OpenWetWare:Presentations/NCI-ICBP

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=Model Construction and Documentation=
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=Examining Communication=
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# Ethnomethodology, Discourse Analysis
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# Data standards as communication
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* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''
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[[Image:Icbp-talk-pyramid.png]]
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Dysfunctional communication!
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[[Image:Icbp-talk-pyramid.png]]
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=Model Construction and Documentation=
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* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''
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Revision as of 02:05, 14 June 2007




Image:OWWEmblem.png

OpenWetWare

A wiki for capturing and sharing biological knowledge

Reshma P. Shetty and Jeremy Muhlich

Problem

Much of the knowledge produced by biological research is passed down by oral tradition.

This makes it difficult for newcomers to enter the field.

Solution: OpenWetWare

Openwetwarehomepage.png

OpenWetWare's contributions

Image:CirEmblemHandwriteLogo2.png
  1. Easy and collaborative content generation
  2. Digitization of biological knowledge, as it is generated

Labs on OpenWetWare

SilverLabhomepage.png

Integrating OpenWetWare into research

SilverProtocolshomepage.png


Examining Communication

  1. Ethnomethodology, Discourse Analysis
  2. Data standards as communication

Image:Icbp-talk-pyramid.png Dysfunctional communication!

Model Construction and Documentation

Models Are Poorly Communicated

Knowledge generated during model building is lost!

It is difficult to:

  1. construct a new model
  2. build on published models
  3. evaluate published models
  4. involve experimentalists

What About MIRIAM, SBML, etc?

  1. MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
  2. SBML - Systems Biology Markup Language

OK for publishing, but too complicated for discovery!

Can we design something more "agile" while utilizing and respecting the established standards?

  1. systematize data
  2. follow so-called "80/20" rule
  3. "living" models
  4. wikis foster communication

YeastPheromoneModel.org

Image:Yeastpheromonemodel home page.png

YeastPheromoneModel.org

Image:Yeastpheromonemodel reaction page.png

OpenWetWare's success

  • 2,800 contributors
  • 100 labs
  • 1.5 million pageviews per month
  • 275,000 sessions per month


http://openwetware.org


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