Introduction to Network Visualisation and Cytoscape
Abstract
Networks are widely used throughout almost every field of study and have been applied to an extraordinarily wide range of problems, such as the structure of language, social group analysis, military communication networks designed for robustness in the event of nuclear attack, co-publication graphs, or who has acted with whom in Hollywood movies.
Within the biosciences, proteins interaction networks, species trees, metabolic networks, gene regulatory networks and many other areas of bioinformatic interest have benefited from network analysis.
The essence of a network is to model pairwise relations between objects by defining a set of nodes, and edges that connect the nodes and represent “being related”.
With such a diverse range of applications, methods of visualisation or drawing of networks to organise, make sense of, and generate hypotheses to test are of great interest.
A well-drawn network simplifies complexity, and can often be the difference between a mass of unstructured data and a new understanding of previously hidden relationships. It will allow you to easily answer questions, such as what are the most important parts of the network? Are there distinct components? How closely related are particular components? What are the most/least highly connected components? How fragile/breakable is the network? And from these observations, find patterns, and make inferences and predictions.
In this hands-on workshop, an introduction will be given to how networks or graphs are defined and methods to visualise them. The primary tool will be Cytoscape, a free, powerful multi-platform application for visualisation and analysis of networks.
Workshop topics covered will include:
- simple formats, including Excel and text documents, for describing and creating networks
- easy interactive network creation in Cytoscape
- different methods of automated layout so that your network is comprehensible and visually pleasing
- changing the style of components of the network by mapping arbitrary attributes to colour, size, shape, or images, or charts
- the Cytoscape App manager for extending Cytoscape’s capabilities
- Cytoscape’s Network Analyser for easy statistics generation and analysis of your networks
- exporting high resolution images for publication, and
- getting help when you are stuck at UQ’s Hacky Hour and online forums.
If there is time, we may also cover sub-sampling, aggregation and pruning as approaches to making sense of “hairballs”.
Examples used will include the classic sociograms of Moreno—describing the changing social relations between schoolchildren, visualising co-publication networks generated from Scopus literature searches, and protein interaction networks.
We also encourage attendees to bring their own networks and problems for visualisation. Please contact Nick or Ollie before the workshop if you have some data you would like to bring.
At the end of this workshop, you will know how to:
- easily describe networks in simple file formats
- import and visualise these into Cytoscape
- highlight and find information in your networks by mapping node and edge attributes to colours, shapes and sizes
- try different layout methods to find the optimum one for your problem, and
- generate publication-quality figures.
Register
Register by emailing either Nick or Ollie.
Instructor biographies
Dr Nick Hamilton is the Institute Bio-Mathematician at UQ's Institute for Molecular Bioscience and an eResearch Analyst with both UQ's Research Computing Centre and QCIF. He holds a PhD in pure mathematics from the University of Western Australia and his research interests are in computational biology, mathematical modelling, bio-imaging, data visualisation and machine learning. He coordinates and runs several training and community events at UQ, such at Hacky Hour, Dr Nick’s Image Clinic, HealthHack, and the annual Winter School in Mathematical and Computational Biology.
Oliver (Ollie) Cairncross is a data visualisation specialist with UQ's Research Computing Centre. He has a Bachelor of Mathematics from QUT and a Bachelor of Business from Charles Darwin University. Ollie has worked within UQ supporting a diverse range of data visualistion requirements. Fields he has covered include the life sciences, physics, engineering and arts, incorporating data sets generated by microscopy imaging, vector field simulation, fluid dynamics, and geospatial mapping.
More information
Dr Nick Hamilton has written an article providing tips on how to use Cytoscape and where to go for help if you need it.