Re: A Level 3 extension for Constraint Based models
23 Mar '11 08:12
Hello All,
I am joining this discussion late but still would like to put my 2 cents in.
1) fba:listOfObjectives
This is in my opinion not SBML material it obviously describes what to
do with the model. Unless SBML changes its doctrine about describing the
model and not the analysis, this part should be removed from the
extension. I nevertheless think that this information should be
captured. It falls under the umbrella of MIASE and should therefore be
encoded in SED-ML.
2) fba:listOfGeneAssociations
This is annotation and should be handled independently from this package
in a general form (e.g. the annotation package)
3) fba:chemicalEquation
This is also annotation and should be handled independently from this
package in a general form (e.g. the annotation package)
This leaves only 1 new edition which is fba:listOfFluxBounds about which
I have some question.
Why are we not using MathML to describe the bounds?
Why do we distinguish between less/lessEqual and
greater/greaterEqual?
The last distinction will make the implementation much harder as it
requires any analysis tool to do algebraic operations since numerically
comparison will not suffice.
Thanks,
Stefan
--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA
| 
23 Mar '11 08:12
