Journal of integrative bioinformatics

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The official bioinformatics tool list for the Journal of Integrative Bioinformatics (JIB).

All bioinformatics tools published in JIB are automatically added to with first authors having the ability to edit their entries and directly import the tools information to


Desktop application 
Systems biology Molecular interactions, pathways and networks Data visualisation Biomedical science 
VANESA is a modeling software for the automatic reconstruction and analysis of biological networks based on life-science database information. Using VANESA, scientists are able to model any kind of biological processes and systems as biological networks. It is now possible for scientists to automatically reconstruct important molecular systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. Users also have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further investigated in the Petri net environment of VANESA. It is platform-independent, free-of-charge, and available at

Screenshot of VANESAScreenshot of VANESAScreenshot of VANESA
JIB Publications
  • Brinkrolf C, Janowski SJ, Kormeier B, et al. VANESA - a software application for the visualization and analysis of networks in system biology applications. J Integr Bioinform. 2014;11(2):239. doi 10.2390/biecoll-jib-2014-239; PubMed 24953454
  • Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA.. J Integr Bioinform. 2018;15(3). doi 10.1515/jib-2018-0018; PubMed 30218605
  • Kormeier B, Hippe K, Arrigo P, Töpel T, Janowski S, Hofestädt R. Reconstruction of biological networks based on life science data integration. J Integr Bioinform. 2010;7(2). doi 10.2390/biecoll-jib-2010-146; PubMed 20978286
  • Hamzeiy H, Suluyayla R, Brinkrolf C, Janowski SJ, Hofestaedt R, Allmer J. Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA.. J Integr Bioinform. 2017;14(1). doi 10.1515/jib-2016-0004; PubMed 28609293