# SBML Software Summary

This page lists software known to us to provide some degree of support for reading, writing, or otherwise working with SBML. For an at-a-glance matrix summarizing key features of these software packages, please see our SBML Software Matrix page. Please use the survey form to notify us about additions and suggestions.

Note that several of the ODE/DAE-based simulators also include some form of stochastic simulation capability, and vice-versa. Also most of the model simulation, development, and analysis tools listed elsewhere on this page include some form of visualization.

## Analysis software (in addition to, or instead of, simulation)

- ABC-SysBio — ABC-SysBio implements likelihood free parameter inference and model selection in dynamical systems. It is designed to work with both stochastic and deterministic models written in Systems Biology Markup Language (SBML). ABC-SysBio is a Python package that combines three algorithms: ABC rejection sampler, ABC SMC for parameter inference and ABC SMC for model selection.
- AMIGO — AMIGO means Advanced Model Identification using Global Optimization. AMIGO is a multi-platform (Windows and Linux) matlab-bsed toolbox which covers all the steps of system identification in systems biology. This includes: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.
- APMonitor — The APMonitor Modeling Language is optimization software for differential and algebraic equations. It is coupled with large-scale nonlinear programming solvers for data reconciliation, real-time optimization, dynamic simulation, and nonlinear predictive control. It is available as a free web service through MATLAB or Python.
- AutoSBW — A frontend around AUTO to simplify bifurcation analysis. The program allows to open SBML models (up to Level 3), and interprets them using AUTO 2000.
- Bifurcation Discovery Tool — The Bifurcation Discovery Tool uses a genetic algorithm to search for Hopf bifurcations, turning points, and bistable switches. The user can select parameters to be searched, admissible parameter ranges, and the nature of the bifurcation to be sought. The tool returns parameter values for the model for which the particular behavior is observed.
- BioBayes — software package for applying the Bayesian inferential methodology to problems in systems biology.
- BioMet Toolbox — The BioMet ToolBox is a web-based resource for analysis of high-throughput data, together with methods for flux analysis (fluxomics) and integration of transcriptome data exploiting the capabilites of metabolic networks described in genome scale models.
- BioNetGen — BioNetGen is a software system for the specification and simulation of rule-based models of biochemical systems. In rule-based models, molecules and molecular complexes are represented using graphs, and molecular interactions and their consequences are represented using graph-rewriting rules. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. (Linux/Mac/Win)
- BioPARKIN — Robust and reliable parameter identification (e.g. rate constants) in biology-related systems described by (sets of) ODEs or DAEs from given measurement data, based on an affine covariant Gauss-Newton algorithm. Additionally, providing a sensible, parameter depending sensitivity analysis for the ODE/DAE systems.
- BoolNet — An R package for the generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
- ByoDyn — ByoDyn includes a set of tools to 1) integrate ordinary differential equations (ODEs), including systems with events, rules (differential algebraic equations, DAE) and delays built from a given biological model; 2) stochastic simulators: SSA and tau-leap; 3) globally optimize the parameters that fit the provided experimental information and evaluate the sensitivity of the model with respect to the different parameters; 4) include the sensitivity of the parameters in an optimal experimental design pipeline based on the Fisher information matrix; and 5) Monte Carlo sampling coupled with cluster analysis and PCA to determine the global shape of the parameter landscape. The program makes use of external software, providing a Python binding schema that allows the user to easily implement new software in the desired calculation protocol. Furtermore, a webserver has been developed to manage the models, calculations and results easily.
- CADLIVE — CADLIVE (Computer-Aided Design of LIVing systEms) is a comprehensive computational tool for constructing large-scale biological network maps, analyzing the topological features of them, and simulating their dynamics. Using CADLIVE, we rationally design a biological system at the molecular interaction level for an engineering purpose.
- CARMEN — CARMEN provides the KGML-based model generation of metabolic pathways based on KEGG database information and the application of template-based models for comparative genomics. This software will be of interest in genome sequencing projects aiming at the rapid analysis and visualization of microbial metabolic features. The KGML-based model generation facilitates a high-speed generated overview of the metabolic repertoire. The comparative analysis of newly sequenced organisms is highly desirable to identify organism-specific features. The reconstructed networks are stored in standardized SBML format.
- CBMPy — PySCeS CBMPy is a new platform for constraint based modelling and analysis. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures used in advanced simulations (LP's, MILP's). PySCeS CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as methods developed specifically for the ecosystem modeling. To cater for a diverse range of modelling needs CBMPy supports user interaction via interactive console for advanced use or as a library for tool development. In addition GUIs are provided for quick access to a visual representation of the model and annotation.
- Cell Collective — The Cell Collective allows laboratory scientists working in different areas of the cell to collectively integrate their knowledge and create large-scale (rule-based) computational models of biological/biochemical networks in a non-technical fashion. Models created in the Cell Collective can be published and made available to the whole community, or shared with a selected group of collaborators, or completely kept private. The software provides an environment not only for the construction and sharing of computational (logic-based) models, but also for real-time, interactive simulations, as well as automated experiments consisting of hundreds of simulations.
- CellNetAnalyzer — CellNetAnalyzer (CNA) is a package for MATLAB and provides a comprehensive and user-friendly environment for structural and functional analysis of biochemical networks. CNA facilitates the analysis of metabolic (stoichiometric) as well as signaling and regulatory networks solely on their network topology, i.e. independent of kinetic mechanisms and parameters. CNA provides a powerful collection of tools and algorithms for structural network analysis which can be started in a menu-controlled manner within interactive network maps. Recently, API functionalities have been added to enable interested users to call algorithms of CNA from external programs. Applications of CNA can be found in systems biology, biotechnology, metabolic engineering, pharmacology, microbiology, chemical engineering.
- CellNOpt — CellNOpt is a software used for creating logic-based models of signal transduction networks using different logic formalisms (Boolean, Fuzzy, or differential equations). CellNOpt uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against high-throughput biochemical data to create cell-specific models. CellNOpt is freely available under GPL license in R and Matlab languages. It can be also accessed through a python wrapper, and a Cytoscape plugin called CytoCopter provides a graphical user interface.
- COBRA — The COnstraint-Based Reconstruction and Analysis Toolbox for Matlab includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models.
- COPASI — 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. Export to: C code, XPP, Berkley Madonna, MathML, TeX Please see the COPASI detailed description for a complete list of features.
- CRdata — CRdata.org offers menu-driven access to the Amazon Elastic Computing Cloud (EC2) and related resources for bioinformatic computing with R and Bioconductor. Users can launch their own processing nodes, and share nodes, scripts, and data with others if they wish.
- DBSolve — DBSolveOptimum is a free software for kinetic modeling of metabolic pathways, analysis, and fitting parameters to experimental data. The program has text-based user interface for model description and graphical interface for data analysis. In addition to standart algorithms of simulation (ODE solver, explicit solver, steady-state analysis) the software includes also the automated local sencetivity analysis, parameters optimization procedures and bifurcaion analysis. The last version of DBSolveOptimum includes the advanced tool for data visualization.
- DEDiscover — Perform simulation and parameter estimation of models described be ordinary and delayed differential equations. Also perform model selection through statistical analysis (Fisher's information, Bootstrapping), residual analysis and sensitivity analysis.
- DOTcvpSB — MatLab toolbox for optimization of models.
- EPISIM — The EPISIM consists of EPISIM Modeller (graphical modeling system) and EPISIM Simulator (simulation environment). Each EPISIM (multi-scale) model comprises a cell behavioral and a biomechanical model (CBM and BM). The BM covers all spatial and biophysical cell properties. Different BMs (lattice and off-lattice) are offered by the simulation environment. A BM can be dynamically linked to a CBM which is graphically modeled with process diagrams in the EPISIM Modeller. Automatic semantic integration of quantitative subcellular SBML models in CBMs is possible. The graphical CBMs are automatically compiled into executable code which is loaded by the EPISIM Simulator conducting an agent-based tissue simulation. EPISIM Simulator embeds COPASI to simulate SBML-based models. This allows linking of discrete (deterministic / stochastic) and continuous models on cellular on subcellular scale. Reaction-Diffusion models of e.g. chemokines can be integrated in a multi-scale tissue model with extracellular diffusion fields.
- Facile — Facile / EasyStoch. A command-line network compiler for systems biology. Facile reads models given in a simple and human-readable textual input format and exports the model in a format for readable by Matlab, Mathematica, Maple, XPP/AUTO. Other tools are supported via SBML export. For stochastic simulations, Facile uses the EasyStoch stochastic simulator. An important feature of EasyStoch that distinguishes it from other Gillespie-algorithm implementations is that it is capable of simulating dynamically changing or noisy biochemical parameters (i.e. extrinsic noise).
- FAME — The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. Manually drawn custom maps that are compatible with FAME are also available for certain species. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/ .
- FASIMU — FASIMU is a command line oriented software implementing the most frequently applied FBA algorithms. It offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins. The platform-independent program is an open-source project, freely available under GNU public license, including manual, tutorial, BiNA and Cytoscape plugin and respective manuals.
- FBASBW — A program allowing to define flux constraints using SBML annotations.
- FlexFlux — FlexFlux is a java tool for metabolic flux and regulatory network analysis. To analyse metabolic fluxes, FlexFlux is based on a mathematical method, FBA which consists in transforming a metabolic network into linear equations and calculate fluxes thanks to linear programming. Concerning the regulatory network analysis, FlexFlux supports multistate qualitative regulatory networks. This regulatory network is composed of components of different natures (genes, mRNAs, proteins, metabolites ...), that interact with each other in different ways and can have an effect on the metabolic network. FlexFlux performs synchronous updates of the regulatory network state from provided initial values. Once a steady-state of this regulatory network is reached, the states are translated into continuous intervals (see the regulation file section) used as constraints for the FBA. We named this pipeline Regulatory Steady-state Analysis (RSA). FlexFlux contains many methods dedicated to regulatory network and flux analysis.
- FluxBalance — Teaching tool for defining flux balance constraints using the SBML Level 3 FBC Package, or SBML L2 annotations.
- Fluxor — Flux analysis. Free, part of BioSpice tool set. Linux.
- Genetic Network Analyzer — Genetic Network Analyzer (GNA) is a computer tool for the modeling, simulation, analysis and verification of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a qualitative model of a genetic regulatory network from knowledge about regulatory interactions and gene expression data. GNA provides a variety of functions to analyze the steady-state and transient dynamics of the network, among other things by exploiting state-of-the-art model-checking tools.
- GINsim — GINsim is dedicated to the logical modelling of regulatory and signalling networks. It allows model definition and provides numerous functionalities for model analyses, including import and export facilities.
- GNU MCSim — GNU MCSim is a free standalone simulation package that allows you to design your own statistical or simulation models. It efficiently performs Bayesian inference through Markov Chain Monte Carlo simulations. Standard Monte Carlo and experimental design optimization are also available. GNU MCSim can import and simulate levels 1 and 2 SBML models
- iBioSim — 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, labeled Petri net, and general biochemical models encoded in the Systems Biology Markup Language (SBML). Models can be constructed using either a schematic or textual editor, 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.
- IBRENA — To aid the analysis of complex biological reaction networks, we have developed a user-friendly program called “Insilico Biochemical REaction Network Analysis (IBRENA)”. This program is written in MATLABTM (The Mathworks, Inc., Natick, MA) with a Graphical User Interface (GUI). In order to reduce computation time, in some cases, ordinary differential equations (ODEs) are solved using Visual FORTRAN (HP-Compaq V6.6, Palo Alto, CA) with integrated IMSL library (Visual Numerics Inc., Houston, TX). This reduces the computational time required for time-consuming sensitivity analysis (described in Chapter 4 of the manual). This application can be deployed on a PC using Windows.
- Jacobian Viewer — The Jacobian matrix is of central importance in the analysis of a computational model. The Jacobian specifies the local dynamics of the model. The entries in the matrix indicate the influence of model variables on the rates of change.The Jacobian Viewer will dynamically show these changes. In order to do so we generate a dependency graph for a computational model, with nodes denoting all species in the model and arcs denoting the influence of one species on the rates of change of another species. This provides insight of how those changes occur. The researcher is of course able to change the time-steps taken by the simulator as well as the starting point of the simulation.
- Jarnac — SBW tool for metabolic analysis, includes dynamic simulation. Simulation engine for JDesigner. BSD License.
- JigCell — JigCell is a set of computational tools with user-friendly interfaces developed for studying complex biochemical regulatory systems in general and the cell cycle control system in particular. For example, The JigCell Model Builder (JCMB) aides the modeler in defining a system to be modeled using SBML with a novel spreadsheet interface, allowing a large amount of data to be displayed in an organized manner. The JigCell Run Manager (JCRM) allows a user to specify a set of specifications for simulation runs using a spreadsheet interface. JigCell Aggregation Connector has been designed to define models in terms of components, for the purpose of being combined in a larger model. JigCell also aims in parameter estimation. A parameter estimator (PET, Parameter Estimation Toolkit) takes a biological model, experimental data, and the relationship between the model and data. Using this information the parameter estimator uses numerical tools to vary the parameters to the model looking for the parameters that best fit the experimental data.
- JSim — JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also supports model archive formats SBML (import and export) and CellML (import only).
- KEGGconverter — KEGGconverter automatically produces merged and converted to SBML fully functional pathway models, enhanced with default kinetics, by inputting only KGML files.The final derived models do not enclose trivial metabolites -reproducing inconsistencies of the KGML visualization-oriented, simplified information pattern- but at the same time they contain all the available information regarding the number of the included reactions in each pathway. Furthermore, additional reactions to neighbouring pathways are constructed which indicate the direction of the metabolic flows in the network and thus providing better stability in the boundary conditions of the models.
- libRoadRunner — libRoadRunner is a high performance SBML simulator (based on an LLVM backend) that includes additional features such as steady state, jacobian, eigenvalues, conservation analysis and sensitivity analysis. It supports full SBML except for delay and non-linear algebraic equations.
- MASS Toolbox — Mathematica based kinetic and constraint-based model building and simulation framework (open source under BSD license). Focus on mass action kinetics and elementary reaction systems. Features include: ODE/DAE integration (delays and events are also supported), high-level plotting commands for time courses and phase portraits, analytical steady-state solutions for complex enzyme mechanisms, static and dynamic pathway visualizations, set operations on models (e.g. obtain the intersection of two models), flux balance analysis, scientific unit support, and many more. SBML import tested against SBML Test Suite.
- MatCont — MatCont is a Matlab software package for the numerical study of parameterized continuous and discrete dynamical systems.
- meneco — meneco is a tool for metabolic network completion. Within a qualitative approach that describes the bio- synthetic capacities of metabolic networks, meneco uses qualitative constraints to express the producibility for a set of metabolites. meneco can be used to check whether a network provides the synthesis routes to comply with the required functionality described by the producibility constraints. In particular it tests whether it is possible to synthesize so called target metabolites from a set of seed metabolites. For networks that fail this test meneco can attempt to complete the network by importing reactions from a metabolic reference network such that the resulting network provides the required functionality. meneco can identify unproducible target metabolites and computes minimal extensions to the network that satisfy the producibil- ity constraints. Additionally, it can compute the union and intersection of all minimal networks extensions without enumerating all minimal network extensions.
- MesoRD — MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
- Metaboflux — Metaboflux is a computational tool for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments. It aims to increase the biological relevance of models by integrating experimental data. The tool is available in two versions : a command line tool optimized for running on HPC servers and a user-friendly interface designed to define model parameters and run simple computations. Metaboflux embedded a stochastic simulator of metabolic networks coupled with a non linear solver (GSL). It solves constraints defined as proportions (for example, metabolite proportions) or as equations. Results can be visualized directly in Metaboflux or within specific tools like Systrip.
- MetaFluxNet — MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way, which allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies.
- MetaNetX — MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. To this end, it integrates a great variety of data sources in a common namespace and tools.
- MetExplore — MetExplore is a web server to link various omics experiments and genome-scale metabolic networks. MetExplore is a fully online tool allowing to navigate content of networks coming from various sources (SBML, KEGG, BIOCYC). SBML networks can be uploaded and all networks (even from KEGG and BioCyc) can be uploaded. It also allows importing data on gene, protein, enzyme, metabolites and reactions. Networks can be visualised using a graph representation online or using Cytoscape. Graph based algorithms are implemented in MetExplore to extract sub-networks.
- MMT2 — Metabolic modeling, model fitting, automated high-performance code generation. (Linux only).
- modelMaGe — modelMaGe is a software application that a) automatically generates SBML or Copasi candidate models by removing specified model components from a given master model, b) automatically documents candidate models, c) automatically fits candidate models to data using CopasiSE, d) provides a ranking of candidate models fits based on the AIC.
- ModeRator — ModeRator - The Model Comparator can give insight about similarity of two reconstructions (models) where entities' external identifiers, like, KEGG ID and ChEBI ID are not included. Metabolites are compared using their names that are available in the model file. Chemical formulas, if available, are used to strengthen or weaken automatic decision about equality of metabolites. Formulas with different charge can be tolerated. Reactions are compared based on their metabolites and stoichiometry. Balanced and imbalanced reactions can be compared through tolerance of missing reactants.
- MonaLisa — MonaLisa is a Petri net based tool for the modeling and analysis of biological networks. It comprises an editor and various analysis techniques. Its main focus is on the analysis and visualization of functional modules in biochemical networks. Thus, the software provides the computation of elementary modes (transition invariants), of mass conservation (place invariants) and MCT-sets (maximal common transition sets), MCS (minimal cut sets) as well as knock-out analysis facilities, and other. The representation of the results is graphically supported. Interfaces to systems biology and special graph formats, such as SBML, KEGG PNT, PNML, APNN, and KEGG, are implemented. Several SBML features, such as annotation with SBO and MIRIAM terms or compounds, are supported.
- Moose — MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. MOOSE uses Python for scripting compatibility with a large range of software and analysis tools. It recognizes model definition standards including SBML, NeuroML, and GENESIS model file formatsGallery MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty.
- Morpheus — Morpheus is a user-friendly modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. 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.
- Odefy — Odefy is a MATLAB and Octave compatible toolbox which a modeling technique called HillCube, a canonical method to convert boolean models into continuous ordinary differential equation (ODE) systems. HillCubes are based on multivariate polynomial interpolation and incorporate Hill kinetics which are known to provide a good approximation of the synergistic dynamics of gene regulation.
- Omix — Omix is a highly customizable editor for biochemical network diagrams, equipped with extensive data visualization features. Highest flexibility in designing networks and visualization is provided. With Omix, sophisticated data visualization can be designed with ease. Especially, time-dependent numerical datasets from experiment and simulation are easily visualized and animated in the context of metabolic network. Omix has extensive import and export capabilities, e.g. for SBML, BioPAX, HDF5, Matlab code, etc. Models can be imported from KEGG or BioCyc. Many plug-ins are available providing modeling and analysis features for Omix. This includes, for instance, stoichiometic analysis, thermodynamic analysis, metabolic flux analysis. As a brand new feature, it is now possible to define the dynamics of a biological network in Omix. You can define kinetic laws for the individual reactions and specify initial concentrations and dynamic changes for metabolites. Furthermore, you can create dynamic events.
- ONDEX — The Ondex data integration platform enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex uses a rich and flexible core data structure, which has the ability to bring together information from structured databases and unstructured sources such as biological sequence data and free text. Ondex also allows users to visualise and analyse the integrated data.
- optflux — OptFlux is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using phenotype prediction methods such as FBA/pFBA, MOMA/LMOMA, ROOM and MiMBl (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard (import/export). OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.
- Pathway Analyser — Flux analysis. Free download, open source (Linux).
- PathwayLab — PathwayLab is a tool for modeling, analysis, and information management of biochemical pathways. It streamlines the pathway building process by a rich and flexible set of graphical building blocks for specifying biochemical entities, reaction, and control mechanisms. The pathway models are built using drag and drop from stencils into a workspace, which makes it very easy to rapidly build models of biochemical reaction networks such as signaling and metabolic pathways as well as gene regulatory networks. PathwayLab depends on Microsoft Visio.
- PET — Parameter optimization and exploration is the primary feature of PET. Some of the other tasks PET can perform are simulations, setting up multiple experiments for a model, comparing parameter sets, and exporting plots for presentations.
- PK-Sim / MoBi — Systems biology software platform for multiscale physiological modeling and simulation with a focus on physiologically-based pharmokinetics and -dynamics (PBPK/PD) including interfaces to MATLAB and R. Available to academic researchers via a free non-commercial license.
- precursor — Compute minimal precursors sets that enable the production of target metabolites. Given a set of desired target metabolites, this tool applies a notion of bio-chemical producebility to metabolic reaction networks and allows to identify the minimal sets of precursors that are required to produce the target metabolites.
- PRISM — PRISM is a probabilistic model checker, a tool for formal verification of systems that exhibit stochastic behaviour. It supports construction and analysis of, amongst others, continuous-time Markov chains (CTMCs) and offers direct input from SBML models. PRISM performs exhaustive model analysis and computes exact values for a range of quantitative queries such as ''what is the probability that ligand A eventually binds to protein B?'' or ''what is the expected amount of protein C at time T?''.
- ProcessDB — ProcessDB helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a diagram-based user interface that helps users formulate, visualize, compare, combine, modify, manage and test their own mechanistic theories of biological function at levels from molecular cell biology to human physiology. All models in ProcessDB can be automatically combined with user-specified experimental protocols and solved using an implementation of CVODE with a flexible graphing interface for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data.
- pybrn — pybrn is a Python package for the analysis of biochemical reaction networks. It is mainly meant as a basic library for researchers developing their own model analysis routines in Python. pybrn currently features: - basic model creation, data handling and evaluation - import of SBML files into pybrn’s data structures - analysis of network conservation relations - computation of steady states and steady state branches - integration of the network’s differential equation
- PyDSTool — PyDSTool is a Python-based Dynamical Systems Toolkit. With PyDSTool we aim to provide a suite of computational tools for the development, simulation, and analysis of dynamical systems that are used for the modeling of physical processes in many scientific disciplines, but especially in the biological sciences. We place emphasis on the support of data analysis and model fitting as a core part of the process of data-driven modeling. Our focus is on models involving ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete mappings.
- PySCeS — PySCeS: the Python Simulator for Cellular Systems is an extendable toolkit for the analysis and investigation of cellular systems. PySCeS is developed in Python and has been designed to be used both interactively or as a library. It utilises a human readable, model description language for describing models as well as being SBML compatible. PySCeS includes stoichiometric, simulation, steady state and Eigen analysis using direct non-linear root finders. It also includes full support for Metabolic Control Analysis (MCA), the characterisation of static bifurcations, multidimensional parameter scanning and 2/3D graph capabilities. Currently an extension PySCeS-CBM is being developed that allows for the interactive manipulation, modelling and optimization of genome scale, constraint based models (e.g. flux balance analysis)
- RAVEN — The RAVEN Toolbox (Reconstruction, Analysis, and Visualization of Metabolic Networks) toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of genome-scale metabolic models (GEMs). The software has three main foci: 1) automatic reconstruction of GEMs based on protein homology, 2) network analysis, modeling and interpretation of simulation results, 3) visualization of GEMs using pre-drawn metabolic network maps.
- SBML Harvester — The SBML Harvester creates a complex ontology-based representation of SBML models, utilizing both the structure of the SBML model and the models' MIRIAM annotations. This representation can then be used for the consistency verification of SBML models as well as complex queries across both models and biomedical ontologies.
- SBML2APM — A large collection of SBML models is found in the Biomodels Database. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through APM MATLAB, APM Python, or through a Web Interface.
- SBML2LaTeX — SBML2LaTeX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate various file types from SBML including PDF, TeX, DVI, PS, EPS, GIF, JPG or PNG. SBML2LaTeX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LaTeX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication.
- SBMLSim — Matlab GUI that allows the user to import a SBML model, simulate it, and visualize the simulations.
- SBSI — SBSI provides high performance fitting of model parameters to experimental data, with especial focus on models with oscillatory components. Additionally SBSI provides a modelling environment for the Bio-PEPA and Kappa languages, as well as standard model editing and simulation capabilities
- SBToolbox2 — MCA: Steady state control coefficients and elasticities; Structural analaysis: conservation relation analysis; model development; simulation; SBML Import/Export; parameter estimation; analysis tools. Requires MatLab (Linux/Win/Mac).
- SBW — Systems Biology Workbench. A framework for connecting and running various applications written in different languages or on different systems, and a collection of available modules for model development, analysis, and simulation. Free/Open Source. (BSD)
- SensA — SensA is a web-based application for sensitivity analysis of mathematical models in SBML format. The sensitivity analysis is based on metabolic control analysis, computing the local, global and time-dependent properties of model components. Interactive visualization facilitates interpretation of usually complex results. SensA can contribute to the analysis, adjustment and understanding of mathematical models for dynamic systems.
- SensSB — A software toolbox for the development and sensitivity analysis of systems biology models
- SimBiology — SimBiology ® is a MATLAB ® product from MathWorks that provides graphical and programmatic tools for computational systems biology and pharmacokinetics. It contains functionality for creating, simulating, and analyzing biological models. The SimBiology desktop lets you build a model using a block diagram editor, a model wizard, or a tabular interface. You can also create a model at the command line or directly from SBML files. SimBiology lets you simulate a model using stochastic or deterministic solvers. The product supports parameter estimation, sensitivity analysis, parameter scans, and other model analysis methods. All SimBiology features can be used together with the MATLAB programming language, letting you customize models, create or modify analysis tasks, and automate your workflow.
- Simulation Tool — The Simulation Tool is an environment for interactive exploration of SBML Models (L1-L3). It allows for simulation and analysis of models, provided capabilites (through simulators like RoadRunner) to define signals and events to interact with the model. Also features Steady State and Frequency Analysis.
- SloppyCell — SloppyCell is focused on parameter estimation and sensitivity analysis for ODE models. In particular, SloppyCell includes semi-analytic sensitivity integration, along with capability for building Bayesian ensembles of parameters sets consistent with given data.
- SOSlib — SOSlib is a programming library and command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in SBML (Systems Biology Markup Language). It is written in ANSI/ISO C and distributed under the GNU Lesser General Public License (LGPL). The package employs libSBML's AST for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems. The native API provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of powerful and efficient analytic applications, hybrid solvers or multi-scale models with interfaces to non SBML data sources. Optional modules (Graphviz and XMGrace) allow a quick inspection of a model's structure and dynamics.
- StochPy — StochPy is a versatile modeling package for stochastic simulation of molecular control networks inside living cells. Its integration with Python’s scientific libraries and PySCeS makes it an easily extensible and a user-friendly simulator. The high-level statistical and plotting functions of StochPy allow for quick and interactive model interrogation at the command-line. Python’s scripting capabilities allow for more complicated and in-depth analysis of stochastic models.
- SYCAMORE — SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations.
- Systems Biology Simulation Core Library — The Systems Biology Simulation Core Library is a fast, accurate, and easily usable application programming interface for dynamic simulation of models. At the moment, only models encoded in the Systems Biology Markup Language (SBML) are supported, but the generic implementation of the framework facilitates the implementation of further standards. 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.
- Systrip — Systrip is a visual environment for the analysis of time-series data in the context of biological networks. This software gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process. Main features : 1. SBML file import and export. 2. Multiple kind of metabolic network representations (3D, force directed, biological convention preserving, hierachical ...). 3. Both graph theoritical measures and metabolic network analysis algorithms (choke points, scope, centrality...). 4. Time-series data import and visualization (table view, parallel coordinates, scatter plot). 5. Visualization of time-series in the context of the metabolic network. 6. 3D molecular visualization. 7. Database querry tools (Kegg, PublicHouse).
- Tide — Tide is a tool for the automatic identification of optimal drug targets in kinetic models based on ordinary differential equations. Give a model in the popular SBML format it will identify promising drug targets for different effective modifier concentrations.
- TinkerCell — TinkerCell is a drawing tool for synthetic biology that supports modular models and is highly extensible. One of the extensions is the COPASI C++ library, which adds most of the analysis capabilities from COPASI. Another extension support SBML import/export as well as the Antimony model definition language. TinkerCell supports over 200 Python and Octave functions, allowing users to add plug-ins written in Python or Octave. Users can also upload their plug-in to a central repository (hosted at Sourceforce); all other TinkerCell users will automatically get this plug-in in TinkerCell in the form of a new button. Hierarchical modeling is another key feature in TinkerCell, which is used in conjunction with a custom ontology for automatically generating one or more models from conceptual diagrams.
- VANTED — This system makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes. Built-in statistic functions allow a fast evaluation of the data (e.g. t-Test or correlation analysis). Vanted can be extended for various functionalities, e.g. flux simulation, database access and 3D visualisation.
- WebCell — Online simulator, model builder, metabolic controal analysis. Includes database of bimodels and JWS models. Registration required.
- WinSCAMP — Windows Binary for SCAMP. Metabolic analysis, ODE solver. Binary download only. Source code on request.
- Wolfram SystemModeler — Wolfram SystemModeler is a high-fidelity modeling software based on the Modelica language. It allows for hierarchical, multidomain, and hybrid systems modeling using a graphical drag and drop environment, and/or an equation based textual interface. And it integrates with the Wolfram technology platform to enable modeling, simulation, and analysis (of many types), all together achieving an agile design optimization loop. Provided with SystemModeler is a large set of built-in model libraries, including the BioChem library - an SBML compatible Modelica library designed for biochemical systems. By making use of the BioChem library, SystemModeler lets you build, simulate, and visualize PKPD and systems biology models. The software also provides SBML import and export functionality to allow Modelica-SBML model exchange.

