This is a one day training course on Network Creation, Visualisation and Partitioning, based on Cytoscape.
Complex natural systems permeate many aspects of everyday life—including human intelligence, social media, biomedicine, agriculture, economics, even our personal and professional relationships. The past decade has seen intensification of research into structural and dynamical properties of complex networks. This course will introduce the basic principles of network theory, and hands-on DIY Network analysis using Cytoscape one of the most widely used global platforms for construction and analysis of biomolecular networks such as gene regulatory interactions, protein complexes, hydrogen-bonding meshwork in active sites and neuronal networks. The aim is to conceptualize your own textual, tabular or genomic datasets as networks, and to understand how simple topological features can help to decipher complex properties of systems and processes.
This is a one day long workshop with lectures, Hands-on modules and exercises for use of Cytoscape in biological data analysis. The course is expected to be data intensive and participants are required to pre-install the software on their own devices as a pre-requisite. This course makes use of the Cytoscape 3.8 architecture. Much of the content is based on the Cytoscape Manual , highly recommended.
Please go to https://cytoscape.org/download.html for downloading and installing the software. This is important to have on your devices before the training course.
If you have any problems with any of these requirements or are at all uncertain about your ability to complete the technical elements of the course, please contact our IT Manager, Paul Judge on [email protected]. or contact Instructor G.Yadav on [email protected]
Morning : Session 1 : Introduction & Set Up
Morning : Session 2 : Creating and Visualizing Networks
Afternoon : Session 3 : Network Partitioning
Afternoon : Session 4 : Network Aesthetics & Export
What is Cytocape? https://cytoscape.org/what_is_cytoscape.html
Cline, M., Smoot, M., Cerami, E. et al. Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2, 2366–2382 (2007). https://doi.org/10.1038/nprot.2007.324
Kohl et al. (2011) Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 696:291-303.(pmid: 21063955)
Shannon et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-504. (pmid: 14597658)
Travel Guide to Cytoscape Plugins: aro Saito, Michael E Smoot, Keiichiro Ono, JohannesRuscheinski, Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012)Nature Methods 9 (11) p. 1069-1076
Mlecnik B, Galon J, Bindea G. Comprehensive functional analysis of large lists of genes and proteins. J Proteomics. 2018 Jan 16;171:2-10. doi: 10.1016/j.jprot.2017.03.016. Epub 2017 Mar 22. PMID: 28343001.
EMBL-EBI: Network Analysis with Cytoscape (Online)
Inferring Co-Expressing Genes and Regulatory Networks from RNA-Seq Data
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Please find the Workshop program here.
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Please tag @gilienv (Instructor) and use Hashtags
#PFHwhen you tweet or post about the event.
Dr Gitanjali Yadav | University of Cambridge / NIPGR
Ms. Citu, NIPGR
Dr. Indu Santhangopalan, University of Cambridge
The Volunteers will be part of the workshop and assist with any issues from set up and installation to data checks and course exercises. Please feel free to request them for any support you may wish to have.
09:30 - 11:00 Introduction & Set Up
Background & Concepts
Basic Topologies & Case Study
Set up & Installation
11:00 - 11:15 COFFEE BREAK (15 minutes)
11:15 - 13:00 Creating and Visualizing Networks
Scale Free Networks
Data Import, Analysis & Layouts
Challenge
13:00 - 14:00 LUNCH BREAK (1 hour)
14:00 - 15:15 Network Partitioning
Clustering Strategies
DIY Network Communities
15:15 - 15:30 COFFEE BREAK (15 minutes)
15:30 - 17:00 Network Aesthetics
Tips and Tricks
Annotate, Download and Export Networks
Exercise
17:00 - 17:30 Saving Workspace, Q & A