1. Building Bioinformatics Tools for Research Scientists Southern California Bioinformatics Summer Institute 2008 Andrew Clark Mentor: Dr. Ping Du, Allergan, Inc August 21, 2008

2. Outline Introduction to Allergan Introduction to Allergan Project objective Project objective Motivation: Why is this important? Motivation: Why is this important? Software development process Software development process Results and conclusion Results and conclusion Acknowledgements Acknowledgements

3. Allergan background Brief history of Allergan Brief history of Allergan Organization structure and operation Organization structure and operation Product areas Product areas Eye, skin careEye, skin care BotoxBotox

4. Project information The Research Data Warehouse is a software application designed to consolidate information from a variety of research databases into a single point of access. The Research Data Warehouse is a software application designed to consolidate information from a variety of research databases into a single point of access. the RDW (web application) R & D SOURCE DATABASES Allergan Scientists

5. Toxicology Chemistry Biology Pharmaco- kinetics Research Dept. The Research Environment at Allergan

6. Project objective Extend the functionality of the “RDW”: Extend the functionality of the “RDW”: Build and integrate a Structure Data File (SDF) export function.Build and integrate a Structure Data File (SDF) export function. SD File RDW Query Result Structure-activity relationship analysis in SARVision. Data manipulation in Excel. Data sharing with external collaborators via email.

7. Why is this important? Structure Data Files are an industry standard for storing chemical compound data. Structure Data Files are an industry standard for storing chemical compound data. The SDF export feature will The SDF export feature will make research scientists’ work simpler.make research scientists’ work simpler. add a useful feature to the RDW.add a useful feature to the RDW.

8. Example SD file 3,7-Dihydro-1,3,7-trimethyl-1H-purine-2,6-dione Marvin 08110810182D Marvin 08110810182D 14 15 0 0 0 0 999 V2000 14 15 0 0 0 0 999 V2000 -1.6702 -2.1687 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 -2.1687 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 -0.8338 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.6702 -0.8338 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.4154 -0.0492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4154 -0.0492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1853 -1.5013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1853 -1.5013 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 -0.6763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 -0.6763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5982 -0.6763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5982 -0.6763 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8838 -1.9137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8838 -1.9137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 -3.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 -3.1513 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4548 -1.9137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4548 -1.9137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4548 -1.0888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4548 -1.0888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 0.1488 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1693 0.1488 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0...... 5 13 1 0 0 0 0 5 13 1 0 0 0 0 13 7 1 0 0 0 0 13 7 1 0 0 0 0 7 14 1 0 0 0 0 7 14 1 0 0 0 0 14 9 1 0 0 0 0 14 9 1 0 0 0 0 9 10 2 0 0 0 0 9 10 2 0 0 0 0 5 10 1 0 0 0 0 5 10 1 0 0 0 0...... M END > > CN1C=NC2=C1C(=O)N(C)C(=O)N2C 353.3255$$$$ Source: http:// chem.sis.nlm.nih.gov/chemidplus/applet/marvin/examples/applets/example-view2.6.html

9. Planning ahead 2.Prepare the requirements specification. 4.Implement and test code, get feedback from managers and RDW users. 3.Design the new feature. 1.Understand the research environment at Allergan.

10. Software Development Process Learn the needs of the users Learn the needs of the users (July 8 – 11)(July 8 – 11) Plan the software program Plan the software program (July 14 – 18)(July 14 – 18) Write the program code Write the program code (July 21 – August 8)(July 21 – August 8) Test and obtain user feedback Test and obtain user feedback (August 11 – 19)(August 11 – 19)

11. Results Example RDW usage: Example RDW usage: Web interfaceWeb interface Search formSearch form Report generationReport generation SDF Export featureSDF Export feature Exported dataExported data

12. The RDW Homepage

13. Selecting a search template

14. The query form

15. Configuring experiment search details

16. Report generated from user search.

17. The SDF Export button

18. The SDF file download prompt

19. Exported SDF data viewed in analysis tool

20. Conclusion Effective bioinformatics research relies on the creative development of software tools.

21. Conclusion Computational resources can: Computational resources can: Standardize access to data through software applications or web services.Standardize access to data through software applications or web services. Perform high power, high precision numerical calculations.Perform high power, high precision numerical calculations. Knowledge of software development and computational methods will help make a well-rounded bioinformatician. Knowledge of software development and computational methods will help make a well-rounded bioinformatician.

22. Acknowledgements Special thanks to Special thanks to The SoCalBSI faculty and staffThe SoCalBSI faculty and staff My mentor at Allergan:My mentor at Allergan: Dr. Ping Du Dr. Ping Du Other supportive individuals at Allergan:Other supportive individuals at Allergan: Dr. Robert Cain, Raju Krishnappa, Gaurang Patel Dr. Robert Cain, Raju Krishnappa, Gaurang Patel All the SoCalBSI summer interns.All the SoCalBSI summer interns.