OpenWetWare:Presentations/NCI-ICBP: Difference between revisions

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<h1>''OpenWetWare''</h1>
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<h2>''A wiki for capturing and sharing biological knowledge''</h2>
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<h2>''[[User:Reshma_P._Shetty|Reshma P. Shetty]] and [[User:Jmuhlich|Jeremy Muhlich]]''</h2>
|<h2>''A wiki for capturing and sharing biological knowledge''</h2>
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|<h2>''[[User:Reshma_P._Shetty|Reshma P. Shetty]] and [[User:Jmuhlich|Jeremy Muhlich]]''</h2>
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=Solution: OpenWetWare=
=Solution: OpenWetWare=
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=OpenWetWare's contributions=
=OpenWetWare's contributions=


#''Democratizing and disseminating content generation''
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#''Digitization of biological knowledge, as it is generated''
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# ''Easy and collaborative content generation''
# ''Community discourse''
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=Courses on OpenWetWare=
=Labs on OpenWetWare=


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=Student contributions to OpenWetWare=
=Integrating OpenWetWare into research=


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=Model Construction and Documentation=
=Examining Communication=
 
'''Ethnomethodology:'''
* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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)''
* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''


'''Discourse Analysis'''
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=Dysfunctionality of Model Publishing=
[[Image:Icbp-talk-pyramid.png]]
[[Image:Icbp-talk-pyramid.png]]
'''figure: Ty Thomson'''
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=Models Are Poorly Communicated=
=Systematization and Data Standards=
<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>


Knowledge generated during model building is lost!
* Standards for models
** MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
** SBML - Systems Biology Markup Language


It is difficult to:
* Communicating with computers, not people
* construct a new model
* Rigid, one-way "conversation"
* build on published models
* evaluate published models
* involve experimentalists
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=What About MIRIAM, SBML, etc?=
=Literate Programming=
 
Donald Knuth, 1981
* MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
* 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?
Write programs primarily for humans, not computers
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=YeastPheromoneModel.org=
=YeastPheromoneModel.org=
''Ty Thomson, MIT''
[[Image:Yeastpheromonemodel home page.png]]
[[Image:Yeastpheromonemodel home page.png]]
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=YeastPheromoneModel.org=
=YeastPheromoneModel.org=
[[Image:Yeastpheromonemodel reaction page.png]]
[[Image:Yeastpheromonemodel reaction page.png]]
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=80-20 Rule / Pareto Principle=
[[Image:Pareto.png]]
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=How do we communicate the final 20% ?=
* Verbal, email, etc.
* Wiki
Conversation is robust, and necessary anyway
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=Agile Informatics effort=
[http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Wiki-based model documentation]
''with Brian Joughin, MIT/ICBP''
To be integrated into OWW
Part of a larger workflow:<br>
[[Image:OverallWorkflow.png]]
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="Living" Models=
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Latest revision as of 07:09, 14 June 2007


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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

  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

figure: Ty Thomson

Systematization and Data Standards

<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>

  • 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

YeastPheromoneModel.org

80-20 Rule / Pareto Principle

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:

"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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