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Tmp index

This interactive index lists SBML-compatible software and their features. The data is provided by the software authors through our SBML Software survey. If the view below is too small, try the full window mode instead.

(Currently disabled.)

Explanation of the feature selectors:

  • Category: How do the software authors classify their software in terms of functionality? Many software tools fall into more than one category. (For example, many simulation systems also have editing and visualization capabilities.)
  • Dependencies: What other software does this software package depend upon? (For example, a few software tools here depend on MATLAB.)
  • Capabilities: What facilities does the package provide by itself (without invoking another software 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 = implementing a database of models (and not merely access to an external database); and Utility = providing other utility functions (e.g., translating SBML to/from other formats).
  • Frameworks: What are the modeling frameworks supported by the software package, regardless of whether the software actually permits simulating models in those frameworks? (For example, an editing tool might allow the creation of models to use various modeling frameworks, but not be able to perform simulation or analysis itself.) ODE = ordinary differential equations; DAE = differential-algebraic equations; PDE = partial differential equations; DDE = delay-differential equations; Stochastic = discrete stochastic simulation; Events = discontinuous event handling; Logical = logical/boolean networks.
  • API: Does the software expose an application programming interface (API), such that users and software can interact with it programmatically? If yes, this will list the languages supported.
  • SBML Import/Export: Does the software support importing SBML or exporting SBML, or both?
  • Supported Versions: What SBML Level and Version combinations does the software support?
  • Supported Features: What are the aspects of SBML that the software supports?
  • Quantitative Understanding: In terms of interpretation/simulation/analysis/output performed by the software, what is the most complex degree of quantitative or mathematical understanding that the software can perform with SBML models? Species, reactions, parameters, compartments = interpret/manipulate/display species, reactions, parameters, and/or compartments; Reaction kinetics = work with reaction kinetics; Stoichiometric relationships = work with stoichiometric relationships/maps; Other mathematical relationships = work with mathematical relationships in a model; Conditional discontinuous events = work with conditional discontinuous events; Time delays = work with time delays (i.e., functions involving time – timedelay).
  • Other Standards: What are other standards that the software is compatible with?
  • Availability: Under what terms, and for which classes of users, is the software available? The two main classes of users distinguished here are academic and non-academic (i.e., commercial) users. In addition, this indicates whether the source code for the software is available, and whether the code may be redistributed by users under open-source terms.
  • Platforms: What are the operating systems supported by the software package?
  • URL Reachable (Computed automatically): Does the software's URL appear to be reacheable? (We run a periodic check of URLs in an effort to detect dead links and orphaned software projects.)
  • Country (Computed automatically): What is the country of origin of the software? (This is based on the IP address of the software's URL.)
  • Last Updated (Computed automatically): How recently has the information in this database been updated by the software's author? In other words, how recently have the authors submitted information to us using the SBML Software survey?

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This page was last modified 19:22, 15 July 2011.



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