Cytoscape WikiTutorials
On November 7th, in simultaneous sessions, Cytoscape users tutorials and developers tutorials were given.
Contents
Cytoscape Tutorials
Tutors
Andrew Garrow, Safety & Environmental Assurance Centre, Unilever, Colworth Park, Sharnbrook, Bedfordshire MK44 1LQ. Andrew{dot}Garrow[at]unilever{dot}com
Yeyejide Adeleye, Safety & Environmental Assurance Centre, Unilever, Colworth Park, Sharnbrook, Bedfordshire MK44 1LQ. Yeyejide{dot}Adeleye[at]unilever{dot}com
Note: Guy Warner was one of the tutors also, but his role will be taken over by Yeyejide
Audience
The intended audience is end users for the software i.e. scientific researchers in fields such as bioinformatics, computational biology, molecular biology and 'omics.
Background required
Basic understanding of molecular biology, knowledge of publicly available bioinformatics databases and some experience of gene expression analysis (or any high-throughput data analysis) is desirable but not essential
Relevance of the tutorial and interest to the community
Traditionally, the results of HTP data analysis are a list of bio-molecules that are believed to be significantly differentially expressed between experimental conditions. As data become more complex (e.g. time series data), statistical approaches such as clustering and classification have been used to reveal patterns within a data set. However, statistical analyses of gene expression data (and any molecular state data) that list differentially expressed genes may not be sufficient to allow researchers to generate new hypothesis and to gain insights into mechanisms underlying the conditions and systems being investigated.
This is because cellular processes are carried out not through individual bio-molecules but via complex interactions between genes, proteins and metabolites: that is, through biological networks. Understanding this organisation and analysing molecular state data in the context of biological networks is crucial to obtaining a picture of cellular activity.
Cytoscape is an open-source software package for the visualisation and analysis of biological networks and the integration of molecular state data. Cytoscape provides functionality to layout and search networks; to visually integrate networks with expression profiles, phenotypes, and other molecular states; and to link to databases of functional annotations.
In this tutorial we hope to provide an introduction to network-based analysis using the Cytoscape software that will be of relevance to researchers with an interest in the analysis of biological data in the context of biological networks and pathways.
Presentations
Developer Tutorials
CyGroups and Implementing a CyGroupViewer
Tutor
Scooter Morris
Description
This tutorial will introduce the new CyGroups mechanism in Cytoscape and walk through the implementation of a CyGroupViewer. The namedSelection and metaNodePlugin2 group viewers will be used as examples.
Links
Layouts - how to implement a new layout algorithm in cytoscape
Tutor
Scooter Morris
Description
This tutorial will walk through some of the steps required to implement a new layout algorithm into Cytoscape. It will cover the CyLayoutAlgorithm interface and the AbstractLayout class that can be used as a starting point. We will also cover the new "Tunables" approach to constructing a Settings panel for users to use to tune the algorithm.
Links
Vizmapper
Tutor
Mike Smoot
Description
Learn how to adapt visual properties of Cytoscape programmatically
Links
Code used during the tutorial is available here:
Webservices
Tutor
Keichiri Ono
Description
How to use the newly developed webservices api.