OpenWetWare:Presentations/NCI-ICBP: Difference between revisions

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=Systematization and Data Standards=
=Systematization and Data Standards=
* A
<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>
* B
 
* Communicating with computers, not people
* Rigid, one-way "conversation"
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=Literate Programming=
Donald Knuth, 1981
 
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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=Data standards=
=Existing Data Standards=
Rigid, one-way communication
* MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
* SBML - Systems Biology Markup Language
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=Model Construction and Documentation=
=80-20 Rule / Pareto Principle=
 
[[Image:Pareto.png]]
* [http://yeastpheromonemodel.org YeastPheromoneModel.org] -- ''Ty Thomson, MIT''
* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''
 
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=Models Are Poorly Communicated=
=How do we communicate the final 20% ?=
 
* Verbal, email, etc.
Knowledge generated during model building is lost!
* Wiki


It is difficult to:
Conversation is robust, and necessary anyway
# construct a new model
# build on published models
# evaluate published models
# involve experimentalists
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=What About MIRIAM, SBML, etc?=
=Agile Informatics effort=
# MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
[http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Wiki-based model documentation]
# SBML - Systems Biology Markup Language


OK for publishing, but too complicated for discovery!
''with Brian Joughin, MIT/ICBP''


Can we design something more "agile" while utilizing and respecting the established standards?
To be integrated into OWW
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# systematize data
="Living" Models=
# follow so-called "80/20" rule
# "living" models
# wikis foster communication
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Revision as of 01:35, 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

http://openwetware.org/images/0/03/Openwetwarehomepage.png

OpenWetWare's contributions

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

Labs on OpenWetWare

http://openwetware.org/images/3/3f/SilverLabhomepage.png

Integrating OpenWetWare into research

http://openwetware.org/images/7/7c/SilverProtocolshomepage.png


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

Systematization and Data Standards

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

  • 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

Existing Data Standards

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

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

"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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