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Thu 14 Jan - Fri 15 Jan 2021
13:00 - 16:30

Venue: Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter)

Provided by: Bioinformatics


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EMBL-EBI: Network Analysis with Cytoscape (Online)

Thu 14 Jan - Fri 15 Jan 2021

Description

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and explore them in full detail. We will subsequently use these networks to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of Cytoscape, an open source software platform for complex network analysis and visualization. The course will also access and analyse the data through Cytoscape apps, including the new IntAct app.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • This workshop is aimed at researchers interested in proteins, network analysis, protein-protein interactions and related areas
  • Biologists and bioinformaticians
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Prerequisites

No prior experience required

Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Thu 14 Jan   13:00 - 16:30 13:00 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter) Pablo Porras,  Kalpana Paneerselvam,  Birgit Meldal
2 Fri 15 Jan   13:00 - 16:30 13:00 - 16:30 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST (GMT+1) in Summer, GMT in Winter) Pablo Porras,  Kalpana Paneerselvam,  Birgit Meldal
Topics covered

Bioinformatics, Pathway or network analysis, Pathway or network visualisation

Objectives

After this course you should be able to:

  • Utilise a range of Cytoscape apps to generate and analyse interaction networks
  • Use different analysis apps within Cytoscape: IntAct, MCODE, ClueGO
  • Import your data into Cytoscape
  • Perform network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials
Aims

During this course you will learn about:

  • Molecular interaction network analysis
  • Basic principles of network analysis
  • Basic Cytoscape functionality and use of apps for access to molecular interaction data (IntAct), clustering (MCODE) and GO enrichment analysis (ClueGO)
Format

Presentations and demonstrations

Timetable

This is subject to change in line with the online training schedule.

Day 1 Topics
Session 1 Introduction: Network analysis basics, Molecular interactions and interaction databases: IntAct and Cytoscape

Comfort Break
Session 2 Cytoscape practical: Accessing interaction data through the IntAct app

Session 3 Q&A session

Day 2 Topics
Session 1 Cytoscape practical: Data integration in Cytoscape

Session 2 Cytoscape practical: Topological analysis in Cytoscape: clustering with MCODE / ClusterMaker2
Comfort Break
Session 3 Cytoscape practical: Enrichment analysis in Cytoscape: ClueGO
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

Two half day sessions

Frequency

Once per year

Related

Related courses
Themes

Booking / availability