19th Annual International Conference on
Intelligent Systems for Molecular Biology and
10th European Conference on Computational Biology

Accepted Posters

Category 'T'- Reviews'
Poster T1
A Framework for the Evaluation of Bioinformatics Methods

José M. Fernández Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO)
Jose M. Rodriguez (Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme); Angela del Pozo (Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme); Iakes Ezkurdia (Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme); Michael L. Tress (Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme); Alfonso Valencia (Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Structural Biology and Biocomputing Programme);
Short Abstract: Our group has been involved in the assessment of bioinformatics methods, including stand alone challenges in protein structure prediction (CASP) and text mining (BioCreAtive) as well as in parallel efforts for continuous assessment EVA/ CAFASP and BCMS.
There are obvious differences in the assessment of protein structure prediction and text mining including scientific, technical and sociological aspects, but there are also many common aspects. In particular: a) the processes of handling training and testing data are similar, b) a similar technology can be used for the continuous assessment of the predictions, c) the evaluation of results can to a large extend be similar, d) results can be represented with similar interfaces and e) in both cases it is very important to deliver properly to the respective communities the legacy data, including the annotated and evaluated data sets.
We believe that these similarities can be extended to other areas of bioinformatics in which methods assessment is equally important.
On this poster, we will describe the status of our developments related with the assessment of function prediction, entity detection and prediction of protein interaction interfaces. We will also depict the general nature of these developments and our views on how they can be adapted to the evaluation of other type of predictions in agreement with the corresponding communities.
Poster T2
eBiomics: an e-Learning Environment on Bioinformatics for Life Scientists

Patrick Koks Wageningen University
Pascale Berthault (SDC Conseil et Edition, -); Guy Bottu (ULB, BiGre); Jacques van Helden (ULB, BiGre); Jean-Pierre Kraehenbuhl (HSeT foundation, -); Frédérique Lisacek (SIB, Proteome Informatics Group); Grégoire Rossier (SIB, Proteome Informatics Group); Jean Sylvestre (SDC Conseil et Edition, -); Jack Leunissen (Wageningen University, Bioinformatics Laboratory);
Short Abstract: With the exponential growth of experimental data in life sciences, data analysis has become more important. The availability of bioinformatics resources to meet these challenges is ever expanding. However, testing, comparing and learning of the appropriate tools is cumbersome. eBiomics offers a solution for the growing demand for training in and evaluation of these tools by providing a didactic guide for on-line tools and databases.

We put much emphasis on the development of a pedagogic strategy. We developed a visually attractive and navigation-friendly, highly cross-linked website. The structure of eBiomics consists of Conceptual Workflows, Protocols, Case-Studies, Resources and Exercises. It delivers defined paths through selections of articles providing complete self-study courses. Alternatively, eBiomics allows for direct access to specific resources and thus acts as a reference base for experienced users. eBiomics builds on previous experience with e-Proxemis (http://e-proxemis.expasy.org/) and adds an improves visual navigation and extension to domains like genomics, transcriptomics and metabolomics.

While building the website (www.ebiomics.org) and writing the content is work in progress, we started forming a test-panel to test the ease of course navigation, content quality and usability. Please join us and write to testpanel@ebiomics.org.
eBiomics offers an e-learning environment that enables us to keep up with frequent additions, upgrades and changes in bioinformatics practice. Guaranteeing the long-term maintenance is challenging in bioinformatics because of the short half-life of many tool and databases. EU, SER and NBIC are funding the setup-phase of our project; we are seeking partners for funding and cooperation in keeping eBiomics up-to-date.
Poster T3
Practical NGS Analysis: A Bioinformatician’s Perspective

