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

Technology Track Presentation Schedule

TT01Sunday, July 17: 10:45 a.m. - 11:10 a.m.
Ensembl Genome Browser: Harnessing the Next Generation Sequencing Wave

Room: J241

Presenting Author: Michael Schuster, EMBL-European Bioinformatics Institute

Abstract:
Recent developments of Ensembl include visualisation of custom next-generation sequencing data and their seamless integration into genome annotation provided by the project. A Variant Effect Predictor allows classification of genetic variants by their overlap with genome annotation. Annotation of regulatory elements has been extended with cell type-specific data sets.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT01: Michael Schuster - Ensembl Genome Browser: Harnessing the Next Generation Sequencing Wave
TOP

TT02Sunday, July 17: 10:45 a.m. - 11:10 a.m.
PubAnatomy: A Rich Internet Application for Integrated Literature and Data Exploration

Room: J565

Presenting Author: Fan Meng and Barbara Mirel, University of Michigan

Abstract:
PubAnatomy is a novel Flash-based literature exploration solution that provides rich interactivity and bi-directional data communication with other Flash RIA in different browser windows to facilitate the integrated exploration of neurobiology literature in relevant biological contexts such as brain structures, pathophysiological processes, gene expression levels and protein-protein interactions

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT02: Fan Meng and Barbara Mirel - PubAnatomy: A Rich Internet Application for Integrated Literature and Data Exploration
TOP

TT03Sunday, July 17: 11:15 a.m. - 11:40 a.m.
UCSC Genome Browser: Visualization tools for high-throughput sequencing

Room: J241

Presenting Author: Rachel Harte, University of California, Santa Cruz

Abstract:
The UCSC Genome Browser and Ensembl offer two presentations featuring Web-based tools for high-throughput sequencing visualization. The Browser allows interactive viewing of BAM files as Custom Tracks. The new Personal Genome SNP format displays variants and the Session tool provides an easy way to share results with others.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT03: Rachel Harte - UCSC Genome Browser: Visualization tools for high-throughput sequencing Show Comments
TOP

TT04Sunday, July 17: 11:15 a.m. - 11:40 a.m.
GenomeSpace

Room: J565

Presenting Author: Michael Reich, Broad Institute

Abstract:
GenomeSpace is a platform that supports an open community of genomics analysis tools. Using GenomeSpace, researchers can construct analyses requiring communication and data transfer between diverse tools such as Web applications and client-side tools. GenomeSpace supports cloud-based storage, handles file format compatibility issues automatically, and enables reproducibility of multi-tool analyses.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT04: Michael Reich - GenomeSpace Show Comments
TOP

TT05Sunday, July 17: 11:45 a.m. - 12:40 p.m.
Enhancing researcher productivity through integrated Bio-medical workflow solutions on SciVerse Platform

Room: J241

Presenting Author: Vishal Gupta, Adriaan Klinkenberg, Elsevier

Abstract:

SciVerse is a platform for trusted scientific content and innovative applications that enhance information search and discovery of researchers by adding semantic search functionality, text and data mining annotation to visualize data and relationships, or integrating data with ontologies and repositories. Using the SciVerse framework, researchers and external developers can build customized workflow solutions that can appear alongside full text articles, abstracts and search results within the SciVerse suite.

This session explores the SciVerse platform that enables collaboration with the scientific community and demonstrates two workflow solutions- NCBI Genome Viewer and Health-mash.



Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT05: Vishal Gupta, Adriaan Klinkenberg - Enhancing researcher productivity through integrated Bio-medical workflow solutions on SciVerse Platform
TOP

TT06Sunday, July 17: 11:45 a.m. - 12:10 p.m.
Bioinformatics@school

Room: J565

Presenting Author: Hienke Sminia, Netherlands Bioinformatics Centre

Abstract:
- Bringing bioinformatics to the classroom -
Bioinformatics is virtually unknown to most high school pupils. Since they are potentially tomorrow's bioinformaticians, the Netherlands Bioinformatics Centre (NBIC) and the Centre for Molecular and Biomolecular Informatics (CMBI) are bringing bioinformatics to the classroom using hands-on student workshops and teacher trainings.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT06: Hienke Sminia - Bioinformatics@school
TOP

TT07Sunday, July 17: 12:15 p.m. - 12:40 p.m.
Supporting Inter-connected Biomedical Open-source Software

Room: J565

Presenting Author: Zhong Li, Columbia University / Broad Institute

Abstract:
One of the unmet needs for open source biomedical software is support. The Molecular Analysis Tools Knowledge Center (MATKC), sponsored by NCI, offers support, expertise, and knowledge resources on selected tools in molecular data management and analysis (caArray, caIntegrator, geWorkbench, and GenePattern). A vibrant online community has been established.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT07: Zhong Li - Supporting Inter-connected Biomedical Open-source Software
TOP

