Cheminformatics in Open Notebook Science
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Cheminformatics in Open Notebook Science Advanced Informatics in Chemistry Education At BCCE, Indiana U. Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University July 29, 2008 Open and Closed Science Open Notebook

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Cheminformatics in Open Notebook Science

Advanced Informatics in Chemistry Education

At BCCE, Indiana U.

Jean-Claude Bradley

E-Learning Coordinator

College of Arts and Sciences

Associate Professor of Chemistry

Drexel University

July 29, 2008


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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(unpublished)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



Open primary research in drug design using web2 0 tools blogs wikis second life mailing lists l.jpg

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


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UsefulChem

BLOG

CDD

WIKI

ChemSpider

GoogleDocs

Mailing List






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Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)



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Link to Raw Data with JSpecView(data in JCAMP-DX format)(by Robert Lancashire)








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Searching with Google Custom Search


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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"


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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



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How did this experiment evolve?

Third party timestamp




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Comparing ExperimentsUgi Master Table





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Imine Formation Mechanism:

talk to the molecules!












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Conclusion

  • Communicate first

  • Standardize second

  • In a Science2.0 world redundancy is king


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