Journal of integrative bioinformatics

Welcome to!

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


The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybrid-dimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies – Three.js, D3.js and PHP – as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at:

Screenshot of CmPIwebScreenshot of CmPIweb
JIB Publications
  • Kovanci G, Ghaffar M, Sommer B. Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios. J Integr Bioinform. 2016;13(4):47–58. doi 10.2390/biecoll-jib-2016-298; PubMed 28187414
  • Sommer B. The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.. J Integr Bioinform. 2019;. doi 10.1515/jib-2019-0057; PubMed 31560649