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:Jmuhlich|Jeremy Muhlich]] and [[User:Reshma_P._Shetty|Reshma P. Shetty]]''</h2>
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''Much of the knowledge produced by biological research is passed down by oral tradition.''
''Much of the knowledge produced by biological research is passed down by oral tradition.''


''This makes it difficult for newcomers, especially in Systems Biology due to its multi-disciplinary nature.''
''This makes it difficult for newcomers to enter the field.''
 
</div>
 
<div class="slide">
 
=Solution: OpenWetWare=
[[Image:Openwetwarehomepage.png|800px]]
 
</div>
 
<div class="slide">
=OpenWetWare's contributions=
 
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# ''Easy and collaborative content generation''
# ''Community discourse''
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<div class="slide">
 
=Labs on OpenWetWare=
 
[[Image:SilverLabhomepage.png|800px]]
 
</div>
</div>


<div class="slide">
<div class="slide">
=OpenWetWare=


''OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.''
=Integrating OpenWetWare into research=


''OpenWetWare seeks to capture information not usually recorded in biological research. It offers a complement to traditional publishing mediums and enables new modes of collaboration.''
[[Image:SilverProtocolshomepage.png|800px]]


</div>
</div>


<div class="slide">
<div class="slide">
=OpenWetWare's contributions=
=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'''
</div>


#''Democratizing and disseminating content generation''
<div class="slide">
#''Digitization of biological knowledge, as it is generated''
=Dysfunctionality of Model Publishing=
[[Image:Icbp-talk-pyramid.png]]
'''figure: Ty Thomson'''
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</div>


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=Courses on OpenWetWare=
=Systematization and Data Standards=
<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>


''[[20.109]], [[Talk:20.109(S07): Measuring calcium in vivo|Student-recorded data]]''
* Standards for models
** MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
** SBML - Systems Biology Markup Language


''"The wiki has also been unspeakably useful in developing curricula with my fellow teaching faculty and teaching assistants. Finally, with all the course material public, researchers and teachers around the world have stumbled into the site and have subsequently contacted me to discuss implemented parts of the curriculum in other settings. Other electronic teaching platforms exist, but none is so collaborative and open."''
* Communicating with computers, not people
* Rigid, one-way "conversation"
</div>


--''[[User:Nkuldell|Natalie Kuldell]], Department of Biological Engineering, MIT''
<div class="slide">
=Literate Programming=
Donald Knuth, 1981


Write programs primarily for humans, not computers
</div>


''"This course has turned out to be a big success. I never expected that the students would engage so well in the class. One reason they have engaged so fully is that the students feel that they have some control over the content and they can see that the materials they post are creating a record and an organized resource. Hosting on OWW also allowed the more reserved students in the class to participate fully by writing down questions and comments on the wiki so they didn't have to depend so much on speaking in class."''
<div class="slide">
=YeastPheromoneModel.org=
''Ty Thomson, MIT''


--''[[User:Hoatlinm|Maureen Hoatlin]], Department of Biochemistry and Molecular Biology, Oregon Health & Science University''
[[Image:Yeastpheromonemodel home page.png]]
</div>


''See [[Courses|all 20 OpenWetWare courses]]''
<div class="slide">
=YeastPheromoneModel.org=
[[Image:Yeastpheromonemodel reaction page.png]]
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</div>


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<div class="slide">
= Model Construction and Documentation=
=80-20 Rule / Pareto Principle=
[[Image:Pareto.png]]
</div>


* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
<div class="slide">
* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''
=How do we communicate the final 20% ?=
* Verbal, email, etc.
* Wiki


Conversation is robust, and necessary anyway
</div>
<div class="slide">
=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]]
</div>
<div class="slide">
="Living" Models=
</div>
</div>


<div class="slide">
<div class="slide">
=OpenWetWare's success=
=OpenWetWare's success=
* 2,800 contributors
 
* 100 labs
* ''2,800 contributors''
* 1.5 million pageviews per month
* ''100 labs''
* 275,000 sessions per month
* ''1.5 million pageviews per month''
* ''275,000 sessions per month''


<br>
<br>
<span style="font-size:300%;">http://openwetware.org</span>
<span style="font-size:300%;">http://openwetware.org</span>
</div>
</div>


__NOTOC__
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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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