Training courses: Biological networks: topological analysis and visualization using Cytoscape software

Course Description

The study of the networks of protein-protein interactions within a cell, called “interactome”, provides information about the organization of the cell and allows us to identify proteins and signaling pathways that are disrupted or deregulated during a disease condition.
In this course, through a practical example, we will use the open-source software Cytoscape and some of its apps to extract protein-protein interaction data, build the network, visualize and explore it in order to detect topological properties, find potential topological clusters and perform functional network enrichment analysis.

Important Dates

• Deadline for applications: 30th November 2024
• Chosen participants will be notified by: 3rd December 2024
• Course date: 10th December 2024

Venue

This is an online course.

Fee

The course does not include a fee

Selection

A maximum of 30 candidates will be selected on a first-come- first-served basis. Selected participants will be notified by 3rd December 2024.

Instructor

• Prof. Luana Licata - University of Rome “Tor Vergata”, ELIXIR-IT, Italy

Helpers

• Alessia Pinto, PhD student, University of Rome “Tor Vergata”, ELIXIR-IT, Italy
• Francesco Gregoris, PhD student, University of Padua
  
  

Organisers

• Prof. Anna Marabotti, University of Salerno, ELIXIR-IT, Italy
• Prof. Luana Licata - University of Rome “Tor Vergata”, ELIXIR-IT, Italy

Contact

For all kinds of queries, please contact the organizer Anna Marabotti or please write to Elixir_training_email.

Target audience

The course is for people participating to the workshop: “Young Minds at Work: Blending Biochemistry and Bioinformatics - 2nd edition”

Aims of the workshop

• To provide practical demonstrations of several freely available protein-protein interactions resources.
• To improve competences in protein-protein network analysis.
• To improve the knowledge of Cytoscape and its network analysis and gene enrichment analysis tools.

Resources and tools covered

• IMEx resources
• STRING
• Cytoscape
• IntactApp
• MCODE
• ClueGo

Learning Outcomes

By the end of this course, the participants will be able to:

• Identify and access public data resources and tools to study protein-protein interactions • Interpret the information given in different molecular interaction databases • Represent networks using Cytoscape • Perform network and functional analysis

Course prerequisites

Participants don’t need to have bioinformatics skills and previous knowledge of the tools that will be presented at the course. Attendees may bring in their own datasets for analysis, although example datasets will be available.

Registration

Please refer directly to the Web site https://www.blendingbb.it/ymw2024/

Programme