## Annotation software

- BioModels Database — BioModels Database is a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided. All models are provided under the terms of the Creative Commons CC0 Public Domain Dedication, cf. our terms of use. This means that the models are available freely for use, modification and distribution, to all users. More information about BioModels Database can be found in the frequently asked questions (FAQ).
- Cell Collective — The Cell Collective allows laboratory scientists working in different areas of the cell to collectively integrate their knowledge and create large-scale (rule-based) computational models of biological/biochemical networks in a non-technical fashion. Models created in the Cell Collective can be published and made available to the whole community, or shared with a selected group of collaborators, or completely kept private. The software provides an environment not only for the construction and sharing of computational (logic-based) models, but also for real-time, interactive simulations, as well as automated experiments consisting of hundreds of simulations.
- CellDesigner — CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system. CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver and Copasi. By using CellDesigner, users can browse and modify existing SBML models with references to existing databases (MIRIAM supported), simulate and view the dynamics through an intuitive graphical interface.
- COPASI — 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. Export to: C code, XPP, Berkley Madonna, MathML, TeX Please see the COPASI detailed description for a complete list of features.
- CySBML — Summary: CySBML is a plugin for the work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations, and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories. Availability and implementation: Freely available for non-commercial purposes via the Cytoscape plugin manager or for download at http://sourceforge.net/projects/cysbml/. Main purpose is an import of SBML with the semantic annotations available within the Cytoscape network visualization.
- GNAT — GNAT is an open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks. It is written in MATLAB and Java. It is thus platform-independent. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms.
- KEGGtranslator — The KEGG PATHWAY database provides a widely used service for pathway-based information. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses its own XML-format “KGML”. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, GML, GraphML, JPG, GIF, LaTeX, etc. KEGG pathways can be obtained from ftp://ftp.genome.jp/pub/kegg/xml/kgml.
- Metannogen — Metannogen is used to browse and annotate existing biological networks given in SBML. It can work together with any network editor that creates SBML files. Its capability of communication with other programs via network sockets allows embedding as a module within other software. It can also be used for network reconstruction to create a network from scratch.
- MetExplore — MetExplore is a web server to link various omics experiments and genome-scale metabolic networks. MetExplore is a fully online tool allowing to navigate content of networks coming from various sources (SBML, KEGG, BIOCYC). SBML networks can be uploaded and all networks (even from KEGG and BioCyc) can be uploaded. It also allows importing data on gene, protein, enzyme, metabolites and reactions. Networks can be visualised using a graph representation online or using Cytoscape. Graph based algorithms are implemented in MetExplore to extract sub-networks.
- Metingear — Metingear is an open source desktop application for creating and curating genome scale metabolic networks with chemical structure. Creating a high-quality genome-scale metabolite reconstruction requires meticulous manual annotation and can take substantial time to complete. Metingear simplifies the process of manual annotation providing a higher-quality and correctly annotated reconstruction in less time.
- MonaLisa — MonaLisa is a Petri net based tool for the modeling and analysis of biological networks. It comprises an editor and various analysis techniques. Its main focus is on the analysis and visualization of functional modules in biochemical networks. Thus, the software provides the computation of elementary modes (transition invariants), of mass conservation (place invariants) and MCT-sets (maximal common transition sets), MCS (minimal cut sets) as well as knock-out analysis facilities, and other. The representation of the results is graphically supported. Interfaces to systems biology and special graph formats, such as SBML, KEGG PNT, PNML, APNN, and KEGG, are implemented. Several SBML features, such as annotation with SBO and MIRIAM terms or compounds, are supported.
- PAYAO — PAYAO is a community collaborative web service platform for gene-regulatory and biochemical pathway model curation.
- PK-Sim / MoBi — Systems biology software platform for multiscale physiological modeling and simulation with a focus on physiologically-based pharmokinetics and -dynamics (PBPK/PD) including interfaces to MATLAB and R. Available to academic researchers via a free non-commercial license.
- PySB — Encode biochemical signaling networks as native Python code for model creation, modification, execution, simulation, and analysis. Use source control tools like git to track model evolution, changes, etc. Access to the full Python numerical and scientific ecosystem.
- Saint — The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive manual process. Modelers need to know and understand both the systems they are modeling and the intricacies of SBML. However, the amount of relevant data for even a relatively small and well-scoped model is overwhelming. Saint, an automated SBML annotation integration environment, aims to aid the modeler and reduce development time by providing extra information about any given SBML model in an easy-to-use interface. Saint accepts SBML-formatted files and integrates information from multiple databases automatically. Any new information that the user agrees with is then automatically added to the SBML model. The purpose of Saint is to aid the researcher in the difficult task of information discovery by seamlessly querying multiple databases and providing the results of that query within the SBML model itself. By providing a modeling interface to existing data integration resources, modelers are able to add information to models quickly and simply.
- SBMLEditor — SBMLeditor a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity and consistency of the final SBML file
- SBMLsqueezer — SBMLsqueezer is a generator for kinetic equations for biochemical networks with access to the rate law database SABIO-RK. When creating equations de novo, it takes the context of each reaction into account by evaluating Systems Biology Ontology (SBO) annotations and further information. It can be used as a stand-alone tool, as a plug-in for CellDesigner, a GARUDA gadget, an online program, through its programming interface, or as a command-line tool. The rate laws that can be produced by SBMLsqueezer are numerous, including traditional and recent approaches for several network types. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.
- SBW — Systems Biology Workbench. A framework for connecting and running various applications written in different languages or on different systems, and a collection of available modules for model development, analysis, and simulation. Free/Open Source. (BSD)
- semanticSBML — Create, check, visualize, retrieve, cluster, annotate, merge SBML models. The program includes a web based graphical user interface. For tool developers a programming interface (Python) and RESTful web-services are provided. It features advanced functions to edit MIRIAM and SBO terms. The latest version of semanticSBML is fully web based and can be accessed under http://semanticsbml.org/semanticSBML/simple/index
- SurreyFBA — SurreyFBA provides constraint-based simulations of genome scale metabolic networks in a free, stand-alone software. In addition to basic simulation protocols the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments. The SurreyFBA is based on a command line interface to the GLPK solver distributed as binary and source code for the three major operating systems. The sfba command line tool, implemented in C++, is easily executed within scripting languages used in the bioinformatics community and provides efficient implementation of tasks requiring iterative calls to the linear programming solver. SurreyFBA includes JyMet, a graphics user interface allowing spreadsheet based model presentation, visualization of numerical results on metabolic networks represented in the Petri net convention, as well as in charts and plots.

