List of all test result submissions

This page provides a list of all the test results publicly available in the SBML Test Suite Database. Updates to these results are made when software authors or representatives upload new results for SBML-compatible software packages.

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RoadRunner 2.10.0 Submitted 1/2/2013 11:01:01 AM by frank.thomas.bergmann@gmail.com View test results

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

 

Recent RoadRunner test run, against full testsuite


BioUML 0.9.5 Submitted 1/15/2013 8:21:03 AM by Ilya View test results

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.

 

BioUML 0.9.4 results. Test suite 2.2. Level 3 version 1. If model was absent, level 2 version 4 model was used instead.


RoadRunner 2.10.0 Submitted 1/16/2013 9:48:12 AM by Fbergmann View test results

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

 

New RoadRunner build using a newer version of the SBMLSupport library that handles comp.


COPASI Build 4.23.189 Submitted 1/16/2013 9:59:48 AM by Fbergmann View test results

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/

 

Results from COPASI snapshot


Simulation Core Library 1.2 Submitted 1/17/2013 7:26:28 AM by RolandKeller View test results

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.

 

The simulation results for Simulation Core Library. AbsTol was set to 10E-14, relTol to 10E-10.


iBioSim 2.4.2 Submitted 1/17/2013 3:54:11 PM by myers View test results

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.

 

Results for iBioSim 2.4.


LibSBMLSim 1.1.0 Submitted 1/31/2013 11:04:58 AM by funa View test results

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.

 

libSBMLSim


iBioSim 2.4.2 Submitted 2/4/2013 2:13:54 PM by myers View test results

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.

 

iBioSim 2.4.2


Simulation Core Library 1.2 Submitted 3/28/2013 5:30:54 AM by RolandKeller View test results

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.

 

The results for simulating all models of the Test Suite with Rosenbrock solver.


BioUML 0.9.5 Submitted 6/4/2013 10:06:31 AM by Ilya View test results

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.

 

BioUML 0.9.5 tests


FluxBalance 1.9 Submitted 7/21/2014 12:10:34 AM by frank_bergmann View test results

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.

 

no description given


libRoadRunner 1.3 Submitted 12/29/2014 3:40:52 PM by lpsmith View test results

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.

 

Results created with libRoadRunner version 1.3


STAR 0.99 Submitted 3/19/2016 9:37:38 PM by mikeev View test results

 

no description given


COPASI Build 4.23.189 Submitted 6/12/2018 1:19:58 AM by frank_bergmann View test results

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/

 

latest build


BioUML 2018.2 Submitted 6/18/2018 1:45:49 AM by Ilya View test results

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.

 

Latest results


WinBEST-KIT 2.0.0 Submitted 12/20/2018 10:33:33 PM by sekiguchi View test results

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.

 

no description given


Morpheus 2.1 Submitted 1/18/2019 6:08:38 AM by Morpheus View test results

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.

 

SBML test results for Morpheus 2.1.0 (https://morpheus.gitlab.io) using SBML Test Suite 3.3.0 (DOI:10.5281/zenodo.1112521)