This document discusses open notebook science initiatives for malaria drug discovery and solubility modeling. It describes a collaboration between researchers from multiple universities using web tools to share primary research on drug design openly. This includes work on a malaria drug target and collecting solubility data in a shared spreadsheet. The document advocates for making raw data, lab notebooks, and interactive spectra publicly available to allow others to verify and build upon the research.

1. Open Notebook Science for Malaria Drug Discovery and Solubility Modeling Jean-Claude Bradley September 30, 2010 Drexel Chemistry Mini Symposium Associate Professor of Chemistry Drexel University

2. Industry is Sharing More

3. Opportunities for Competitive Collaboration

4. Some Initiatives Promoting More Openness in Drug Discovery

5. Motivation: Faster Science, Better Science

6. TRUST PROOF

7. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

8. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org

9. The Ugi Reaction

10. Outcome of Guha-Bradley-Rosenthal collaboration

11. References to papers, blog posts, lab notebook pages, raw data

12. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?

13. Crowdsourcing Solubility Data

14. ONS Challenge Judges

15. ONS Submeta Award Winners

16. Solubilities collected in a Google Spreadsheet

17. Rajarshi Guha’s Live Web Query using Google Viz API

18. Data provenance: From Wikipedia to…

19. … the lab notebook and raw data

20. Interactive NMR spectra using JSpecView and JCAMP-DX

21. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)

22. Raw Data As Images Splatter? Some liquid

23. YouTube for demonstrating experimental set-up

24. The importance of raw data availability Missed in a prior publication on solubility for this compound

25. The Intersection of Open Notebooks (Bradley/Todd) and IP implications Open Notebook could have blocked patent if done earlier

26. Convenient web services for solubility measurement and prediction (Andrew Lang)

27. Other Web Services… (Andrew Lang) General Transparent Solubility Prediction

28. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)

29. Integration of Multiple Web Services to Recommend Solvents for Reactions (Andrew Lang)

32. Solubility Prediction (Andy Lang uses Abraham Model)

33. Reaction Attempts Book

34. Reaction Attempts Book: Reactants listed Alphabetically

35. For all Formats of ONS Projects