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Re: Introduction

From: Oliver Ruebenacker <curoli@gmail.com>
Date: Mon, 5 Jan 2009 21:40:52 -0500
Message-ID: <5639badd0901051840m3e188f9eqb4694534eeedad28@mail.gmail.com>
To: "Kei Cheung" <kei.cheung@yale.edu>
Cc: public-semweb-lifesci@w3.org

     Hello Kei, All,

  I don't know NEURON or it's format, but after a brief glance, my
first impression is that NEURON works quite like a typical
SBML-compatible simulator (tracking concentrations in an arrangement
of compartments), so there should be a way to convert to and from
SBML, or otherwise it should be possible to convince some one to
create such a way. Do you know people involved with NEURON you could
ask?

     Take care
     Oliver

On Fri, Jan 2, 2009 at 11:24 PM, Kei Cheung <kei.cheung@yale.edu> wrote:
> 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/
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>



-- 
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, 6 January 2009 02:41:29 GMT

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