Posts Tagged ‘networks’

VIZBI 2014 tutorial – Network visualisation and analysis of high dimensional data using BioLayout Express3D

Thursday, January 16th, 2014

BioLayout Express3D is a powerful tool for the visualization and analysis of network graphs. Network-based approaches are becoming increasingly popular for the analysis of complex systems of interaction and high dimensional data. In biology, networks can be generated from interactions between individuals, disease transmission, sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades, gene expression, etc. BioLayout Express3D has been specifically designed for visualisation, clustering, exploration and analysis of very large network graphs in 2- and 3-dimensional space derived primarily, but not exclusively, from biological data.

This tutorial is designed to cover the basics of network visualisation and analysis using this tool with particular emphasis on the analysis of high dimensional data such as that generated by microarray analysis or RNA-seq analyses. If time is available we will also demonstrate the use of the tool in the context of pathway modelling.

Participants will need to bring with them a laptop of any flavour (the program does not run on tablets) with the program and Java installed. To make the most use of the session it would be preferable to have at least a medium range graphics card e.g. AMD or Nvidia and a three-button mouse to allow to exploration of reasonable sized graphs in 3D space.

If in doubt – run the webstart version on the website and if you have any issues or questions contact support@biolayout.org.

VIZBI 2014 tutorial – ‘Exploring biological networks by means of visualization: Use R and NetBioV’

Tuesday, January 7th, 2014

The analysis of biological networks starts with the visualization of the networks. This can be seen as a form of an exploratory analysis. The main aim of an effective visualization is to highlight key structural properties of a network. Besides the connectivity of the nodes, there is a large variety of structural features of a network that can instead be exploited for an effective visualization. For example, modules, shortest paths or hierarchical levels.

We developed an R package called NetBioV (network biology visualization) that provides many easy to use functions, layout styles and color schemes to visualize biological networks

The tutorial is organized as follows:
• Introduction of biological networks
• Overview of standard graph layout algorithms
• Overview of visualization software
• Network visualization using R
• Visualization of biological networks using NetBioV, emphasizing structural components:
– Global view
– Modular view
– Hierarchical view
• Conclusions

Registration is now open for the EMBL Advance Course ‘Cytoscape Developer’

Wednesday, December 18th, 2013

A week after the VIZBI 2014, on March 10-11, EMBL Advanced Course ‘Cytoscape Developer’ will be held at EMBL Heidelberg. This two-day course will teach participants to develop Apps for the Cytoscape 3.x series.

Cytoscape is an open source software platform for visualisation of molecular networks and biological pathways. The system allows annotation and integration of these networks with gene expression profiles and other state data. While Cytoscape was initially built for biologists, the platform can be adapted to a broad range of network-related projects including bioinformatics, social network analysis and semantic web. Cytoscape has a very active App developer community which means that new functionalities and tailored solutions are constantly being added to the platform.

As part of the course, the participants will be introduced to the app development process as well as the key aspects of the Cytoscape API necessary to manipulate Cytoscape tables, networks, and user interface. The participants will then be guided on how to set up development environments on multiple platforms, and develop an initial Cytoscape App. The second day of this course will provide time for each participant to interact with the instructor and other participants to plan and develop their own Cytoscape app.

The registration is now open until Friday 31 January 2014. Please register here.