(last update Oct. 11 2011)

IT Workshop - The X-meeting 2011 will have a special session on IT infrastructure. The main motivation for this workshop is the identification of an imbalance, in many of our institutions, between the needs of the bioinformaticians and the way the IT infrastructure is setup (restrictions, network setup, access, etc.). The objective of this parallel session will be to describe the needs of bioinformaticians to the IT professionals and discuss examples where satisfactory solutions were developed and others where improvements are necessary. In addition, solutions for bioinformatics hardware implementations will be discussed..

Bioinformatic tools and methods to build and study gene coexpression and protein interaction networks (Instructor: Dr. Javier De Las Rivas) - Introduction to the basic concepts, terminology and types of biological networks, with special focus on gene coexpression networks and protein-protein interaction networks. Overview of the most important databases storing biomolecular network information. Definition of protein-protein interaction networks and presentation of tools to build and explore this type of networks. Use of Cytoscape, open-source program for the visualisation and analysis of networks. Exercises guided to the construction of your own gene/protein networks in Cytoscape.

Reactome (Instructor: Robin Haw) - Reactome Pathway and Network Analysis (Instructor: Robin Haw) - Reactome is an expert-authored, manually-curated, peer-reviewed database of reactions, pathways and biological processes. This practical course will introduce the Reactome database, website and our suite of pathway and network analysis tools. Participants will learn to: browse and query pathway knowledge, integrate network and pathway data, ?use pathway and expression analysis tools to analyze experimental datasets, annotate gene lists using Reactome BioMart, and discover network patterns related to cancer and other diseases using the Reactome Functional Interaction Network Cytoscape plug-in.

De novo assembly bacterial genome using next generation sequencing data (Instructors: Vasco Azevedo, Artur Silva, Rommel Ramos, Louise Cerdeira, Anderson Santos, Luis Guimaraes and Vinicius Abreu) - Day 1: Overview NGS Technologies / Improving data quality / Introduction to genome assembly. Day 2: De novo bacterial genome assembly / Finishing genomes / In silico gaps closure. Day 3: Overview structural annotation / Automated pipeline for structural annotation.

FreeBit Workshop. Developing free software (Instructor: Jose R. Valverde) - Developing free software provides many advantages, both to the academic and the commercial developer. This course will provide a summary introduction to the advantages of the Free Software model answering the most relevant practical questions for developers, such as: What kind of Free Software licenses are there and which one should I use? How do I share the workload with other developers all over the world? What tools are best suited to Free Software development? How do I exploit and support Free Software? 

Macromolecular structure, protein function (Instructor: Cesar Avila) - Modern Deep Sequencing and Proteomics are producing a large amount of data about known and novel proteins in a large variety of organisms. Annotating genes and understanding the role of new proteins is a major challenge that has driven major research efforts to mine collected data and provide scientists with suitable, free and easy to use tools addressing this problem. Attendants to this course will learn about the various approaches that can be used, from sequence analysis, to structural analysis and modelling, and will come out with a large arsenal of Free Software tools they can use at their home institution to efficiently analyze protein function.