## Conversion tool (SBML to/from another format)

- Antimony — libAntimony is a C/C++ library that can parse Antimony-formatted models, convert them to SBML, and provides an API to allow other tools access to model elements. Antimony models are modular, text-based, human readable and writable, largely compatible with SBML, and have a special syntax for creating genetic networks. QTAntimony is a simple text editor that lets you create and translate Antimony models to and from SBML and CellML.
- CellDesigner — CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system. CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver and Copasi. By using CellDesigner, users can browse and modify existing SBML models with references to existing databases (MIRIAM supported), simulate and view the dynamics through an intuitive graphical interface.
- CellML2SBML — Converts CELLML to SBML
- COPASI — 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. Export to: C code, XPP, Berkley Madonna, MathML, TeX Please see the COPASI detailed description for a complete list of features.
- ecellJ — Converts between Ecell models and various other formats including SBML and open office spreadsheets.
- GINsim — GINsim is dedicated to the logical modelling of regulatory and signalling networks. It allows model definition and provides numerous functionalities for model analyses, including import and export facilities.
- JarnacLite — JarnacLite allows to edit SBML through a simple script based format. It is integrated with SBW, so that a model created with JarnacLite can be quickly simulated and analyzed with a variety of tools. JarnacLite is available on all platforms, and as translator also online. It is released under the BSD license.
- jNeuroML — There are a number of repositories in active development under GitHub for handling NeuroML and LEMS with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation. jNeuroML can be used to import SBML and convert it to LEMS, and can export some NeuroML 2/LEMS files to SBML. See https://github.com/OpenSourceBrain/SBMLShowcase
- KEGGtranslator — The KEGG PATHWAY database provides a widely used service for pathway-based information. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses its own XML-format “KGML”. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, GML, GraphML, JPG, GIF, LaTeX, etc. KEGG pathways can be obtained from ftp://ftp.genome.jp/pub/kegg/xml/kgml.
- MetaNetX — MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. To this end, it integrates a great variety of data sources in a common namespace and tools.
- MetExplore — MetExplore is a web server to link various omics experiments and genome-scale metabolic networks. MetExplore is a fully online tool allowing to navigate content of networks coming from various sources (SBML, KEGG, BIOCYC). SBML networks can be uploaded and all networks (even from KEGG and BioCyc) can be uploaded. It also allows importing data on gene, protein, enzyme, metabolites and reactions. Networks can be visualised using a graph representation online or using Cytoscape. Graph based algorithms are implemented in MetExplore to extract sub-networks.
- MonaLisa — MonaLisa is a Petri net based tool for the modeling and analysis of biological networks. It comprises an editor and various analysis techniques. Its main focus is on the analysis and visualization of functional modules in biochemical networks. Thus, the software provides the computation of elementary modes (transition invariants), of mass conservation (place invariants) and MCT-sets (maximal common transition sets), MCS (minimal cut sets) as well as knock-out analysis facilities, and other. The representation of the results is graphically supported. Interfaces to systems biology and special graph formats, such as SBML, KEGG PNT, PNML, APNN, and KEGG, are implemented. Several SBML features, such as annotation with SBO and MIRIAM terms or compounds, are supported.
- Moose — MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. MOOSE uses Python for scripting compatibility with a large range of software and analysis tools. It recognizes model definition standards including SBML, NeuroML, and GENESIS model file formatsGallery MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty.
- Morpheus — Morpheus is a user-friendly modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. 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.
- MoSeC — MoSeC is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence. Both CellML and SBML models constructed using virtual parts can be converted into standard GenBank, EMBL or SBOL files ready for synthesising.
- PathSBML plugin for PathVisio — The PathSBML plugin allows researchers to visualize and overlay data on the same pathway models they use in simulation experiments. Exporting these models as GPML would also allow them to be uploaded to Wikipathways for community curation.
- PyDSTool — PyDSTool is a Python-based Dynamical Systems Toolkit. With PyDSTool we aim to provide a suite of computational tools for the development, simulation, and analysis of dynamical systems that are used for the modeling of physical processes in many scientific disciplines, but especially in the biological sciences. We place emphasis on the support of data analysis and model fitting as a core part of the process of data-driven modeling. Our focus is on models involving ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete mappings.
- SBML Translators — translators from SBML to a wide variety of other formats such as: •C / C++ / C# •Jarnac •Java •Matlab / Mathematica •XPP To name but a few. All translators are available from one UI.
- SBML2APM — A large collection of SBML models is found in the Biomodels Database. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through APM MATLAB, APM Python, or through a Web Interface.
- SBML2LaTeX — SBML2LaTeX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate various file types from SBML including PDF, TeX, DVI, PS, EPS, GIF, JPG or PNG. SBML2LaTeX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LaTeX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication.
- SBML2SMW — CellDesigner plugin for extracting Celldesigner model information, storing this information to a Semantic Mediawiki server and context-sensitive restoring and integration of this information in a Celldesigner model.
- SBtab — Data tables in the form of spreadsheets or delimited text files are the most utilised data format in Systems Biology. However, they are often not sufficiently structured and lack clear naming conventions that would be required for modelling. We propose the SBtab format as an attempt to establish an easy-to-use table format that is both flexible and clearly structured. It comprises defined table types for different kinds of data; syntax rules for usage of names, shortnames, and database identifiers used for annotation; and standardised formulae for reaction stoichiometries. Predefined table types can be used to define biochemical network models and the biochemical constants therein. The user can also define own table types, adjusting SBtab to other types of data. Software code, tools, and further information can be found at www.sbtab.net.
- sbtranslate — sbtranslate is a command-line translation tool that converts models between antimony, core SBML, SBML with the Hierarchical Model Composition package, and CellML. Antimony itself has a separate listing.
- SBW — Systems Biology Workbench. A framework for connecting and running various applications written in different languages or on different systems, and a collection of available modules for model development, analysis, and simulation. Free/Open Source. (BSD)

## Data integration and management software

- AMIGO — AMIGO means Advanced Model Identification using Global Optimization. AMIGO is a multi-platform (Windows and Linux) matlab-bsed toolbox which covers all the steps of system identification in systems biology. This includes: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.
- BioPathwise — BioPathwise is a pathway-centric environment for interdisciplinary collaborative research. The main interface is a pathway whiteboard that allows graphic representation of pathways, visualization of experimental data, pathway simulation, statistical analysis and regression. Extensible via an open API.
- CADLIVE — CADLIVE (Computer-Aided Design of LIVing systEms) is a comprehensive computational tool for constructing large-scale biological network maps, analyzing the topological features of them, and simulating their dynamics. Using CADLIVE, we rationally design a biological system at the molecular interaction level for an engineering purpose.
- CARMEN — CARMEN provides the KGML-based model generation of metabolic pathways based on KEGG database information and the application of template-based models for comparative genomics. This software will be of interest in genome sequencing projects aiming at the rapid analysis and visualization of microbial metabolic features. The KGML-based model generation facilitates a high-speed generated overview of the metabolic repertoire. The comparative analysis of newly sequenced organisms is highly desirable to identify organism-specific features. The reconstructed networks are stored in standardized SBML format.
- Cell Collective — The Cell Collective allows laboratory scientists working in different areas of the cell to collectively integrate their knowledge and create large-scale (rule-based) computational models of biological/biochemical networks in a non-technical fashion. Models created in the Cell Collective can be published and made available to the whole community, or shared with a selected group of collaborators, or completely kept private. The software provides an environment not only for the construction and sharing of computational (logic-based) models, but also for real-time, interactive simulations, as well as automated experiments consisting of hundreds of simulations.
- CySBML — Summary: CySBML is a plugin for the work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations, and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories. Availability and implementation: Freely available for non-commercial purposes via the Cytoscape plugin manager or for download at http://sourceforge.net/projects/cysbml/. Main purpose is an import of SBML with the semantic annotations available within the Cytoscape network visualization.
- Insilico Discovery — modeling and simulation platform for graphically oriented setup, management and engineering of cellular networks
- insilicoIDE — insilicoIDE (ISIDE) assists users to build models of physiological functions with multilevel hierarchical structure and to run simulations. A model is built as a functional network of ''modules'' which represent physiological entities. In each module, equations such as ODEs and PDEs, parameters and morphological information can be defined. Besides, a module can include a model written in SBML. The SBML model is functionally embedded in the module network. There is an open model database at www.physiome.jp. Users can use models in the database freely as parts to build their own model. The modularity of the model representation in ISIDE makes reuse and integration of multiple models easier. The simulator included in ISIDE supports parallel computing.
- jNeuroML — There are a number of repositories in active development under GitHub for handling NeuroML and LEMS with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation. jNeuroML can be used to import SBML and convert it to LEMS, and can export some NeuroML 2/LEMS files to SBML. See https://github.com/OpenSourceBrain/SBMLShowcase
- JSim — JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also supports model archive formats SBML (import and export) and CellML (import only).
- KEGGconverter — KEGGconverter automatically produces merged and converted to SBML fully functional pathway models, enhanced with default kinetics, by inputting only KGML files.The final derived models do not enclose trivial metabolites -reproducing inconsistencies of the KGML visualization-oriented, simplified information pattern- but at the same time they contain all the available information regarding the number of the included reactions in each pathway. Furthermore, additional reactions to neighbouring pathways are constructed which indicate the direction of the metabolic flows in the network and thus providing better stability in the boundary conditions of the models.
- KEGGtranslator — The KEGG PATHWAY database provides a widely used service for pathway-based information. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses its own XML-format “KGML”. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. KEGGtranslator is an easy-to-use stand-alone application that can visualize and convert KGML formatted files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g., MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator converts KEGG files (KGML formatted XML-files) to SBML, GML, GraphML, JPG, GIF, LaTeX, etc. KEGG pathways can be obtained from ftp://ftp.genome.jp/pub/kegg/xml/kgml.
- Medicel — commercial data integration framework. (now euformatics)
- MEMOSys — MEMOSys is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. It currently contains 9 annotated microbial metabolic models.
- MetaCrop — MetaCrop is a database that contains manually curated, highly detailed information about metabolic pathways in crop plants, including location information, transport processes, and reaction kinetics. The web interface supports an easy exploration of the information from overview pathways to single reactions and therefore helps users understanding the metabolism of crop plants. It also allows automatic data export for the creation of detailed models of metabolic pathways to support simulation approaches.
- Metannogen — Metannogen is used to browse and annotate existing biological networks given in SBML. It can work together with any network editor that creates SBML files. Its capability of communication with other programs via network sockets allows embedding as a module within other software. It can also be used for network reconstruction to create a network from scratch.
- Metingear — Metingear is an open source desktop application for creating and curating genome scale metabolic networks with chemical structure. Creating a high-quality genome-scale metabolite reconstruction requires meticulous manual annotation and can take substantial time to complete. Metingear simplifies the process of manual annotation providing a higher-quality and correctly annotated reconstruction in less time.
- MIRIAM Resources — a set of online services created in support of MIRIAM, a set of guidelines for the annotation and curation of computational models.
- ONDEX — The Ondex data integration platform enables data from diverse biological data sets to be linked, integrated and visualised through graph analysis techniques. Ondex uses a rich and flexible core data structure, which has the ability to bring together information from structured databases and unstructured sources such as biological sequence data and free text. Ondex also allows users to visualise and analyse the integrated data.
- Pathway Access — PathwayAccess is a suite of CellDesigner plugins which directly interact with pathway datasources
- Pathway Tools — Extracts and integrates information from pathway/genome databases (see BioCyc); metabolic analysis; gene code prediction; operon prediction; gene expression analysis. Optional support: Oracle or MySQL, Browser, BLAST, Marvin Msketch, JME/OpenBabel. SBML support via BioCyc. Free academic; fee for commercial. License application must be reviewed by SRIC before download. SRI unique license. (Linux/Windows/Solaris/Mac).
- PATIKAweb — Pathway database integration; pathway visualization and analysis. Online tool only. (Acad/NP)
- PK-Sim / MoBi — Systems biology software platform for multiscale physiological modeling and simulation with a focus on physiologically-based pharmokinetics and -dynamics (PBPK/PD) including interfaces to MATLAB and R. Available to academic researchers via a free non-commercial license.
- ProcessDB — ProcessDB helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a diagram-based user interface that helps users formulate, visualize, compare, combine, modify, manage and test their own mechanistic theories of biological function at levels from molecular cell biology to human physiology. All models in ProcessDB can be automatically combined with user-specified experimental protocols and solved using an implementation of CVODE with a flexible graphing interface for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data.
- PROTON — Integrated modeling environment. Reconstructs biochemical systems from molecular databases in an automated and user-centric way. Fuses information from distributed databases and the reconstruction of systems is interactively controlled by the user. The approach is based on different layers which allow the integrative modelling of biochemical systems at multiple levels. ODE based modeling and simulation. (Free Download. Optional Server, Windows; Client: Linus/Windows/Mac).
- PySB — Encode biochemical signaling networks as native Python code for model creation, modification, execution, simulation, and analysis. Use source control tools like git to track model evolution, changes, etc. Access to the full Python numerical and scientific ecosystem.
- ReMatch — ReMatch is a web-based tool for integration of user-given stoichiometric metabolic models into a database collected from public data sources such as KEGG, MetaCyc, CheBI and ARM. ReMatch is geared particularly towards 13C metabolic flux analysis: it is possible to augment the model with carbon mappings and export the model to analysis in 13C flux analysis software
- SABIO-RK — SABIO-RK is a curated database for biochemical reaction kinetics data. The data is drawn from different sources: by extraction from published literature or direct submission by experimenters, and is supplemented with additional data from other databases. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. It can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML. SABIO-RK facilitates the exchange of kinetic data between experimentalists and modellers, and thereby supports the setup of quantitative computer models.
- Saint — The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive manual process. Modelers need to know and understand both the systems they are modeling and the intricacies of SBML. However, the amount of relevant data for even a relatively small and well-scoped model is overwhelming. Saint, an automated SBML annotation integration environment, aims to aid the modeler and reduce development time by providing extra information about any given SBML model in an easy-to-use interface. Saint accepts SBML-formatted files and integrates information from multiple databases automatically. Any new information that the user agrees with is then automatically added to the SBML model. The purpose of Saint is to aid the researcher in the difficult task of information discovery by seamlessly querying multiple databases and providing the results of that query within the SBML model itself. By providing a modeling interface to existing data integration resources, modelers are able to add information to models quickly and simply.
- SBML Harvester — The SBML Harvester creates a complex ontology-based representation of SBML models, utilizing both the structure of the SBML model and the models' MIRIAM annotations. This representation can then be used for the consistency verification of SBML models as well as complex queries across both models and biomedical ontologies.
- SBMLsqueezer — SBMLsqueezer is a generator for kinetic equations for biochemical networks with access to the rate law database SABIO-RK. When creating equations de novo, it takes the context of each reaction into account by evaluating Systems Biology Ontology (SBO) annotations and further information. It can be used as a stand-alone tool, as a plug-in for CellDesigner, a GARUDA gadget, an online program, through its programming interface, or as a command-line tool. The rate laws that can be produced by SBMLsqueezer are numerous, including traditional and recent approaches for several network types. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.
- SBMM assistant — Systems Biology Metabolic Modeling assistant (SBMM assistant) is a web application to consult basic metabolic information, to build metabolic models, and to annotate them in SBML files with external resource annotations suggested by MIRIAM
- SBO — The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.
- SCIpath — microarray data management. (Linux/Windows).
- semanticSBML — Create, check, visualize, retrieve, cluster, annotate, merge SBML models. The program includes a web based graphical user interface. For tool developers a programming interface (Python) and RESTful web-services are provided. It features advanced functions to edit MIRIAM and SBO terms. The latest version of semanticSBML is fully web based and can be accessed under http://semanticsbml.org/semanticSBML/simple/index
- SIGNALIGN — online pathway alignment service.
- SignaLink — SignaLink is a multi-layered (onion-like) database made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network of human and two invertebrate model organisms, C. elegans and D. melanogaster.
- SigPath — Bioinformatic database and pathway management (GPL).
- SimBiology — SimBiology ® is a MATLAB ® product from MathWorks that provides graphical and programmatic tools for computational systems biology and pharmacokinetics. It contains functionality for creating, simulating, and analyzing biological models. The SimBiology desktop lets you build a model using a block diagram editor, a model wizard, or a tabular interface. You can also create a model at the command line or directly from SBML files. SimBiology lets you simulate a model using stochastic or deterministic solvers. The product supports parameter estimation, sensitivity analysis, parameter scans, and other model analysis methods. All SimBiology features can be used together with the MATLAB programming language, letting you customize models, create or modify analysis tasks, and automate your workflow.
- SRS — Data integration for bioinformatics. Commercial.
- SYCAMORE — SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations.
- VANTED — This system makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes. Built-in statistic functions allow a fast evaluation of the data (e.g. t-Test or correlation analysis). Vanted can be extended for various functionalities, e.g. flux simulation, database access and 3D visualisation.

