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Open Notebook Science for Collaborative Drug Development. University of Manchester. Jean-Claude Bradley. E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University. Sept 5, 2008. Open and Closed Science . Open Notebook

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Presentation Transcript
slide1

Open Notebook Science for

Collaborative Drug Development

University of Manchester

Jean-Claude Bradley

E-Learning Coordinator

College of Arts and Sciences

Associate Professor of Chemistry

Drexel University

Sept 5, 2008

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(unpublished)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

slide3

Motivations for ONS

  • Faster Science
  • Better Science
slide4

A recent example in Southampton

Sept 3, 2008 usefulchem.wikispaces.com/exp207

slide8

The Results in a GoogleDoc

reliable

unreliable

slide11

Open Notebook Science

Grand Challenge

Round one

  • design procedures to determine the solubility of compounds in organic solvents
  • teams or individuals welcome
  • Open Notebooks will be validated by experts
  • “mystery prizes” for creativity, productivity, reproducibility and other metrics of scientific quality
  • details coming soon…..
usefulchem project open primary research in drug design using web2 0 tools

UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools

Rajarshi Guha

Indiana U

Tsu-Soo Tan

Nanyang Inst.

Docking

JC Bradley

Drexel U

Synthesis

Phil Rosenthal

UCSF

(malaria)

Dan Zaharevitz

NCI

(tumors)

Testing

slide13

Architecture: Distributed, Interlinked and Redundant

BLOG

CDD

WIKI

Nature Precedings

FriendFeed

JoVE

ChemSpider

GoogleDocs

Mailing List

slide25

How are people finding our experiments?

Specific Compounds

Experimental Conditions

NMR in TFA

Phenylacetaldehyde

c4h6o2 nmr

methylene chloride/methanol

h'nmr of benzophenone

sulfuric acid pka

tertbutylamine

tosyl isocyanide

amino furan

dichloromethane polar?

Reaction between Benzaldehyde and NaBH4

phosphoric acid pka

veratraldehyde wiki

kinetics boc deprotection

Rf value in polar solvent

why glycerol is immiscible with ether

side reaction of imines

5.8 ppm nmr

nmr cdcl3 chloroform side reaction

diasterotopic wiki

adding anhydrous MgSO4 to the dichlormethane ether extraction

hnmr doublet of doublet

Boc-protected NMR

chromatotron recipe

triplet cdcl3 "13c nmr"

slide26

How are people finding UsefulChem?

Educational

Big Picture

free downloading chemistry video

organic chemistry project + high school

how to make poster in second life

organic chem. quiz

3d periodic tables

animation protein docking

docking animation

why are acid-base reactions exothermic?

lysosomal targets

protease and malaria

cheminformatics project proposal

automated reactions

malaria review project synthesis

CHEMISTRY WEB 2.0

projects on QSAR & drug design

chemistry experiment results database

slide34

How did this experiment evolve?

Third party timestamp

slide49

Imine Formation Mechanism:

talk to the molecules!

conclusion
Conclusion
  • Communicate first
  • Standardize second
  • In a Science2.0 world redundancy is king