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Automates repetitive tasks in model building and simulation. SBpipe builds a sequence of repeated model simulations or parameter estimations, performs analyses from this generated sequence, and finally generates a LaTeX/PDF report. It can execute models implemented in Copasi, Python or coded in any other programming language using Python as a wrapper module. The software aims to encourage the development of pipelines for systems modelling into a single community activity.

AMICI / Advanced MATLAB Interface for CVODES and IDAS

Provides a MATLAB interface for the SUNDIALS solvers CVODES and IDAS. AMICI allows the user to specify differential equation models in terms of symbolic variables in MATLAB and automatically compiles such models as MEX simulation files. In contrast to the SUNDIALSTB interface, all necessary functions are transformed into native C code, which allows for a significantly faster compilation. The interface was designed to provide routines for efficient gradient computation in parameter estimation of biochemical reaction models but is also applicable to a wider range of differential equation constrained optimization problems.


Facilitates the simulation and analysis of complex network models. Epigrass aims to help designing and simulating network-epidemic models with any kind of node behavior. It enables researchers to perform comprehensive spatio-temporal simulations incorporating epidemiological data and models for disease transmission and control. This is done in order to create complex scenario analyses. It permits multiple edge sets in order to represent multiple contact networks in a single model.

LIFESPAN / Longitudinal Interactive Front End Study Planner

Promotes systematic searches within the study design space. LIFESPAN generates a set of alternative models with equal statistical power to detect hypothesized effects, and delineates trade-off relations among relevant parameters, such as total study time and the number of measurement occasions. It boosts the efficiency, breadth, and precision of the search for optimal longitudinal designs. The tool helps researchers to craft and select longitudinal designs that have optimal power to detect random effects of change, based the change process under investigation.


Enables generation of networks with a specified degree distribution, measuring fundamental network characteristics. EpiFire is an application programming interface (API) allowing user to perform these functions in a point-and-click environment and provides intuitive graphical results of epidemic simulations. It includes a continuous time, stochastic mass-action simulation class to permit users to create hybrid models or to compare the results of mass-action and network-based models.

PUA / Prediction Uncertainty Analysis

Performs optimal experiment design (OED) for models that cope with large parameter uncertainty. PUA is not limited to any specific error model or assumption regarding the parameter distribution. It enables the modeller to select specific predictions of interest that require decreased uncertainty thereby focus the experimental efforts in order to save time and resources. Furthermore, it allows the prediction of interest to be any quantity that can be obtained from simulations.


Calculates the marginal state occupation probabilities, the state entry and exit time distributions, and the marginal integrated transition hazard for a general, possibly non-Markov, multistate system under left-truncation and right censoring. msSurv also performs nonparametric estimation for state dependent right censored and possibly left truncated data. This package provides functions to find the state occupation probabilities at a specific time and to find the transition probabilities between any two times.