UsefulChem: An Open Notebook Science Project

UsefulChem:An Open Notebook Science Project

Jean-Claude Bradley

E-Learning Coordinator College of Arts and Sciences

Associate Professor of ChemistryDrexel University

Oct 23, 2007

ASIS&T Panel :Opening Science to All: Implications of Blogs and Wikis

for Social and Scholarly Scientific Communication

Open and Closed ScienceOpen and Closed Science

TraditionalLab Notebook(unpublished)

TraditionalJournal Article

Open Access Journal Article

Open Notebook Science (full transparency)

CLOSED

OPEN

Where is Science headed?Where is Science headed?

WE ARE HEREWE ARE HERE

How will this happen?How will this happen?

Self-organizing redundant processesSelf-organizing redundant processes Agents can Read/Write with zero cost Agents can Read/Write with zero cost

(free hosted services – e.g. Google)(free hosted services – e.g. Google) Publication of all aspects of the Publication of all aspects of the

scientific process: scientific process: Open Notebook Open Notebook ScienceScience

How can machines know what How can machines know what is important?is important?

Ask the humansAsk the humans

UsefulChem BlogUsefulChem Blog

What chemists think is What chemists think is important in 2005important in 2005

Malaria is a Logical Application Malaria is a Logical Application of Open Scienceof Open Science

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

•Not a lucrative market: IP control less important

Find-A-DrugFind-A-Drug

Diketopiperazine LibraryDiketopiperazine LibraryEvolves to: on pot Evolves to: on pot

Ugi Ugi reaction/cyclizationreaction/cyclization

First iteration: First iteration: Solid Support Solid Support

SynthesisSynthesis

The Molecules BlogThe Molecules Blog

The Experiments BlogThe Experiments Blog

Comments from peersComments from peers

The UsefulChem WikiThe UsefulChem Wiki

Telling the story of the failuresTelling the story of the failures

Experiments moved to wikiExperiments moved to wiki

Experiment HistoryExperiment History

Experiment EditsExperiment Edits

Third Party Time-Stamp on Third Party Time-Stamp on Experiment VersionsExperiment Versions

Monitoring experimental Monitoring experimental progressprogress

How are people finding our How are people finding our experiments?experiments?

Molecules found by InChIMolecules found by InChI

Graphical Mining of Data with Graphical Mining of Data with JSpecViewJSpecView

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

usefulchem.blogspot.comusefulchem.blogspot.com

The blog as an integrative The blog as an integrative tooltool

Processing Molecules on Processing Molecules on ChemSpiderChemSpider

Open Primary Research in Drug Design Open Primary Research in Drug Design using Web2.0 toolsusing Web2.0 tools

(blogs, wikis, Second Life, mailing (blogs, wikis, Second Life, mailing lists)lists)

Docking

Synthesis

Testing

Rajarshi GuhaIndiana U

JC BradleyDrexel U

Phil RosenthalUCSF

(malaria)

Dan ZaharevitzNCI

(tumors)

Tsu-Soo TanNanyang Inst.

Mailing List Facilitates inter-Mailing List Facilitates inter-group collaborationgroup collaboration

UsefulChem and Open UsefulChem and Open Science in Second LifeScience in Second Life

scifooliveson.wikispaces.com

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

YESYES QuestionQuestion: What if I make a mistake in my data, never fix it, : What if I make a mistake in my data, never fix it,

no one catches it, and then someone dies because a no one catches it, and then someone dies because a medical decision was based on my "findings"? Isn't this medical decision was based on my "findings"? Isn't this exactly why we have formal peer review in formal exactly why we have formal peer review in formal publications? publications?

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

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

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

For UsefulChem, wiki is for chemists, blog for wider For UsefulChem, wiki is for chemists, blog for wider audienceaudience

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

We’ll find out….We’ll find out…. QuestionQuestion: Can scientists establish their : Can scientists establish their

credibilities/reputation by writing blogs and wikis? credibilities/reputation by writing blogs and wikis? Certainly we’ve found collaborators this wayCertainly we’ve found collaborators this way