Programs (co-)developed in this group for applications in systems biology and bioinformatics

Our group develops, maintains and contributes to many large software projects and libraries for applications in systems biology and bioinformatics.

Most projects are managed on the GitHub page of the group:

Contributions to collaboratively developed projects can be found on the GitHub pages of the  SBML and SBGN.


Conversion between Escher-JSON, SBML and SBGN-ML

With this Java™-based program, popular file formats that are used for graphical representations in systems biology modelling can be converted into one another: Escher's JSON dialect as well as the standardized formats SBML and SBGN-ML. The program can be operated either via its graphical user interface or via the command line.


Integrated and cross-platform analysis of microarray data and networks

InCroMAP offers a variety of possibilities to visualize data sets or to apply methods for integrated cross-platform analysis. Currently, numerous data formats such as mRNA, miRNA, DNA methylation and protein modification are supported. InCroMAP can map and analyze all data in the context of biological networks.


A modular framework for research projects

InSilico is a project based on Eclipse and JavaFX for the integration and management of various apps to facilitate the processing of scientific models and data as well as the development of end-user software. Here you will find detailed Dokumentation and further project descriptions.


A complete and platform-independent programming interface for SBML processing with Java™

A joint project for a free, open source, programming library for reading, writing and modifying SBML files and data streams based exclusively on Java™ It is an alternative to the native implementation of ​​​​​​​libSBML.


Convert from KEGG database to standardized file formats

KEGGtranslator offers a visual representation of biological networks from the popular KEGG database as well as a variety of options for converting the files submitted there into standardized formats. The Java™-based program supports current versions of​​ BioPAX, SBML, GraphML, and numerous other formats.


Automatic preparation of biological models

ModelPolisher uses the information stored in the BiGG Models Database to include cross-references to all components contained in given models. This process also resolves common problems.


Nasal community modeling workflow

A metabolic modeling workflow for communities of organisms in an nasal medium. This implements functionality to analyze the interaction of metabolic models within a community.


Tissue-specific reconstruction of genome-scale metabolic models

An advanced re-implementation of the mCADRE algorithm in Python. This tool constructs tissue-specific metabolic models by leveraging gene expression data and literature-based evidence, along with network topology information.


StandAlone BINding specificity Estimator

SABINE is a tool for the prediction of the binding specificity of transcription factors using machine learning methods.


A documentation tool for systems biology models in SBML format

SBML2LaTeX generates human-readable reports in LaTeX format about the content of ​​​​​​​ SBML files. These can then be converted into various formats, such as PDF files. The generated content can also be integrated directly into publications since the equations contained in SBML are also translated into formulas.


Store models of metabolism and expression in SBML

SBMLme is a converter that stores JSON-based files from COBRAme into valid​​​​​​​ SBML ​​​​​​​without any loss of information.


An efficient Java™ implementation for SBML

SBMLsimulator provides a graphical user interface for the systems biology simulation core and connects it with a graph-based dynamic view as well as with the versatile optimization tool EvA2.


Generator for kinetic equations in biochemical networks

SBMLsqueezer analyzes biochemical reactions and automatically suggests a set of applicable kinetic equations. Either the equations can be generated automatically for the entire reaction system at once, or for selected biochemical reactions. The program creates contained kinetic parameters and derives their unit itself. This feature makes it easy to convert structural models to dynamic models and then simulate them.


Systems Biology Simulation Core Library

SBSCL is a comprehensive implementation of systems biology simulation methods in Java™. SBSCL can solve complex differential equation systems (including delays, algebraic systems, spontaneous events, and rules) as well as flow balance analysis using the Simplex method. Currently, an interpreter for SBML models is built in. Extensions for other formats are possible. Due to the integrated support of SED-ML, simulation experiments can be clearly repeated.


A simple editor for SBML models that relies on a table display

JavaFX-based cross-platform and highly extensible application that provides functions for reading, writing, modifying and validating SBML files. The user interface is based on SBtab.


Systems Biology Visualizer and format Converter

A standalone application with a graphical user interface for viewing and converting files with systems biological content.


Identification and structural characterization of transcription factors

TFpredict uses methods of monitored machine learning to differentiate transcription factors or σ factors from other proteins and then characterize them structurally.


A Java™ library with numerous functions

The SysBio project significantly simplifies and unifies software development by providing numerous implementations for everyday objects and recurring patterns.


A graphical editor for systems biology models

A simple graphical viewer and editor for systems biology models.