ECCB 2010 NEXT-GEN SEQUENCING TUTORIAL PDF

Visualizing the next generation of sequencing data with GenomeView .. .. A .. Why inverse proteins are relatively abundant, J.-C. Nebel and C. Walawage, Protein & Peptide Letters, 17(7), Michal Nánási ([email protected] ) Website: (free download, tutorials, manual, . Next generation sequencing presents new challenges in large scale data at the European Conference of Computational Biology (ECCB) , Ghent. Tutorials, workshops and seminars To do bioinformatics well, you need to learn 3 things. ECCB Next-gen sequencing Tutorial (Thomas [email protected]).

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Going back in time, the fourteen previous editions of ECCB have been held in: 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.

Presenters

He subsequently moved to the Pathogen Genomics group at the Wellcome Trust Sanger Institute to work on sequence assembly of several pathogens such as Plasmodium falciparum strains, Trypanosoma brucei, and several other pathogen genomes. The ECCB organizing committee congratulates all these dynamic young scientists for their enthusiasm, which is essential to the future of research in computational biology. After thorough consideration and discussion, the ECCB theme co- chairs selected 24 proposals out of 71 submissions, mainly on the criteria of compatibility with the ECCB objectives, wide impact in the life sciences and the potential for attracting a large audience to the conference.

All poster abstracts are available on the conference web site.

Submissions to this track should cross the boundaries of traditional academic science, or show developments that are directly relevant beyond academia or have potential for it. Thanks to our academic and commercial sponsors and to the careful control of conference costs, we could satisfy about two-thirds of the requests.

Introduction to structural variation Summary of different types of structural variants Large insertions, deletions, inversions, translocations, copy number variants Overview of algorithms tutorrial tools for calling structural variants Practical examples of calling structural variants Visualisation of structural variants.

Next generation sequencing

The Application Track is an initiative to promote application of computational biology in industry and other fields beyond academia. The conference topics span all areas of methodological developments for computational biology and innovative applications of computational methods to molecular biology and biomedicine.

Together, the Programme Committee PC was composed of reviewers and 35 co-reviewers. We also gratefully acknowledge the hard and diligent work performed by dequencing reviewers over a short period of time.

We thank all theme co-chairs for their availability throughout the reviewing process, for their very positive attitude in the final selection and for their valuable help in re-examining the modified submissions.

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It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Working with next-generation sequencing data Tutorial 2: Recent data obtained by high-throughput experiments accelerate the genome-wide identification of regulatory elements but also provide additional bioinformatics challenges.

Next generation sequencing | Taverna

Submission authors were asked to rank the five themes for fit of their paper. Today’s software and CPU time availability on clusters, super computers, and the grid allow for easy improvement of old files. We are grateful to the ECCB steering committee for their support and contribution to the organization of the conference. To present a more unified view of where the science has gone over recent years, new to ECCB this year is that the conference presentations are divided over five broad themes: Working with next-generation sequencing data – A short primer on QC, alignment, and variation analysis of next-generation sequencing data Presenters Thomas Keane completed his PhD degree in the area of distributed computing and high-throughput phylogenomics from NUI Maynooth Ireland in Many people contributed to the local organization of the conference, often much beyond the call of duty, and we owe them a great debt, in particular Femke Francissen and Jacintha van Beemen, both at the Dutch Techcentre for Life Sciences DTL for their relentless logistic and organizational support.

Following the call for Proceedings papers, we received submissions. His current work includes downstream analysis of next-generation sequencing data in order to identify putative SNPs and indels. Finally, the ELIXIR track proved to be a very popular addition, with 50 high-quality submissions for only 12 presentation slots. Use of semantic web resources in computational biology and bioinformatics Tutorial 3: After the reviewers reached a consensus, a final ranking and selection for each theme was carried out by the theme co- chairs.

This distinction was intended to create more clarity for both the reviewers and authors; the reviewing criteria were therefore explicitly stated in the submission guidelines.

Learning resources | BacPathGenomics

Linking sequence patterns and functionality of alpha-helical antimicrobial peptides. 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.

Citing articles via Web of Science 1. These technologies have resulted in a huge reduction in the cost of sequencing and has meant that many new researchers now have access to raw sequencing data.

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. Working with next-generation sequencing data – A short primer on QC, alignment, and variation analysis of next-generation sequencing data.

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We also arranged with FResearch http: 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.

Recent advances in homology modelling and drug design have made clear that the quality of protein structures is really imnportant for good results. Related articles in Web of Science Google Scholar. Gkoutos University of Birmingham, UK.

These rankings were subsequently used to assign papers to themes and to arrive at an optimally balanced distribution of submissions over the themes. The ECCB edition features keynote lectures by distinguished speakers.

Friday, 01 April Submissions to the Poster Track were evaluated based on a word abstract and will be shown at the conference along the five main conference themes. This workshop will teach the participants how to use a series of protein structure validation tools and how to interpret the results. We also thank, as our further supporting sponsors, Gemeentemuseum Den Haag, where also the opening reception will be held, the Municipality of The Hague, Bayer sponsoring the morning run and The Utrecht Bioinformatics Centre sponsoring the Poster Award.

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.

Computational analysis platforms are challenged by the enormous complexity of biological systems and the sheer amount of data resulting from high-throughput measuring techniques, such as single-cell or single-molecule measurements. Finally, all these efforts would be meaningless without the many participants from all over the world.

Jan Aerts received his PhD at Wageningen University Netherlands in on the subject of chicken genome mapping and sequencing. Discovery of statistically significant post-translational modification motifs. The type and volume of the data produced by next-generation sequencing machines presents many previously unseen informatics challenges.

In this short course, we will introduce the participants to sequfncing 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.

Taken together, the workshops demonstrate how extensively seuencing have found their way into large-scale practical applications: We thank all those who provided financial support to the conference.