OpenWetWare:Presentations/NCI-ICBP

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=Solution: OpenWetWare=
=Solution: OpenWetWare=
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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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=Labs on OpenWetWare=
=Labs on OpenWetWare=
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=Integrating OpenWetWare into research=
=Integrating OpenWetWare into research=
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=Dysfunctionality of Model Publishing=
=Dysfunctionality of Model Publishing=
[[Image:Icbp-talk-pyramid.png]]
[[Image:Icbp-talk-pyramid.png]]
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'''figure: Ty Thomson'''
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<div class="slide">
<div class="slide">
=Systematization and Data Standards=
=Systematization and Data Standards=
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* A
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<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>
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* B
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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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* Communicating with computers, not people
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* Rigid, one-way "conversation"
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=Literate Programming=
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Donald Knuth, 1981
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Write programs primarily for humans, not computers
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=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]]
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=Data standards=
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=80-20 Rule / Pareto Principle=
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Rigid, one-way communication
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[[Image:Pareto.png]]
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=Model Construction and Documentation=
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=How do we communicate the final 20% ?=
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* Verbal, email, etc.
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* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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* Wiki
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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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Conversation is robust, and necessary anyway
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<div class="slide">
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=Models Are Poorly Communicated=
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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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Knowledge generated during model building is lost!
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''with Brian Joughin, MIT/ICBP''
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It is difficult to:
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# construct a new model
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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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=What About MIRIAM, SBML, etc?=
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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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OK for publishing, but too complicated for discovery!
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To be integrated into OWW
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Can we design something more "agile" while utilizing and respecting the established standards?
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Part of a larger workflow:<br>
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[[Image:OverallWorkflow.png]]
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<div class="slide">
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# systematize data
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="Living" Models=
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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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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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