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Re: Introduction

From: Kei Cheung <kei.cheung@yale.edu>
Date: Fri, 02 Jan 2009 23:24:31 -0500
Message-ID: <495EE87F.6090908@yale.edu>
To: Oliver Ruebenacker <curoli@gmail.com>
CC: public-semweb-lifesci@w3.org

Hi Oliver,

Thanks for the information. I've gone through the list of Vcell models 
available at http://vcell.org/applications/published%20_models.html. I 
found two models related to Purkinje cell or neuron:

http://www.ncbi.nlm.nih.gov/pubmed/16169982?dopt=Abstract
http://www.ncbi.nlm.nih.gov/pubmed/18487300?ordinalpos=10&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum

These two models may be complementary to some of the purkinje cell 
related models listed in SenseLab's ModelDB

http://senselab.med.yale.edu/modeldb/ModelList.asp?id=271

If so, it might be interesting.

Cheers,

-Kei

 Oliver Ruebenacker wrote:

>     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/
>>>
>>>
>>>      
>>>
>>    
>>
>
>
>
>  
>
Received on Saturday, 3 January 2009 04:25:15 GMT

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