Presentation held at the CDK workshop 2009.

1. Accessing and scripting CDK from Bioclipse Ola Spjuth [email_address] Dept. Pharmaceutical Biosciences Uppsala University, Sweden http://www.bioclipse.net http://bioclipse.blogspot.com

7. Component based architecture Bioclipse Proteochemometrics 2D 3D Data analysis Spectra Molecular dynamics

9. Software updates After installation and restart we have new functionality and more options!

10. Install Sample Data Menu: File > New… Use name: Sample Data

12. Toolbar Perspective bar Stacked views Welcome Jmol Editor Outline Navigator Properties Javascript Console The Bioclipse Workbench

14. Cheat Sheets Step by step tutorials inside the Workbench Interactive with actions to perform Menu: Help > Cheat Sheets

20. Some basic CDK commands in Bioclipse Don’t forget tab-completion!

21. I/O and GUI interaction 1) Type 2) Drag and drop

25. Example script: Download and visualize proteins Script: /Sample Data/Javascripts/dnaiso.js Gist: 95779

26. Multiple molecules Script: /Sample Data/Javascripts/multimol.js Gist: 95790

27. Scripting Jmol Jmol manager: jmol.spinOn() Run general Jmol script: jmol.run(“spin on”)

28. 2D coordinates

29. 3D coordinates

30. 2D/3D complete script Script: /Sample Data/Javascripts/gencoords.js Gist: 95755

31. Script JCP editing Script: /Sample Data/Javascripts/buildmol.js Gist: 96594

35. Calculating CDK properties Command: qsar.calculate( molecule, descriptor) Script: /Sample Data/Javascripts/qsar.js Gist: 95194

36. Calculating CDK properties: Multiple molecules, multiple descriptors Command: qsar.calculateNoParams( molecules, descriptors) Script: /Sample Data/Javascripts/qsar-multi.js Gist: 95189

39. Use R on QSAR dataset

41. Some ongoing Bioclipse projects

42. Speclipse: Spectrum analysis in Bioclipse More information: Stefan Kuhn and Dr. Christoph Steinbeck, EBI, UK

43. MetaPrint2D: Site-of-metabolism prediction Collaboration with Dr. Lars Carlsson, AstraZeneca, SE and Prof. Robert Glenn, Cambridge University, UK

44. Pharmacophores Collaboration with Dr. John Van Drie (Van Drie Research LLC) and Dr . Rajarshi Guha (Indiana University)

45. Brunn: High Throughput Screening Collaboration with Prof. Rolf Larsson, Dept Clinical Pharmacology, Uppsala University, Sweden www.brunn.sf.net More information: Jonathan Alvarsson, Uppsala University, Sweden

46. Data analysis Collaboration with Genetta Soft AB, Sweden. www.genettasoft.com