Open Notebook Science for Collaborative Drug Discovery Jean-Claude Bradley July 23, 2009 BrightTALK Associate Professor of...
WE ARE HERE How can the scientific process become more automated?
The Robot Scientist
<ul><li>Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) </li></ul><ul><li>Self-org...
UsefulChem Project:  Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha India...
Malaria Target: falcipain-2  involved in hemoglobin metabolism Dana.org
Outcome of Guha-Bradley-Rosenthal collboration
The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
Open and Closed Science  Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Op...
Motivation:  Faster Science,   Better Science
Open Notebook Science Logos  (Andy Lang, Shirley Wu) Sharing: how much and when
There are NO FACTS,  only measurements embedded within assumptions Open Notebook Science maintains the integrity of data p...
TRUST PROOF
The solubility of 4-chlorobenzaldehyde
The Log makes Assumptions Explicit
Results and Workflows in Machine-Friendly Format
The Rationale of Findings Explicit
Raw Data Made Public Splatter? Some liquid
YouTube for demonstrating experimental set-up
Calculations Made Public on  Google Spreadsheets
Link to Docking Results:  Lists of SMILES in GoogleDocs  (Rajarshi Guha)
Link to Docking Procedure  (Rajarshi Guha)
Revision History on  Google Spreadsheets
Wiki Page History
Comparing Wiki Page Versions
Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
Linking to Molecules in Chemistry Databases
Experimental Spectra and User-Deposited Data on ChemSpider
(Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
Database Curation via Game Playing
Over 50,000 spectrum views so far - worldwide
Link Spectral Game to Open Educational Content
NMR game in Second Life (Andy Lang)
Crowdsourcing Solubility Data
ONS Challenge Students
ONS Challenge Judges
Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files  (Andy Lang)
Teaching Lab: Brent Friesen (Dominican University)
Solubility Experiment List
Solubilities collected in a Google Spreadsheet
Rajarshi Guha’s Live Web Query using Google Viz API
Rajarshi Guha and Andy Lang: Chemical Space Explorer
Solubility Measurement Requests:  DoSol sheet <ul><li>Outlier Bot:  flags measurements with high standard deviation to mea...
Solvent mixture and temperature: multidimensional solubility data Actual Data  (4-nitrobenzaldehyde) From quadratic regres...
Comparing Experiments Ugi Master Table
Crowdsourcing Reaction Requests:  DoUgi sheet
Raw data reveal a problem Missed in a prior publication on solubility for this compound
Data provenance:  From Wikipedia to…
… the lab notebook and raw data
Including links to the literature
Collaborative Drug Discovery (CDD) Database
<ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul><ul><l...
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
XML reports from MiniMapper robot
GoogleDoc to program and report
Best Yield: 66% 0.4 M methanol 1.2 eq imine
Reaction Optimization Visualization in Second Life
Paper written on Wiki
References to papers, blog posts, lab notebook pages, raw data
Paper on Journal of Visualized Experiments (JoVE)
Pre-print on Nature Precedings
ChemSpider Automated Mark-up of Chemical Names
Archiving and Curation of ONS and other new forms of scholarship?
Cameron Neylon’s Notebooks Other Open Notebooks
Anthony Salvagno’s Notebook (Steve Koch group)
Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Jenny Hale (Southampton U.) </li></ul><ul><li>David Bulge...
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BrightTALK Open Notebook Science

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Jean-Claude Bradley presents on "Open Notebook Science for Collaborative Drug Discovery" on July 23, 2009.

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BrightTALK Open Notebook Science

  1. 1. Open Notebook Science for Collaborative Drug Discovery Jean-Claude Bradley July 23, 2009 BrightTALK Associate Professor of Chemistry Drexel University
  2. 2. WE ARE HERE How can the scientific process become more automated?
  3. 3. The Robot Scientist
  4. 4. <ul><li>Agents can participate with zero or near-zero cost (free hosted services – e.g. Google) </li></ul><ul><li>Self-organizing redundant processes </li></ul>How radical openness can assist in the automation of science
  5. 5. 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.
  6. 6. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  7. 7. Outcome of Guha-Bradley-Rosenthal collboration
  8. 8. The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?
  9. 9. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING
  10. 10. Motivation: Faster Science, Better Science
  11. 11. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  12. 12. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  13. 13. TRUST PROOF
  14. 14. The solubility of 4-chlorobenzaldehyde
  15. 15. The Log makes Assumptions Explicit
  16. 16. Results and Workflows in Machine-Friendly Format
  17. 17. The Rationale of Findings Explicit
  18. 18. Raw Data Made Public Splatter? Some liquid
  19. 19. YouTube for demonstrating experimental set-up
  20. 20. Calculations Made Public on Google Spreadsheets
  21. 21. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  22. 22. Link to Docking Procedure (Rajarshi Guha)
  23. 23. Revision History on Google Spreadsheets
  24. 24. Wiki Page History
  25. 25. Comparing Wiki Page Versions
  26. 26. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  27. 27. Linking to Molecules in Chemistry Databases
  28. 28. Experimental Spectra and User-Deposited Data on ChemSpider
  29. 29. (Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)
  30. 30. Database Curation via Game Playing
  31. 31. Over 50,000 spectrum views so far - worldwide
  32. 32. Link Spectral Game to Open Educational Content
  33. 33. NMR game in Second Life (Andy Lang)
  34. 34. Crowdsourcing Solubility Data
  35. 35. ONS Challenge Students
  36. 36. ONS Challenge Judges
  37. 37. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  38. 38. Teaching Lab: Brent Friesen (Dominican University)
  39. 39. Solubility Experiment List
  40. 40. Solubilities collected in a Google Spreadsheet
  41. 41. Rajarshi Guha’s Live Web Query using Google Viz API
  42. 42. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  43. 43. Solubility Measurement Requests: DoSol sheet <ul><li>Outlier Bot: flags measurements with high standard deviation to mean ratios </li></ul><ul><li>Google Analytics queries – new solvent/solute searches </li></ul><ul><li>Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study </li></ul><ul><li>Application based models – high priority Ugi reactants </li></ul>
  44. 44. Solvent mixture and temperature: multidimensional solubility data Actual Data (4-nitrobenzaldehyde) From quadratic regression of 5D space Feeds DoSol Sheet the next points to measure to best cover the space
  45. 45. Comparing Experiments Ugi Master Table
  46. 46. Crowdsourcing Reaction Requests: DoUgi sheet
  47. 47. Raw data reveal a problem Missed in a prior publication on solubility for this compound
  48. 48. Data provenance: From Wikipedia to…
  49. 49. … the lab notebook and raw data
  50. 50. Including links to the literature
  51. 51. Collaborative Drug Discovery (CDD) Database
  52. 52. <ul><li>Concentration (0.4, 0.2, 0.07 M) </li></ul><ul><li>Solvent (methanol, ethanol, acetonitrile, THF) </li></ul><ul><li>Excess of some reagents (1.2 eq.) </li></ul>How does Open Notebook Science fit with traditional publication?
  53. 53. Mettler-Toledo MiniMapper
  54. 54. Mettler-Toledo MiniBlock System
  55. 55. XML reports from MiniMapper robot
  56. 56. GoogleDoc to program and report
  57. 57. Best Yield: 66% 0.4 M methanol 1.2 eq imine
  58. 58. Reaction Optimization Visualization in Second Life
  59. 59. Paper written on Wiki
  60. 60. References to papers, blog posts, lab notebook pages, raw data
  61. 61. Paper on Journal of Visualized Experiments (JoVE)
  62. 62. Pre-print on Nature Precedings
  63. 63. ChemSpider Automated Mark-up of Chemical Names
  64. 64. Archiving and Curation of ONS and other new forms of scholarship?
  65. 65. Cameron Neylon’s Notebooks Other Open Notebooks
  66. 66. Anthony Salvagno’s Notebook (Steve Koch group)
  67. 67. Acknowledgements <ul><li>Khalid Mirza (Drexel) </li></ul><ul><li>Jenny Hale (Southampton U.) </li></ul><ul><li>David Bulger (Oral Roberts U.) </li></ul><ul><li>Tim Bohinsky (Drexel) </li></ul><ul><li>Kevin Owens (Drexel) </li></ul><ul><li>Tom Osborne (Mettler-Toledo) </li></ul><ul><li>Antony Williams (ChemSpider) </li></ul><ul><li>Andrew Lang (Oral Roberts U.) </li></ul><ul><li>Rajarshi Guha (Indiana U.) </li></ul><ul><li>Cameron Neylon (Southampton U.) </li></ul>

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