Re: Handwritten sbml model. Please look.
07 Mar '07 07:39
> Hi thanks for the replys everyone.
> Hello shoops. That method of removing the reactions all together is very interesting, can most models be represented in alternate forms like that?
> Hello Frank Bergmann. You say you shouldn't write SBML by hand, but rather use a tool to help you? What generator do you use? Whats the best one out there etc?
> If i had a rule or a number of rules that define each of my models, as described in shoops post:
> dx1/dt = u - k * x1
> Is there a generator that could generate sbml from that alone, or would I still have to supply the various species, reactions, compartments etc?
As far as I know, Henning Schmidt's Matlab package in its latest or
upcoming release can generate even the SBML reaction network from such
ODEs, but I guess you might need a some additional information on
Generally I would recommend to have the full reaction network in SBML
rather then ODEs (SBML rate rules) only. This just contains more
information about the model and allows a range of software/algorithms to
better analyse your system. It also makes extensions of the models, or
integration with other models, easier.
> Once again thank you for your help.
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