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Cloud-Based Bioinformatics

 

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Thursday, 11 October


NGS Analysis Workflow Optimization 

7:45 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:30 Chairperson’s Opening Remarks

Michelle Munson, President & Co-Founder, Aspera, Inc.

8:35 Optimizing Bioinformatics Workflows for Data Analysis Using Cloud Management Techniques

Ivona BrandicIvona Brandic’, Ph.D., Vienna University of Technology

With the rapid development of high-throughput technologies in recent years, huge amounts of data are being generated and stored in databases in life sciences, which necessitates significant advances in computing capacity and performance. An example of such technologies is the high-throughput sequencing of the transcriptome (RNASeq), which has the potential to transform how gene structure and gene expression profiling are studied. Scientific workflow applications are crucial in enabling scientists to data mine important information from the huge amount of stored data. In this talk we discuss how the application of cloud computing technologies can support the work of scientists working in the field of high-throughput sequencing.

9:05 Tavaxy: A Workflow System with Taverna and Galaxy Capabilities and Cloud Computing Support

Mohamed AbouelhodaMohamed Abouelhoda, Ph.D., Assistant Professor, Center for Informatics Science, Nile University

Taverna and Galaxy, which are the most popular workflow systems in bioinformatics, are not interoperable. That is, workflows written for one system cannot run on the other. In this talk, we introduce a new workflow system called Tavaxy that enables hybrid composition of Taverna and Galaxy workflows in addition to other tools. Tavaxy supports use of cloud computing and supports different use case scenarios to use the cloud on the whole system level or sub-workflow level.

Aspera9:35 High-Speed Data Movement for Effective Global Collaboration in Genomic Research

Michelle Munson, President & Co-Founder, Aspera, Inc.

To collaborate effectively, scientific organizations need to implement large-scale computing and networking infrastructure, select storage systems and integrate high-speed transport technologies to power the collection and distribution of terabytes of sequencing data to researchers globally. Learn about best practices, requirements and challenges of IT infrastructure designs and how Aspera powers data movement in support of global research.

10:05 Coffee Break in the Exhibit Hall with Poster Viewing

10:45 Creating a Collaborative Bioinformatics Resource for the New York Genome Center and its 11 Institutional Founding Members

Dirk Evers Dirk Evers, Ph.D., SVP Informatics, New York Genome Center

The New York Genome Center aims to open in mid 2013. It will be home to researchers in Genomics and provide research and clinical sequencing services, a high performance computing infrastructure as well as bioinformatics analysis resources and personnel. The unique challenge is to build a collaborative center that will act as the hub to 11 world-class research institutions. This presentation will go over the plan for the high performance computing infrastructure and the bioinformatics resource framework as planned and also give an update on the current state of the build-out.
 

11:15 Critical Parameters of NGS Outsourcing

Herbert AuerHerbert Auer, Director, Functional Genomics Core, Institute for Research in Biomedicine, Parc Cientific de Barcelona

A good number of service providers offer already Next Generation Sequencing (NGS) as a service. In addition to pricing, time for completion of projects, and methods offered by NGS service providers, quality of data is of paramount importance. We have been working with five different providers on two continents across a numbers of projects. Experiences and positive and negative surprises will be described in this presentation. We performed a project on somatic mutations in non-cancerous diseases with one of these providers. Since this project needed extremely accurate results, reliability of data, documentation of processing and quality control had to be carefully evaluated and these experiences will be described.

11:45 ARB and SILVA: Tools and Reference Databases for Large Scale rDNA Analysis

Elmar Pruesse, Ph.D., Micobial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology

The SILVA project was initiated in 2007 to facilitate the transition of rDNA centered workflows to an environment defined by superabundant sequence data. SILVA provides regularly updated, high-grade rDNA reference databases geared for phylogenetic analysis and diversity studies. The databases comprise quality controlled, aligned sequence data rich in contextual data (including multiple taxonomies). In this talk we present our ongoing efforts to enhance both integrative workflow efficiency and scalability of the ARB/SILVA tandem, as well as the tools and databases offered by SILVA for high-throughput sequence analysis.

12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own


Open Bioinformatics 

13:45 Chairperson’s Remarks

13:50 Next Generation Bioinformatics Data Analysis Tools in HPC Environments

Hesham AliHesham Ali, Ph.D., Professor and Dean, College of Information Science and Technology, University of Nebraska at Omaha

The availability of vast amounts of biological and medical data continues to represent unlimited opportunities as well as great challenges in biomedical research. Developing innovative data mining techniques and clever parallel computational methods to implement them will surely play an important role in efficiently extracting useful knowledge from the raw data currently available. This presentation focuses on addressing key issues related to the effective utilization of High Performance Computing (HPC) in biomedical research, with a particular focus on systems biology approaches and energy awareness in Biomedical Informatics.

14:20 Quantitative, Systematic Analysis of Post-Translational Modifications from Complex Proteome Mixtures Using Cloud Computing

Shi-Jian DingShi-Jian Ding, Ph.D., Assistant Professor, Pathology and Microbiology, University of Nebraska Medical Center

Systematic analysis of post-translational modifications (PTMs) from complex proteome mixtures is a challenging task. Here we describe the development and application of a novel algorithm, ISPTM (iterative search for peptide identifications with PTMs), for tackling this challenge. ISPTM has been implemented in academic and industry cloud computing environments, open science grid and Amazon EC2. Furthermore, ISPTM was coupled to our UNiquant software to enable quantitative, systematic analysis of PTMs from complex proteome mixtures.

14:50 Visualizing Metabolite Fluxes on WikiPathways Pathways Using a PathVisio Plugin

Anwesha DuttaAnwesha Dutta, Ph.D. Fellow, Department of Bioinformatics – BiGCaT, Maastricht University

Biological pathways provide intuitive frameworks to integrate and co-analyze different kinds of data, such as system-wide transcriptomic, proteomic, and metabolomic measurements. The same life processes that are visualized in pathways are also described by quantitative models. For example, the arrows that connect entities within metabolic pathways actually represent metabolite fluxes. The integration of large scale data analysis with modeled or measured fluxomics data, will help to gain more insights into the mechanism of the biological process.

15:20 WikiBioPath - A Biological Knowledge Base and Associated Analysis Tools

Pavel HradeckyPavel Hradecky, MD, Biomedical Research Director, AltraBio

WikiBioPath (WBP) is a web application combining an integrated life science knowledge database of genomic data and functional annotations with a suite of search and visualization tools allowing the user to perform targeted interpretation of large experimental data sets. The backbone of WikiBioPath is formed by a knowledge graph consisting of biological objects and their functional relationships that can be contextualized (filtered) to a particular biological topic of interest. WikiBioPath will also be released as an open source software package.

15:50 Refreshment Break in the Exhibit Hall with Poster Viewing

16:15 Breakout Discussion

Group 1: Private-Public Partnership for Drug Discovery

Moderator: Mollie Shields Uehling, CEO, SAFE-BioPharma Association

Group 2: Genomic Data Analysis Workflow Optimization

Moderator: Anwesha Dutta, Ph.D. Fellow, Department of Bioinformatics – BiGCaT, Maastricht University

Group 3: Open Innovation: Where Do You Draw the Line?

Moderator: Nour Shublaq, BEng MSc PhD (Oxon) MIET, Dr, University College London

 

17:15 Close of Conference



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