Software

Open-source software developed by the research group:

Vanted

Vanted (Visualisation and Analysis of Networks conTaining Experimental Data) is a tool for the visual exploration and analysis of multimodal data in the context of biological networks. It helps to integrate and process data from different areas (such as transcriptomics, proteomics, metabolomics) and to present the results in a user-friendly way. Extensions based on Vanted address, for example, metabolic modelling (FBA-SimVis), an information system for experimental data (DBE2), network analysis methods (CentiLib), and spatial data investigations/image processing (Hive).

www.vanted.org  

B. H. Junker et al.: ‘Vanted: a system for advanced data analysis and visualization in the context of biological networks’ BMC Bioinformatics 7: 109.1-13, 2006.


Meta-All & MetaCrop

Meta-All is a database and information system for multi-level representation of metabolic processes,  MetaCrop is a special instance of the system for detailed plant metabolism. MetaCrop is both a large collection of manually curated pathways and metabolic information in crop plants at different levels of detail (from overviews down to kinetic parameters) and a repository for metabolic models supporting standards such as SBML and SBGN.

metacrop.ipk-gatersleben.de

F. Schreiber et al.: ‘MetaCrop 2.0: managing and exploring information about crop plant metabolism’ Nucleic Acids Research 40(1): D1173-D1177, 2012.


SBGN-ED

SBGN (Systems Biology Graphical Notation) is a standard for the graphical representation of biological networks and cellular systems. The software SBGN-ED supports editing, validation and interactive navigation of SBGN  maps as well as mapping of data onto biological networks and cellular processes represented in SBGN, and their analysis. 

www.sbgn-ed.org

T. Czauderna et al.: ‘Editing, validating, and translating of SBGN maps’ Bioinformatics 26(18): 2340-2341, 2010.


CELLmicrocosmos

CELLmicrocosmos (short Cm) aims at the spatial analysis and interactive 3D visualisation of intracellular interactions and consists of different software applications such as Cm PathwayIntegration and Cm MembraneEditor. Cm PathwayIntegration supports the localisation and visualisation of biological pathways and other protein-/gene-related networks in the context of 3D cell models. Cm MembraneEditor generates models of molecular membranes and vesicular structures using PDB files ready for molecular dynamic simulations.

www.cellmicrocosmos.org

B. Sommer and F. Schreiber: 'Integration and virtual reality exploration of biomedical data with CmPI and Vanted' it - Information Technology (to appear), 2017.


Contributions to software projects

ScaffoldHunter

Scaffold Hunter is a tool for the visual analysis of data from the life sciences, aiming at intuitive access to large and complex data sets that offers a variety of views and analysis methods. It originates from drug discovery and has evolved into a reusable open source platform for a wider range of applications.

Path2Models

Path2Models automatically generates mathematical models from biological pathway representations using a suite of freely available software. Computed models from over 2600 organisms  encoded in SBML and SBGN are available through the BioModels Database.

OGDF & libSBGN

We contribute to open source libraries such as OGDF and libSBGN. OGDF is a self-contained C++ class library for the automatic layout of diagrams and offers sophisticated algorithms and data structures which can be used within your own applications or scientific projects. libSBGN is a software library for working with SBGN-ML files.

Optimas-DW

The Optimas Data  Warehouse is a comprehensive data collection for maize and integrates data from different domains such as transcriptomics, metabolomics, ionomics, proteomics and phenomics. It provides interactive access to and analysis of the data.

Former software projects of the research group

HTPheno

Image analysis pipeline for high throughput plant phenotyping.

MAVisto, CentiBiN & CentiLib

Investigation of structural network properties (motifs, centralities, and global graph properties) especially for biological networks. Initially stand-alone programs, the newer developments are now part of the Vanted tool suite and further developed there.

BioPath

Representation, visualisation and exploration of biochemical pathways; an electronic version of the Boehringer pathway chart.