Cheminformatics in Open Notebook Science
Download
1 / 55

Cheminformatics in Open Notebook Science - PowerPoint PPT Presentation

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

Related searches for Cheminformatics in Open Notebook Science

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha

Download Presentation

Cheminformatics in Open Notebook Science

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


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

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(unpublished)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


Older Males Prefer Organic Chemistry!


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


UsefulChem

BLOG

CDD

WIKI

ChemSpider

GoogleDocs

Mailing List


Where’s the Beef?


Link to Lab Notebook Page in Wiki


Link to Molecules


Link to Docking Procedure (Rajarshi Guha)


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


Procedure Section


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


Using ChemSpider to archive compound characterization


ChemSpider predicted vs. experimental NMRs


The Most Important Section!The Log


Conclusion is Fully Supported


Table of Contents


Indexing the Experiments in Google


Searching with Google Custom Search


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"


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


How Should Open Notebook Science be Used?


How did this experiment evolve?

Third party timestamp


http://usefulchem.wikispaces.com/page/diff/Exp037/1577428


http://usefulchem.wikispaces.com/SO+Research+Report


Comparing ExperimentsUgi Master Table


Collaborative Drug Discovery (CDD) Database


YouTube for demonstrating experimental set-up


Mailing List Facilitates inter-group collaboration


Imine Formation Mechanism:

talk to the molecules!


Interacting with NMR spectra (JCAMP-DX)


Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)


Gus Rosania’s Notebook


Cameron Neylon’s Notebook


Using ExcelVBA to automate kinetics analysis


Reaction profile plotted automatically


Results in Machine-Friendly Format


Mettler-Toledo MiniMapper


Mettler-Toledo MiniBlock System


Where is Science headed?

WE ARE HERE


Conclusion

  • Communicate first

  • Standardize second

  • In a Science2.0 world redundancy is king


ad
  • Login