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

[Peter Hunter]

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...
> 
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