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.
| COPASI Build 4.34.251 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/ |
| iBioSim 2.4.2 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. |
| SBMLToolbox 4.1.0 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 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. |
| LibSBMLSim 1.1.0 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. |
| BioUML 0.9.5 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. |
| Vcell 5.1 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). |
| CBMPy 0.7.0 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). |
| FluxBalance 1.9 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. |
| STAR 0.99 |
| BioUML 2018.2 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. |
| WinBEST-KIT 2.0.0 WinBEST-KIT is a biochemical reaction simulator for analyzing complicated metabolic pathways. One particularly notable feature is that users can define original mathematical equations to represent unknown kinetic mechanisms and customize them as GUI components for representing reaction steps. Thus, users can visually arrange their original mathematical equations as GUI components to create the models to be analyzed. Derivation of the mass balance equations, execution of the numerical calculations, and visualization of the simulation results are all performed automatically on the basis of the created model. |
| Morpheus 2.1 Morpheus is a user-friendly and extensible modeling environment for multiscale, multicellular and spatio-temporal systems biology. Morpheus supports the simulation and statistical analysis of (stochastic) spatial cell-based models coupled bi-directionally with ordinary differential equations, reaction-diffusion systems and SBML models. It allows rapid development of multiscale models in biological terms and mathematical expressions rather than programming code. Its graphical user interface supports the entire workflow from model construction and simulation to visualization, archiving and batch processing. For example SBML models can be imported as intra-cellular submodels into existing spatial tissue models. Morpheus is open-source (https://gitlab.com/morpheus.lab/morpheus) and pre-compiled installers are available for Mac/Win/Linux. |
| AMICI 0.11.8 AMICI provides a multi-language (Python, C++, Matlab) interface for the SUNDIALS solvers CVODES (for ordinary differential equations) and IDAS (for algebraic differential equations). AMICI allows the user to read differential equation models specified as SBML and automatically compiles such models as .mex simulation files (Matlab), C++ executables or Python modules. In contrast to the (no longer maintained) sundialsTB Matlab interface, all necessary functions are transformed into native C++ code, which allows for a significantly faster simulation. Beyond forward integration, the compiled simulation file also allows for forward sensitivity analysis, steady state sensitivity analysis and adjoint sensitivity analysis for likelihood based output functions. The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but it is also applicable to a wider range of differential equation constrained optimization problems. |
| Systems Biology Simulation Core Library (SBSCL) 2.1 The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java™ implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution. This library is based on the JSBML project and can be used on every operating system for which a Java Virtual Machine is available. Please note that this project does not contain any user interface, neither a command-line interface, nor a graphical user interface. This project has been developed as a pure programming library. To support the MIASE effort, it understands SED-ML files. Its abstract type and interface hierarchy facilitates the implementation of further community standards, such as CellML. |
| BioStoch/BioSANS 1.0 Symbolic and Numeric Software for Systems Biology |
| SBML_result_files 1.0 This is the original results file from SBML semantic test suite. Just checking if it can perfect score. |
| modelbase 1.2.1 modelbase is a python package to help you build and analyze dynamic mathematical models of biological systems. It has originally been designed for the simulation of metabolic systems, but can be used for virtually any processes, in which some substances get converted into others. |
| SBMLToolkit.jl-Rodas4 0.1.8 |
| libRoadRunner 2.2.0 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. libRoadRunner comes with an extensive documentation including a significant C API, C++ API, Python bindings, ODE solver, structural analysis code, sensitivity, steady state analyses, event handling and stochastic simulation support. It includes significant improvements to performance, back-end design, by using LLVM to compile SBML models to machine code. |
| BioUML 2022.1 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. |
| iBioSim 3.1 iBioSim has been developed for the modeling, analysis, and design of genetic circuits. It supports modeling and visualization support for multi-cellular and spatial models, importing and exporting models specified using the Systems Biology Markup Language (SBML), and is one of the first tools to also support the Synthetic Biology Open Language (SBOL). |