Flux Balance Constraints
SBML Level 3 Flux Constraints Package Activity Status Page
Contents |
Package objectives
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.
Active proposals
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 | (3) |
| 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.
FBC Package Working Group
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
Active specifications
There are no active specifications for the SBML Level 3 Annotations package at this time.
A provisional definition for SBML Flux Constraints has been produced by Olivier and Bergmann and has been in use since 2009. This implementation utilizes SBML Level 2 annotation elements to store additional information.
Flux Constraints related workshops, meetings 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)