Dräger Lab

The Systems Biology Simulation Core Library (SBSCL) provides an efficient and exhaustive Java implementation of methods to interpret the content of models encoded in the Systems Biology Markup Language (SBML) and its numerical solution.

Cross platform highly-extensible JavaFx based application which provides functions for reading, writing, manipulating, and validating SBML files.

Encoding ME models in SBML

A parser for systems biology models published in a table form that produces standardized files, such as SBML.

A standalone program that reads files created with the graphical network editor Escher and converts them to files in community standard formats.

pymCADRE enables the reconstruction of tissue-specific metabolic models in Python using transcriptomic data and information of the network topology.

Systems Biology Visualizer and Converter

FERN (Framework for Evaluation of Reaction Networks) is an extensible and comprehensive framework for efficient simulations and analysis of chemical reaction networks written in Java.

A demo repository with example code for using the Systems Biology Simulation Core Library (SBSCL).

A Java-based software for visualizing and translating the KEGG PATHWAY database. Conversion of KGML files into BioPAX, SBML, GraphML, GML, and various other formats.