Software

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.

https://github.com/draeger-lab/EscherConverter/

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.

https://github.com/draeger-lab/InCroMAP/

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.

https://github.com/draeger-lab/insilico/

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.

https://github.com/sbmlteam/jsbml/

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.

https://github.com/draeger-lab/KEGGtranslator/

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.

https://github.com/draeger-lab/ModelPolisher/

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.

https://github.com/manuelgloeckler/ncmw

The refineGEMs application automates numerous steps that need to be performed to create genome-scale metabolic models, drastically reducing the remaining manual curation.

The documentation can be found here.

https://github.com/draeger-lab/refinegems

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

https://github.com/draeger-lab/SABINE/

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.

https://github.com/draeger-lab/SBML2LaTeX/

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

https://github.com/draeger-lab/SBMLme/

SBOannotator automatically assigns SBO terms to multiple entities of a given SBML model. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks.

Web application hosted at TueVis is accessible and ready to use at sbo-annotator-tuevis.cs.uni-tuebingen.de.

https://github.com/draeger-lab/SBOannotator

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.

https://github.com/draeger-lab/SBMLsimulator/

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.

https://github.com/draeger-lab/SBMLsqueezer/

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.

https://github.com/draeger-lab/SBSCL/

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.

https://github.com/draeger-lab/SBTabEditor/

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

https://github.com/draeger-lab/SBVC/

SPECIMEN is a collection of different workflows designed for the automated and standardized curation of genome-scale models. It is mainly based on the refineGEMs toolbox, but also includes additional tools like CarveMe.

https://github.com/draeger-lab/SPECIMEN

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

https://github.com/draeger-lab/TFpredict/

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

https://github.com/draeger-lab/SysBio/

A simple graphical viewer and editor for systems biology models.

https://github.com/draeger-lab/BioModelsEd/