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Re: Introduction

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Tue, 16 Dec 2008 19:25:13 +0100
Message-ID: <5639badd0812161025y1393788aybe5f25934c08a9ba@mail.gmail.com>
To: "Kei Cheung" <kei.cheung@yale.edu>
Cc: public-semweb-lifesci@w3.org

     Hello Kei, All,

  Thanks for the interest. I think yes, there are also neuron models.

  Here are models published by VCell users, which you can access by
logging onto the VCell:

  http://vcell.org/applications/published%20_models.html

  You can also import any model in SBML, for example from here:

  http://biomodels.net/

  Our project (http://vcell.org/biopax) is opening the way for BioPAX
import to the VCell. We recommend most BioPAX data from Reactome:

  http://reactome.org/

  Other pathway databases supporting BioPAX can be found here:

  http://www.biopaxwiki.org/cgi-bin/moin.cgi/

  I think all of these sources have models relating to neurons.

     Take care
     Oliver


On Sun, Dec 14, 2008 at 5:36 AM, Kei Cheung <kei.cheung@yale.edu> wrote:
> Hi Oliver,
>
> Thanks for the introduction. I just wonder if Virtual Cell includes model of
> neurons (a kind of nerve cell).
>
> Cheers,
>
> -Kei
>
> Oliver Ruebenacker wrote:
>
>>    Hello All,
>>
>>  I just joined the SWHCLSIG and thought I introduce myself:
>>
>>  I work for the Virtual Cell [1] at the Center for Cell Analysis and
>> Modeling [2] at the University of Connecticut Health Center [3].
>>
>>  My current project [4] aims to integrate formats for molecular
>> pathways, especially BioPAX [5] and SBML [6], aiming to include other
>> formats in the future. For this project, we have developed a Java
>> application called Systems Biology Linker (Sybil), which makes
>> extensive use of Semantic Web technologies (including querying,
>> reasoning and program-based ontology-building) with the help of Jena
>> [7] and an ontology we developed called Systems Biology Pathway
>> Exchange (SBPAX).
>>
>>  I am also facilitating the bi-weekly meetings of the BioPAX-OBO
>> group [8], which aims to integrate BioPAX into the OBO Foundry [9], a
>> task that requires an extensive revision of BioPAX.
>>
>>  I am looking forward to working with others on the greater goal of
>> integrating biomedical knowledge using Semantic Web technologies.
>>
>>    Take care
>>    Oliver
>>
>>  [1]  Virtual Cell - http://vcell.org
>>  [2]  Center for Cell Analysis and Modeling - http://www.ccam.uchc.edu
>>  [3]  University of Connecticut Health Center - http://www.uchc.edu
>>  [4]  My current project - http://vcell.org/biopax/
>>  [5]  BioPAX - http://www.biopax.org/, http://www.biopaxwiki.org/
>>  [6]  SBML - http://sbml.org
>>  [7]  Jena - http://jena.sourceforge.net/
>>  [8] Every second, fourth and last Tuesday, 3pm to 6pm, in Stata
>> Center, MIT. Contact me if interested.
>>  [9]  OBO Foundry - http://www.obofoundry.org/
>>
>>
>
>



-- 
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
Received on Tuesday, 16 December 2008 18:25:49 GMT

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