Science Commons Open Notebook Science Talk
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Transcript of Science Commons Open Notebook Science Talk
Using Free Hosted Web2.0 Tools for Open Notebook
Science
Jean-Claude Bradley
February 20, 2010
Science Commons Symposium
Associate Professor of ChemistryDrexel University
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?
How bad is our current system? Try to find the solubility EGCG?
=2.3 g/L
WTF?!
The End of the Chain of Provenance
The NaH oxidation controversy
Information spreads quickly through the blogosphere
15% NMR yield
Khalid Mirza and Marshall Moritz
Top results on a Google search
The Scandal of Bell’s Lab Notebook
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
provenance by making assumptions explicit
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 YouTube for demonstrating experimental set-upset-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
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 100,000 spectrum views so far - worldwide
Link Spectral Game to Open Educational Content
The Ugi reaction: can we predict precipitation?
Can we predict solubility in organic solvents?
Crowdsourcing Solubility Data
ONS Submeta Award Winners
ONS Challenge Judges
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
WE ARE HEREWE ARE HERE
How can the scientific process become more automated?
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)
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
Solubility Prediction (Andy Lang’s Model)
Understanding in addition to empirical modeling
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
•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?
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
BUT…
Open Access: the Choice that Keeps Giving.. and Giving…
Beware of your addiction to metrics: redundancy will reduce
them
Cameron Neylon’s NotebooksCameron Neylon’s Notebooks
Other Open NotebooksOther Open Notebooks
Anthony Salvagno’s Notebook Anthony Salvagno’s Notebook (Steve Koch group)(Steve Koch group)
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?
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
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
Good concept but.....
Most pages look like this....
Where We Began: The ONS backup spreadsheet and ONSPreserver
Publishing Google Spreadsheets as XLS
Where We Are Now
ONSArchive: Semi-Automated Snapshot of the Entire Scientific Record
Snapshot is Self-Contained and Live on the Internet
Lulu.com Data Disks
DSpace – Handle (hdl)
Lulu.com - ISBN
Google Spreadsheet
s
Google Documents
Web Services
ChemSpider & Indiana
Real Time Linear Regression, Unit
Conversions, Style Sheet, etc
Data Book
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)
More about the ONSarchive project:
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