Science Commons Open Notebook Science Talk
Upcoming SlideShare
Loading in...5
×
 

Science Commons Open Notebook Science Talk

on

  • 3,857 views

Jean-Claude Bradley presents at the Science Commons Symposium on Feb 20, 2010 at the Microsoft Campus in Redmond. The talk covers doing Open Notebook Science using free and hosted tools, including ...

Jean-Claude Bradley presents at the Science Commons Symposium on Feb 20, 2010 at the Microsoft Campus in Redmond. The talk covers doing Open Notebook Science using free and hosted tools, including new archiving protocols developed with Andrew Lang.

Statistics

Views

Total Views
3,857
Views on SlideShare
3,448
Embed Views
409

Actions

Likes
8
Downloads
14
Comments
2

15 Embeds 409

http://scienceroll.com 254
http://usefulchem.blogspot.com 77
http://ways.org 60
http://translate.googleusercontent.com 3
http://chemistry4up.blogspot.com 2
http://translate.yandex.net 2
http://usefulchem.blogspot.ca 2
http://www.slideshare.net 2
http://static.slideshare.net 1
http://usefulchem.blogspot.in 1
http://usefulchem.blogspot.de 1
http://usefulchem.blogspot.tw 1
http://feeds.feedburner.com 1
http://usefulchem.blogspot.com.es 1
url_unknown 1
More...

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
  • Böyle ilginç bir blog görmek iyidir. Güncelleme için teşekkürler.
    en ucuz iphone
    Are you sure you want to
    Your message goes here
    Processing…
  • thank u ~~i love this!
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

Science Commons Open Notebook Science Talk Science Commons Open Notebook Science Talk Presentation Transcript

  • Using Free Hosted Web2.0 Tools for Open Notebook Science Jean-Claude Bradley February 20, 2010 Science Commons Symposium Associate Professor of Chemistry Drexel University
  • The case for Open Notebook Science
    • Is our current system working?
    • Is ONS difficult or expensive to implement?
    • Does ONS prevent peer-reviewed publication?
    • Can ONS data be easily discoverable?
    • Can ONS information be easily archived and cited?
    • 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 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
  • 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 HERE How can the scientific process become more automated?
  • Semi-Automated Measurement of solubility via web service analysis of JCAMP-DX files (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 Notebooks Other Open Notebooks
  • Anthony Salvagno’s Notebook (Steve Koch group)
  • 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 Where do Libraries fit in the communication of science and education in 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 Spreadsheets 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
    • Is our current system working? NO
    • Is ONS difficult or expensive to implement? NO
    • Does ONS prevent peer-reviewed publication? NO – but depends of publisher
    • Can ONS data be easily discoverable? YES
    • Can ONS information be easily archived and cited? YES
    • Is ONS compatible with IP protection? Maybe to a limited extent