Software

Topological Filtering

Model space exploration for ODE models based on approximate parameter space exploration.

YouScope is a free, open-source microscope control software compatible with most present-day automized microscopes. YouScope allows to easily automatize complex microscopy protocols using an user-friendly graphical interface.

openBIS LIMS-ELN

openBIS LIMS-ELN is an Electronic Laboratory Notebook and a Laboratory Information Management System solution suitable for the academic life science laboratories.

odeSD

odeSD is a specialized ODE integrator for efficient computation of parameter sensitivities

CellX

CellX is a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. The image segmentation package is also available for MATLAB.

efmtool

efmtool computes elementary flux modes (EFMs) of metabolic networks.

polco

The polco tool enumerates extreme rays of polyhedral cones. It can also be used to enumerate vertices of polytopes, and for the dual problem, the enumeration of facets given the extreme points (aka convex hull).

HYPERSPACE

A MATLAB package to sample high-dimensional parameter spaces in dynamical systems models of regulatory circuits in cell and developmental biology.

SDE evaluation package

MATLAB package for evaluation of parameter points in models based on stochastic differential equations.

Mapping Tool

A tool to assist name mapping if different nomenclatures are used by different models (e.g. metabolic networks).

Convert2Sbml / Convert2Matlab

Java tool to convert various metabolic network source files into SBML / MATLAB files.

Java Libraries

Assorted general-purpose Java libraries.

GTSbox

A MATLAB-based toolbox to estimate mechanistic non-linear mixed effect models (NMLEs) from single-cell data using a flexible and scalable global two-stage approach.