Abhishek Pratap University of Maryland Baltimore County / DOE- Joint Genome Institute
Short Abstract: The motivation for this poster comes from the questions I see across bioinfo mailing lists on how to handle NGS (Next Generation Sequencing) Data. I plan to present various analysis methods and techniques that I have used or developed for analysis of data from Illumina class of sequencers in the last three years or so.
The focus remains on asking biologically pertinent questions efficiently in a timely manner from the raw data. More importantly making sure the conclusions make biological sense. I plan to address the following questions via this poster and engage in exciting discussions with my peers at ISMB.
1. Data quality conversions. Why should you convert Illumina QScores to SangerQ?
2. Error Corrections : Dynamic v/s Static trims
3. Can I sequence more from the same library? : Evaluating Library Complexity
4. Alignment: Which aligner is right for your data and question and why?
5. Exome Capture : Knowing you captured the right region
6. RNA Seq : issues with read count and expression analysis
7. SNP Calling : Specificity v/s Sensitivity
8. How to identify disease causing mutations with case and controls?
9. Data exchange formats: How should I store and transfer my NGS data?
Many techniques that will be shown will use some of already available open source tools. My goal is to provide review for those and describe how I threaded different pipelines together to answer the questions that principal investigator’s asked of the data.
Poster T4
A Review of Software for Visualization and Interpretation of Genome Wide Association Studies Results

Armita Zarnegar National ICT Australia (NICTA)
Adam Kowalczyk (The University of Melbourne, National ICT Australia (NICTA)); Andrew Stranieri (University of Ballarat, Information Technology and Mathematical Sciences); Izhak Haviv (Baker IDI Institute, -);
Short Abstract: A Review of Software for Visualization and Interpretation of Genome Wide Association Studies Results

Experimental techniques for Genome Wide Association Studies produce a wealth of results which demand flexible, highly interactive visualization tools to facilitate their biological interpretation.
The biological interpretation of such results is heavily dependent on steps such as linkage disequilibrium analysis, collection of information related to each single nucleotide polymorphism (SNP) and annotation of reference genes. Software for this purpose has to collect information from several data sources and visualize them in a proper and informative way.

In this review, we describe the existing software and tools for visualization and interpretation of the results of Genome Wide Association Studies. We highlight the state-of-the-art methods which have the ability to show epsistatic interactions or act in a large scale.
As a result of this overview, we found the shortcomings of the existing softwate tools. We suggest two new features required for handling the epistasis interactions. We propose a framework that provides a summary of existing features and an evaluation of the existing software based on these key features. Having such a systematic review is currently lacking and our review can assist researchers with choosing the most appropriate software for their purpose.

Accepted Posters

Attention Poster Authors: The ideal poster size should be max. 1.30 m (130 cm) high x 0.90 m (90 cm) wide. Fasteners (Velcro / double sided tape) will be provided at the site, please DO NOT bring tape, tacks or pins. View a diagram of the the poster board here

Posters Display Schedule:

Odd Numbered posters:
  • Set-up timeframe: Sunday, July 17, 7:30 a.m. - 10:00 a.m.
  • Author poster presentations: Monday, July 18, 12:40 p.m. - 2:30 p.m.
  • Removal timeframe: Monday, July 18, 2:30 p.m. - 3:30 p.m.*
Even Numbered posters:
  • Set-up timeframe: Monday, July 18, 3:30 p.m. - 4:30 p.m.
  • Author poster presentations: Tuesday, July 19, 12:40 p.m. - 2:30 p.m.
  • Removal timeframe: Tuesday, July 19, 2:30 p.m. - 4:00 p.m.*
* Posters that are not removed by the designated time may be taken down by the organizers and discarded. Please be sure to remove your poster within the stated timeframe.

Delegate Posters Viewing Schedule

Odd Numbered posters:
On display Sunday, July 17, 10:00 a.m. through Monday, June 18, 2:30 p.m.
Author presentations will take place Monday, July 18: 12:40 p.m.-2:30 p.m.

Even Numbered posters:
On display Monday, July 18, 4:30 p.m. through Tuesday, June 19, 2:30 p.m.
Author presentations will take place Tuesday, July 19: 12:40 p.m.-2:30 p.m

Want to print a poster in Vienna - try these options:

Repacopy- next to the congress venue link [MAP]

Also at Karlsplatz is in the Ring Center, Kärntner Str. 42, link [MAP]

If you need your poster on a thicker material, you may also use a plotter service next to Karlsplatz: http://schiessling.at/portfolio/

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