Science Commons Open Notebook Science Talk
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Transcript of Science Commons Open Notebook Science Talk
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Using Free Hosted Web2.0 Tools for Open Notebook
Science
Jean-Claude Bradley
February 20, 2010
Science Commons Symposium
Associate Professor of ChemistryDrexel University
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The case for Open Notebook Science
1. Is our current system working?2. Is ONS difficult or expensive to
implement?3. Does ONS prevent peer-reviewed
publication?4. Can ONS data be easily discoverable?5. Can ONS information be easily
archived and cited?6. Is ONS compatible with IP protection?
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How bad is our current system? Try to find the solubility EGCG?
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=2.3 g/L
WTF?!
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The End of the Chain of Provenance
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The NaH oxidation controversy
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Information spreads quickly through the blogosphere
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15% NMR yield
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Khalid Mirza and Marshall Moritz
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Top results on a Google search
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The Scandal of Bell’s Lab Notebook
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Motivation: Faster Science, Better Science
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Open Notebook Science Logos (Andy Lang, Shirley Wu)
Sharing: how much and when
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There are NO FACTS, only measurements embedded
within assumptions
Open Notebook Science maintains the integrity of data
provenance by making assumptions explicit
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TRUST
PROOF
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The solubility of 4-chlorobenzaldehyde
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The Log makes Assumptions Explicit
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The Rationale of Findings Explicit
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Raw Data Made Public
Splatter?
Some liquid
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YouTube for demonstrating experimental YouTube for demonstrating experimental set-upset-up
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Calculations Made Public on Google Spreadsheets
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Revision History on Google Spreadsheets
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Wiki Page History
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Comparing Wiki Page Versions
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Proof of Purity with interactive NMR spectrum using JSpecView and
JCAMP-DX
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Linking to Molecules in Chemistry Databases
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Experimental Spectra and User-Deposited Data on ChemSpider
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(Andy Lang, Tony Williams)
Open Data JCAMP spectra for education
(Andy Lang, Tony Williams, Robert Lancashire)
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Database Curation via Game Playing
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Over 100,000 spectrum views so far - worldwide
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Link Spectral Game to Open Educational Content
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The Ugi reaction: can we predict precipitation?
Can we predict solubility in organic solvents?
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Crowdsourcing Solubility Data
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ONS Submeta Award Winners
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ONS Challenge Judges
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Teaching Lab: Brent Friesen (Dominican University)
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Solubility Experiment List
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Solubilities collected in a Google Spreadsheet
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Rajarshi Guha’s Live Web Query using Google Viz API
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WE ARE HEREWE ARE HERE
How can the scientific process become more automated?
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Semi-Automated Semi-Automated Measurement of solubility via Measurement of solubility via
web service analysis of web service analysis of JCAMP-DX files JCAMP-DX files
(Andy Lang)(Andy Lang)
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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
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Solubility Prediction (Andy Lang’s Model)
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Understanding in addition to empirical modeling
Missed in a prior publication on
solubility for this compound
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Data provenance: From Wikipedia to…
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…the lab notebook and raw data
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Including links to the literature
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•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)
How does Open Notebook Science fit with traditional publication?
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Paper written on Wiki
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References to papers, blog posts, lab notebook pages, raw
data
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Paper on Journal of Visualized Experiments (JoVE)
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Pre-print on Nature Precedings
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ChemSpider Automated Mark-up of Chemical Names
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BUT…
Open Access: the Choice that Keeps Giving.. and Giving…
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Beware of your addiction to metrics: redundancy will reduce
them
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Cameron Neylon’s NotebooksCameron Neylon’s Notebooks
Other Open NotebooksOther Open Notebooks
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Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)
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TraditionalLab Notebook(unpublished)
TraditionalJournal Article
Open Access Journal Article
Open Notebook Science (full transparency)
CLOSED OPEN
TraditionalPaper TextbookF2F lectures
Lectures Notes public
Assigned problems public
Archived Lectures Public and free online textbooks
RESEARCH
TEACHING
Where do Libraries fit in the Where do Libraries fit in the communication of science and education in communication of science and education in
the Open/Closed Continuum? the Open/Closed Continuum?
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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
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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
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Good concept but.....
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Most pages look like this....
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Where We Began: The ONS backup spreadsheet and ONSPreserver
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Publishing Google Spreadsheets as XLS
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Where We Are Now
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ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
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Snapshot is Self-Contained and Live on the Internet
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Lulu.com Data Disks
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DSpace – Handle (hdl)
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Lulu.com - ISBN
Google Spreadsheet
s
Google Documents
Web Services
ChemSpider & Indiana
Real Time Linear Regression, Unit
Conversions, Style Sheet, etc
Data Book
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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)
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More about the ONSarchive project:
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Conclusions
1. Is our current system working? NO2. Is ONS difficult or expensive to
implement? NO 3. Does ONS prevent peer-reviewed
publication? NO – but depends of publisher
4. Can ONS data be easily discoverable? YES
5. Can ONS information be easily archived and cited? YES
6. Is ONS compatible with IP protection? Maybe to a limited extent