Open Notebook Science
NASA
Goddard Space Flight Center
Jean-Claude Bradley
Associate Professor o...
Open and Closed Science
Open Notebook
Traditional Traditional
...
Motivation: Faster Science, Better Science
Open Notebook Science Logos
(Andy Lang, Shirley Wu)
Sharing: how much and when
Where is Science headed?
WE ARE HERE
There are NO FACTS,
only measurements embedded
within assumptions
Open Notebook Science maintains
the integrit...
TRUST
PROOF
The solubility of 4-chlorobenzaldehyde
The Log makes Assumptions Explicit
The Rationale of Findings Explicit
Raw Data Made Public
Splatter?
Some liquid
YouTube for demonstrating experimental set-up
Calculations Made Public on
Google Spreadsheets
Revision History on
Google Spreadsheets
Wiki Page History
Comparing Wiki Page Versions
Proof of Purity with interactive NMR
spectrum using JSpecView and JCAMP-DX
Indexing Molecules on Google
Linking to Molecules in Chemistry
Databases
Experimental Spectra and User-
Deposited Data on ChemSpider
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams)
(Andy Lang, Tony Williams, Robert ...
Database Curation via Game Playing
Over 50,000 spectrum views so far -
worldwide
Link Spectral Game to Open Educational
Content
Remixing Code and Content (Andy
Lang)
Prizes not Punishment to motivate
students
NMR game in Second Life (Andy Lang)
Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
Imine Formation Mechanism:
talk to the molecules!
Student Projects in Second Life
Spring 09 projects: networking in
Second Life and FriendFeed
Crowdsourcing Solubility Data
ONS Challenge Students
ONS Challenge Judges
Teaching Lab: Brent Friesen
(Dominican University)
Solubility Experiment List
Summary of Solubility Experiments
Solubilities collected in a Google
Spreadsheet
Rajarshi Guha’s Live Web Query
using Google Viz API
Substructure Searching of solubility data
Rajarshi Guha and Andy Lang:
Chemical Space Explorer
Andy Lang: Chemical Space Explorer in
Second Life
From Wikipedia to…
…the lab notebook and raw data
Including links to the literature
Temperature info automatically
plotted
Exploring Solubility in Second Life (Andy Lang)
Pierre Lindenbaum’s Solubility Data
as RDF Triples
Results and Workflows in Machine-
Friendly Format
Experiments in Chemical Markup Language
UsefulChem Workflows in
myExperiment
UsefulChem Project: Open Primary
Research in Drug Design using Web2.0
tools
Rajarshi Guha ...
Malaria Target: falcipain-2
involved in hemoglobin metabolism
Dana.org
Architecture: Distributed, Interlinked and
Redundant
BLOG
CDD WIKI...
Where’s the Beef?
Link to Lab Notebook Page in Wiki
Link to Docking Procedure
(Rajarshi Guha)
Link to Docking Results:
Lists of SMILES in GoogleDocs
(Rajarshi Guha)
Comparing Experiments
Ugi Master Table
Reaction to Optimize
•Concentration (0.4, 0.2, 0.07 M)
•Solvent (methanol, ethanol, acetonitrile, THF)
•Excess of some...
Mettler-Toledo MiniMapper
Mettler-Toledo MiniBlock System
XML reports from MiniMapper robot
GoogleDoc to program and report
Paper written on Wiki
References to papers, blog posts,
lab notebook pages, raw data
ChemSpider Automated Mark-up of
Chemical Names
Paper on Journal of Visualized
Experiments (JoVE)
Pre-print on Nature Precedings
Reaction Optimization Visualization in
Second Life
Collaborative Drug Discovery (CDD) Database
Outcome of Guha-Bradley-Rosenthal
collboration
Google Spreadsheet linked to
Open Web Services
= Chemistry Dashboard
Semi-Automated Measurement of
solubility via web service analysis
of JCAMP-DX files
(Andy Lang)
Archiving and Curation of ONS and
other new forms of scholarship?
Publishing Google Spreadsheets as XLS
Other Open Notebooks
Gus Rosania’s Notebook (recently terminated)
Cameron Neylon’s Notebook
Anthony Salvagno’s Notebook
(Steve Koch group)
Acknowledgements
Khalid Mirza (Drexel)

Jenny Hale (Southampton U.)

David Bulger (Oral Roberts U.)

...
NASA Open Notebook Science Talk
NASA Open Notebook Science Talk
of 82

NASA Open Notebook Science Talk

Jean-Claude Bradley discusses Open Notebook Science on April 15, 2009 at the NASA Goddard Space Flight Center. This includes recent material such as ONS logos, the ChemTiles and Spectral Games, automated backup of Google Spreadsheets and automated solubility determinations using web services called from within Google Spreadsheets.
Published on: Mar 3, 2016
Published in: Education      Technology      
Source: www.slideshare.net


