Test results for SBML-compatible software systems

The following is an alphabetical list of all software systems represented in the SBML Test Suite Database along with the most recent results made publicly available by their authors. Updates to these results are made when software authors or their representatives upload new results for SBML-compatible software packages.

BioUML 0.9.5 Latest submission Website BioUML is an open source integrated Java platform for building virtual cell and virtual physiological human. It spans a comprehensive range of capabilities, including access to databases with experimental data, tools for formalized description of biological systems structure and functioning, as well as tools for their visualization, simulation, parameters fitting and analyses. Due to scripts (R, JavaScript) and workflow support it provides powerful possibilities for analyses of high-throughput data. The plug-in based architecture (Eclipse run time from IBM is used) allows to add new functionality using plug-ins.
CBMPy 0.7.0 (Not yet available) Website PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist (metabolites, reactions, compartments) while transparently translating these into the underlying mathematical structures used in advanced analysis (LP, MILP).
COPASI Build 42 Latest submission Website COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. For a complete list of feature please see: http://copasi.org/Support/Features/
FluxBalance 1.9 Latest submission Website FluxBalance is a teaching tool for Flux Balance analysis. It fully supports the SBML Level 3 Flux Balance Constraints Package, as well as the SBML Layout Package. It can also be used with SBML Level 2 models using these packages as annotations.
iBioSim 2.4.2 Latest submission Website The iBioSim tool supports the modeling, analysis, and design of genetic circuits with applications in both systems and synthetic biology. It includes editors to construct genetic circuit models (GCM), Systems Biology Markup Language (SBML) models (L2V4 and L3V1 supported), and labeled Petri net (LPN) models. Models can be constructed by hand, imported from model databases, or learned from experimental data. These models can be analyzed using a variety of ODE and stochastic simulators as well as Markov chain analysis. The efficiency of these analysis methods is enhanced using a variety of automatic reaction-based and logical abstractions. The analysis results can be plotted as graphs or visualized upon the genetic circuit schematic.
libRoadRunner 1.3 Latest submission Website A high performance and portable simulation engine for systems and synthetic biology, libRoadRunner can run on many platforms including Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the original C# roadRunner developed by Frank Bergmann and Herbert Sauro. The same original functionality however remains, including the original C API, the structural analysis code, sensitivity and steady state analyses, but with significant improvements to performance, back-end design, better event handling, new C++ API and stochastic simulation support.
libRoadRunner-legacyC 1.2.3 (Not yet available) Website libRoadRunner is a high performance and portable simulation engine for systems and synthetic biology. It can run on many platforms including Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the original C# roadRunner developed by Frank Bergmann and Herbert Sauro. The same original functionality however remains, including the original C API, the structural analysis code, sensitivity and steady state analyses, but with significant improvements to performance, back-end design, better event handling, new C++ API and stochastic simulation support. In this version of the software, instead of the default LLVM compiler, the 'legacy C' compiler is used instead, which does not have all the capabilities of the default LLVM version.
LibSBMLSim 1.1.0 Latest submission Website LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs), Differential Algebraic Equations (DAEs) and Delay Differential Equations (DDEs). LibSBMLSim provides simple command-line tool and APIs for several programming languages (C, C++, Java, C#, Python and Ruby) to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.
RoadRunner 2.10.0 Latest submission Website roadRunner is a high performance simulator for cellular networks. roadRunner accepts standard SBML (Levels 1-3) and generates the necessary ordinary differential equations that are solved either by CVODE to generate time course data or NLEQ to compute the steady state. roadRunner supports many functions, including: 1.ODE simulation and steady state analysis; 2.Conservation analysis to ensure a non-singular Jacobian; 3.Steady state metabolic control analysis; 4.Frequency domain metabolic control analysis; 5.Simple continuation of steady states
SBMLToolbox 4.1.0 (Not yet available) Website SBMLToolbox is built on top of libSBML and provides a set of basic functions allowing SBML models to be used in both MATLAB and Octave. SBMLToolbox provides functions for creating and validating models; and manipulating and simulating these models using ordinary differential equation solvers.
Simulation Core Library 1.2 Latest submission Website Simulation Core Library is a fast, accurate, and easily usable program for dynamic simulation of models encoded in the Systems Biology Markup Language (SBML). In order to ensure a high reliability of this software, it has been benchmarked against the entire SBML Test Suite (all levels and versions) and all models from the Biomodels.net database. Simulation Core Library is included into SBMLsimulator, which includes a large collection of nature-inspired heuristic optimization procedures for efficient model calibration and provides an intuitive Graphical User Interface (GUI). Simulation Core Library runs on all platforms that provide a standard Java Virtual Machine and is based on the open-source library JSBML.
STAR 0.99 Latest submission Website
Vcell 5.1 (Not yet available) Website VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. Free, registration required. Open source, source code available upon request. (Linux/Mac/Win/Web).