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Facilitates the complicated and cumbersome model development process by providing a simple method to translate such models to human-readable reports. SBML2LaTeX is a Java-based stand-alone program to fill this gap. A convenient web service also allows users to directly convert SBML to various formats, including DVI, LATEX and PDF, and provides many settings for customization. It covers all constructs defined in the latest specification of SBML (Level 2 Version 4) and is able to typeset complex kinetic formulas.


Serves for modeling spatial management problems, for designing and analyzing policies and for comparing given policies by simulation. GMDPtoolbox is a toolbox dedicated to the Graph-Based Markov Decision Process (GMDP) framework. It is composed of two algorithms providing local policies by approximating the optimal solution of GMDP. This toolbox offers user a structure to encode GMDP problems, as well as modeling tools, solution algorithms, and analysis tools for evaluating and comparing policies.

FEBiO / Finite Elements for Biomechanics

Offers a nonlinear finite element solver for biomechanical applications. FEBiO provides modeling scenarios, constitutive models and boundary conditions. The application supplies algorithms to model tied or sliding contact under large deformations between elastic, biphasic, or multiphasic materials. Users can run five different types of analysis: (i) nonlinear elasticity and viscoelasticity; (ii) rigid body mechanics; (iii) multiphasic mechanics; (iv) interstitial growth mechanics and (v) heat conduction.

GenSSI / Generating Series for testing Structural Identifiability

Allows structural identifiability analysis of models describing biological systems under multiple experimental conditions. GenSSI is a software toolbox that performs structural identifiability analysis of linear and nonlinear ordinary differential equation (ODE) models. The software provides a Systems Biology Markup Language (SBML) import, automatic methods for multi-experiment structural identifiability analysis, and methods for the transformation of models. It permits users to obtain subsets/combinations of structurally identifiable parameters, which can be used to reformulate the model.

SBSI / Systems Biology Software Infrastructure

Affords a suite for model analysis and data integration. SBSI is composed of three major software: (i) SBSINumerics, containing a library with parallelized implementations of global optimization algorithms; (ii) SBSIDispatcher, providing access to back-end HPC machines; and (iii) SBSIVisual, a client application to configure parameter optimization jobs, to link with external databases and to view the results of optimizations. There are no dependencies between modules.


Assists users in simplifing forward modelling of the effect of different intervention options. fluEvidenceSynthesis is a package that allows users to infer parameters using a Bayesian approach, perform forward modelling of the likely results of the proposed intervention and finally perform cost effectiveness analysis of the results. It is based on a method to inform vaccination strategies for influenza, with extensions to make it easily adaptable to other diseases and data sources.

REANIMATE / REAlistic Numerical Image-based Modelling of biologicAl Tissue substratEs

Conducts realistic computational experiments that naturally incorporates the variability and heterogeneity found between biological samples. REANIMATE consists of two steps: (1) a solution is sought from a set of coupled fluid dynamics models that describe steady-state vascular and interstitial fluid transport; and (2) the steady-state solution is used to parameterize a time-dependent model that describes the vascular and interstitial uptake of exogenously administered material.

MAGPIE / Modeling and Analysis Generic Platform with Integrated Evaluation

Offers a platform dedicated to models’ community management. MAGPIE is accessible through three different ways: (i) a demo platform hosted on a web application; (ii) a source code allowing a local installation; and (iii) a R API. The application provides a repository of models and analysis tools that can be freely customized by multiple users. It also includes additional features for easing the visualization of results and a sharing results system based on twitter's hashtags model.


Simplifies parameter inference for complex biological systems. PyDREAM is an open-source implementation of the DREAM(ZS) and MT-DREAM(ZS) sampling algorithms for efficient inference of complex, high-dimensional, and posterior parameter distributions. It uses a common multi-chain architecture and creates candidate points in each chain on the fly via differential evolution. This tool focuses on three points: (1) specification of the prior parameter distribution, (2) selection of an appropriate likelihood function, and (3) Markov chain Monte Carlo (MCMC) simulation.

SSCC TD Simulator / Simultaneous and Serial Configural-cue Compound Stimuli Temporal Difference model simulator

Provides a model for representing compound stimulus configurations in a real-time architecture. SSCC TD Simulator is an extension of the Temporal Difference model which can be used for determining the hypothetic compound representation which can result from two or more stimuli that coexist according to specific conditions. It is also able to represent the formation of a compound representation of serial stimulus compounds.

APMonitor / Advanced Process Monitor

Permits users to optimize mixed-integer and differential algebraic equations. APMonitor is able to: (1) construct model, (2) fit parameters to data, (3) optimize over a future predictive horizon, and (4) transform differential equations into sets of algebraic equations. It employs a model to byte-code and is based on analysis of the sparsity structure of the model. This tool is able to solve the differential and algebraic equations using a simultaneous or sequential solution approach.

Repast Simphony

Allows users to generate agent-based models and simulations. Repast Simphony is an open source platform providing a graphic user interface developed for small computing clusters application. The application includes various features such as libraries for genetic algorithms and neural networks, an automated Monte Carlo simulation framework and tools for the integration of external models. The software supports various formats including ReLogo, Groovy, or Java which can be interleaved.


Generates agent-based models and simulations. Repast is an open source suite that is composed of two main components: (i) Repast Simphony, designed for working on small computing clusters, that provides a graphic user interface including libraries for genetic algorithms, neural networks and specialized mathematics; and (ii) Repast for High Performance Computing, designed for a parallel environment, that supplies an advanced command-line version developed for large computing clusters.


Offers a modeling environment for simulating complex phenomena. NetLogo is available through both a standalone software and a web application coupled to a homepage that displays a library of models and extensions. The software encompasses a large model application area including spread of disease, fractals, cellular automata or crystallization. Additionally, the program includes a feature for saving models as Java applets, for facilitating the publication of the simulations from the tool to a Web page.

DBSCAN / Density-Based Spatial Clustering of Applications with Noise

Assists in clustering spatial data. DBSCAN is a non-parametric, density based clustering technique. It provides features that useful when detecting objects/class/patterns/structures of different shapes and sizes. This algorithm is a good candidate to find ‘natural’ clusters and their arrangement within the data space when they have a comparable density without any preliminary information about the groups present in a data set.