OpenWetWare:Presentations/NCI-ICBP

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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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|<h1>''OpenWetWare''</h1>
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<h2>''[[User:Reshma_P._Shetty|Reshma P. Shetty]] and [[User:Jmuhlich|Jeremy Muhlich]]''</h2>
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|<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.''
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''This makes it difficult for newcomers, especially in Systems Biology due to its multi-disciplinary nature.''
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''This makes it difficult for newcomers to enter the field.''
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<div class="slide">
<div class="slide">
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=Solution: OpenWetWare=
 
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[[Image:Openwetwarehomepage.png]]
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=Solution: OpenWetWare=
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[[Image:Openwetwarehomepage.png|800px]]
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=OpenWetWare's contributions=
=OpenWetWare's contributions=
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#''Democratizing and disseminating content generation''
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{|
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#''Digitization of biological knowledge, as it is generated''
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|[[Image:CirEmblemHandwriteLogo2.png]]
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# ''Easy and collaborative content generation''
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# ''Community discourse''
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<div class="slide">
<div class="slide">
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=Courses on OpenWetWare=
 
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''[[20.109]], [[Talk:20.109(S07): Measuring calcium in vivo|Student-recorded data]]''
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=Labs on OpenWetWare=
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''"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."''
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[[Image:SilverLabhomepage.png|800px]]
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--''[[User:Nkuldell|Natalie Kuldell]], Department of Biological Engineering, MIT''
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''"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."''
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=Integrating OpenWetWare into research=
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--''[[User:Hoatlinm|Maureen Hoatlin]], Department of Biochemistry and Molecular Biology, Oregon Health & Science University''
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[[Image:SilverProtocolshomepage.png|800px]]
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''See [[Courses|all 20 OpenWetWare courses]]''
 
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</div>
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<div class="slide">
<div class="slide">
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=Model Construction and Documentation=
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=Examining Communication=
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'''Ethnomethodology:'''
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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)''
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* [http://yeastpheromonemodel.org YeastPheromoneModel.org]  -- ''Ty Thomson, MIT''
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'''Discourse Analysis'''
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* [http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Agile Informatics project] -- ''Jeremy Muhlich, HMS/CDP; Brian Joughin, MIT/ICBP''
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</div>
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<div class="slide">
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=Dysfunctionality of Model Publishing=
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[[Image:Icbp-talk-pyramid.png]]
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'''figure: Ty Thomson'''
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</div>
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<div class="slide">
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=Systematization and Data Standards=
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<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>
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* Standards for models
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** MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
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** SBML - Systems Biology Markup Language
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* Communicating with computers, not people
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* Rigid, one-way "conversation"
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</div>
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<div class="slide">
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=Literate Programming=
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Donald Knuth, 1981
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Write programs primarily for humans, not computers
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</div>
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<div class="slide">
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=YeastPheromoneModel.org=
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''Ty Thomson, MIT''
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[[Image:Yeastpheromonemodel home page.png]]
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</div>
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<div class="slide">
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=YeastPheromoneModel.org=
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[[Image:Yeastpheromonemodel reaction page.png]]
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</div>
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<div class="slide">
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=80-20 Rule / Pareto Principle=
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[[Image:Pareto.png]]
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</div>
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<div class="slide">
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=How do we communicate the final 20% ?=
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* Verbal, email, etc.
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* Wiki
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Conversation is robust, and necessary anyway
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</div>
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<div class="slide">
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=Agile Informatics effort=
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[http://ome-sorger7.mit.edu/~jmuhlich/mwtest/ Wiki-based model documentation]
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''with Brian Joughin, MIT/ICBP''
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To be integrated into OWW
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Part of a larger workflow:<br>
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[[Image:OverallWorkflow.png]]
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</div>
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<div class="slide">
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="Living" Models=
</div>
</div>

Current revision




Image: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

OpenWetWare's contributions

Image:CirEmblemHandwriteLogo2.png
  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

Image:Icbp-talk-pyramid.png figure: Ty Thomson

Systematization and Data Standards

  • 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

Image:Yeastpheromonemodel home page.png

YeastPheromoneModel.org

Image:Yeastpheromonemodel reaction page.png

80-20 Rule / Pareto Principle

Image: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:
Image: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


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