TT08Sunday, July 17: 2:30 p.m. - 3:25 p.m.
MONGKIE: Modular Network Generation and Visualization Platform with Knowledge Integration Environment

Room: J241

Presenting Author: Sanghyuk Lee, Korean Bioinformation Center

Abstract:
MONGKIE is an integrated network visualization platform which allows us to explore and analyze interconnected biological data in an interactive manner with knowledge integration environment providing functional modules such as Import/Export Network, Expression Overlay, Network Clustering/Ranking, Pathway Integration/Visualization, Gene Set Enrichment Analysis(GO/Pathway) and Analysis Pipelines consisting of other modules.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT08: Sanghyuk Lee - MONGKIE: Modular Network Generation and Visualization Platform with Knowledge Integration Environment
TOP

TT09Sunday, July 17: 2:30 p.m. - 2:55 p.m.
Cloud Computing for Computational Biology

Room: J565

Presenting Author: Attila Berces, Omixon

Abstract:
We demonstrate some free utilities that help biologist to take advantage of cloud computing. In addition we demonstrate next generation sequencing data analysis on the Omixon portal starting with short reads and ending with annotated variants and aligned reads in a genome browser.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT09: Attila Berces - Cloud Computing for Computational Biology
TOP

TT10Sunday, July 17: 3:00 p.m. - 3:25 p.m.
Accurate Genome Variant Detection

Room: J565

Presenting Author: Attila Berces, Omixon

Abstract:
We demonstrate Omixon Variant Toolkit, an easy-TO-USE NEXT generation sequencing DATA analysis pipeline especially designed FOR the most accurate genomic variant detection. We shall demonstrate several biologically relevant variants FOUND only BY this tool but NOT BY the most popular tools AND were subsequently validate BY Sanger sequencing.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT10: Attila Berces - Accurate Genome Variant Detection
TOP

TT11Sunday, July 17: 3:30 p.m. - 4:25 p.m.
Efficient Graph Based Assembly of Short-Read Sequences on a Hybrid Core Architecture

Room: J241

Presenting Author: George Vacek, Convey Computer

Abstract:
Convey’s Graph Constructor takes advantage of increased random-access memory bandwidth to dramatically reduce run time and memory usage of Velvet for short-read, de novo assembly. Results will be presented for a variety of datasets. Performance improvements facilitate multiple runs with varying parameters, ultimately resulting in higher quality assemblies.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT11: George Vacek - Efficient Graph Based Assembly of Short-Read Sequences on a Hybrid Core Architecture
TOP

TT12Sunday, July 17: 3:30 p.m. - 4:25 p.m.
Functional Synergy Analysis of OMICs Data of Different Types in Cancer Research

Room: J565

Presenting Author: Yuri Nikolsky, Thomson Reuters

Abstract:
We developed and applied several methods of functional data analysis for revealing of functional correlation between the datasets of different types (NGS, expression, epigenetics) regardless of gene content overlap between them. I will describe the basic techniques of pathway, network and interactome – based correlation and summarize the results of collaborative studies on cancer.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT12: Yuri Nikolsky - Functional Synergy Analysis of OMICs Data of Different Types in Cancer Research
TOP

TT13Monday, July 18: 10:45 a.m. - 11:40 a.m.
Analyzing Next Gen Sequencing Data with Pipeline Pilot

Room: J241

Presenting Author: Scott Markel, Ruth Dunn, Accelrys

Abstract:
Pipeline Pilot® provides a software environment where algorithms and data come together into a data-pipelining model that allows quick and customizable application integration, data analysis, and reporting of results. Pipeline Pilot already integrates chemistry, text analytics, statistics, and sequence analysis. Now next generation sequencing is supported.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT13: Scott Markel, Ruth Dunn - Analyzing Next Gen Sequencing Data with Pipeline Pilot Show Comments
TOP

TT14Monday, July 18: 10:45 a.m. - 11:10 a.m.
ProBiS: a web server for detection of protein binding sites

Room: J565

Presenting Author: Janez Konc, National Institute of Chemistry

Abstract:
We present new features of the recently enhanced ProBiS 2.0 web server, and provide a brief tutorial of its usage on an example of protein function prediction.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT14: Janez Konc - ProBiS: a web server for detection of protein binding sites
TOP

TT15Monday, July 18: 10:45 a.m. - 11:10 a.m.
RightField: The Semantic Annotation of Experimental Data using Spreadsheets

Room: Lounge 1

Presenting Author: Katy Wolstencroft, University of Manchester

Abstract:
RightField is an open source application for embedding ontology annotation in spreadsheets. Cells can be restricted to ranges of allowed classes or instances from chosen ontologies and presented as a simple drop-down list in the spreadsheet. The result is “semantic annotation by stealth” and consistently annotated standards compliant data.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT15: Katy Wolstencroft - RightField: The Semantic Annotation of Experimental Data using Spreadsheets
TOP

TT16Monday, July 18: 11:15 a.m. - 11:40 a.m.
UK PubMed Central: a database of life science research articles.

