Tutorials

ECCB 2010 will feature four one-day tutorial sessions on Sunday, September 26, 2010.

The purpose of the tutorial program is to provide participants with lectures and instruction covering  topics relevant to the bioinformatics field. It offers participants an opportunity to learn about new areas of bioinformatics research, to get an introduction to important established topics, or to develop advanced skills in areas about which they are already familiar.

TUTORIAL 1: WORKING WITH NEXT-GENERATION SEQUENCING DATA

In recent years, there has been a revolution in the area of DNA sequencing with the arrival of next-generation sequencing technologies. The type and volume of the data produced by next-generation sequencing machines presents many previously unseen informatics challenges. This tutorial will help people who are getting started on next-gen sequencing get an idea of the tools, flows, and procedures that they may need to set up to handle this data. In this short course, we will introduce the participants to the different next-generation sequencing technologies, show how to do some basic quality checking of the data, how to run the various next-generation alignment tools, create de novo sequence assemblies, and call variants (such as SNPs, short indels, and structural variants) from a reference sequence.

TUTORIAL 2: USE OF SEMANTIC WEB RESOURCES IN COMPUTATIONAL BIOLOGY AND BIOINFORMATICS

The Semantic Web is a set of technologies, or a framework, which is designed to make data integration possible via the web, with the addition of a precise semantic characterization of entities and relations (ontologies). As data integration is a pre-requisite for systems biology and translational research, the Semantic Web can bring relevant benefits in these areas. The aim of this tutorial is to briefly introduce the key basic principles needed to understand what it means to represent information on the Semantic Web, and then to provide the attendees with basic hands on competences to start using biomedical information resources which are now available on this framework. 

TUTORIAL 3: CURRENT METHODS AND APPLICATIONS FOR REGULATORY SEQUENCE ANALYSIS

The annotation of the non-coding genome with gene regulatory function is lagging far behind the annotation of protein-coding genes and improved annotation will depend both on deeper biological insight into cis-regulatory logic and on more efficient computational prediction algorithms. Recent data obtained by high-throughput experiments accelerate the genome-wide identification of regulatory elements but also provide additional bioinformatics challenges. In the light of these developments, this tutorial will focus on bioinformatics methods to predict cis-regulatory elements and to aid the process of regulatory annotation. Participants will be provided with an overview of existing resources (databases, tools) and methods for detecting cis-regulatory elements in genome sequences, and generate testable hypotheses about the binding specificity of transcription factors (motifs discovery), their precise binding locations (binding site prediction), and their target genes (target identification), and go towards regulatory networks.

TUTORIAL 4: PROTEIN STRUCTURE VALIDATION

Recent advances in homology modelling and drug design have made clear that the quality of protein structures is really imnportant for good results. Today's software and CPU time availability on clusters, super computers, and the grid allow for easy improvement of old files. It is therefore important for all protein structure bioinformaticians to be able to evaluate the quality of the structures used in their studies and to know when it might be beneficial to ask an NMR spectroscopist or X-ray crystallographer to help bring an old file up to today's standards. This workshop will teach the participants how to use a series of protein structure validation tools and how to interpret the results. The origins of problems are discussed as well as their importance for follow up studies.