Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"
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.178 some interesting comments, although not totally accurate... begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"
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.178 some interesting comments, although not totally accurate... ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:Peter Hunter FRS n:Hunter;Peter org:University of Auckland;Auckland Bioengineering Institute (ABI) adr:70 Symonds St;;Level 6;Auckland;;;New Zealand email;internet:[EMAIL PROTECTED] title:Director tel;work:+649 373 7599 x88395 tel;fax:+649 367 7157 tel;home:+649 307 6662 tel;cell:+6421 505033 url:http://www.bioeng.auckland.ac.nz/ version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"
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.178 some interesting comments, although not totally accurate... ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion begin:vcard fn:James Lawson n:Lawson;James org:Auckland Bioengineering Institute;CellML Model Repository Curator, CellML Team adr:;;University of AucklandNew Zealand email;internet:[EMAIL PROTECTED] title:James Lawson url:http://www.cellml.org version:2.1 end:vcard ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] in case you haven't seen it | "Why Are Computational Neuroscience and Systems Biology So Separate?"
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.178 some interesting comments, although not totally accurate... >>> >>> ___ >>> cellml-discussion mailing list >>> cellml-discussion@cellml.org >>> http://www.cellml.org/mailman/listinfo/cellml-discussion >> ___ >> cellml-discussion mailing list >> cellml-discussion@cellml.org >> http://www.cellml.org/mailman/listinfo/cellml-discussion >> > > ___ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion > ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
