Software tools and packages under active development and maintanance
MDS and MCDS (Optimal solutions) - Implementation of the ILP formulations for MDS and MCDS problems in the Sage software system using the glpk solver underlying gene regulatory networks. - BMC Systems Biology (2016)
Mebitoo - Mebitoo is a bioinformatics tool to embrace computational analysis methods with a uniform graphical user interface. Moreover, the software enables persistent storage with an incorporated database engine, which supports XML files for customized data structures. - BICoB (2015)
PPICompare - PPICompare detects rewiring events in protein interaction networks.
TFmiR - TFmiR is a web service that builds a TF and miRNA co-regulatory network based on user parameters set and generate general and disease-specific co-regulatory networks. - Nucleic Acid Research (2015)
Software no longer in active development
Brownmove - A many-particle Brownian-Dynamics simulation package.
CESIP (cellular simulation package) in C++
EPOSBP - Ensemble of Pockets on Protein Surfaces with BALLPass.
PROPORES (PROtein PORE identification toolS) - “PROPORES” is a novel toolkit for identifying pockets, cavities and channels of protein structures. - Proteins: Structure, Function, and Bioinformatics (2012)
QVADIS Java3D program package to characterize proton transfer pathways in biomolecules accounting for side chain flexibility and transfer kinetics.
SnvDMiR - Associating the genomic proximity of genetic variants with deregulated miRNAs and differentially methylated regions. (R code)