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Dear Brett and Frank,

This looks great. I'd like to release the yeast network
(http://yeast.sf.net/) using the L3 extension rather than Cobra
dialect right away, but don't want to lose my user base. To that end I
have a few questions:

* You mention there is a command-line converter Cobra to Flux
Constraints. Is this publicly available, and does it work in the other
direction (Flux Constraints to Cobra)?

* Are you / the Cobra folks planning to write a parser for direct import
of your models to Cobra?

* If there is no bound defined for a flux, it is unbounded -Inf < J <
Inf. If J is marked reversible="false", should we assume 0 <= J? (I
think this is the assumption made in Cobra right now)

* You mention that (e.g.) a ChEBI annotation could conflict with
fba:chemicalEquation. The same annotation could conflict with fba:charge.

* I'm interpreting "obj3" as "maximise 1.J2 + 1.J3" - is that correct?
So should the other two objectives be interpreted as the same ("maximise
1.J2" and "minimise -1.J2"), or does the presence of a "minimise" mean
its coefficients should be negated?

* I'm a bit worried about the introduction of strict inequalities
("less" and "greater"). Such problems won't generally have a solution
(e.g. minimise x, subject to x > 0), and I think they should be steered
clear of.

Cheers,
Kieran


On 18/03/2011 14:59, Brett G. Olivier wrote:
> Dear SBML Community
>
> We are pleased to announce that version 2 of the SBML L3 extension
> for describing Constraint Based models has been reformulated and is
> now available as a package proposal on sbml.org:
>
> http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Flux_Constraints
>
>In a nutshell: "The Flux Constraints package is a proposed SBML
> Level 3 extension that allows the definition of constraint based
> (a.k.a steady state, flux balance analysis or FBA) models".
>
> We are now interested in hearing your thoughts and comments.
>
> Best regards Brett Olivier& Frank Bergmann

--
kieran smallbone
kieran.smallbone@manchester.ac.uk
http://u003f.com/

manchester centre for integrative systems biology
manchester interdisciplinary biocentre
131 princess street
manchester m1 7dn. uk
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