OpenWetWare:Presentations/NCI-ICBP

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{{Slides}}
{{Slides}}
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{{:OpenWetWare:Presentations/jmuhlich1.css}}
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=Solution: OpenWetWare=
=Solution: OpenWetWare=
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[http://openwetware.org http://openwetware.org/images/0/03/Openwetwarehomepage.png]
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[[Image:Openwetwarehomepage.png|800px]]
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# ''Easy and collaborative content generation''
# ''Easy and collaborative content generation''
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#''Digitization of biological knowledge, as it is generated''
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# ''Community discourse''
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<div class="slide">
<div class="slide">
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=Courses on OpenWetWare=
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=Labs on OpenWetWare=
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[http://openwetware.org/wiki/20.109 http://openwetware.org/images/2/2b/20.109homepage.png]
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[[Image:SilverLabhomepage.png|800px]]
</div>
</div>
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<div class="slide">
<div class="slide">
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=Student contributions to OpenWetWare=
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=Integrating OpenWetWare into research=
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[http://openwetware.org/wiki/Talk:20.109%28S07%29:_Measuring_calcium_in_vivo http://openwetware.org/images/2/2a/20.109studentdatapage.png]
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[[Image:SilverProtocolshomepage.png|800px]]
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<div class="slide">
<div class="slide">
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=Model Construction and Documentation=
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=Examining Communication=
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'''Ethnomethodology:'''
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* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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A sociological discipline which focuses on the ways in which people make sense of their world, display this understanding to others, and produce the mutually shared social order in which they live. ''(Wikipedia)''
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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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'''Discourse Analysis'''
</div>
</div>
<div class="slide">
<div class="slide">
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=Dysfunctionality of Model Publishing=
[[Image:Icbp-talk-pyramid.png]]
[[Image:Icbp-talk-pyramid.png]]
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'''figure: Ty Thomson'''
</div>
</div>
<div class="slide">
<div class="slide">
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=Models Are Poorly Communicated=
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=Systematization and Data Standards=
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<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>
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Knowledge generated during model building is lost!
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* Standards for models
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** MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
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** SBML - Systems Biology Markup Language
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It is difficult to:
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* Communicating with computers, not people
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# construct a new model
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* Rigid, one-way "conversation"
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# build on published models
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# evaluate published models
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# involve experimentalists
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</div>
</div>
<div class="slide">
<div class="slide">
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=What About MIRIAM, SBML, etc?=
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=Literate Programming=
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# MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
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Donald Knuth, 1981
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# SBML - Systems Biology Markup Language
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OK for publishing, but too complicated for discovery!
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Write programs primarily for humans, not computers
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Can we design something more "agile" while utilizing and respecting the established standards?
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</div>
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<div class="slide">
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# systematize data
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# follow so-called "80/20" rule
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# "living" models
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# wikis foster communication
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</div>
</div>
<div class="slide">
<div class="slide">
=YeastPheromoneModel.org=
=YeastPheromoneModel.org=
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''Ty Thomson, MIT''
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[[Image:Yeastpheromonemodel home page.png]]
[[Image:Yeastpheromonemodel home page.png]]
</div>
</div>
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=YeastPheromoneModel.org=
=YeastPheromoneModel.org=
[[Image:Yeastpheromonemodel reaction page.png]]
[[Image:Yeastpheromonemodel reaction page.png]]
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</div>
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<div class="slide">
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=80-20 Rule / Pareto Principle=
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[[Image:Pareto.png]]
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</div>
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<div class="slide">
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=How do we communicate the final 20% ?=
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* Verbal, email, etc.
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* Wiki
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Conversation is robust, and necessary anyway
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</div>
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<div class="slide">
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=Agile Informatics effort=
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[http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Wiki-based model documentation]
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''with Brian Joughin, MIT/ICBP''
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To be integrated into OWW
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Part of a larger workflow:<br>
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[[Image:OverallWorkflow.png]]
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</div>
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<div class="slide">
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="Living" Models=
</div>
</div>

Current revision




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

OpenWetWare's contributions

Image:CirEmblemHandwriteLogo2.png
  1. Easy and collaborative content generation
  2. Community discourse

Labs on OpenWetWare

Integrating OpenWetWare into research


Examining Communication

Ethnomethodology: A sociological discipline which focuses on the ways in which people make sense of their world, display this understanding to others, and produce the mutually shared social order in which they live. (Wikipedia)

Discourse Analysis

Dysfunctionality of Model Publishing

Image:Icbp-talk-pyramid.png figure: Ty Thomson

Systematization and Data Standards

  • Standards for models
    • MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
    • SBML - Systems Biology Markup Language
  • Communicating with computers, not people
  • Rigid, one-way "conversation"

Literate Programming

Donald Knuth, 1981

Write programs primarily for humans, not computers

YeastPheromoneModel.org

Ty Thomson, MIT

Image:Yeastpheromonemodel home page.png

YeastPheromoneModel.org

Image:Yeastpheromonemodel reaction page.png

80-20 Rule / Pareto Principle

Image:Pareto.png

How do we communicate the final 20% ?

  • Verbal, email, etc.
  • Wiki

Conversation is robust, and necessary anyway

Agile Informatics effort

Wiki-based model documentation

with Brian Joughin, MIT/ICBP

To be integrated into OWW

Part of a larger workflow:
Image:OverallWorkflow.png

"Living" Models

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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