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Hello

I just wanted to know whether some efforts are underway to incorporate a
flux annotation standard into the SBML specifications (l2v2 or l3?). I
understand from my dicussion with Jeremy Zucker at the Hackathon 2005 that
the Harvard group is working on it. Fluxor does support some flux
annotations at the moment.

A crucial point for decision would be whether the SBML file should contain

(a) flux annotations that would be used as input by a 'flux-simulator',
which would include the objective function (which however, presumes the
use of FBA) and flux constraints, or

(b) flux annotations that would be output by a simulator, which would
include predicted flux values for all fluxes, as solved by the simulator,
based on the given constraints and objective functions (I think Fluxor
uses this idea).

To me, (a) appears better in some ways, as it would be a model definition,
rather than a simulation output. However, (b) is useful if someone is
publishing, say, the conclusions and results of their FBA.

Kindly give your comments.

Thanks

Regards
Karthik Raman


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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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