The first version of **CyPathia** was developed for Cytoscape (3.6.1 +). It provides a user friendly and straightforward interface. The CyPathia app is based on **Hipathia Bioconductor** package, allowing the Cytoscape community for the first time the possibility of using mechanistic models.
In order to call [http://bioconductor.org/packages/release/bioc/html/hipathia.html Hipathia] , we have to invoke R from **Cytoscape**. Thus **JRI Java/R Interface** have been used (Fig.1). JRI allows to run a R session inside Java applications as a single thread.
**CyPathia 1.0.0** provides two functionality , first one is the computation of signal transduction along KEGG signaling pathways from transcriptomic data. The user has to load both of the expression matrix file and experimental design file which has at least two groups. In the current version, CyPathia supports **145 networks from KEGG** for three species (**Human**, **Mouse** and **Rat**). Next version will support directed networks.
**CyPathia** use **wilcoxon test** to compare the signal values -which are already calculated using Hipathia- between different conditions loaded previously in the experimental design file.
The second functionality is to import generated report (sifs, natt and eatt files) from both [hipathia web](http://hipathia.babelomics.org) or [Hipathia package](http://bioconductor.org/packages/release/bioc/html/hipathia.html).
**Case study 1:** [Differential signaling using cypathia and Breast Cancer dataset.](https://youtu.be/Mz2VZXtnavk)