Re: [sbml-arrays] Comment on arrays spec

[Fengkai Z. <zha...@ni...>]

Multi takes phorsphorylation status of multiple domains as use cases. I 
would think that array could use them to build cases for 
multidimensional arrays.

Multi applies the "don't care" concept to simplify rules. Also, the 
"occur" attributes allow to model changes of the phorsphorylation status 
of multiple copies of domains without referring individual domains. For 
example, a protein has 2 sites phorsphorylated from 5 phorsphorylation 
sites and two more sites (any two from the remaining 3 unphorsphorylated 
sites) are phorsphorylated in a reason. Not sure if array can do that or 
if it is reasonable to use array for those cases.

Fengkai


On 05/15/2017 04:47 PM, Leandro Watanabe wrote:
> I like Bruce's idea. We talked about the possibility of representing
> some rule-based models using arrays. Maybe we could check with the multi
> group if this is possible.
>
> Leandro
>
> On Mon, May 15, 2017 at 2:25 PM, Bruce Shapiro
> <bru...@gm... <mailto:bru...@gm...>> wrote:
>
>     You could use a multidimensional array to model the states of a
>     reaction that has multiple binding sites, where each dimension
>     represents the occupancy level (e.g., number of phosphorylations) of
>     the site, and the number of dimensions is equal to the number of
>     binding sites. You might similarly build toy models to represent
>     multi-state reactions in this way. This might not  always be the
>     best way to do it in SBML but it parallels a very effective
>     mathematical description. I leave it to others to do the
>     implementations, though.
>

====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Systems Biology, DIR, NIAID
9000 Rockville Pike
Building 4, Room 137
MSC 0421
Bethesda MD 20892
Phone: 301.761.5442
Fax: 301.480.1660
NIAID, National Institutes of Health, DHHS

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