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Arrays and Sets

SBML Level 3 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Information on this page is likely to be out of date with current developments.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.

Package objectives

The primary motivation for proposing this capability is that many types of models use large numbers of more-or-less identical components, and it is convenient (if not practically necessary in very large models) to be able to use an indexing scheme to reference these components. (Or as Bruce Shapiro put it succinctly in 2006, "Arrays allow us to describe a bunch of stuff without listing every item explicitly every time".) Another motivation is the desire to support models having elements and structures whose spatial geometries are not important; these elements might more conveniently be referenced as indexed entities rather than individually-named entities. A final motivation is to support abstract mathematical models. Additional motivations and history of the arrays and sets effort in SBML are available on a separate page.

The short label for this package is arrays.

Package specifications

A separate page is dedicated to the specification development activities involving this package.

Package 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 Arrays and Sets in SBML Level 3:

Proposal name or identification Date Comments
Proposal by Finney et al. 2003-09-05 (1), (2), (3)
Proposal by Shapiro et al. 2004-12-21 (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.

These proposals largely overlap, but differ in their support for dynamic creation/destruction of components. Both of these proposals need significant updating to fit into the syntax and organization emerging for SBML Level 3. These proposals also need to be combined into one consensus 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-arrays mailing list.

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This page was last modified 02:47, 9 July 2013.

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