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Open and Closed 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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Presentation Transcript
slide1
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

open and closed science
Open and Closed Science

Open Notebook

Science (full transparency)

Traditional

Lab Notebook

(unpublished)

Traditional

Journal Article

Open Access Journal Article

RESEARCH

OPEN

CLOSED

TEACHING

Archived Lectures Public and free online textbooks

Lectures Notes public

Traditional

Paper Textbook

F2F lectures

Assigned problems public

slide5
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?
slide9
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
slide11
Diketopiperazine Library

First iteration: Solid Support Synthesis

Evolves to: on pot Ugi reaction/cyclization

slide23
The blog as an integrative tool

usefulchem.blogspot.com

slide27
Graphical Mining of Data with JSpecView

usefulchem.wikispaces.com/Exp070 (48h 7 min)

open primary research in drug design using web2 0 tools blogs wikis second life mailing lists

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

Rajarshi Guha

Indiana U

Tsu-Soo Tan

Nanyang Inst.

Docking

JC Bradley

Drexel U

Synthesis

Phil Rosenthal

UCSF

(malaria)

Dan Zaharevitz

NCI

(tumors)

Testing

open science connectivity
Open science connectivity

More info on open source science here

http://usefulchem.wikispaces.com

slide39
Falcipain-2 inhibitor?

Khalid Mirza

http://usefulchem.wikispaces.com/Exp148

slide41
Raw Experimental Data

neurodatabase.org

slide42
Selected Experiments (some failed)

Orgprepdaily.wordpress.com

slide43
Generalized Protocols

Openwetware.org

slide44
Vendor Reliability

Orgprepdaily.wordpress.com

slide46
Discussing Hypotheses

RRResearch.blogspot.com

slide48
UsefulChem and Open Science in Second Life

scifooliveson.wikispaces.com

slide50
Question: 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
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