## Framework or library

- CLEML — Carbon Labeling Experiment Markup Language. The libCLEML is freely downloadable (GPL). (Linux/Win).
- CL-SBML — Common Lisp implementation of the SBML Standard (Level 2). I/O library for SBML in Common Lisp.
- pybrn — pybrn is a Python package for the analysis of biochemical reaction networks. It is mainly meant as a basic library for researchers developing their own model analysis routines in Python. pybrn currently features: - basic model creation, data handling and evaluation - import of SBML files into pybrn’s data structures - analysis of network conservation relations - computation of steady states and steady state branches - integration of the network’s differential equation

## Framework or library (for use in developing software applications)

- AMIGO — AMIGO means Advanced Model Identification using Global Optimization. AMIGO is a multi-platform (Windows and Linux) matlab-bsed toolbox which covers all the steps of system identification in systems biology. This includes: local and global sensitivity analysis, local and global ranking of parameters, parameter estimation, identifiability analysis and optimal experimental design.
- Antimony — libAntimony is a C/C++ library that can parse Antimony-formatted models, convert them to SBML, and provides an API to allow other tools access to model elements. Antimony models are modular, text-based, human readable and writable, largely compatible with SBML, and have a special syntax for creating genetic networks. QTAntimony is a simple text editor that lets you create and translate Antimony models to and from SBML and CellML.
- APMonitor — The APMonitor Modeling Language is optimization software for differential and algebraic equations. It is coupled with large-scale nonlinear programming solvers for data reconciliation, real-time optimization, dynamic simulation, and nonlinear predictive control. It is available as a free web service through MATLAB or Python.
- BioPARKIN — Robust and reliable parameter identification (e.g. rate constants) in biology-related systems described by (sets of) ODEs or DAEs from given measurement data, based on an affine covariant Gauss-Newton algorithm. Additionally, providing a sensible, parameter depending sensitivity analysis for the ODE/DAE systems.
- BioSPICE Dashboard — Large collection of tools, integrated via a 'Dashboard.' Free download (BSD), various platforms.
- BiVeS — BiVeS (Biomodel Version Control System) able to detect differences between two versions of a computational model and to communicate these changes. Focusing on SBML and CellML, BiVeS (Biomodel Version Control System) accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions.
- FlexFlux — FlexFlux is a java tool for metabolic flux and regulatory network analysis. To analyse metabolic fluxes, FlexFlux is based on a mathematical method, FBA which consists in transforming a metabolic network into linear equations and calculate fluxes thanks to linear programming. Concerning the regulatory network analysis, FlexFlux supports multistate qualitative regulatory networks. This regulatory network is composed of components of different natures (genes, mRNAs, proteins, metabolites ...), that interact with each other in different ways and can have an effect on the metabolic network. FlexFlux performs synchronous updates of the regulatory network state from provided initial values. Once a steady-state of this regulatory network is reached, the states are translated into continuous intervals (see the regulation file section) used as constraints for the FBA. We named this pipeline Regulatory Steady-state Analysis (RSA). FlexFlux contains many methods dedicated to regulatory network and flux analysis.
- JSBML — open-source, Java library for reading, writing, and manipulating SBML files
- JSim — JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also supports model archive formats SBML (import and export) and CellML (import only).
- libAnnotationSBML — Java library for reading and writing MIRIAM-compliant SBML annotations
- libSBML — LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux.
- libSBMLSim — LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.
- libStruct — The structural analysis library is a C/C++ portable software library for analyzing the structural properties of stoichiometric networks. The library supports the analysis of both flux balance and moiety conservation. The library will accept models in the form of either standard SBML or raw stoichiometry matrices. The software is distributed under the BSD license and was developed through funding from NIH grant 1R01GM081070-01.
- Metannogen — Metannogen is used to browse and annotate existing biological networks given in SBML. It can work together with any network editor that creates SBML files. Its capability of communication with other programs via network sockets allows embedding as a module within other software. It can also be used for network reconstruction to create a network from scratch.
- Moose — MOOSE is the Multiscale Object-Oriented Simulation Environment. It is the base and numerical core for large, detailed simulations including Computational Neuroscience and Systems Biology. MOOSE spans the range from single molecules to subcellular networks, from single cells to neuronal networks, and to still larger systems. MOOSE uses Python for scripting compatibility with a large range of software and analysis tools. It recognizes model definition standards including SBML, NeuroML, and GENESIS model file formatsGallery MOOSE is open source software, licensed under the LGPL (Lesser GNU Public License). It has absolutely no warranty.
- Odefy — Odefy is a MATLAB and Octave compatible toolbox which a modeling technique called HillCube, a canonical method to convert boolean models into continuous ordinary differential equation (ODE) systems. HillCubes are based on multivariate polynomial interpolation and incorporate Hill kinetics which are known to provide a good approximation of the synergistic dynamics of gene regulation.
- PyDSTool — PyDSTool is a Python-based Dynamical Systems Toolkit. With PyDSTool we aim to provide a suite of computational tools for the development, simulation, and analysis of dynamical systems that are used for the modeling of physical processes in many scientific disciplines, but especially in the biological sciences. We place emphasis on the support of data analysis and model fitting as a core part of the process of data-driven modeling. Our focus is on models involving ordinary differential equations (ODEs), differential-algebraic equations (DAEs), and discrete mappings.
- PySB — Encode biochemical signaling networks as native Python code for model creation, modification, execution, simulation, and analysis. Use source control tools like git to track model evolution, changes, etc. Access to the full Python numerical and scientific ecosystem.
- PySCeS — PySCeS: the Python Simulator for Cellular Systems is an extendable toolkit for the analysis and investigation of cellular systems. PySCeS is developed in Python and has been designed to be used both interactively or as a library. It utilises a human readable, model description language for describing models as well as being SBML compatible. PySCeS includes stoichiometric, simulation, steady state and Eigen analysis using direct non-linear root finders. It also includes full support for Metabolic Control Analysis (MCA), the characterisation of static bifurcations, multidimensional parameter scanning and 2/3D graph capabilities. Currently an extension PySCeS-CBM is being developed that allows for the interactive manipulation, modelling and optimization of genome scale, constraint based models (e.g. flux balance analysis)
- SBML Layout — SBML Layout encompasses: 1. a online application for layouting / rendering an SBML file , 2. a library for reading / writing SBML Layout and Rendering information as well as SBGN-ML and 3. a standalone application for displaying files with the SBML Layout or Rendering information. It is written in .net and available under the BSD for all platforms.
- SBML2APM — A large collection of SBML models is found in the Biomodels Database. To use these models in APM, they must first be converted with the following utility. Once converted, the model can be simulated through APM MATLAB, APM Python, or through a Web Interface.
- semanticSBML — Create, check, visualize, retrieve, cluster, annotate, merge SBML models. The program includes a web based graphical user interface. For tool developers a programming interface (Python) and RESTful web-services are provided. It features advanced functions to edit MIRIAM and SBO terms. The latest version of semanticSBML is fully web based and can be accessed under http://semanticsbml.org/semanticSBML/simple/index
- SimBiology — SimBiology ® is a MATLAB ® product from MathWorks that provides graphical and programmatic tools for computational systems biology and pharmacokinetics. It contains functionality for creating, simulating, and analyzing biological models. The SimBiology desktop lets you build a model using a block diagram editor, a model wizard, or a tabular interface. You can also create a model at the command line or directly from SBML files. SimBiology lets you simulate a model using stochastic or deterministic solvers. The product supports parameter estimation, sensitivity analysis, parameter scans, and other model analysis methods. All SimBiology features can be used together with the MATLAB programming language, letting you customize models, create or modify analysis tasks, and automate your workflow.
- SloppyCell — SloppyCell is focused on parameter estimation and sensitivity analysis for ODE models. In particular, SloppyCell includes semi-analytic sensitivity integration, along with capability for building Bayesian ensembles of parameters sets consistent with given data.
- SOSlib — SOSlib is a programming library and command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in SBML (Systems Biology Markup Language). It is written in ANSI/ISO C and distributed under the GNU Lesser General Public License (LGPL). The package employs libSBML's AST for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems. The native API provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of powerful and efficient analytic applications, hybrid solvers or multi-scale models with interfaces to non SBML data sources. Optional modules (Graphviz and XMGrace) allow a quick inspection of a model's structure and dynamics.
- StochPy — StochPy is a versatile modeling package for stochastic simulation of molecular control networks inside living cells. Its integration with Python’s scientific libraries and PySCeS makes it an easily extensible and a user-friendly simulator. The high-level statistical and plotting functions of StochPy allow for quick and interactive model interrogation at the command-line. Python’s scripting capabilities allow for more complicated and in-depth analysis of stochastic models.
- Systems Biology Simulation Core Library — The Systems Biology Simulation Core Library is a fast, accurate, and easily usable application programming interface for dynamic simulation of models. At the moment, only models encoded in the Systems Biology Markup Language (SBML) are supported, but the generic implementation of the framework facilitates the implementation of further standards. 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.
- TERANODE Suite — Suite of tools for model management, design, and simulation. (Linux/Mac/Windows) Commercial (30-day trial available).
- TinkerCell — TinkerCell is a drawing tool for synthetic biology that supports modular models and is highly extensible. One of the extensions is the COPASI C++ library, which adds most of the analysis capabilities from COPASI. Another extension support SBML import/export as well as the Antimony model definition language. TinkerCell supports over 200 Python and Octave functions, allowing users to add plug-ins written in Python or Octave. Users can also upload their plug-in to a central repository (hosted at Sourceforce); all other TinkerCell users will automatically get this plug-in in TinkerCell in the form of a new button. Hierarchical modeling is another key feature in TinkerCell, which is used in conjunction with a custom ontology for automatically generating one or more models from conceptual diagrams.

