Difference between revisions of "Main Page"

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='''[http://www.biopax.org BioPAX] : Biological Pathways Exchange'''=
 
='''[http://www.biopax.org BioPAX] : Biological Pathways Exchange'''=
  
BioPAX is a collaborative effort to create a data exchange format for biological pathway data.  
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[http://www.biopax.org/ BioPAX] is a collaborative effort to create a data exchange format for biological pathway data. BioPAX activity is now mostly documented on this wiki and [http://groups.google.com/group/biopax-discuss?lnk=li BioPAX Forum].
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* [[Level3Announcement | BioPAX Level3 Announcenment]]
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* [[Specification]]
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* [[FAQ]]
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* [http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html BioPAX Paper Published in Nature Biotechnology ]
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* [[Previous Presentations and Publications]]
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* [http://groups.google.com/group/biopax-discuss?lnk=li BioPAX Discussion] is the main public forum for all BioPAX discussions and questions.
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* Archives
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** [http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]
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** [http://groups.google.com/group/BioPAX-Boston biopax-boston]
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** [http://archive.biopaxwiki.org Original Wiki Archive]
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* [[Special:Categories | Wiki Pages by Category]]
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== BioPAX Workgroup Coordination ==
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*[[L4Workgroups| Level 4 Workgroups]]
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<!-- *Level 4 [[BioPAX Workgroup Coordination L4]] Page -->
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*Level 3 [[BioPAX Workgroup Coordination]] Page
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* Next Workshop: [http://co.mbine.org/events/HARMONY_2013 Harmony 2013]
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* Last Workshop:  [http://co.mbine.org/events/COMBINE_2012 COMBINE 2012 Toronto, ON]
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* See [[Past meetings]] to find notes from previous meetings.
  
* [[:Category:SPECIFICATION|BioPAX Specification]]
 
* [[:Category:SOFTWARE|BioPAX Software]]
 
* [[:Category:COMMUNITY|BioPAX Community]]
 
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==[[Level3Announcement]]==
 
==[http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html BioPAX Paper Published in Nature Biotechnology ]==
 
 
== Using BioPAX ==
 
== Using BioPAX ==
 
*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
 
*<b>For biologists and computational biologists interested in downloading and analyzing pathway data</b>
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**[[Software Development Tools]]
 
**[[Software Development Tools]]
  
== [[Documents | Documentation]] ==
 
*[http://www.biopax.org/release/biopax-level3-documentation.pdf Level 3 Documentation (pdf)]
 
*[http://biopax.org/release/biopax-level2-documentation.pdf Level 2 Documentation (pdf)] [http://www.biopax.org/release/biopax-level2.owl another, automatically generated version]
 
*[http://www.biopax.org/release/biopax-level1-documentation.pdf Level 1 Documentation (pdf)] [http://www.biopax.org/release/biopax-level1.owl another, automatically generated version]
 
 
* BioPAX Homepage: http://www.biopax.org/. Note: BioPAX activity is now mostly documented on this wiki.
 
* [[FAQ]]
 
* [[Presentations and Publications]]
 
 
== Community ==
 
* Mailing Lists:
 
**[http://groups.google.com/group/biopax-discuss?lnk=li biopax discuss] - This is the main mailing list for all BioPAX community discussion.
 
* Old Mailing list (Archives still available)
 
**[http://www.biopax.org/mailman/listinfo/biopax-discuss biopax-discuss]
 
**[http://groups.google.com/group/BioPAX-Boston biopax-boston]
 
 
== BioPAX Workgroup Coordination ==
 
*[[L4Workgroups| Level 4 Workgroups]]
 
<!-- *Level 4 [[BioPAX Workgroup Coordination L4]] Page -->
 
*Level 3 [[BioPAX Workgroup Coordination]] Page
 
* Next Workshop: [http://co.mbine.org/events/HARMONY_2013 Harmony 2013]
 
* Last Workshop:  [http://co.mbine.org/events/COMBINE_2012 COMBINE 2012 Toronto, ON]
 
* See [[Past meetings]] to find notes from previous meetings.
 
 
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==Note==
 
==Note==

Revision as of 22:57, 27 March 2013

BioPAX : Biological Pathways Exchange

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. BioPAX activity is now mostly documented on this wiki and BioPAX Forum.



BioPAX Workgroup Coordination

Using BioPAX


Note

BioPAX wiki pages were auto-converted from the MoinMoin to MediaWiki, and this was not perfect. We encourage everyone to review and fix them, e.g., by simply picking up a Random Page.

Original Wiki Archive is still available (readonly).

Known Issues:

  • not all pages were copied, but they are available in the archive (exception: see the next issue)
  • after the conversion, a sub-page name became, e.g., "Page/SubPage", but the parent "Page" still refers to it as [[/SubPage]]. This has to be changed manually to [[Page/SubPage]]
  • attachments were not copied; images can be easily uploaded and linked, but PDF, OWL, etc., cannot
    (there is no simple solution, because the wiki is SourceForge's globally configured and shared application). So, we manually uploaded them to "/other" directory
  • you may find some pages look ugly due to extra spaces before * or # or broken nested lists (must be *, **, ***, etc. or #, ##, ###,..)