First login?
Lost password?
 
 
cellml-discussion AT lists.cellml.org 
CellML Discussion List

Text archives Help


[cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"


Chronological Thread 
  • From: e.crampin at auckland.ac.nz (Edmund J. Crampin)
  • Subject: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"
  • Date: Tue, 03 Jun 2008 19:01:08 +1200
James, I thought yours was a rhetorical question, no?
Edmund

James Lawson wrote:
> Hi Peter,
>
> I guess I framed it as a question to the community, but it was more of
> a leading question that I'd like to address in the paper on the
> repository. What I'm really talking about is the common preconception
> that SBML and CellML are designed to fill the same niches. The niches
> overlap but are not the same; I see the idea of CellML as part of the
> Physiome Project as being quite a powerful way of explaining its niche.
>
> With respect to the existence of multiple standards, I would go even
> further: it is essential to have more than one standard for
> representing this kind of information, lest the standard define the
> field, rather than the field defining the standard.
>
> Cheers,
> James Lawson
>
>
> Peter Hunter wrote:
>> Hi James,
>>
>> Re your final question - the Physiome Project at the moment is
>> largely about (i) the development of the markup languages CellML and
>> FieldML (& maybe ModelML for the physics) and their associated model
>> repositories and software tools, and (ii) strategies for bridging
>> spatial and temporal scales. I see no reason at all not to include
>> neuroscience in this picture - in fact there are a number of
>> initiatives relating to a 'brain physiome' just getting underway. The
>> essence of the Physiome is the recognition of the need to link models
>> of structure and function across spatial scales from nm to m and
>> temporal scales from brownian motion to human lifetime turnover of
>> proteins. Easy to say ...
>>
>> While CellML and SBML are in some way competing standards, both
>> communities are helping one another greatly by promoting the idea of
>> modelling standards .. and provided we can convert between them,
>> there's no particular disadvantage in having two standards.
>>
>> Cheers,
>> Peter
>>
>> James Lawson wrote:
>>> Hi folks,
>>>
>>> Pretty interesting read. I actually came to what I do now through a
>>> heavy cellular neurosci background so this disconnect between
>>> systems biology and neurosci is something that has really bugged me.
>>> They mention in the paper that SBML doesn't provide the spatial
>>> support needed for it to be useful to computational neuroscientists.
>>> CellML with its emphasis on multiscalar integration and modularity
>>> along with FieldML to describe the geometric information could
>>> address these issues.
>>>
>>> Also, I'm always interested in how CellML is represented in these
>>> kinds of publications. It is usually seen (as in this paper,) by
>>> systems biologists as a competing language for describing systems
>>> biology, which is understandable but only partly true. I think we
>>> need to seriously market CellML as a Physiome language, a lot more
>>> than we do. This will be a topic in the upcoming paper about the
>>> CellML repository I'm starting to put together - that is: the name
>>> of the software is Physiome Model Repository 2 - what has it got to
>>> do with the Physiome Project then?
>>>
>>>
>>> Kind regards,
>>> James
>>>
>>> David Nickerson wrote:
>>>> Why Are Computational Neuroscience and Systems Biology So Separate?
>>>> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000078
>>>>
>>>>
>>>>
>>>> some interesting comments, although not totally accurate...
>>>
>>> _______________________________________________
>>> cellml-discussion mailing list
>>> cellml-discussion at cellml.org
>>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>> _______________________________________________
>> cellml-discussion mailing list
>> cellml-discussion at cellml.org
>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>


Archive powered by MHonArc 2.6.18.

Top of page