## Model creation/development/editing software

- ALC — ALC (Automated Layer Construction) (Koschorreck et al., BMC Systems Biology 2008, 2:91) is a computer program that highly simplifies the building of reduced modular models, according to the layer-based approach. The model is defined using a simple but powerful rule-based syntax that supports the concepts of modularity and macrostates. ALC performs consistency checks on the model definition and provides the model output in different formats (C MEX, MATLAB, Mathematica and SBML) as ready-to-run simulation files. ALC also provides additional documentation files that simplify the publication or presentation of the models. The tool can be used offline (which requires Perl) or via a form on the ALC website. ALC can be downloaded from the ALC website or from SourceForge.
- Antimony — libAntimony is a C/C++ library that can parse Antimony-formatted models, convert them to SBML, and provides an API to allow other tools access to model elements. Antimony models are modular, text-based, human readable and writable, largely compatible with SBML, and have a special syntax for creating genetic networks. QTAntimony is a simple text editor that lets you create and translate Antimony models to and from SBML and CellML.
- APMonitor — The APMonitor Modeling Language is optimization software for differential and algebraic equations. It is coupled with large-scale nonlinear programming solvers for data reconciliation, real-time optimization, dynamic simulation, and nonlinear predictive control. It is available as a free web service through MATLAB or Python.
- Asmparts — Produces models of biological systems by assembling models from biological parts.
- Athena — Athena is a graphical modeling tool experimenting with modular systems. Athena is integrated with SBW and allows the analysis of models through a multitude of plugins. It is available for windows only, and released under the BSD license.
- BALSA — Front end for Sigtran (inactive?)
- BenTen — Ben(Zai)Ten is a novel graphical model editor, designed to make it easy to construct kinetic biological models on the one side and produce standards compliant, well annotated computational models at the same time. Supported Standards: SBO, SBGN - PD, SBML (including L3), MIRIAM Supported Operating Systems: Windows / Linux / OS X License: BSD
- Bio Sketch Pad — graphical model design tool, front end for BioCharon
- BioCharon — BioCharon includes a suite of tools for developing models for use with CHARON. It includes the graphical BioSketchPad for desigining models, a hybrid SBML/C++ language model builder, and a metabolic analyzer.
- Biological Networks — Pathway model development supports SBML Import/Export (only supports simple mass action kinetics); visualization; data management; network/metabolic analysis; clustering. No simulation engine. Free academic download (Java web start, Windows/Linux/Mac).
- BioNetGen — BioNetGen is a software system for the specification and simulation of rule-based models of biochemical systems. In rule-based models, molecules and molecular complexes are represented using graphs, and molecular interactions and their consequences are represented using graph-rewriting rules. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. (Linux/Mac/Win)
- BioSpreadsheet — SBML model editor. Part of the UTK/ORNL Bio-SPICE tool set which includes the Exact Stochastic Simulator (ESS). Requires BioSpice Dashboard. Free download. Includes Source code.
- BioTapestry — Graphical model development and simulation tool for genetic regulatory networks based on JRE. Uses Java Web Start. Free download. SBML export.
- BioUML — platform for building virtual cell and virtual physiological human
- CARMEN — CARMEN provides the KGML-based model generation of metabolic pathways based on KEGG database information and the application of template-based models for comparative genomics. This software will be of interest in genome sequencing projects aiming at the rapid analysis and visualization of microbial metabolic features. The KGML-based model generation facilitates a high-speed generated overview of the metabolic repertoire. The comparative analysis of newly sequenced organisms is highly desirable to identify organism-specific features. The reconstructed networks are stored in standardized SBML format.
- Cell Illustrator — Graphical model editor; Petri-net based simulation algorithm; SBML Import. Commercial. (Linux/Mac/Win).
- CellDesigner — CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system. CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver and Copasi. By using CellDesigner, users can browse and modify existing SBML models with references to existing databases (MIRIAM supported), simulate and view the dynamics through an intuitive graphical interface.
- Cellerator — Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multi-compartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations that can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.. Cellerator is superseeded by xCellerator.
- CompuCell3D — CompuCell3D (CC3D) is a documented and supported open-source environment for building and running multi-cell, multi-scale simulations based on the Cellular Potts Model/ Glazier Graner Hogeweg model, which implements biochemical network modeling using components from the Systems Biology Workbench (SBW) suite. Building CC3D models with its model-description language CC3DML and Python scripting requires much less specialized knowledge of numerical analysis or computer science than do hard-coded methods and allows easy model publication, sharing, reuse and validation. CC3D’s architecture allows experienced programmers to build very sophisticated extensions. It scripting capability makes CC3D more similar to general-use packages like Matlab than to specialized research code.
- DBSolve — DBSolveOptimum is a free software for kinetic modeling of metabolic pathways, analysis, and fitting parameters to experimental data. The program has text-based user interface for model description and graphical interface for data analysis. In addition to standart algorithms of simulation (ODE solver, explicit solver, steady-state analysis) the software includes also the automated local sencetivity analysis, parameters optimization procedures and bifurcaion analysis. The last version of DBSolveOptimum includes the advanced tool for data visualization.
- EPISIM — The EPISIM consists of EPISIM Modeller (graphical modeling system) and EPISIM Simulator (simulation environment). Each EPISIM (multi-scale) model comprises a cell behavioral and a biomechanical model (CBM and BM). The BM covers all spatial and biophysical cell properties. Different BMs (lattice and off-lattice) are offered by the simulation environment. A BM can be dynamically linked to a CBM which is graphically modeled with process diagrams in the EPISIM Modeller. Automatic semantic integration of quantitative subcellular SBML models in CBMs is possible. The graphical CBMs are automatically compiled into executable code which is loaded by the EPISIM Simulator conducting an agent-based tissue simulation. EPISIM Simulator embeds COPASI to simulate SBML-based models. This allows linking of discrete (deterministic / stochastic) and continuous models on cellular on subcellular scale. Reaction-Diffusion models of e.g. chemokines can be integrated in a multi-scale tissue model with extracellular diffusion fields.
- Facile — Facile / EasyStoch. A command-line network compiler for systems biology. Facile reads models given in a simple and human-readable textual input format and exports the model in a format for readable by Matlab, Mathematica, Maple, XPP/AUTO. Other tools are supported via SBML export. For stochastic simulations, Facile uses the EasyStoch stochastic simulator. An important feature of EasyStoch that distinguishes it from other Gillespie-algorithm implementations is that it is capable of simulating dynamically changing or noisy biochemical parameters (i.e. extrinsic noise).
- FAME — The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. Manually drawn custom maps that are compatible with FAME are also available for certain species. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/ .
- Genetic Network Analyzer — Genetic Network Analyzer (GNA) is a computer tool for the modeling, simulation, analysis and verification of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a qualitative model of a genetic regulatory network from knowledge about regulatory interactions and gene expression data. GNA provides a variety of functions to analyze the steady-state and transient dynamics of the network, among other things by exploiting state-of-the-art model-checking tools.
- GINsim — GINsim is dedicated to the logical modelling of regulatory and signalling networks. It allows model definition and provides numerous functionalities for model analyses, including import and export facilities.
- GNU MCSim — GNU MCSim is a free standalone simulation package that allows you to design your own statistical or simulation models. It efficiently performs Bayesian inference through Markov Chain Monte Carlo simulations. Standard Monte Carlo and experimental design optimization are also available. GNU MCSim can import and simulate levels 1 and 2 SBML models
- HSMB — Hybrid SBML Model Builder for BioCharon.
- HybridSBML — Hybrid SBML Model Builder for BioCharon
- iBioSim — 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, labeled Petri net, and general biochemical models encoded in the Systems Biology Markup Language (SBML). Models can be constructed using either a schematic or textual editor, 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.
- insilicoIDE — insilicoIDE (ISIDE) assists users to build models of physiological functions with multilevel hierarchical structure and to run simulations. A model is built as a functional network of ''modules'' which represent physiological entities. In each module, equations such as ODEs and PDEs, parameters and morphological information can be defined. Besides, a module can include a model written in SBML. The SBML model is functionally embedded in the module network. There is an open model database at www.physiome.jp. Users can use models in the database freely as parts to build their own model. The modularity of the model representation in ISIDE makes reuse and integration of multiple models easier. The simulator included in ISIDE supports parallel computing.
- JACOBIAN — numerical engine underlying OpenBio
- Jarnac — SBW tool for metabolic analysis, includes dynamic simulation. Simulation engine for JDesigner. BSD License.
- JarnacLite — JarnacLite allows to edit SBML through a simple script based format. It is integrated with SBW, so that a model created with JarnacLite can be quickly simulated and analyzed with a variety of tools. JarnacLite is available on all platforms, and as translator also online. It is released under the BSD license.
- JDesigner — Graphical model design tool. Typically uses RoadRunner as a simulation engine via SBW. Free/Open Source (BSD).
- JigCell — JigCell is a set of computational tools with user-friendly interfaces developed for studying complex biochemical regulatory systems in general and the cell cycle control system in particular. For example, The JigCell Model Builder (JCMB) aides the modeler in defining a system to be modeled using SBML with a novel spreadsheet interface, allowing a large amount of data to be displayed in an organized manner. The JigCell Run Manager (JCRM) allows a user to specify a set of specifications for simulation runs using a spreadsheet interface. JigCell Aggregation Connector has been designed to define models in terms of components, for the purpose of being combined in a larger model. JigCell also aims in parameter estimation. A parameter estimator (PET, Parameter Estimation Toolkit) takes a biological model, experimental data, and the relationship between the model and data. Using this information the parameter estimator uses numerical tools to vary the parameters to the model looking for the parameters that best fit the experimental data.
- Karyote* — Online model development tool based on online database of parts. Claims to have some sort of simulator and SBML support. Level unclear. Documentation absent.
- MASS Toolbox — Mathematica based kinetic and constraint-based model building and simulation framework (open source under BSD license). Focus on mass action kinetics and elementary reaction systems. Features include: ODE/DAE integration (delays and events are also supported), high-level plotting commands for time courses and phase portraits, analytical steady-state solutions for complex enzyme mechanisms, static and dynamic pathway visualizations, set operations on models (e.g. obtain the intersection of two models), flux balance analysis, scientific unit support, and many more. SBML import tested against SBML Test Suite.
- MEMOSys — MEMOSys is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. It currently contains 9 annotated microbial metabolic models.
- MetaFluxNet — MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way, which allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies.
- Metingear — Metingear is an open source desktop application for creating and curating genome scale metabolic networks with chemical structure. Creating a high-quality genome-scale metabolite reconstruction requires meticulous manual annotation and can take substantial time to complete. Metingear simplifies the process of manual annotation providing a higher-quality and correctly annotated reconstruction in less time.
- MetNetMaker — MetNetMaker is the simplest way to create SBML-format metabolic models based on the KEGG LIGAND ontology. Models can be visualised in Cytoscape and are ready for FBA using the COBRA toolbox.
- modelMaGe — modelMaGe is a software application that a) automatically generates SBML or Copasi candidate models by removing specified model components from a given master model, b) automatically documents candidate models, c) automatically fits candidate models to data using CopasiSE, d) provides a ranking of candidate models fits based on the AIC.
- Monod — Modeler's Notebook and Data Store' model annotation manager. (Linux/Mac OS) Open Source, Must build from source (LGPL).
- Morpheus — Morpheus is a user-friendly modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. 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.
- NetBuilder' — NetBuilder' is a software tool that is intended to help experimentalists creating and manipulating the mathematical representations they need to predict the behaviour of their systems. NetBuilder' has a graphical user interface, which allows its users to create a picture of the (known) components and interactions in the system, and enter quantitative information, such as know or estimated quantities and rates. A (hidden) translator converts the picture and the other data into a mathematical description, whereupon NetBuilder's ''simulation engine'' may be used to find out how the modelled system responds to changing input.
- Omix — Omix is a highly customizable editor for biochemical network diagrams, equipped with extensive data visualization features. Highest flexibility in designing networks and visualization is provided. With Omix, sophisticated data visualization can be designed with ease. Especially, time-dependent numerical datasets from experiment and simulation are easily visualized and animated in the context of metabolic network. Omix has extensive import and export capabilities, e.g. for SBML, BioPAX, HDF5, Matlab code, etc. Models can be imported from KEGG or BioCyc. Many plug-ins are available providing modeling and analysis features for Omix. This includes, for instance, stoichiometic analysis, thermodynamic analysis, metabolic flux analysis. As a brand new feature, it is now possible to define the dynamics of a biological network in Omix. You can define kinetic laws for the individual reactions and specify initial concentrations and dynamic changes for metabolites. Furthermore, you can create dynamic events.
- Pathway Builder — Graphical model design. Part of Bio-Spice. (BioSpice BSD License)
- PathwayLab — PathwayLab is a tool for modeling, analysis, and information management of biochemical pathways. It streamlines the pathway building process by a rich and flexible set of graphical building blocks for specifying biochemical entities, reaction, and control mechanisms. The pathway models are built using drag and drop from stencils into a workspace, which makes it very easy to rapidly build models of biochemical reaction networks such as signaling and metabolic pathways as well as gene regulatory networks. PathwayLab depends on Microsoft Visio.
- ProcessDB — ProcessDB helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a diagram-based user interface that helps users formulate, visualize, compare, combine, modify, manage and test their own mechanistic theories of biological function at levels from molecular cell biology to human physiology. All models in ProcessDB can be automatically combined with user-specified experimental protocols and solved using an implementation of CVODE with a flexible graphing interface for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data.
- ProMoT — The process modeling tool ProMoT is a software for the set-up and manipulation of models of complex technical or biological systems. Key features are the support of modular models, modeling libraries for different application areas, efficient and robust numerical algorithms, its own modeling language MDL and advanced graphical support. Dynamic models can contain DAE and discrete events for simulation in DIVA, Diana or MATLAB. Logical (Boolean) models are exported to CellNetAnalyzer. Process-Interaction-Models can be exported into BNGL format or transformed into logical models.
- PyLESS — PyLESS is a software for dimension reduction in dynamic models. It has been developed as a B.Sc. thesis and more information on the software can be found at https://www2.hu-berlin.de/biologie/theorybp/docs/bsc_marvin_schulz.pdf
- RAVEN — The RAVEN Toolbox (Reconstruction, Analysis, and Visualization of Metabolic Networks) toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of genome-scale metabolic models (GEMs). The software has three main foci: 1) automatic reconstruction of GEMs based on protein homology, 2) network analysis, modeling and interpretation of simulation results, 3) visualization of GEMs using pre-drawn metabolic network maps.
- Saint — The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive manual process. Modelers need to know and understand both the systems they are modeling and the intricacies of SBML. However, the amount of relevant data for even a relatively small and well-scoped model is overwhelming. Saint, an automated SBML annotation integration environment, aims to aid the modeler and reduce development time by providing extra information about any given SBML model in an easy-to-use interface. Saint accepts SBML-formatted files and integrates information from multiple databases automatically. Any new information that the user agrees with is then automatically added to the SBML model. The purpose of Saint is to aid the researcher in the difficult task of information discovery by seamlessly querying multiple databases and providing the results of that query within the SBML model itself. By providing a modeling interface to existing data integration resources, modelers are able to add information to models quickly and simply.
- SBML2NEURON — Note: SBML2NEURON is currently obsolete. The Import/export features of jNeuroML (https://github.com/NeuroML/jNeuroML) offer a more complete path for getting SBML models into NEURON (via conversion to LEMS.
- SBMLEditor — SBMLeditor a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity and consistency of the final SBML file
- SBML-shorthand — Specification and conversion tools for a simple human-readable shorthand notation for a subset of SBML. Used for rapid building of SBML models without using a sophisticated GUI tool.
- SBMLsqueezer — SBMLsqueezer is a generator for kinetic equations for biochemical networks with access to the rate law database SABIO-RK. When creating equations de novo, it takes the context of each reaction into account by evaluating Systems Biology Ontology (SBO) annotations and further information. It can be used as a stand-alone tool, as a plug-in for CellDesigner, a GARUDA gadget, an online program, through its programming interface, or as a command-line tool. The rate laws that can be produced by SBMLsqueezer are numerous, including traditional and recent approaches for several network types. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.
- SBMLToolbox — Manipulation of SBML in both the MATLAB and Octave environments. Some simulation support but the main focus is on allowing users to adapt SBML to their existing MATLAB/Octave functions.
- SED-ML Web Tools — The SED-ML Web tools represent a suite of tools for creating, editing, simulating and validating SED-ML files.SED-ML descriptions can be created directly by uploading an SBML model.
- SigTran — SigTran is a modeling environment especially designed to enable biological researchers to carry out large scale simulations and analysis of complex signal transduction networks. (inactive?)
- SImpleSBML — SimpleSBML is a package that can be used to construct biological models in SBML format using Python without interacting directly with the libSBML package. Using libSBML to build models can be difficult and complicated, even when the model is relatively simple, and it can take time for a user to learn how to use the package properly. This package is intended as an intuitive interface for users who are not already familiar with libSBML. It can be used to construct models with only a few lines of code, print out the resulting models in SBML format, and simplify existing models in SBML format by finding the SimpleSBML methods that can be used to build a libSBML version of the model.
- SloppyCell — SloppyCell is focused on parameter estimation and sensitivity analysis for ODE models. In particular, SloppyCell includes semi-analytic sensitivity integration, along with capability for building Bayesian ensembles of parameters sets consistent with given data.
- TinkerCell — TinkerCell is a drawing tool for synthetic biology that supports modular models and is highly extensible. One of the extensions is the COPASI C++ library, which adds most of the analysis capabilities from COPASI. Another extension support SBML import/export as well as the Antimony model definition language. TinkerCell supports over 200 Python and Octave functions, allowing users to add plug-ins written in Python or Octave. Users can also upload their plug-in to a central repository (hosted at Sourceforce); all other TinkerCell users will automatically get this plug-in in TinkerCell in the form of a new button. Hierarchical modeling is another key feature in TinkerCell, which is used in conjunction with a custom ontology for automatically generating one or more models from conceptual diagrams.
- Virtual Cell — VCell is a unique computational environment for modeling and simulation of cell biology which supports multiple simulation frameworks (spatial/nonspatial, deterministic/stochastic) from the same user-specified physiological model. VCell was specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. VCell is deployed as a distributed application that can leverage remote computational, database and data storage resources or perform computations locally. Our original focus was spatial modeling and simulation within experimental cellular geometry, but has grown to include ode, pde, particle, SSA, and hybrid mathematical frameworks as well rule-based modeling , biological pathway integration, and moving boundary problems.
- Virtual Parts Repository — A repository of standard virtual parts which are reusable, modular and composable models of physical biological parts. These models can be joined together computationally in order to facilitate the model-driven design of large-scale biological systems. The Virtual Parts Repository has a REST-based Web service interface to access information about, and models of, biological parts and their interactions computationally. Moreover, the repository can be programmatically accessed using the JParts API, which also provides methods to join models of parts and interactions to create simulatable models.
- Wolfram SystemModeler — Wolfram SystemModeler is a high-fidelity modeling software based on the Modelica language. It allows for hierarchical, multidomain, and hybrid systems modeling using a graphical drag and drop environment, and/or an equation based textual interface. And it integrates with the Wolfram technology platform to enable modeling, simulation, and analysis (of many types), all together achieving an agile design optimization loop. Provided with SystemModeler is a large set of built-in model libraries, including the BioChem library - an SBML compatible Modelica library designed for biochemical systems. By making use of the BioChem library, SystemModeler lets you build, simulate, and visualize PKPD and systems biology models. The software also provides SBML import and export functionality to allow Modelica-SBML model exchange.

## Repository or database

- BASIS — BASIS is a project developing web-based services for quantitative study of the biology of ageing. The project also hosts the Stochastic Test Suite.
- BiGG — Database of human, yeast and bacterial metabolites, pathways and reactions as well as SBML reconstructions for metabolic modeling.
- BioCyc — Collection of pathway/genome databases. May be downloaded in SBML, BioPAX, or flat format. Free limited academic license (detailed). May be explored with Pathway Tools
- BioGRID — BioGRID is an online interaction repository with data compiled through comprehensive curation efforts.
- BioModels Database — BioModels Database is a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided. All models are provided under the terms of the Creative Commons CC0 Public Domain Dedication, cf. our terms of use. This means that the models are available freely for use, modification and distribution, to all users. More information about BioModels Database can be found in the frequently asked questions (FAQ).
- BioModels Importer — The database component of BioModels.net is especially designed for working with annotated computational models: each model is carefully reviewed and augmented by human annotators on the BioModels.net team to add metadata linking the model elements to other biological databases and resources. The BioModels Database at the EBI system goes far beyond other collections of models by being a true database, featuring browsing, cross-referencing, searching, and facilities for visualization, exporting models in different formats, and remote API access. The BioModels Importer is such a tool, allowing to search for a specific model (or to quickly access them all). Integrated with SBW the Importer sends a model to JDesigner, Jarnac or any other tool in a snap.
- BRENDA — the BRaunschweig ENzyme Database is a comprehensive information system covering enzymes and their activities. The majority of the data are manually extracted from the primary literature. The content covers information on function, structure, occurrence, preparation and application of enzymes as well as properties of mutants and engineered variants. In 2011, BRENDA introduced the ability to output data in SBML format.
- CADLIVE — CADLIVE (Computer-Aided Design of LIVing systEms) is a comprehensive computational tool for constructing large-scale biological network maps, analyzing the topological features of them, and simulating their dynamics. Using CADLIVE, we rationally design a biological system at the molecular interaction level for an engineering purpose.
- ConsensusPathDB — integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks
- CRdata — CRdata.org offers menu-driven access to the Amazon Elastic Computing Cloud (EC2) and related resources for bioinformatic computing with R and Bioconductor. Users can launch their own processing nodes, and share nodes, scripts, and data with others if they wish.
- CycSim — CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. it supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes and direct visualization of both on metabolic maps. CycSim also functions as an online repository of genome-scale metabolic models.
- insilicoIDE — insilicoIDE (ISIDE) assists users to build models of physiological functions with multilevel hierarchical structure and to run simulations. A model is built as a functional network of ''modules'' which represent physiological entities. In each module, equations such as ODEs and PDEs, parameters and morphological information can be defined. Besides, a module can include a model written in SBML. The SBML model is functionally embedded in the module network. There is an open model database at www.physiome.jp. Users can use models in the database freely as parts to build their own model. The modularity of the model representation in ISIDE makes reuse and integration of multiple models easier. The simulator included in ISIDE supports parallel computing.
- iPathways+ — A Web-based Pathway Publishing Platform to browse public pathways, to publish your pathways online, to share your pathways by embedding your pathways to your website, via emails, via SNS (Facebook, TwiBer, Google+), and visualize (map) your data. iPathways+ support CellDesigner ver 4.x format.
- JWS Online — Online database and simulator.
- KiMoSys — We are now suggesting our subject-specific repository KiMoSys (see BioSharing entry:000631) for appreciation by SBML team. KiMoSys is an experimental data repository for KInetic MOdels of biological SYStems. Despite all the existing resources available, there is a growing requirement for the search and exchange of experimental data and protocols, kinetic models, as well as applications to support, the construction of large-scale kinetic models for the wider systems biology community. We propose KiMoSys, a web-based unified platform, constituted by a repository of published experimental data useful for building and validating kinetic models. Moreover, KiMoSys ensure long-term persistence and preservation of the data and associated kinetic models; provide curation, support community standard format (e.g. SBML, SBtab and COMBINE archive); provide stable data identifiers and static URL for submitted datasets; keep datasets private, share with specific users or allow public access for the global community.
- Kineticon — Online resource for kinetic data, reactions, enzymes, pathways. SBML L2V1 Export.
- MEMOSys — MEMOSys is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. It currently contains 9 annotated microbial metabolic models.
- Meta-All — Pathway database manager.
- MetaCrop — MetaCrop is a database that contains manually curated, highly detailed information about metabolic pathways in crop plants, including location information, transport processes, and reaction kinetics. The web interface supports an easy exploration of the information from overview pathways to single reactions and therefore helps users understanding the metabolism of crop plants. It also allows automatic data export for the creation of detailed models of metabolic pathways to support simulation approaches.
- MetaNetX — MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. To this end, it integrates a great variety of data sources in a common namespace and tools.
- NetPath — NetPath' is a curated resource of signal transduction pathways in humans. All pathways are freely available in BioPAX, PSI-MI and SBML formats. The pathways are freely available under an adaptive Creative Commons License which stipulates that the pathways may be used if adequate credit is given to the authors. Feedback on the NetPath website and its contents can be sent to info@netpath.org.
- NetPro — Molecular interaction database (commercial).
- PANTHER Pathway — Pathway database (online resource).
- PathArt — Pathway database collection. (Commercial)
- PAYAO — PAYAO is a community collaborative web service platform for gene-regulatory and biochemical pathway model curation.
- Reactome — Pathway database (online resource).
- SABIO-RK — SABIO-RK is a curated database for biochemical reaction kinetics data. The data is drawn from different sources: by extraction from published literature or direct submission by experimenters, and is supplemented with additional data from other databases. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. It can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML. SABIO-RK facilitates the exchange of kinetic data between experimentalists and modellers, and thereby supports the setup of quantitative computer models.
- SBMLEditor — SBMLeditor a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity and consistency of the final SBML file
- SGMP — The UCSD Signaling Gateway Molecule Pages provide essential information on over 4000 proteins involved in cellular signaling. Each Molecule Page contains regularly updated information derived from public data sources as well as sequence analysis, references and links to other databases. Published Molecule Pages contain an expert-authored review article that describes the biological activity, regulation and localization of the protein. This review is supplemented by highly structured data that illustrate protein-protein interactions, post-translational modifications, subcellular localization and biological function. Prior to publication, there is rigorous peer and editorial review of each Molecule Page. The published pages are citable by digital object identifiers (DOIs). All data in the Molecule Pages are freely available to the public.
- Sigmoid* — Model database, explorer, visualization, Cellerator-based simulations as a web service.
- SignaLink — SignaLink is a multi-layered (onion-like) database made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network of human and two invertebrate model organisms, C. elegans and D. melanogaster.
- SPDBS — SBML-Based Biochemical Pathway Database System
- SYCAMORE — SYCAMORE is a system that provides you with a faciliated access to a number of tools and methods in order to build models of biochemical systems, view, analyse and refine them, as well as perform quick simulations.
- Virtual Cell — VCell is a unique computational environment for modeling and simulation of cell biology which supports multiple simulation frameworks (spatial/nonspatial, deterministic/stochastic) from the same user-specified physiological model. VCell was specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. VCell is deployed as a distributed application that can leverage remote computational, database and data storage resources or perform computations locally. Our original focus was spatial modeling and simulation within experimental cellular geometry, but has grown to include ode, pde, particle, SSA, and hybrid mathematical frameworks as well rule-based modeling , biological pathway integration, and moving boundary problems.
- Virtual Parts Repository — A repository of standard virtual parts which are reusable, modular and composable models of physical biological parts. These models can be joined together computationally in order to facilitate the model-driven design of large-scale biological systems. The Virtual Parts Repository has a REST-based Web service interface to access information about, and models of, biological parts and their interactions computationally. Moreover, the repository can be programmatically accessed using the JParts API, which also provides methods to join models of parts and interactions to create simulatable models.

