Difference between revisions of "OpenWetWare:Presentations/NCI-ICBP"

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{{Slides}}
 
{{Slides}}
  
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<div class="slide cover">  
 
{|
 
{|
|rowspan=10|[[Image:OWWEmblem.png]]  
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|[[Image:OWWEmblem.png]]  
|-
+
|
|-
+
<h1>''OpenWetWare''</h1>
|-
+
 
|-
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<h2>''A wiki for capturing and sharing biological knowledge''</h2>
|<h1>''OpenWetWare''</h1>
+
 
|-
+
<h2>''[[User:Reshma_P._Shetty|Reshma P. Shetty]] and [[User:Jmuhlich|Jeremy Muhlich]]''</h2>
|<h2>''A wiki for capturing and sharing biological knowledge''</h2>
 
|-
 
|<h2>''[[User:Reshma_P._Shetty|Reshma P. Shetty]] and [[User:Jmuhlich|Jeremy Muhlich]]''</h2>
 
|-
 
|-
 
|-
 
|-
 
 
|}
 
|}
 
</div>  
 
</div>  
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=Solution: OpenWetWare=
 
=Solution: OpenWetWare=
[http://openwetware.org http://openwetware.org/images/0/03/Openwetwarehomepage.png]
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[[Image:Openwetwarehomepage.png|800px]]
  
 
</div>
 
</div>
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|[[Image:CirEmblemHandwriteLogo2.png]]
 
|[[Image:CirEmblemHandwriteLogo2.png]]
 
|  
 
|  
# ''Democratizing and disseminating content generation''
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# ''Easy and collaborative content generation''
#''Digitization of biological knowledge, as it is generated''
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# ''Community discourse''
 
|}
 
|}
 
</div>
 
</div>
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<div class="slide">
 
<div class="slide">
  
=Courses on OpenWetWare=
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=Labs on OpenWetWare=
  
[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">
  
=Student contributions to OpenWetWare=
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=Integrating OpenWetWare into research=
  
[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]]
  
 
</div>
 
</div>
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<div class="slide">
 
<div class="slide">
=Model Construction and Documentation=
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=Examining Communication=
 
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'''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'''
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
 +
=Dysfunctionality of Model Publishing=
 
[[Image:Icbp-talk-pyramid.png]]
 
[[Image:Icbp-talk-pyramid.png]]
 +
'''figure: Ty Thomson'''
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
=Models Are Poorly Communicated=
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=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"
 +
</div>
  
Knowledge generated during model building is lost!
+
<div class="slide">
 +
=Literate Programming=
 +
Donald Knuth, 1981
  
It is difficult to:
+
Write programs primarily for humans, not computers
# construct a new model
 
# build on published models
 
# evaluate published models
 
# involve experimentalists
 
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
=What About MIRIAM, SBML, etc?=
+
=YeastPheromoneModel.org=
# MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
+
''Ty Thomson, MIT''
# SBML - Systems Biology Markup Language
+
 
 +
[[Image:Yeastpheromonemodel home page.png]]
 +
</div>
  
OK for publishing, but too complicated for discovery!
+
<div class="slide">
 +
=YeastPheromoneModel.org=
 +
[[Image:Yeastpheromonemodel reaction page.png]]
 +
</div>
  
Can we design something more "agile" while utilizing and respecting the established standards?
+
<div class="slide">
 +
=80-20 Rule / Pareto Principle=
 +
[[Image:Pareto.png]]
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
# systematize data
+
=How do we communicate the final 20% ?=
# follow so-called "80/20" rule
+
* Verbal, email, etc.
# "living" models
+
* Wiki
# wikis foster communication
+
 
 +
Conversation is robust, and necessary anyway
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
=YeastPheromoneModel.org=
+
=Agile Informatics effort=
[[Image:Yeastpheromonemodel home page.png]]
+
[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]]
 
</div>
 
</div>
  
 
<div class="slide">
 
<div class="slide">
=YeastPheromoneModel.org=
+
="Living" Models=
[[Image:Yeastpheromonemodel reaction page.png]]
 
 
</div>
 
</div>
  

Latest revision as of 06:09, 14 June 2007


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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

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

Labs on OpenWetWare

SilverLabhomepage.png

Integrating OpenWetWare into research

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

Icbp-talk-pyramid.png 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 home page.png

YeastPheromoneModel.org

Yeastpheromonemodel reaction page.png

80-20 Rule / Pareto Principle

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:
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