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Multistate and Multicomponent Species

(Active proposals)
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Revision as of 14:57, 28 March 2009

SBML Level 3 Package Activity Status Page

Contents

Package objectives

Many models and modelers want to represent biochemical species that have internal structure or state properties. These may involve molecules that have multiple potential states, such as a protein that may be covalently modified, and molecules that combine to form heterogeneous complexes located among multiple compartments. The resulting system of reactions needs to be generated based on the combinatorial possibilities inherent in the definition of the species and on user-specified rules. The purpose of the SBML Level 3 Multistate and Multicomponent Species package is to provide a means for doing this in SBML.

The short label for this package is multi.

Active proposals

The SBML Development Process for SBML Level 3 defines two stages: a proposal stage, and a specification development stage. The following is a list of the active proposals for Multistate and Multicomponent Species in SBML Level 3:

Proposal name or identification Date Comments
Multistate and Multicomponent Species Proposal 2008-08-27 (3)

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.

Active specifications

There are no active specifications for the SBML Level 3 Multistate and Multicomponent Species package at this time.

History of proposals

Proposals for supporting multistates and multicomponent species have a long history in SBML. Here is a reconstruction in chronological order:

  • In March 2004, before the the 2nd SBML hackathon, Andrew Finney published an updated proposal to encode complex species made up of several components. Planed as an extension for SBML Level 3, the document also described SpeciesTypes that would later be incorporated to SBML Level 2, from version 2 onward.
  • In October 2004, Michael Blinov published, together with Jim Fader, Byron Goldstein, Andrew Finney and Bill Hlavacek, an alternative proposal for encoding multi-component species, that also contained some possibilities of encoding multistate features.
  • Anika Oellrich started to implement a new SBML L2 support for StochSim in spring 2007, storing multistate information in proprietary annotations. This led in June 2007 to a proposal for Level 3 by Le Nov&egravere and Oellrich and Le Novere proposal multistates, meant to work in conjunction with 2004 Finney's multicomponents proposal. The proposal was presented at the 12th SBML forum meeting. A light correction was published in December 2007.


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