SBML Level 3 Package Activity Status Page
Quantitative methods for modeling biologicals network require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. For most biologicals networks, this knowledge is missing. This has led to the development of many qualitative modeling methods using, for example, information such as gene expression data coming from functional genomic experiments. The components used in these models are fundamentally different from species and reactions used in current SBML models. For example, entity pools in these models represent discrete levels of activities rather than amounts of matter; the processes involving them cannot be described as reactions per se (i.e., they are not events-per-time) but rather as transitions between states. Boolean networks, logical models and some petri-nets are examples of this type of model. Despite these differences from traditional SBML models, it is still desirable to somehow bring these classes of models together. The purpose of the Qualitative Models package for SBML Level 3 is to support the necessary additions to SBML.
The short label for this package is qual.
A separate page is dedicated to the specification development activities involving this package.
This proposal was accepted by community vote and has now entered the specification phase.
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 Qualitative Models in SBML Level 3:
|Proposal name or identification||Date||Comments|
|SBML-L3-qual-proposal_2.1.pdf||2011-05-14||(1), (2), (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.
Package Working Group (PWG)
After a vote by the SBML community to accept the above proposal as something that addresses a valid need and takes a reasonable approach, we formed a working group to help complete the proposal and resolve any implementation issues that might arise. Membership of this group is open to all interested members of the SBML community; all you need to do is sign up for the sbml-qual mailing list.