Flux Balance Constraints
SBML Level 3 Flux Constraints Package Activity Status Page
Please note: This page is for the proposal of this SBML Level 3 package.
Information on this page is likely to be out of date with current developments.
Current development is focused on the specification of this package.
Specification activity is described on a separate page.
The Flux Balance Constraints package is a proposed SBML Level 3 extension that allows the definition of constraint based (a.k.a steady state, flux balance analysis, FBA) models. The proposal also introduces an outline for the annotation of Genome Scale Reconstructions that are typical of this model type.
The short label for this package currently falls under the description fbc.
A separate page is dedicated to the specification development activities involving this package.
The following is a list of the active proposals for Flux Balance Constraints in SBML Level 3:
|Proposal name or identification||Date||Comments|
|Flux Balance Constraints v3 (2012) by B.G. Olivier & F.T. Bergmann||2012|
|Flux Balance v2 (2011) by Brett G. Olivier & Frank T. Bergmann||2011|
Legend for editorial comments:
(1) Proposal has not yet been structured according to the recommended format for SBML Level 3 package proposals.
(2) Proposal needs to be updated for SBML Level 3.
(3) Work in progress—the authors have not finalized this proposal.
Package Working Group (PWG)
After a vote by the SBML community to accept the above proposal as addressing a valid need and taking a reasonable approach towards addressing this need, a working group has been formed to help complete the proposal and work on any implementation issues that may arise. Membership of this group is open to anyone by signing up for the mailing list at: https://lists.sourceforge.net/lists/listinfo/sbml-flux
Activities: FBC-related presentations and material
- 2009 Brett G. Olivier: L3 FBA package discussion (SBML Forum presentation, initial package proposal)
- 2010 Frank T. Bergmann and Brett G. Olivier: SBML Level 3 Package Proposal: Flux (Document: proposal v1)
- 2010 Brett G. Olivier: The SBML Flux Balance Analysis Package (SBML Forum presentation: proposal v1)
- 2011 Brett G. Olivier: The SBML Flux Balance Analysis Package (COMBINE presentation: proposal v2)
- 2011 Brett G. Olivier and Frank T. Bergmann: Flux Balance Constraints Proposal (Document: proposal v2)
- 2011 Brett G. Olivier: Updates to the SBML Level 3 Package: Flux Balance Constraints (COMBINE presentation: updates to v2)
- 2011 Frank T. Bergmann: libSBML FBC package implemented in experimental.
- 2012 Brett G. Olivier and Frank T. Bergmann: Specification currently being drafted: working document available: version 0.2-alpha (20120816).