Transcripts - NASA Open Notebook Science Talk

  • 1. Open Notebook Science NASA Goddard Space Flight Center Jean-Claude Bradley Associate Professor of Chemistry Drexel University April 15, 2009
  • 2. Open and Closed Science Open Notebook Traditional Traditional Open Access Science (full Lab Notebook Journal Journal Article transparency) (unpublished) Article RESEARCH OPEN CLOSED TEACHING Archived Lectures Traditional Assigned Lectures Notes Paper problems Public and public Textbook public free online F2F lectures textbooks
  • 3. Motivation: Faster Science, Better Science
  • 4. Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when
  • 5. Where is Science headed? WE ARE HERE
  • 6. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
  • 7. TRUST PROOF
  • 8. The solubility of 4-chlorobenzaldehyde
  • 9. The Log makes Assumptions Explicit
  • 10. The Rationale of Findings Explicit
  • 11. Raw Data Made Public Splatter? Some liquid
  • 12. YouTube for demonstrating experimental set-up
  • 13. Calculations Made Public on Google Spreadsheets
  • 14. Revision History on Google Spreadsheets
  • 15. Wiki Page History
  • 16. Comparing Wiki Page Versions
  • 17. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
  • 18. Indexing Molecules on Google
  • 19. Linking to Molecules in Chemistry Databases
  • 20. Experimental Spectra and User- Deposited Data on ChemSpider
  • 21. Open Data JCAMP spectra for education (Andy Lang, Tony Williams) (Andy Lang, Tony Williams, Robert Lancashire)
  • 22. Database Curation via Game Playing
  • 23. Over 50,000 spectrum views so far - worldwide
  • 24. Link Spectral Game to Open Educational Content
  • 25. Remixing Code and Content (Andy Lang)
  • 26. Prizes not Punishment to motivate students
  • 27. NMR game in Second Life (Andy Lang)
  • 28. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  • 29. Imine Formation Mechanism: talk to the molecules!
  • 30. Student Projects in Second Life
  • 31. Spring 09 projects: networking in Second Life and FriendFeed
  • 32. Crowdsourcing Solubility Data
  • 33. ONS Challenge Students
  • 34. ONS Challenge Judges
  • 35. Teaching Lab: Brent Friesen (Dominican University)
  • 36. Solubility Experiment List
  • 37. Summary of Solubility Experiments
  • 38. Solubilities collected in a Google Spreadsheet
  • 39. Rajarshi Guha’s Live Web Query using Google Viz API
  • 40. Substructure Searching of solubility data
  • 41. Rajarshi Guha and Andy Lang: Chemical Space Explorer
  • 42. Andy Lang: Chemical Space Explorer in Second Life
  • 43. From Wikipedia to…
  • 44. …the lab notebook and raw data
  • 45. Including links to the literature
  • 46. Temperature info automatically plotted
  • 47. Exploring Solubility in Second Life (Andy Lang)
  • 48. Pierre Lindenbaum’s Solubility Data as RDF Triples
  • 49. Results and Workflows in Machine- Friendly Format
  • 50. Experiments in Chemical Markup Language
  • 51. UsefulChem Workflows in myExperiment
  • 52. UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Rajarshi Guha Tsu-Soo Tan Docking Indiana U Nanyang Inst. JC Bradley Synthesis Drexel U Phil Rosenthal Dan Zaharevitz Testing UCSF NCI (malaria) (tumors)
  • 53. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
  • 54. Architecture: Distributed, Interlinked and Redundant BLOG CDD WIKI Nature FriendFeed Precedings JoVE ChemSpider GoogleDocs Mailing List
  • 55. Where’s the Beef?
  • 56. Link to Lab Notebook Page in Wiki
  • 57. Link to Docking Procedure (Rajarshi Guha)
  • 58. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  • 59. Comparing Experiments Ugi Master Table
  • 60. Reaction to Optimize •Concentration (0.4, 0.2, 0.07 M) •Solvent (methanol, ethanol, acetonitrile, THF) •Excess of some reagents (1.2 eq.)
  • 61. Mettler-Toledo MiniMapper
  • 62. Mettler-Toledo MiniBlock System
  • 63. XML reports from MiniMapper robot
  • 64. GoogleDoc to program and report
  • 65. Paper written on Wiki
  • 66. References to papers, blog posts, lab notebook pages, raw data
  • 67. ChemSpider Automated Mark-up of Chemical Names
  • 68. Paper on Journal of Visualized Experiments (JoVE)
  • 69. Pre-print on Nature Precedings
  • 70. Reaction Optimization Visualization in Second Life
  • 71. Collaborative Drug Discovery (CDD) Database
  • 72. Outcome of Guha-Bradley-Rosenthal collboration
  • 73. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
  • 74. Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang)
  • 75. Archiving and Curation of ONS and other new forms of scholarship?
  • 76. Publishing Google Spreadsheets as XLS
  • 77. Other Open Notebooks Gus Rosania’s Notebook (recently terminated)
  • 78. Cameron Neylon’s Notebook
  • 79. Anthony Salvagno’s Notebook (Steve Koch group)
  • 80. Acknowledgements Khalid Mirza (Drexel)  Jenny Hale (Southampton U.)  David Bulger (Oral Roberts U.)  Tim Bohinsky (Drexel)  Kevin Owens (Drexel)  Tom Osborne (Mettler-Toledo)  Antony Williams (ChemSpider)  Andrew Lang (Oral Roberts U.)  Rajarshi Guha (Indiana U.)  Cameron Neylon (Southampton U.) 