## Scripting module

- MatCont — MatCont is a Matlab software package for the numerical study of parameterized continuous and discrete dynamical systems.
- pybrn — pybrn is a Python package for the analysis of biochemical reaction networks. It is mainly meant as a basic library for researchers developing their own model analysis routines in Python. pybrn currently features: - basic model creation, data handling and evaluation - import of SBML files into pybrn’s data structures - analysis of network conservation relations - computation of steady states and steady state branches - integration of the network’s differential equation

## Simulation software

- BetaWB — BetaWB is a collection of tools based on the programming language BlenX, explicitly designed to represent biological entities and their interactions. The BetaWB includes the BetaWB simulator, a stochastic simulator based on an efficient variant of the Gillespie Stochastic Simulation Algorithm (SSA), the BetaWB designer, a graphical editor for developing models and the BetaWB plotter, a tool to analyse the results of a stochastic simulation run.
- BIOCHAM — Programming environment with GUI, simulator, and rule-based modeling language. SBML import & export.
- BioNessie — BioNessie is a free, state-of-the-art platform-independent biochemical networks simulation and analysis software environment software. It is developed using Java technology and can run on many platforms that support JRE (Java Runtime Environment 1.5 or higher). It provides a full user-friendly Graphical User Interface (GUI) which allows the user to import, create, edit and export the biochemical models with the SBML (Systems Biology Markup Language) standard. The unique Concurrent Versions Syst ...
- BioNetGen — BioNetGen is a software system for the specification and simulation of rule-based models of biochemical systems. In rule-based models, molecules and molecular complexes are represented using graphs, and molecular interactions and their consequences are represented using graph-rewriting rules. Open source. Download requires email based registration. Requires Perl. Optional GUI uses JRE. (Linux/Mac/Win)
- BioPARKIN — Robust and reliable parameter identification (e.g. rate constants) in biology-related systems described by (sets of) ODEs or DAEs from given measurement data, based on an affine covariant Gauss-Newton algorithm. Additionally, providing a sensible, parameter depending sensitivity analysis for the ODE/DAE systems.
- BioRica — BioRica is a high-level hierarchical modeling framework integrating discrete and continuous multi-scale dynamics. The co-existence of continuous and discrete dynamics is assured by flux connections with the continuous parts of the model. Once connected, these parts of the model act as components that can be queried for the function value, but also modified, therefore accounting for any trajectory modification induced by discrete parts of the model. BioRica is available upon request.
- BioSyS — a system that facilitates the study of biological systems that are described by Ordinary Differential Equations (ODEs). This software is designed to be capable of performing distributed simulations using Grid computing, stores the results in a database and allow further studies, incorporating various types of analysis such as charts, population dynamics, algorithms of clustering, classification, user-defined rules, stability and bifurcations, using data mining techniques. BioSyS 1.0 makes it easier for researchers with a number of tools and algorithms that allow them to carry out investigations in an easier way.
- BioTapestry — Graphical model development and simulation tool for genetic regulatory networks based on JRE. Uses Java Web Start. Free download. SBML export.
- BoolNet — An R package for the generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
- braincirc — Braincirc is an open source model development and simulation environment developed primarily for linux platforms, originally developed to simulate brain circulation (Linux).
- ByoDyn — ByoDyn includes a set of tools to 1) integrate ordinary differential equations (ODEs), including systems with events, rules (differential algebraic equations, DAE) and delays built from a given biological model; 2) stochastic simulators: SSA and tau-leap; 3) globally optimize the parameters that fit the provided experimental information and evaluate the sensitivity of the model with respect to the different parameters; 4) include the sensitivity of the parameters in an optimal experimental design pipeline based on the Fisher information matrix; and 5) Monte Carlo sampling coupled with cluster analysis and PCA to determine the global shape of the parameter landscape. The program makes use of external software, providing a Python binding schema that allows the user to easily implement new software in the desired calculation protocol. Furtermore, a webserver has been developed to manage the models, calculations and results easily.
- Cain — Cain is an application that performs stochastic and deterministic simulations of chemical reactions. It stores models, simulation parameters, and simulation results in an XML format. The models and simulation parameters can be read from input files or edited within the program. Cain offers a variety of solvers including: Gillespie's direct method, Gillespie's first reaction method, Gibson and Bruck's next reaction method, tau-leaping, hybrid direct/tau-leaping, and ODE integration.
- Cell Illustrator — Graphical model editor; Petri-net based simulation algorithm; SBML Import. Commercial. (Linux/Mac/Win).
- CellNetAnalyzer — CellNetAnalyzer (CNA) is a package for MATLAB and provides a comprehensive and user-friendly environment for structural and functional analysis of biochemical networks. CNA facilitates the analysis of metabolic (stoichiometric) as well as signaling and regulatory networks solely on their network topology, i.e. independent of kinetic mechanisms and parameters. CNA provides a powerful collection of tools and algorithms for structural network analysis which can be started in a menu-controlled manner within interactive network maps. Recently, API functionalities have been added to enable interested users to call algorithms of CNA from external programs. Applications of CNA can be found in systems biology, biotechnology, metabolic engineering, pharmacology, microbiology, chemical engineering.
- CellNOpt — CellNOpt is a software used for creating logic-based models of signal transduction networks using different logic formalisms (Boolean, Fuzzy, or differential equations). CellNOpt uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against high-throughput biochemical data to create cell-specific models. CellNOpt is freely available under GPL license in R and Matlab languages. It can be also accessed through a python wrapper, and a Cytoscape plugin called CytoCopter provides a graphical user interface.
- Cellware — Block diagram model editor & simulator. SBML import. Free download (Academic/Non-Profit) (Linux/Mac/Win).
- CompuCell3D — CompuCell3D (CC3D) is a documented and supported open-source environment for building and running multi-cell, multi-scale simulations based on the Cellular Potts Model/ Glazier Graner Hogeweg model, which implements biochemical network modeling using components from the Systems Biology Workbench (SBW) suite. Building CC3D models with its model-description language CC3DML and Python scripting requires much less specialized knowledge of numerical analysis or computer science than do hard-coded methods and allows easy model publication, sharing, reuse and validation. CC3D’s architecture allows experienced programmers to build very sophisticated extensions. It scripting capability makes CC3D more similar to general-use packages like Matlab than to specialized research code.
- CRdata — CRdata.org offers menu-driven access to the Amazon Elastic Computing Cloud (EC2) and related resources for bioinformatic computing with R and Bioconductor. Users can launch their own processing nodes, and share nodes, scripts, and data with others if they wish.
- Cyto-Sim — Stochastic simulator based on automata theory (P system). Free download. JVM Based.
- DBSolve — DBSolveOptimum is a free software for kinetic modeling of metabolic pathways, analysis, and fitting parameters to experimental data. The program has text-based user interface for model description and graphical interface for data analysis. In addition to standart algorithms of simulation (ODE solver, explicit solver, steady-state analysis) the software includes also the automated local sencetivity analysis, parameters optimization procedures and bifurcaion analysis. The last version of DBSolveOptimum includes the advanced tool for data visualization.
- DEDiscover — Perform simulation and parameter estimation of models described be ordinary and delayed differential equations. Also perform model selection through statistical analysis (Fisher's information, Bootstrapping), residual analysis and sensitivity analysis.
- Dizzy — Chemical kinetics simulator. SBML Import/Export (L1 Subset). Includes Gillespie, Gibson-Bruck and Tau Leap stochastic and ODE/RK5 deterministic methods. LGPL, open source, Free download. (Linux/Mac/Windows).
- E-CELL — (Linux RPM/Win). Requires Python, Numpy, GSL, Boost. Command line, scripting, and GUI. Supports ODE/DAE and Gibson-Bruck SSA models. GUI requires Gnome, gnome-python2, and pygtk. GPL with exceptions. SBML import via SBML2EML converter. Limited SBML export via ecellj converter.
- EPISIM — The EPISIM consists of EPISIM Modeller (graphical modeling system) and EPISIM Simulator (simulation environment). Each EPISIM (multi-scale) model comprises a cell behavioral and a biomechanical model (CBM and BM). The BM covers all spatial and biophysical cell properties. Different BMs (lattice and off-lattice) are offered by the simulation environment. A BM can be dynamically linked to a CBM which is graphically modeled with process diagrams in the EPISIM Modeller. Automatic semantic integration of quantitative subcellular SBML models in CBMs is possible. The graphical CBMs are automatically compiled into executable code which is loaded by the EPISIM Simulator conducting an agent-based tissue simulation. EPISIM Simulator embeds COPASI to simulate SBML-based models. This allows linking of discrete (deterministic / stochastic) and continuous models on cellular on subcellular scale. Reaction-Diffusion models of e.g. chemokines can be integrated in a multi-scale tissue model with extracellular diffusion fields.
- ESS — Exact Stochastic Simulator. Part of the UTK/ORNL Bio-SPICE tool set which includes the BioSpreadsheet SBML model editor. Requires BioSpice Dashboard. Free download. Includes Source code.
- Facile — Facile / EasyStoch. A command-line network compiler for systems biology. Facile reads models given in a simple and human-readable textual input format and exports the model in a format for readable by Matlab, Mathematica, Maple, XPP/AUTO. Other tools are supported via SBML export. For stochastic simulations, Facile uses the EasyStoch stochastic simulator. An important feature of EasyStoch that distinguishes it from other Gillespie-algorithm implementations is that it is capable of simulating dynamically changing or noisy biochemical parameters (i.e. extrinsic noise).
- FASIMU — FASIMU is a command line oriented software implementing the most frequently applied FBA algorithms. It offers the first freely available implementation of (i) weighted flux minimization, (ii) fitness maximization for partially inhibited enzymes, and (iii) the concentration-based thermodynamic feasibility constraint. It allows heterogenous computation series suited for network pruning, leak analysis, FVA, and systematic probing of metabolic objectives for network curation controlled by an intuitive description file. The metabolic network can be supplied in SBML, CellNetAnalyzer, and plain text format. FASIMU uses the optimization capabilities of free (lp solve and GLPK) and commercial solvers (CPLEX, LINDO). The results can be visualized in Cytoscape or BiNA using newly developed plugins. The platform-independent program is an open-source project, freely available under GNU public license, including manual, tutorial, BiNA and Cytoscape plugin and respective manuals.
- FERN — FERN is a Java framework for the efficient simulation of chemical reaction networks. It provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. Furthermore, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modeled easily with FERN.
- FlexFlux — FlexFlux is a java tool for metabolic flux and regulatory network analysis. To analyse metabolic fluxes, FlexFlux is based on a mathematical method, FBA which consists in transforming a metabolic network into linear equations and calculate fluxes thanks to linear programming. Concerning the regulatory network analysis, FlexFlux supports multistate qualitative regulatory networks. This regulatory network is composed of components of different natures (genes, mRNAs, proteins, metabolites ...), that interact with each other in different ways and can have an effect on the metabolic network. FlexFlux performs synchronous updates of the regulatory network state from provided initial values. Once a steady-state of this regulatory network is reached, the states are translated into continuous intervals (see the regulation file section) used as constraints for the FBA. We named this pipeline Regulatory Steady-state Analysis (RSA). FlexFlux contains many methods dedicated to regulatory network and flux analysis.
- Genetdes — Network optimization using Simulated Annealing. SBML Import/Export. Free download, requires email license (CCL- AN). (Linux)
- Genetic Network Analyzer — Genetic Network Analyzer (GNA) is a computer tool for the modeling, simulation, analysis and verification of genetic regulatory networks. The aim of GNA is to assist biologists and bioinformaticians in constructing a qualitative model of a genetic regulatory network from knowledge about regulatory interactions and gene expression data. GNA provides a variety of functions to analyze the steady-state and transient dynamics of the network, among other things by exploiting state-of-the-art model-checking tools.
- Gepasi — Forerunner of COPASI. ODE simulations, metabolic analysis. SBML L1 Inport/Export. (Windows or Linux under Wine). Limited license.
- Gillespie2 — from the BASIS Project. Source code.
- GNAT — GNAT is an open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks. It is written in MATLAB and Java. It is thus platform-independent. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms.
- GNU MCSim — GNU MCSim is a free standalone simulation package that allows you to design your own statistical or simulation models. It efficiently performs Bayesian inference through Markov Chain Monte Carlo simulations. Standard Monte Carlo and experimental design optimization are also available. GNU MCSim can import and simulate levels 1 and 2 SBML models
- iBioSim — 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, labeled Petri net, and general biochemical models encoded in the Systems Biology Markup Language (SBML). Models can be constructed using either a schematic or textual editor, 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.
- Jarnac — SBW tool for metabolic analysis, includes dynamic simulation. Simulation engine for JDesigner. BSD License.
- JigCell — JigCell is a set of computational tools with user-friendly interfaces developed for studying complex biochemical regulatory systems in general and the cell cycle control system in particular. For example, The JigCell Model Builder (JCMB) aides the modeler in defining a system to be modeled using SBML with a novel spreadsheet interface, allowing a large amount of data to be displayed in an organized manner. The JigCell Run Manager (JCRM) allows a user to specify a set of specifications for simulation runs using a spreadsheet interface. JigCell Aggregation Connector has been designed to define models in terms of components, for the purpose of being combined in a larger model. JigCell also aims in parameter estimation. A parameter estimator (PET, Parameter Estimation Toolkit) takes a biological model, experimental data, and the relationship between the model and data. Using this information the parameter estimator uses numerical tools to vary the parameters to the model looking for the parameters that best fit the experimental data.
- jNeuroML — There are a number of repositories in active development under GitHub for handling NeuroML and LEMS with Java. To make it easier to access all of this functionality, we've created a single package, jNeuroML, which allows access to most of this functionality through a simple command line interface and requires minimal installation. jNeuroML can be used to import SBML and convert it to LEMS, and can export some NeuroML 2/LEMS files to SBML. See https://github.com/OpenSourceBrain/SBMLShowcase
- Kinsolver — A simulator for biochemical and gene regulatory networks
- libRoadRunner — libRoadRunner is a high performance SBML simulator (based on an LLVM backend) that includes additional features such as steady state, jacobian, eigenvalues, conservation analysis and sensitivity analysis. It supports full SBML except for delay and non-linear algebraic equations.
- libSBMLSim — LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.
- MASS Toolbox — Mathematica based kinetic and constraint-based model building and simulation framework (open source under BSD license). Focus on mass action kinetics and elementary reaction systems. Features include: ODE/DAE integration (delays and events are also supported), high-level plotting commands for time courses and phase portraits, analytical steady-state solutions for complex enzyme mechanisms, static and dynamic pathway visualizations, set operations on models (e.g. obtain the intersection of two models), flux balance analysis, scientific unit support, and many more. SBML import tested against SBML Test Suite.
- MatCont — MatCont is a Matlab software package for the numerical study of parameterized continuous and discrete dynamical systems.
- MesoRD — MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
- Metaboflux — Metaboflux is a computational tool for predicting flux distribution in metabolic networks under multiple and various constraints deducted from the experiments. It aims to increase the biological relevance of models by integrating experimental data. The tool is available in two versions : a command line tool optimized for running on HPC servers and a user-friendly interface designed to define model parameters and run simple computations. Metaboflux embedded a stochastic simulator of metabolic networks coupled with a non linear solver (GSL). It solves constraints defined as proportions (for example, metabolite proportions) or as equations. Results can be visualized directly in Metaboflux or within specific tools like Systrip.
- MetaFluxNet — MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way, which allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies.
- Modesto — Merged ODE and Stochastic Simulator. Source code only. Linux. (MPL 1.1)
- Moleculizer — Command line stochastic simulator. Open source. (Linux) (GPL)
- Narrator — Graphical model design and simulation. Java-based, platform independent. Open source/free download (LGPL).
- nemo — RANGE will generate large random transcription networks, with up to 16,000 genes, in the NEMO language. NEMO's compiler (nemo2sbml) uses lex and yacc to output a Systems Biology Markup Language (SBML) model for either user-specified and/or randomized gene input functions. The SBML model of the known network may be input to a biochemical simulator (i.e. COPASI), allowing the generation of synthetic microarray data for algorithm development purposes. Alternately, NEMO may be used by itself to simply describe and SBML-ize your existing biochemical network.
- NetBuilder' — NetBuilder' is a software tool that is intended to help experimentalists creating and manipulating the mathematical representations they need to predict the behaviour of their systems. NetBuilder' has a graphical user interface, which allows its users to create a picture of the (known) components and interactions in the system, and enter quantitative information, such as know or estimated quantities and rates. A (hidden) translator converts the picture and the other data into a mathematical description, whereupon NetBuilder's ''simulation engine'' may be used to find out how the modelled system responds to changing input.
- Odefy — Odefy is a MATLAB and Octave compatible toolbox which a modeling technique called HillCube, a canonical method to convert boolean models into continuous ordinary differential equation (ODE) systems. HillCubes are based on multivariate polynomial interpolation and incorporate Hill kinetics which are known to provide a good approximation of the synergistic dynamics of gene regulation.
- optflux — OptFlux is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using phenotype prediction methods such as FBA/pFBA, MOMA/LMOMA, ROOM and MiMBl (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard (import/export). OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.
- Oscill8 — Bifurcation and Simulation. Windows Binary. (BSD).
- Pathway Solver — ODE based simulation. Commercial. (formerly runSMBL)
- PathwayLab — PathwayLab is a tool for modeling, analysis, and information management of biochemical pathways. It streamlines the pathway building process by a rich and flexible set of graphical building blocks for specifying biochemical entities, reaction, and control mechanisms. The pathway models are built using drag and drop from stencils into a workspace, which makes it very easy to rapidly build models of biochemical reaction networks such as signaling and metabolic pathways as well as gene regulatory networks. PathwayLab depends on Microsoft Visio.
- PET — Parameter optimization and exploration is the primary feature of PET. Some of the other tasks PET can perform are simulations, setting up multiple experiments for a model, comparing parameter sets, and exporting plots for presentations.
- PhysioLab Modeler — Whole organism modeling environment. Commercial.
- PNK — Petri Net Simulator (JRE/SBW required) (GPL).
- PySCeS — PySCeS: the Python Simulator for Cellular Systems is an extendable toolkit for the analysis and investigation of cellular systems. PySCeS is developed in Python and has been designed to be used both interactively or as a library. It utilises a human readable, model description language for describing models as well as being SBML compatible. PySCeS includes stoichiometric, simulation, steady state and Eigen analysis using direct non-linear root finders. It also includes full support for Metabolic Control Analysis (MCA), the characterisation of static bifurcations, multidimensional parameter scanning and 2/3D graph capabilities. Currently an extension PySCeS-CBM is being developed that allows for the interactive manipulation, modelling and optimization of genome scale, constraint based models (e.g. flux balance analysis)
- RAVEN — The RAVEN Toolbox (Reconstruction, Analysis, and Visualization of Metabolic Networks) toolbox is a complete environment for reconstruction, analysis, simulation, and visualization of genome-scale metabolic models (GEMs). The software has three main foci: 1) automatic reconstruction of GEMs based on protein homology, 2) network analysis, modeling and interpretation of simulation results, 3) visualization of GEMs using pre-drawn metabolic network maps.
- roadRunner — 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
- SBML2NEURON — Note: SBML2NEURON is currently obsolete. The Import/export features of jNeuroML (https://github.com/NeuroML/jNeuroML) offer a more complete path for getting SBML models into NEURON (via conversion to LEMS.
- SBML-PET-MPI — SBML-PET-MPI is a parallel parameter estimation tool for Systems Biology Markup Language (SBML) based models. The tool allows the user to perform parameter estimation, parameter uncertainty and identifiability analysis by collectively fitting multiple experimental data sets. SBML-PET-MPI can run on Windows, Linux and Mac OS X systems.
- SBMLR — This package uses the R package XML to bring SBML models into and out of R.
- SBML-SAT — SBML-SAT implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface.
- SBMLToolbox — Manipulation of SBML in both the MATLAB and Octave environments. Some simulation support but the main focus is on allowing users to adapt SBML to their existing MATLAB/Octave functions.
- SBToolbox2 — MCA: Steady state control coefficients and elasticities; Structural analaysis: conservation relation analysis; model development; simulation; SBML Import/Export; parameter estimation; analysis tools. Requires MatLab (Linux/Win/Mac).
- sbw: javasim — Set of Java simulators implementing; Chemical Langevin, CVODE, Gibson NRM, Gillespie DM, Gillespie FRM, and LSODA.
- sbw: stochastic simulator — GillespieGUI is a new user interface for biochemical networks that has been designed to integrate both tasks of interest to biologists - namely, simulating a model and analyzing the data. The data simulation is carried out by a stochastic simulator, whose parameters such as simulation start and end times, as well as data or time sampling options can be set prior to starting the simulation. This being a tool designed for statistical analysis, users can specify the number of runs of the model that the simulation should generate. Once the data for the specified number of runs has been generated, the tool then computes correlations between various species, along with their power spectral densities and transfer functions. In particular the following capabilities are supported:
- SED-ML Web Tools — The SED-ML Web tools represent a suite of tools for creating, editing, simulating and validating SED-ML files.SED-ML descriptions can be created directly by uploading an SBML model.
- SIMBA — Wastewater simulation. SBML Support unspecified. Commercial(?).
- Simulation Tool — The Simulation Tool is an environment for interactive exploration of SBML Models (L1-L3). It allows for simulation and analysis of models, provided capabilites (through simulators like RoadRunner) to define signals and events to interact with the model. Also features Steady State and Frequency Analysis.
- SmartCell — Stochastic Reaction/Diffusion Simulator (Linux/Mac/Win) (Acad/NP).
- Snoopy — a software tool to design and animate hierarchical graphs, among others Petri nets. To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but being specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the GUI adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools.
- SOSlib — SOSlib is a programming library and command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in SBML (Systems Biology Markup Language). It is written in ANSI/ISO C and distributed under the GNU Lesser General Public License (LGPL). The package employs libSBML's AST for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems. The native API provides fine-grained interfaces to all internal data structures, symbolic operations and numerical routines, enabling the construction of powerful and efficient analytic applications, hybrid solvers or multi-scale models with interfaces to non SBML data sources. Optional modules (Graphviz and XMGrace) allow a quick inspection of a model's structure and dynamics.
- STEPS — STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh. While STEPS was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role. We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.
- StochKit — C++ library that provides various SSA, tau-leaping and adaptive step size algorithms. Source code only. (Linux) (Acad/NP).
- StochPy — StochPy is a versatile modeling package for stochastic simulation of molecular control networks inside living cells. Its integration with Python’s scientific libraries and PySCeS makes it an easily extensible and a user-friendly simulator. The high-level statistical and plotting functions of StochPy allow for quick and interactive model interrogation at the command-line. Python’s scripting capabilities allow for more complicated and in-depth analysis of stochastic models.
- StochSim — STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.
- STOCKS — SSA, Gibson-Bruck, and Tau-Leaping algorithms. Command line based tool. (source code, Linux/Windows) (GPL).
- SurreyFBA — SurreyFBA provides constraint-based simulations of genome scale metabolic networks in a free, stand-alone software. In addition to basic simulation protocols the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments. The SurreyFBA is based on a command line interface to the GLPK solver distributed as binary and source code for the three major operating systems. The sfba command line tool, implemented in C++, is easily executed within scripting languages used in the bioinformatics community and provides efficient implementation of tasks requiring iterative calls to the linear programming solver. SurreyFBA includes JyMet, a graphics user interface allowing spreadsheet based model presentation, visualization of numerical results on metabolic networks represented in the Petri net convention, as well as in charts and plots.
- SynBioSS — a suite of software tools for the modeling and simulation of synthetic gene constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale (stochastic-discrete, stochastic-continuous and continuous-deterministic simulation) algorithms. A user can enter a sequence of BioBricks to synthesize a new gene network, obtain a set of biochemical reactions and model the dynamic behavior.
- Systems Biology Simulation Core Library — The Systems Biology Simulation Core Library is a fast, accurate, and easily usable application programming interface for dynamic simulation of models. At the moment, only models encoded in the Systems Biology Markup Language (SBML) are supported, but the generic implementation of the framework facilitates the implementation of further standards. 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.
- Trelis — Monte Carlo Simulator.
- VANTED — This system makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes. Built-in statistic functions allow a fast evaluation of the data (e.g. t-Test or correlation analysis). Vanted can be extended for various functionalities, e.g. flux simulation, database access and 3D visualisation.
- Virtual Cell — VCell is a unique computational environment for modeling and simulation of cell biology which supports multiple simulation frameworks (spatial/nonspatial, deterministic/stochastic) from the same user-specified physiological model. VCell was specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. VCell is deployed as a distributed application that can leverage remote computational, database and data storage resources or perform computations locally. Our original focus was spatial modeling and simulation within experimental cellular geometry, but has grown to include ode, pde, particle, SSA, and hybrid mathematical frameworks as well rule-based modeling , biological pathway integration, and moving boundary problems.
- WebCell — Online simulator, model builder, metabolic controal analysis. Includes database of bimodels and JWS models. Registration required.
- Wolfram SystemModeler — Wolfram SystemModeler is a high-fidelity modeling software based on the Modelica language. It allows for hierarchical, multidomain, and hybrid systems modeling using a graphical drag and drop environment, and/or an equation based textual interface. And it integrates with the Wolfram technology platform to enable modeling, simulation, and analysis (of many types), all together achieving an agile design optimization loop. Provided with SystemModeler is a large set of built-in model libraries, including the BioChem library - an SBML compatible Modelica library designed for biochemical systems. By making use of the BioChem library, SystemModeler lets you build, simulate, and visualize PKPD and systems biology models. The software also provides SBML import and export functionality to allow Modelica-SBML model exchange.
- xCellerator — Mathematica based ODE simulator. SBML inport/export uses MathSBML. Requires Mathematica. Free download (LGPL). (Linux/Mac/Win).
- Xholon — Model development environment, tool set, simulation. (Linux/Win) Open Source (LGPL).
- XPPAUT — ODE solver, analysis tool. Open Source. Free download. (Linux/Mac/Win)

