ACRL Open Notebook Science talk
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The document discusses the concept of open notebook science, emphasizing the importance of transparency in scientific research and data sharing. It highlights tools and methods for public access to experimental data, collaborative projects, and the integration of web technologies in chemistry education and research. Key examples and case studies demonstrate how open approaches can improve scientific accuracy and engagement in educational settings.
ACRL Open Notebook Science talk
- 1. Open Notebook Science Jean-Claude Bradley Feb 17, 2009 Association of College and Research Libraries Associate Professor of Chemistry Drexel University
- 2. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures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
- 3. Motivation: Faster Science, Better Science
- 4. Where is Science headed? WE ARE HERE
- 5. There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit
- 6. TRUST PROOF
- 7. The solubility of 4-chlorobenzaldehyde
- 8. The Log makes Assumptions Explicit
- 9. The Rationale of Findings Explicit
- 10. Raw Data Made Public Splatter? Some liquid
- 11. YouTube for demonstrating experimental set-up
- 12. Calculations Made Public on Google Spreadsheets
- 13. Revision History on Google Spreadsheets
- 15. Comparing Wiki Page Versions
- 16. Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX
- 17. Indexing Molecules on Google
- 18. Linking to Molecules in Chemistry Databases
- 19. Experimental Spectra and User-Deposited Data on ChemSpider
- 20. The Spectra Game (Andy Lang, Tony Williams)
- 22. NMR game in Second Life (Andy Lang)
- 23. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
- 24. Imine Formation Mechanism: talk to the molecules!
- 25. Student Projects in Second Life
- 29. Teaching Lab: Brent Friesen (Dominican University)
- 31. Solubilities collected in a Google Spreadsheet
- 32. Rajarshi Guha’s Live Web Query using Google Viz API
- 33. Substructure Searching of solubility data
- 34. Rajarshi Guha and Andy Lang: Chemical Space Explorer
- 35. Andy Lang: Chemical Space Explorer in Second Life
- 37. … the lab notebook and raw data
- 38. Including links to the literature
- 40. Temperature info automatically plotted
- 41. Exploring Solubility in Second Life (Andy Lang)
- 42. Pierre Lindenbaum’s Solubility Data as RDF Triples
- 43. Results and Workflows in Machine-Friendly Format
- 44. Experiments in Chemical Markup Language
- 45. UsefulChem Workflows in myExperiment
- 46. 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.
- 47. Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org
- 48. BLOG WIKI Mailing List GoogleDocs Architecture: Distributed, Interlinked and Redundant ChemSpider CDD FriendFeed Nature Precedings JoVE
- 50. Link to Lab Notebook Page in Wiki
- 51. Link to Docking Procedure (Rajarshi Guha)
- 52. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
- 53. Comparing Experiments Ugi Master Table
- 54. Concentration (0.4, 0.2, 0.07 M) Solvent (methanol, ethanol, acetonitrile, THF) Excess of some reagents (1.2 eq.) Reaction to Optimize
- 57. XML reports from MiniMapper robot
- 58. GoogleDoc to program and report
- 59. Paper written on Wiki
- 60. References to papers, blog posts, lab notebook pages, raw data
- 61. ChemSpider Automated Mark-up of Chemical Names
- 62. Paper on Journal of Visualized Experiments (JoVE)
- 63. Pre-print on Nature Precedings
- 64. Reaction Optimization Visualization in Second Life
- 66. Collaborative Drug Discovery (CDD) Database
- 67. Outcome of Guha-Bradley-Rosenthal collboration
- 68. Google Spreadsheet linked to Open Web Services = Chemistry Dashboard
- 69. Potential Trends for the Future of Chemistry Fast, Fuzzy, Open, Automated, Green, Crowdsourced, Simple (e.g. mix and filter)
- 70. Gus Rosania’s Notebook Other Open Notebooks
- 72. Anthony Salvagno’s Notebook (Steve Koch group)
- 73. 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.)