Software Packages

The software developed in our group is generally released as free and open source software. However, the use of the software does not imply any support or warranties. The software should not be relied on for any purpose where incorrect results could result in loss of property or personal injury. No liability of any kind, either direct or consequential, resulting from your use of these files is accepted. Please follow the links of the tools to learn more about copyright and licenses. If you have doubts or questions please do not hesitate to contact us.


BiVeS (Biomodel Version Control System) is a library to detect differences between two versions of a computational model and to communicate these changes.


BudHat is our prototype that implements a version control system for computational models. BudHat uses BiVeS to detect and communicate differences between versions of a model.


COMODI is an ontology serves as a basis for scientists and software developers to characterise model updates at the level of single changes. These annotations can help to determine the relevance of a change in a given context.

CombineArchive Library

A Java library to read, write, create, and manipulate COMBINE Archives.

CombineArchive Web

The CombineArchive WebInterface (WebCAT) is a web based user interface to create, modify, and share CombineArchives. It helps sharing of reproducible research. No need for registration. No database. Just start using the web interface!


The GEMtractor helps extracting views into genome-scale metabolic models. It is a Django platform for trimming and extracting models encoded in SBML. It can be used to extract subnetworks, for example focusing on reaction- and enzyme-centric views into the model.


M2CAT is a web based tool to export reproducible research results. It links the graph based database MASYMOS to the CombineArchiveToolkit (CAT).

Software Developed for Publications

Martin Scharm, Vasundra Touré, Dagmar Waltemath
CombineArchive ShowCase
A fully featured COMBINE Archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. It is supposed to help demonstrating the concepts and best practices on COMBINE Archives.

Lai X, Bhattacharya A, Schmitz U, Kunz M, Vera J, Wolkenhauer O,
A systems biology approach to study microRNA-mediated gene regulatory networks
Submitted for publication

Kossow C, Rybacki S, Millat T, Rateitschak K, Jaster R, Uhrmacher AM, Wolkenhauer O (2014)
An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers
submitted for publication, developed in cooperation with the Modelling and Simulation Research Group (University of Rostock)

Schmidt V, Baum K, Lao A, Rateitschak K, Schmitz Y, Teichmann A, Wiesner B, Petersen CM, Nykjaer A, Wolf J, Wolkenhauer O, Willnow T (2012)
Quantitative modeling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease
EMBO Journal 31: 187-200

Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O (2012)
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease
BMC Systems Biology 6:74

Lai X, Schmitz U, Gupta S, Bhattacharya A, Kunz M, Wolkenhauer O, Vera J
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs
Nucleic Acids Research, 40: 8818-8834.

Resources for Theses

Liebal, Thesis data
Regulation of the General Stress Response of Bacillus subtilis
The zip-file contains the figures and software executable for Matlab and Visual Basic for the thesis 'Regulation of the General Stress Response of Bacillus subtilis' by Ulf Liebal.