11 Solution = LabSynch + JChem Step One 12

7 Solution = LabSynch + JChem Step Two 13 Solution = LabSynch + JChem Batch Registration Compound Batch Registration Automatically filled in if an existing structure is entered in marvin sketch. 14

8 Solution = LabSynch + JChem Resulting LabSynch Page LabSynch ID IJC Compound ID External ID From Hypothesis To Conclusion Behind the Scenes <iframe> JSP Structure Form Embedded JS <iframe> PHP Batch Form Embedded JS Redirect JChem Base Tomcat MySQL LabSynch Server PHP 16

9 Connecting JChem JSP to LabSynch PHP After registering a structure, the Structure form redirects the iframe to a LabSynch form, passing the compound ID of the structure as a query parameter if (structureadded){ // new structure was created, redirect user to compound registration step String redirecturl = serverbase + "/server/ijc_compoundregistration.php?cd_id=" + insertedid; response.sendredirect(redirecturl); } else { // existing structure was found, redirect user to compound batch registration step String redirecturl = serverbase + "/server/ijc_compoundbatchregistration.php?cd_id=" + insertedid; response.sendredirect(redirecturl); } If the user enters a structure that has already been registered, the compound ID for that structure is returned, and the iframe is redirected to the Compound Batch Registration form instead of Compound Registration 17 Future: Cross Linking Java Web Start Open URL in Browser 18

10 Summary IJC and JChem Base provide cost-effective tools for small groups - Low entry barrier buy what we need - Simple server set-up uses existing LabSynch server and backup systems Adding structure Items to LabSynch was straight-forward using JChem Base and LabSynch API Structure Items work in both IJC and LabSynch No changes were required to existing biology forms and data Users get new capability science is tracked and shared better 19 Thanks To Ambrx Melanie Nelson, Ph. D. Zhenwei Miao, Ph. D. Junjie Liu, Ph. D. Ying Sun, Ph. D. Mike Trout Bruce Kimmel, Ph. D. John McNeil & Co., Inc. On Khongsaly Guy Oshiro, Ph. D. Matthew Shaw 20