## Software for use in interactive environments (e.g., MATLAB, R, ...)

- acslXtreme — commercial modeling environment that uses a script language called CSL. Has SBML import. Windows only.
- BioSens — ODE Simulation & Sensitivity analysis for BioSpice Dashboard Dashboard. Requires dashboard, Matlab, XPP, Cygwin, libSBML, DASPK, Tapenade. Requires Biospice dashboard, Matlab, XPP, Cygwin, libSBML, DASPK, Tapenade. Free download (License unspecified). (Windows)
- BoolNet — An R package for the generation, reconstruction, simulation and analysis of synchronous, asynchronous, and probabilistic Boolean networks
- BSTLab — GMA and S-Systems based toolbox for Biochemical Systems Theory.
- CBMPy — PySCeS CBMPy is a new platform for constraint based modelling and analysis. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures used in advanced simulations (LP's, MILP's). PySCeS CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as methods developed specifically for the ecosystem modeling. To cater for a diverse range of modelling needs CBMPy supports user interaction via interactive console for advanced use or as a library for tool development. In addition GUIs are provided for quick access to a visual representation of the model and annotation.
- CellNetAnalyzer — CellNetAnalyzer (CNA) is a package for MATLAB and provides a comprehensive and user-friendly environment for structural and functional analysis of biochemical networks. CNA facilitates the analysis of metabolic (stoichiometric) as well as signaling and regulatory networks solely on their network topology, i.e. independent of kinetic mechanisms and parameters. CNA provides a powerful collection of tools and algorithms for structural network analysis which can be started in a menu-controlled manner within interactive network maps. Recently, API functionalities have been added to enable interested users to call algorithms of CNA from external programs. Applications of CNA can be found in systems biology, biotechnology, metabolic engineering, pharmacology, microbiology, chemical engineering.
- COBRA — The COnstraint-Based Reconstruction and Analysis Toolbox for Matlab includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models.
- DOTcvpSB — MatLab toolbox for optimization of models.
- GNAT — GNAT is an open source MATLAB-based toolbox. It provides functions for reading, writing, manipulation, visualization and simulation of glycan structures and glycosylation reaction networks. It is written in MATLAB and Java. It is thus platform-independent. It has been tested in Windows (Windows 7), Linux (Ubuntu), and Mac OS (X Lion) platforms.
- libRoadRunner — libRoadRunner is a high performance SBML simulator (based on an LLVM backend) that includes additional features such as steady state, jacobian, eigenvalues, conservation analysis and sensitivity analysis. It supports full SBML except for delay and non-linear algebraic equations.
- MathSBML — SBML import/export and simulation within Mathematica.
- Metatool — A tool for metabolic pathway analysis with the main focus in elementary modes calculation. Enzyme subsets and conservation relations are also determined.
- PottersWheel — ODE based Simulation, model fitting, visualization, clustering, model design. (Free download; Optimization toolbox recommended).
- RANGE — Random network generator. Noise added by R-script. Source code in C, yacc, lex. (GPL).
- RMBNToolbox — Toolbox for generating random notebooks (GPL).
- RSBML — SBML interface library for R (GPL). (available from CRAN).
- SBMLR — This package uses the R package XML to bring SBML models into and out of R.
- SBMLToolbox — Manipulation of SBML in both the MATLAB and Octave environments. Some simulation support but the main focus is on allowing users to adapt SBML to their existing MATLAB/Octave functions.
- SBToolbox2 — MCA: Steady state control coefficients and elasticities; Structural analaysis: conservation relation analysis; model development; simulation; SBML Import/Export; parameter estimation; analysis tools. Requires MatLab (Linux/Win/Mac).
- Simpathica — ODE based simulation. Part of BioSpice.
- Tide — Tide is a tool for the automatic identification of optimal drug targets in kinetic models based on ordinary differential equations. Give a model in the popular SBML format it will identify promising drug targets for different effective modifier concentrations.
- xCellerator — Mathematica based ODE simulator. SBML inport/export uses MathSBML. Requires Mathematica. Free download (LGPL). (Linux/Mac/Win).

## Utility software

- CL-SBML — Common Lisp implementation of the SBML Standard (Level 2). I/O library for SBML in Common Lisp.
- ModeRator — ModeRator - The Model Comparator can give insight about similarity of two reconstructions (models) where entities' external identifiers, like, KEGG ID and ChEBI ID are not included. Metabolites are compared using their names that are available in the model file. Chemical formulas, if available, are used to strengthen or weaken automatic decision about equality of metabolites. Formulas with different charge can be tolerated. Reactions are compared based on their metabolites and stoichiometry. Balanced and imbalanced reactions can be compared through tolerance of missing reactants.

