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

From OpenWetWare
Jump to: navigation, search
 
(9 intermediate revisions by 2 users not shown)
Line 29: Line 29:
  
 
=Solution: OpenWetWare=
 
=Solution: OpenWetWare=
[http://openwetware.org http://openwetware.org/images/0/03/Openwetwarehomepage.png]
+
[[Image:Openwetwarehomepage.png|800px]]
  
 
</div>
 
</div>
Line 40: Line 40:
 
|  
 
|  
 
# ''Easy and collaborative content generation''
 
# ''Easy and collaborative content generation''
#''Digitization of biological knowledge, as it is generated''
+
# ''Community discourse''
 
|}
 
|}
 
</div>
 
</div>
Line 48: Line 48:
 
=Labs on OpenWetWare=
 
=Labs on OpenWetWare=
  
[http://openwetware.org/wiki/Silver http://openwetware.org/images/3/3f/SilverLabhomepage.png]
+
[[Image:SilverLabhomepage.png|800px]]
  
 
</div>
 
</div>
Line 56: Line 56:
 
=Integrating OpenWetWare into research=
 
=Integrating OpenWetWare into research=
  
[http://openwetware.org/wiki/Silver:_Protocols http://openwetware.org/images/7/7c/SilverProtocolshomepage.png]
+
[[Image:SilverProtocolshomepage.png|800px]]
  
 
</div>
 
</div>
Line 72: Line 72:
 
=Dysfunctionality of Model Publishing=
 
=Dysfunctionality of Model Publishing=
 
[[Image:Icbp-talk-pyramid.png]]
 
[[Image:Icbp-talk-pyramid.png]]
 +
'''figure: Ty Thomson'''
 
</div>
 
</div>
  
Line 77: Line 78:
 
=Systematization and Data Standards=
 
=Systematization and Data Standards=
 
<html><img src="http://www.fotosearch.com/thumb/ICL/ICL154/BIM_116.jpg"</img></html>
 
<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
 
* Communicating with computers, not people
Line 99: Line 104:
 
=YeastPheromoneModel.org=
 
=YeastPheromoneModel.org=
 
[[Image:Yeastpheromonemodel reaction page.png]]
 
[[Image:Yeastpheromonemodel reaction page.png]]
</div>
 
 
<div class="slide">
 
=Existing Data Standards=
 
* MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
 
* SBML - Systems Biology Markup Language
 
 
</div>
 
</div>
  
Line 127: Line 126:
  
 
To be integrated into OWW
 
To be integrated into OWW
 +
 +
Part of a larger workflow:<br>
 +
[[Image:OverallWorkflow.png]]
 
</div>
 
</div>
  

Latest revision as of 06:09, 14 June 2007


<html> <script> function addStylesheet(url) {

   // presentation mode
   if (document.createStyleSheet) {
       document.createStyleSheet(url);
   }
   else {
       var styles = "@import url('" + url +  "');";
       var newSS=document.createElement('link');
       newSS.rel='stylesheet';
       newSS.href='data:text/css,'+escape(styles);
       document.getElementsByTagName("head")[0].appendChild(newSS);
   }

} if (location.href.indexOf('action=render') > 0) {

   document.write("<head><title>Presentation</title></head>"); // need this for some browsers for addStylesheet to work
   addStylesheet('http://www.w3.org/Talks/Tools/Slidy/slidy.css');
   addStylesheet("/skins/monobook/main.css");
   addStylesheet("/index.php?title=MediaWiki:Common.css&usemsgcache=yes&action=raw&ctype=text/css&smaxage=18000");
   addStylesheet("/index.php?title=MediaWiki:Monobook.css&usemsgcache=yes&action=raw&ctype=text/css&smaxage=18000");
   addStylesheet("/index.php?title=-&action=raw&gen=css&maxage=18000&smaxage=0&ts=20070606210926");
   document.write('<script src="http://www.w3.org/Talks/Tools/Slidy/slidy.js" type="text/javascript"><' + '/script>');
   document.write('<script type="text/javascript">wgBreakFrames = false;<' + '/script>'); // for wikibits.js
   document.write('<script src="/skins/common/wikibits.js" type="text/javascript"><' + '/script>');
   document.write('<script src="/index.php?title=-&action=raw&smaxage=0&gen=js" type="text/javascript"><' + '/script>');

} else {

   // wiki mode
   if (wgServer)
       document.write('<a href="' + wgServer + '/index.php?title=' + wgPageName + '&action=render"><b><em>=> Start web presentation</em></b></a>');

} </script> </html>



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