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Hi Nick

I think Ben does have some of these in mind. In the Hackathon at Tokyo, I
had indeed discussed with him about people writing some add-on codes to
libSBML, such as extracting a stoichometric matrix, that would be of great
use (there's an example working code for this on the libsbml-discuss web
interface).

It would be great if this and other such routine model tasks would be
integrated into libSBML.

Regards

Karthik

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KARTHIK RAMAN
Graduate Research Student
Supercomputer Education and Research Centre
Indian Institute of Science
Bangalore - 560 012

Phone: +91-80-22932469 (Ext 24)
+91-80-23601409 (Ext 24)
+91-98862-22404 (Mobile)

E-mail : karthik AT rishi.serc.iisc.ernet.in
Webpage : http://rishi.serc.iisc.ernet.in/~karthik/
Blog : karthikraman.blogspot.com

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On Wed, 6 Jul 2005, Nicholas Allen wrote:

>
> It's been roughly 3 years since the idea of SBML L2 was proposed. Since that time, I think that the underlying SBML libraries have gotten quite good at the mechanics of reading and writing SBML. There's still a lot of work left to be done to actually understand and use SBML, but that task is shared with SBML applications. So, I thought I'd ask everyone for their opinions on what SBML libraries should do to help make that happen, and what support is most important. I've come up with a few ways that SBML libraries could support applications better and I'd like to know about other ideas people have.
>
> - Validating models for semantic correctness. libSBML already can do a number of consistency checks on a model mentioned in the L2 specification, but there are some specification requirements left unchecked and it can be difficult to get feedback about what needs to be changed to make a model valid. JigCell has a smaller number of consistency checks, and I'd like to improve on this.
>
> - Translating id references in the model to the actual definition that is being referenced. References in an SBML model give an identifier, and it's up to you to figure out what that identifier actually means. It can be tricky to get this correct because of the way default units work and namespace clashes. I've been adding a number of methods to JigCell to resolve identifiers and I know Ben has mentioned doing this for libSBML as well.
>
> - Support for unit consistency checking and conversion. I know this is a big one as many SBML applications do a pretty poor job handling units at the current time. JigCell does the bare minimum to handle units and leaves it up to applications deal with the problem currently.
>
> - Tools for working with MathML. I think that libSBML has facilities for performing infix<->MathML conversions and JigCell does too, but it's still quite hard to interpret and manipulate MathML expressions after the SBML library has gone over the model.
>
> - Computing higher-level information about a model. There's a lot of duplicated code for computing stoichiometry matrices, differential equations, moiety conservation relations, and the like from a model. SBML libraries could provide these services so that people don't have to write their own. I'm thinking about moving a number of these computations from JigCell applications to the SBML library so that they're available to users.
>
> -- Nick Allen
> nallen@vt.edu
>
>