A scientific meeting entitled „Network Biology Workshop: Cytoscape” was organized at the Center for Medical Genomics OMICRON. A one week course that took place between 11th and 15th of January 2016 gathered 20 participants. Three main speakers Matt Z. Rogon from Centre for Biomolecular Network Analysis, EMBL (Heidelberg, Germany), Rob Ewing from Centre for Biological Sciences (University of Southampton, Great Britain) and Pablo Porras Millan from Scientific Database Curator – Orchard team: Molecular Interactions (EMBL-EBI, Great Britain) skilfully introduced the topic of bioinformatic tools that can be used to analyze high-throughput genomic, transcriptomic and proteomic data in the context of systems biology. The course included extensive coverage of pathway analysis and introduced the participants to several molecular interaction databases (PSICQUIC, IntAct). The participant had an opportunity to apply their newly gathered knowledge to real life data during computational exercises. The meeting was funded by the Leading National Research Center Jagiellonian University Medical College.