OpenWetWare:Presentations/NCI-ICBP: Difference between revisions
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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> | ||
<div class="slide"> | <div class="slide"> | ||
=Problem= | =Problem= | ||
''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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=Solution: OpenWetWare= | =Solution: OpenWetWare= | ||
[[Image:Openwetwarehomepage.png|800px]] | |||
[[Image:Openwetwarehomepage.png]] | |||
</div> | </div> | ||
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=OpenWetWare's contributions= | =OpenWetWare's contributions= | ||
#'' | {| | ||
#'' | |[[Image:CirEmblemHandwriteLogo2.png]] | ||
| | |||
# ''Easy and collaborative content generation'' | |||
# ''Community discourse'' | |||
|} | |||
</div> | </div> | ||
<div class="slide"> | <div class="slide"> | ||
= | =Labs on OpenWetWare= | ||
[[Image: | [[Image:SilverLabhomepage.png|800px]] | ||
</div> | </div> | ||
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<div class="slide"> | <div class="slide"> | ||
= | =Integrating OpenWetWare into research= | ||
[[Image: | [[Image:SilverProtocolshomepage.png|800px]] | ||
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= | =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> | ||
<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"> | ||
= | =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> | ||
<div class="slide"> | <div class="slide"> | ||
= | =Literate Programming= | ||
Donald Knuth, 1981 | |||
Write programs primarily for humans, not computers | |||
</div> | </div> | ||
<div class="slide"> | <div class="slide"> | ||
=YeastPheromoneModel.org= | =YeastPheromoneModel.org= | ||
''Ty Thomson, MIT'' | |||
[[Image:Yeastpheromonemodel home page.png]] | [[Image:Yeastpheromonemodel home page.png]] | ||
</div> | </div> | ||
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=YeastPheromoneModel.org= | =YeastPheromoneModel.org= | ||
[[Image:Yeastpheromonemodel reaction page.png]] | [[Image:Yeastpheromonemodel reaction page.png]] | ||
</div> | |||
<div class="slide"> | |||
=80-20 Rule / Pareto Principle= | |||
[[Image:Pareto.png]] | |||
</div> | |||
<div class="slide"> | |||
=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> | ||
Latest revision as of 07:09, 14 June 2007
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