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SBML Software Matrix2

This matrix provides an at-a-glance summary of software known to us to provide some degree of support for reading, writing, or otherwise working with SBML. The columns' meanings are explained below. For a list of longer descriptions grouped into themes, please see our SBML Software Summary page.

The columns of this table should be read in the following way:

  • Capabilities summarizes the facilities that a package provides by itself (i.e., without invoking another package) for working with SBML: "Creation" = creating/editing models, "Simulation" = performing time-series simulation of models, "Analysis" = analyzing models (e.g., sensitivity analysis, flux-balance analysis, etc.), "Database" = providing a database of models, and "Utility" = providing other utility functions (e.g., translating SBML to/from other formats).
  • Frameworks summarizes the modeling frameworks supported by a package, regardless of whether the package also supports simulation or analysis using those same frameworks: "ODE" = ordinary differential equations, "DAE" = differential-algebraic equations, "PDE" = partial differential equations, "Stochastic" = discrete stochastic simulation, "Events" = discrete events, "Logical" = logical (e.g., Boolean) models, and "Other" = frameworks not listed here.
  • API indicates whether a package exposes an application programming interface to other software systems; entries in this column are the programming languages for which that API is provided. "WS" = web services.
  • Dep. indicates dependencies on other software environments. "MMA" = Mathematica, "BSP" = Bio-SPICE.
  • Platforms indicates the operating systems for under which the software runs. "L" = Linux, "W" = Windows, "M" = MacOS, "B" = web browser-based.
  • SBML indicates whether a package allows importing or exporting SBML, or both. (Level and Version of SBML are not indicated because it is impossible to determine this in all cases without exhaustive research.)
  • Availabil. indicates the availability of the software. "Open source" indicates whether the source code is offered. "Academic use" indicates whether the software is free (F) or for-cost ($) to academic users. "Commericial use" indicates the same for nonacademic use.

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Bruce E. Shapiro and Michael Hucka.

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This page was last modified 20:13, 5 June 2009.

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