Open Notebook Science:
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Publication of all aspects of the scientific process: Open Source Science / Open ... Third Party Time-Stamp on Experiment Versions. Monitoring experimental ...

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Open Notebook Science:

Research in Real Time

Sigma Xi

Swarthmore College Chapter

Jean-Claude Bradley

E-Learning Coordinator

College of Arts and Sciences

Associate Professor of Chemistry

Drexel University

Nov 27, 2007

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Open and Closed Science

Open Notebook

Science (full transparency)


Lab Notebook



Journal Article

Open Access Journal Article





Archived Lectures Public and free online textbooks

Lectures Notes public


Paper Textbook

F2F lectures

Assigned problems public

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How will this happen?

  • Self-organizing redundant processes

  • Fully Open Access (Read and Write)

  • Publication of all aspects of the scientific process: Open Source Science / Open Notebook Science

  • Using semantically rich formats and automation at zero publication cost – is this the way to the technological singularity?

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Malaria is a Logical Application of Open Science

  • Very large problem: 300-500 million cases per year with one million deaths

  • Not a lucrative market: IP control less important

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Diketopiperazine Library

First iteration: Solid Support Synthesis

Evolves to: on pot Ugi reaction/cyclization

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The blog as an integrative tool

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Graphical Mining of Data with JSpecView (48h 7 min)

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Open Primary Research in Drug Design using Web2.0 tools JSpecView(blogs, wikis, Second Life, mailing lists)

Rajarshi Guha

Indiana U

Tsu-Soo Tan

Nanyang Inst.


JC Bradley

Drexel U


Phil Rosenthal



Dan Zaharevitz




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Open science connectivity JSpecView

More info on open source science here

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Falcipain-2 inhibitor? JSpecView

Khalid Mirza

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Raw Experimental Data JSpecView

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Selected Experiments (some failed) JSpecView

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Generalized Protocols JSpecView

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Vendor Reliability JSpecView

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Discussing Hypotheses JSpecView

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UsefulChem and Open Science in Second Life JSpecView

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  • Question JSpecView: Is it really a good thing to let anyone who thinks they have a scientific breakthrough have access to free, open, public, Googleable media?

  • YES

  • Question: What if I make a mistake in my data, never fix it, no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal publications?

  • Peer review is not designed to catch errors from the analysis of raw data

  • Open Notebook Science is more difficult where human subjects are involved

  • Question: Who is the audience for science blogs and wikis anyway? Scientists or laypeople?

  • For UsefulChem, wiki is for chemists, blog for wider audience

  • Question: Can you get published if you've already posted your results to your blog/wiki?

  • We’ll find out….

  • Question: Can scientists establish their credibility/reputation by writing blogs and wikis?

  • Certainly we’ve found collaborators this way