## Utility software (other than conversion)

- BiNoM — Biological Network Manager. Network design and manipulation. Visualization. Model conversion (CellDesigner, BioPAX); Structural Analysis; BioPAX Queries. Available as an independent library or Cytoscape plugin.
- BioPAX2SBML — The BioPAX2SBML converter translates BioPAX formats (Level 2 and 3) into SBML format (Level 3 Version 1 with qual) including reactions and relations in one model. Thus, the resulting models can be used for further quantitative and qualitative modeling purposes.
- BiVeS — BiVeS (Biomodel Version Control System) able to detect differences between two versions of a computational model and to communicate these changes. Focusing on SBML and CellML, BiVeS (Biomodel Version Control System) accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions.
- CellMC — CellMC is a program generator that emits highly optimized executables realizing the stochastic simulation algorithm (SSA) given a model expressed as SBML (Level 2). It works on Intel/AMD based PCs and Cell/BE platforms (e.g. Sony PS3, IBM QS22).
- GRENDEL — GRENDEL (Gene Regulatory Network Decoding Evaluations tooL), generates random gene regulatory networks according to user specified constraints on the network topology and kinetics (in addition to generating random topologies, it can also take a predefined topology as input). It then outputs SBML to define the state of each regulatory network under various user specified experimental designs, which can be integrated to produce simulated gene expression data.
- KEGGconverter — KEGGconverter automatically produces merged and converted to SBML fully functional pathway models, enhanced with default kinetics, by inputting only KGML files.The final derived models do not enclose trivial metabolites -reproducing inconsistencies of the KGML visualization-oriented, simplified information pattern- but at the same time they contain all the available information regarding the number of the included reactions in each pathway. Furthermore, additional reactions to neighbouring pathways are constructed which indicate the direction of the metabolic flows in the network and thus providing better stability in the boundary conditions of the models.
- MuVal (Multi-valued logic) — MuVal— Multi-valued logic (MuVal) is a free web service that can convert CellNetAnalyzer (CNA) compliant logic models of signalling networks in a way that facilitates handling of combinatorial regulation. Inhibition or activation of reactions by multiple regulators is a common situation in cell physiology. By the sequential use of MuVal and CNA signaling, the models of the networks can be simulated in terms of multi-valued logic with graded-inhibitory (or activation) responses. MuVal provides an effective alternative to the currently applied assumptions of concerted or independent inhibitory mechanisms, which lead to false inferences in “classical” Boolean (or multi-valued) treatment if the reactions analyzed are being influenced by several regulators simultaneously.
- PathSBML plugin for PathVisio — The PathSBML plugin allows researchers to visualize and overlay data on the same pathway models they use in simulation experiments. Exporting these models as GPML would also allow them to be uploaded to Wikipathways for community curation.
- PINT — New pathway databases generally display pathways by retrieving information from a database dynamically. Some of them even provide their pathways in SBML or other exchangeable formats. Integrating these models is a challenging work, because these models were not built in the same way. Pathways integration Tool (PINT) may integrate the standard SBML files. Since these files may be obtained from different sources, any inconsistency in component names can be revised by using an annotation editor upon uploading a pathway model. This integration function greatly simplifies the building of a complex model from small models. To get new users started, about 190 curated public models of human pathways were collected by PINT. Relevant models can be selected and sent to the workbench by using a user-friendly query interface, which also accepts a gene list derived from high-throughput experiments. The models on the workbench, from either a public or a private source, can be integrated and painted. The painting function is useful for highlighting important genes or even their expression level on a merged pathway diagram, so that the biological significance can be revealed. This tool is freely available.
- SBFC — The System Biology Format Converter (SBFC) aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biology. Although there are various tools available to convert models from one format to another, most of them have been independently developed and cannot easily be combined, specially to provide support for more formats. The framework is written in Java and can be used as a standalone executable. This is a collaborative project and we hope that developers will provide support for more formats by creating new modules.SBFC allows anyone to easily add new converters and to integrate existing converters with a minimum of changes.
- SBML Harvester — The SBML Harvester creates a complex ontology-based representation of SBML models, utilizing both the structure of the SBML model and the models' MIRIAM annotations. This representation can then be used for the consistency verification of SBML models as well as complex queries across both models and biomedical ontologies.
- SBML Reaction Finder — The SBML Reaction Finder retrieves and extracts individual chemical reactions from curated SBML models.
- SBML2BioPax — SBML2BioPax is a tool to convert any SBML files into BioPax. It can create BioPax level 2 or BioPax level 3. It uses the MIRIAM annotations as well as the SBO terms present in the SBML model to improve the BioPAX file generated. The tool is developed inside the SBFC (http://sbfc.sourceforge.net/) framework.
- SBML2LaTeX — SBML2LaTeX is a tool to convert files in the System Biology Markup Language SBML) format into LATEX files. A convenient online version is available, which allows the user to directly generate various file types from SBML including PDF, TeX, DVI, PS, EPS, GIF, JPG or PNG. SBML2LaTeX can also be downloaded and used locally in batch mode or interactively with its Graphical User Interface or several command line options. The purpose of SBML2LaTeX is to provide a way to read the contents of XML-based SBML files. This is helpful and important for, e.g., error detection, proofreading and model communication.
- SBML2Octave — SBML2Octave is a tool to convert any SBML files into Octave. It will create a .m file that should be usable inside MATLAB as well. It support all the SBML elements until SBML level 3 core 1 apart for delay. The tool is developed inside the SBFC (http://sbfc.sourceforge.net/) framework.
- SBML2XPP — Converter between SBML and XPPAut or Oscill8.
- SBML-SAT — SBML-SAT implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface.
- SBML-shorthand — Specification and conversion tools for a simple human-readable shorthand notation for a subset of SBML. Used for rapid building of SBML models without using a sophisticated GUI tool.
- sbmltidy — A wrapper around the tidy command-line utility that will reformat ('pretty-print') an SBML file.
- SyBiL — SyBiL is short for Systems Biology Linker. Biological pathways, reaction and signaling networks are made publicly availabel in formats standardized to the Biological Pathway eXchange format (BioPAX). Simulation tools for biological pathways are standardized to other Markup languages such as Systems Biology Markup Language (SBML) and Virtual Cell Markup Language (VCML). To take full advantage of scientific advances requires the mapping and integration of simulation markup languages with BioPAX. Sybil is developed to convert models between BioPAX and SBML/VCML.
- UTKornTools — UTK/ORNL Bio-SPICE tool set (inactive)

## Visualization/display/formatting software

- Arcadia — Arcadia is an open-source, light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways. It automatically translates SBML files into SBGN maps (using additional semantic information such as SBO terms when available). The default layout can be improved semi-automatically, e.g. by ''cloning'' (duplicating) highly connected species, or focusing on the neighborhood around a given species or reaction. The resulting map can be saved in the SBML file itself (using the layout extension) or exported as a vector image (PDF or SVG)
- AVIS — AVIS is a Google gadget compatible web-based viewer of interactive cell signaling networks. AVIS is an implementation of AJAX (Asynchronous JavaScript with XML) with the usage of the libraries GraphViz, ImageMagic (PerlMagic) and overLib. AVIS provides web-based visualization of text-based signaling networks with dynamical zooming, panning and linking capabilities. AVIS is a cross-platform web-based tool that can be used to visualize network maps as embedded objects in any web page. AVIS was implemented for visualization of PathwayGenerator, a tool that displays over 4000 automatically generated mammalian cell signaling maps; NodeNeighborhood a tool to visualize first and second interacting neighbors of yeast and mammalian proteins; and for Genes2Networks, a tool to connect lists of genes and protein using background protein interaction networks.
- BiNoM Cytoscape Plugin — BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.
- BioModels Database — BioModels Database is a reliable repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources. The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided. All models are provided under the terms of the Creative Commons CC0 Public Domain Dedication, cf. our terms of use. This means that the models are available freely for use, modification and distribution, to all users. More information about BioModels Database can be found in the frequently asked questions (FAQ).
- BiVeS — BiVeS (Biomodel Version Control System) able to detect differences between two versions of a computational model and to communicate these changes. Focusing on SBML and CellML, BiVeS (Biomodel Version Control System) accurately detect and describe differences between versions of a model with respect to (i) the models’ encoding, (ii) the structure of biological networks, and (iii) mathematical expressions.
- CompuCell3D — CompuCell3D (CC3D) is a documented and supported open-source environment for building and running multi-cell, multi-scale simulations based on the Cellular Potts Model/ Glazier Graner Hogeweg model, which implements biochemical network modeling using components from the Systems Biology Workbench (SBW) suite. Building CC3D models with its model-description language CC3DML and Python scripting requires much less specialized knowledge of numerical analysis or computer science than do hard-coded methods and allows easy model publication, sharing, reuse and validation. CC3D’s architecture allows experienced programmers to build very sophisticated extensions. It scripting capability makes CC3D more similar to general-use packages like Matlab than to specialized research code.
- CySBML — Summary: CySBML is a plugin for the work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts based on SBML structure, access to MIRIAM and SBO-based annotations, and SBML validation. CySBML includes an importer for BioModels to load SBML from standard repositories. Availability and implementation: Freely available for non-commercial purposes via the Cytoscape plugin manager or for download at http://sourceforge.net/projects/cysbml/. Main purpose is an import of SBML with the semantic annotations available within the Cytoscape network visualization.
- Cytoscape — open source software platform for visualizing complex-networks and integrating these with any type of attribute data
- DEDiscover — Perform simulation and parameter estimation of models described be ordinary and delayed differential equations. Also perform model selection through statistical analysis (Fisher's information, Bootstrapping), residual analysis and sensitivity analysis.
- EPE — Edinburgh Pathway Editor is a biological pathway drawing/editing application. Currently it can draw diagrams using SBGN PD Level 1, Cytoscape and Metabolic notations. It can export SBML Level 2 v3 and BioPAX Level 3 from the metabolic notation and BioPAX export for SBGN will be coming soon. It is completely customisable and can be configured to support a wide variety of graphical notations. In addition it has an extensible architecture that allows addition exporters to be added. The ability to import SBML models will come soon.
- FAME — The Flux Analysis and Modeling Environment (FAME) is the first web-based modeling tool that combines the tasks of creating, editing, running, and analyzing/visualizing stoichiometric models into a single program. Analysis results can be automatically superimposed on familiar KEGG-like maps. Manually drawn custom maps that are compatible with FAME are also available for certain species. FAME is written in PHP and uses the Python-based PySCeS-CBM for its linear solving capabilities. It comes with a comprehensive manual and a quick-start tutorial, and can be accessed online at http://f-a-m-e.org/ .
- iPathways — Explore biological pathways on your palm!! In comprehending the biological complexity of living systems in disease and healthy states, molecular pathway maps form an integral part of a researcher’s arsenal. iPathways, developed by The Systems Biology Institute, Tokyo, brings your pathways from the desktop to the device for the first time!! iPathways provides access to molecular maps constructed in CellDesigner™ , compatible with SBML (Systems Biology Markup Language) and SBGN( Systems Biology Graphical Notation) standards. Browse pathways from your account and explore publications and genes of interest. Features (1.1): - Register Free! or use a guest login - Navigate pathway information by tapping on a gene or protein molecule or a reaction box - View publications associated with a reaction by tapping the PUBMED id on a reaction - Explore genes of interest on IHOP or Entrez directly from your pathways
- iPathways+ — A Web-based Pathway Publishing Platform to browse public pathways, to publish your pathways online, to share your pathways by embedding your pathways to your website, via emails, via SNS (Facebook, TwiBer, Google+), and visualize (map) your data. iPathways+ support CellDesigner ver 4.x format.
- MesoRD — MesoRD is a stochastic and deterministic simulator of coupled chemical reactions and diffusions in space.
- MoSeC — MoSeC is a Java application for synthetic biology design that takes a model annotated with the DNA sequence information of genetic elements and converts it into a DNA sequence. Both CellML and SBML models constructed using virtual parts can be converted into standard GenBank, EMBL or SBOL files ready for synthesising.
- NetBuilder' — NetBuilder' is a software tool that is intended to help experimentalists creating and manipulating the mathematical representations they need to predict the behaviour of their systems. NetBuilder' has a graphical user interface, which allows its users to create a picture of the (known) components and interactions in the system, and enter quantitative information, such as know or estimated quantities and rates. A (hidden) translator converts the picture and the other data into a mathematical description, whereupon NetBuilder's ''simulation engine'' may be used to find out how the modelled system responds to changing input.
- Omix — Omix is a highly customizable editor for biochemical network diagrams, equipped with extensive data visualization features. Highest flexibility in designing networks and visualization is provided. With Omix, sophisticated data visualization can be designed with ease. Especially, time-dependent numerical datasets from experiment and simulation are easily visualized and animated in the context of metabolic network. Omix has extensive import and export capabilities, e.g. for SBML, BioPAX, HDF5, Matlab code, etc. Models can be imported from KEGG or BioCyc. Many plug-ins are available providing modeling and analysis features for Omix. This includes, for instance, stoichiometic analysis, thermodynamic analysis, metabolic flux analysis. As a brand new feature, it is now possible to define the dynamics of a biological network in Omix. You can define kinetic laws for the individual reactions and specify initial concentrations and dynamic changes for metabolites. Furthermore, you can create dynamic events.
- optflux — OptFlux is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using phenotype prediction methods such as FBA/pFBA, MOMA/LMOMA, ROOM and MiMBl (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard (import/export). OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph.
- PathSBML plugin for PathVisio — The PathSBML plugin allows researchers to visualize and overlay data on the same pathway models they use in simulation experiments. Exporting these models as GPML would also allow them to be uploaded to Wikipathways for community curation.
- PaVESy — Pathway Visualization Editing System. Java based. (Linux/Mac/Win). Free download.
- PET — Parameter optimization and exploration is the primary feature of PET. Some of the other tasks PET can perform are simulations, setting up multiple experiments for a model, comparing parameter sets, and exporting plots for presentations.
- ProMoT — The process modeling tool ProMoT is a software for the set-up and manipulation of models of complex technical or biological systems. Key features are the support of modular models, modeling libraries for different application areas, efficient and robust numerical algorithms, its own modeling language MDL and advanced graphical support. Dynamic models can contain DAE and discrete events for simulation in DIVA, Diana or MATLAB. Logical (Boolean) models are exported to CellNetAnalyzer. Process-Interaction-Models can be exported into BNGL format or transformed into logical models.
- SBML Layout — SBML Layout encompasses: 1. a online application for layouting / rendering an SBML file , 2. a library for reading / writing SBML Layout and Rendering information as well as SBGN-ML and 3. a standalone application for displaying files with the SBML Layout or Rendering information. It is written in .net and available under the BSD for all platforms.
- SBML2TikZ — SBML2TikZ provides automatic generation of TeX Macros to illustrate Systems Biology Markup Language (SBML) graphs. The rendering is dependent on the SBML Render Extension proposed by Gauges et al. and the rendering library is built on the existing SBML Layout Library.
- SBW: Auto Layout — The SBW AutoLayout module automatically creates lucid layouts of biochemical models. The SBW AutoLayout module has a graphical user interface (GUI) and an application programming interface (API). The GUI provides a typical window application for using AutoLayout's functionality, while the API allows programmers to incorporate AutoLayout's functionality into their own programs
- Simulate3D — Traditionally simulation results are available as either data tables or X-Y plots. Data tables are helpful for further processing by other computational tools. X-Y plots, on the other hand, tend to get complex even for a limited number of species. In creating a new visualization tool, we had two goals in mind. A first goal was to tie simulation results strongly to the model. A next goal was to be able to view the simulation in real time to refine or broaden it where necessary. These goals have been realized in form of a 3D Time-course Visualization module.
- SimWiz — Visualizes simulation outputs from tools such as Copasi and STODE. (Linux/Win) (European Media License)
- Snoopy — a software tool to design and animate hierarchical graphs, among others Petri nets. To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but being specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the GUI adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools.
- SurreyFBA — SurreyFBA provides constraint-based simulations of genome scale metabolic networks in a free, stand-alone software. In addition to basic simulation protocols the tool also implements the analysis of minimal substrate and product sets, which is useful for metabolic engineering and prediction of nutritional requirements in complex in vivo environments. The SurreyFBA is based on a command line interface to the GLPK solver distributed as binary and source code for the three major operating systems. The sfba command line tool, implemented in C++, is easily executed within scripting languages used in the bioinformatics community and provides efficient implementation of tasks requiring iterative calls to the linear programming solver. SurreyFBA includes JyMet, a graphics user interface allowing spreadsheet based model presentation, visualization of numerical results on metabolic networks represented in the Petri net convention, as well as in charts and plots.
- Systrip — Systrip is a visual environment for the analysis of time-series data in the context of biological networks. This software gathers bioinformatics and graph theoretical algorithms that can be assembled in different ways to help biologists in their visual mining process. Main features : 1. SBML file import and export. 2. Multiple kind of metabolic network representations (3D, force directed, biological convention preserving, hierachical ...). 3. Both graph theoritical measures and metabolic network analysis algorithms (choke points, scope, centrality...). 4. Time-series data import and visualization (table view, parallel coordinates, scatter plot). 5. Visualization of time-series in the context of the metabolic network. 6. 3D molecular visualization. 7. Database querry tools (Kegg, PublicHouse).
- Virtual Parts Repository — A repository of standard virtual parts which are reusable, modular and composable models of physical biological parts. These models can be joined together computationally in order to facilitate the model-driven design of large-scale biological systems. The Virtual Parts Repository has a REST-based Web service interface to access information about, and models of, biological parts and their interactions computationally. Moreover, the repository can be programmatically accessed using the JParts API, which also provides methods to join models of parts and interactions to create simulatable models.

## Authors

Frank T. Bergmann, Bruce E. Shapiro and Mike Hucka.