NITLE Open Notebook Science Talk

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Slide 1: Open Notebook Science for Research and Teaching National Institute for Technology in Liberal Education Jean-Claude Bradley Associate Professor of Chemistry Drexel University Andrew Lang Professor of Mathematics Oral Roberts University February 18, 2010 Slide 2: The NaH oxidation controversy Slide 3: Information spreads quickly through the blogosphere Slide 4: 15% NMR yield Slide 6: Khalid Mirza and Marshall Moritz Slide 8: Top results on a Google search Slide 9: How bad is our current system? Try to find the solubility EGCG? Slide 10: WTF?! =2.3 g/L Slide 11: The End of the Chain of Provenance Slide 12: The Scandal of Bell’s Lab Notebook Slide 13: Motivation: Faster Science, Better Science Slide 14: Open Notebook Science Logos (Andy Lang, Shirley Wu) Sharing: how much and when Slide 15: There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit Slide 16: TRUST PROOF Slide 17: The solubility of 4-chlorobenzaldehyde Slide 18: The Log makes Assumptions Explicit Slide 19: The Rationale of Findings Explicit Slide 20: Raw Data Made Public Splatter? Some liquid Slide 21: YouTube for demonstrating experimental set-up Slide 22: Calculations Made Public on Google Spreadsheets Slide 23: Revision History on Google Spreadsheets Slide 24: Wiki Page History Slide 25: Comparing Wiki Page Versions Slide 26: Proof of Purity with interactive NMR spectrum using JSpecView and JCAMP-DX Slide 27: Linking to Molecules in Chemistry Databases Slide 28: Experimental Spectra and UserDeposited Data on ChemSpider Slide 29: Open Data JCAMP spectra for education (Andy Lang, Tony Williams) (Andy Lang, Tony Williams, Robert Lancashire) Slide 30: Database Curation via Game Playing Slide 31: Over 100,000 spectrum views so far worldwide Slide 32: Link Spectral Game to Open Educational Content Slide 33: NMR game in Second Life (Andy Lang) Slide 34: The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents? Slide 35: Crowdsourcing Solubility Data Slide 36: ONS Submeta Award Winners Slide 37: ONS Challenge Judges Slide 38: Teaching Lab: Brent Friesen (Dominican University) Slide 39: Solubility Experiment List Slide 40: Solubilities collected in a Google Spreadsheet Slide 41: Rajarshi Guha’s Live Web Query using Google Viz API Slide 42: How can the scientific process become more automated? WE ARE HERE Slide 43: Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (Andy Lang) Slide 44: Solubility Measurement Requests: DoSol sheet •Outlier Bot: flags measurements with high standard deviation to mean ratios •Google Analytics queries – new solvent/solute searches •Solubility request form – researcher in Israel requesting pyrene in acetonitrile solubility for environmental soil contamination study •Application based models – high priority Ugi reactants Slide 45: Solubility Prediction (Andy Lang’s Model) Slide 46: Solubility prediction can generate requests for additional measurements Slide 47: 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 Slide 48: Understanding in addition to empirical modeling Missed in a prior publication on solubility for this compound Slide 49: Data provenance: From Wikipedia to… Slide 50: …the lab notebook and raw data Slide 51: Including links to the literature Slide 52: Pierre Lindenbaum’s Solubility Data as RDF Triples Slide 53: How does Open Notebook Science fit with traditional publication? •Concentration (0.4, 0.2, 0.07 M) •Solvent (methanol, ethanol, acetonitrile, THF) •Excess of some reagents (1.2 eq.) Slide 54: Paper written on Wiki Slide 55: References to papers, blog posts, lab notebook pages, raw data Slide 56: Paper on Journal of Visualized Experiments (JoVE) Slide 57: Pre-print on Nature Precedings Slide 58: ChemSpider Automated Mark-up of Chemical Names Slide 59: Open Access: the Choice that Keeps Giving.. and Giving… BUT… Slide 60: Beware of your addiction to metrics: redundancy will reduce them Slide 61: Other Open Notebooks Cameron Neylon’s Notebooks Slide 62: Anthony Salvagno’s Notebook (Steve Koch group) Slide 63: Educational “Open Notebooks” Slide 64: Educational “Open Notebooks” Slide 65: Educational “Open Notebooks” Slide 66: Crowdsourcing ChemInfo Resource Collection Slide 67: Where do Libraries fit in the communication of science and education in the Open/Closed Continuum? Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) RESEARCH CLOSED TEACHING Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks OPEN Slide 68: The Missing Pieces of the Puzzle • Automatic Backup of Science 2.0 Data • Archiving of Open Notebooks • Science 2.0 Community Needed Resources Preservation, Cataloging, Archiving, Cite-ability Slide 69: Librarians and Science 2.0 "The Internet Archive is a 501(c)(3) non-profit that was founded to build an Internet library, with the purpose of offering permanent access for researchers, historians, and scholars to historical collections that exist in digital format." The internet Archive is not practical for practitioners of Open Notebook Science or Science 2.0 Slide 70: Good concept but..... Slide 71: Most pages look like this.... Slide 72: Where We Began: The ONS backup spreadsheet and ONSPreserver Slide 73: Publishing Google Spreadsheets as XLS Slide 74: Where We Are Now Slide 75: ONSPreserverLite Daily Backup of Crucial Data Slide 76: ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record Slide 77: Snapshot is Self-Contained and Live on the Internet Slide 78: Lulu.com Data Disks Slide 79: DSpace – Handle (hdl) Slide 80: Lulu.com - ISBN Google Spreadsheets Google Documents Web Services ChemSpider & Indiana Real Time Linear Regression, Unit Conversions, Style Sheet, etc Data Book Slide 83: Bradley, Jean-Claude; Lang Andrew. Solubilities Summary Sheet. Open Notebook Science Challenge. 2009-12-11. URL:http://spreadsheets.google.com/pub? key=plwwufp30hfq0udnEmRD1aQ&output=xls. Accessed: 2009-12-11. (Archived by WebCite® at http://www.webcitation.org/5lx5ry3BV) Slide 84: More about the ONSarchive project: