SBML Software Matrix
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. Please use the survey form to notify us about omissions, updates and suggestions.
The columns of this table should be read in the following way:
- Recent contact indicates whether we have heard from the software's developer(s) or maintainer(s) within roughly a year's time. It can be taken as some indication that the software appears to be maintained actively.
- 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.
- 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.
Please use the survey form to notify us about additions and suggestions.
Frank Bergmann, Bruce E. Shapiro and Michael Hucka.