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

CmPI - CELLmicrocosmos 4 PathwayIntegration

Desktop application 
Molecular interactions, pathways and networks Bioinformatics Cell biology Computer science Structural biology 
Detailed investigation of socially important diseases with modern experimental methods has resulted in the generation of large volume of valuable data. However, analysis and interpretation of this data needs application of efficient computational techniques and systems biology approaches. In particular, the techniques allowing the reconstruction of associative networks of various biological objects and events can be useful. In this publication, the combination of different techniques to create such a network associated with an abstract cell environment is discussed in order to gain insights into the functional as well as spatial interrelationships. It is shown that experimentally gained knowledge enriched with data warehouse content and text mining data can be used for the reconstruction and localization of a cardiovascular disease developing network beginning with MUPP1/MPDZ (multi-PDZ domain protein).

Screenshot of CmPI - CELLmicrocosmos 4 PathwayIntegrationScreenshot of CmPI - CELLmicrocosmos 4 PathwayIntegration
JIB Publications
  • Sommer B, Tiys ES, Kormeier B, et al. Visualization and Analysis of a Cardio Vascular Diseaseand MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches. J Integr Bioinform. 2010;7(1). doi 10.2390/biecoll-jib-2010-148; PubMed 21068463
  • 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