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{{Slides}}
{{Slides}}


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{|
|[[Image:OWWEmblem.png]]
|
<h1>''OpenWetWare''</h1>
 
<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 class="slide">
=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.''
 
</div>
 
<div class="slide">
 
=Solution: OpenWetWare=
[[Image:Openwetwarehomepage.png|800px]]
 
</div>
 
<div class="slide">
=OpenWetWare's contributions=
 
{|
|[[Image:CirEmblemHandwriteLogo2.png]]
|
# ''Easy and collaborative content generation''
# ''Community discourse''
|}
</div>
 
<div class="slide">
 
=Labs on OpenWetWare=
 
[[Image:SilverLabhomepage.png|800px]]
 
</div>
 
<div class="slide">
 
=Integrating OpenWetWare into research=
 
[[Image:SilverProtocolshomepage.png|800px]]
 
</div>
 
 
<div class="slide">
=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>
 
<div class="slide">
=Dysfunctionality of Model Publishing=
[[Image:Icbp-talk-pyramid.png]]
'''figure: Ty Thomson'''
</div>
 
<div class="slide">
=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>


<div class="slide">
<div class="slide">
<h1>OpenWetWare</h1>
=Literate Programming=
Donald Knuth, 1981


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


''OpenWetWare seeks to capture information not usually recorded in biological research and offers a complement to traditional publishing mediums.''
<div class="slide">
=YeastPheromoneModel.org=
''Ty Thomson, MIT''
 
[[Image:Yeastpheromonemodel home page.png]]
</div>
</div>


<div class="slide">
<div class="slide">
<h1>Motivation</h1>
=YeastPheromoneModel.org=
[[Image:Yeastpheromonemodel reaction page.png]]
</div>


''As engineers learning biology, we struggle with the fact that much of biological research can't be learned from books and papers.''
<div class="slide">
=80-20 Rule / Pareto Principle=
[[Image:Pareto.png]]
</div>
</div>


<div class="slide">
<div class="slide">
<h1>OpenWetWare's contributions</h1>
=How do we communicate the final 20% ?=
* Verbal, email, etc.
* Wiki


#''Democratizing and disseminating content generation''
Conversation is robust, and necessary anyway
#''Digitization of biological knowledge, as it is generated''
#''Making biological research easier''
</div>
</div>


<div class="slide">
<div class="slide">
<h1>Courses on OpenWetWare</h1>
=Agile Informatics effort=
[http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Wiki-based model documentation]
 
''with Brian Joughin, MIT/ICBP''
 
To be integrated into OWW


''[[20.109]], [[Talk:20.109(S07): Measuring calcium in vivo|Student-recorded data]]''
Part of a larger workflow:<br>
[[Image:OverallWorkflow.png]]
</div>


''"The collaborative environment [of OpenWetWare] is a powerful pedagogical tool, requiring my students become responsible contributors to the subject. The wiki has also been unspeakably useful in developing curricula with my fellow teaching faculty and teaching assitants. 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."''
<div class="slide">
="Living" Models=
</div>
 
<div class="slide">
=OpenWetWare's success=


--''[[User:Nkuldell|Natalie Kuldell]], Department of Biological Engineering, MIT''
* ''2,800 contributors''
* ''100 labs''
* ''1.5 million pageviews per month''
* ''275,000 sessions per month''


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


''See [[Courses|all OpenWetWare courses]]''
</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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