Room: J565

Presenting Author: Jo McEntyre, EMBL-EBI

Abstract:
UK PubMed Central is a database of about two million full-text life science research articles and 25 million abstracts (from CiteXplore), overlaid with semantic enrichment, database links, and citation networks. It is free to use, and the open access articles are made available in full.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT16: Jo McEntyre - UK PubMed Central: a database of life science research articles.
TOP

TT17Monday, July 18: 11:15 a.m. - 11:40 a.m.
Software for the data-driven researcher: Annotation of Next Generation Sequencing SNP Data using scientific workflows

Room: Lounge 1

Presenting Author: Paul Fisher, University of Manchester

Abstract:
In this demonstration we will showcase the Taverna 2 workflow engine and Taverna Server, and illustrate how scientific workflows deployed on the cloud can provide a means of addressing the data analysis requirements for the annotation of SNP from Next Generation Sequencing.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT17: Paul Fisher - Software for the data-driven researcher: Annotation of Next Generation Sequencing SNP Data using scientific workflows Show Comments
TOP

TT18Monday, July 18: 11:45 a.m. - 12:10 p.m.
GeneCards: The Human Gene ReSearcher

Room: J241

Presenting Author: Irina Dalah, Weizmann Istitute of Science

Abstract:
GeneCards (www.genecards.org) is a comprehensive, searchable compendium of annotative information about human genes, used worldwide for >15 years.
Our presentation will demonstrate how GeneCards facilitates life-science research, showcasing the powerful search, with sortable results shown as expandable, structured minicards, and with gene-sets exportable to GeneALaCart and GeneDecks, enabling systems-biology insights.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT18: Irina Dalah - GeneCards: The Human Gene ReSearcher
TOP

TT19Monday, July 18: 11:45 a.m. - 12:10 p.m.
Integrating Heterogeneous Data using the Ontological Discovery Environment

Room: J565

Presenting Author: Elissa Chesler, The Jackson Laboratory

Abstract:
The Ontological Discovery Environment (ODE) is an approach to large-scale data analysis of heterogeneous life science data using biclique enumeration and highlights the advantages of unifying discretized data into graph structures. We will present its work flow processes by analyzing a diverse set of use cases in complex trait disorders.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT19: Elissa Chesler - Integrating Heterogeneous Data using the Ontological Discovery Environment
TOP

TT20Monday, July 18: 11:45 a.m. - 12:10 p.m.
End user tools for data interoperability

Room: Lounge 1

Presenting Author: Christine Chichester, NBIC

Abstract:
In the NBIC interoperability task force, we work towards a sustainable future for a large-scale, community editable store of disambiguated scientific assertions, exemplifying a new paradigm in life sciences data accumulation. We will demonstrate some of the tools we have created as end user applications.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT20: Christine Chichester - End user tools for data interoperability Show Comments
TOP

TT21Monday, July 18: 12:15 p.m. - 12:40 p.m.
PRIDE Inspector

Room: J241

Presenting Author: Florian Reisinger, EMBL-EBI

Abstract:
Public data deposition and distribution has become a necessity in proteomics and is increasingly requested by journals. As a MS proteomics repository, PRIDE (http://www.ebi.ac.uk/pride) provides valuable tools to the community which support submission and visualization/validation of proteomics findings. PRIDE Inspector (http://code.google.com/p/pride-toolsuite/wiki/PRIDEInspector) is the latest addition to the PRIDE tool suite.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT21: Florian Reisinger - PRIDE Inspector
TOP

TT22Monday, July 18: 12:15 p.m. - 12:40 p.m.
SUPERFAMILY

Room: J565

Presenting Author: Julian Gough, University of Bristol

Abstract:
We will be: giving an overview of SUPERFAMILY and a practical demonstration of how to use it; inviting feedback and requests from existing users and questions from potential users; and showcasing many powerful analysis features, currently under-exploited, such as: domain-centric GO, tree of sequenced life, evolutionary analyses and comparative genomics.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT22: Julian Gough - SUPERFAMILY
TOP

TT23Monday, July 18: 12:15 p.m. - 12:40 p.m.
Enacting Taverna Workflows through Galaxy

Room: Lounge 1

Presenting Author: Kostas Karasavvas, NBIC - LUMC

Abstract:
We demonstrate making Galaxy and Taverna, two widely used bioinformatics pipeline platforms, more interoperable. We show how Taverna workflows can be wrapped as Galaxy tools automatically, via myExperiment, using our generator. We then show how the Taverna workflow becomes part of the Galaxy pipeline with an example.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT23: Kostas Karasavvas - Enacting Taverna Workflows through Galaxy
TOP

TT24Monday, July 18: 2:30 p.m. - 2:55 p.m.
EMBOSS: New developments and extended data access

Room: J241

Presenting Author: Peter Rice, European Bioinformatics Institute

Abstract:
EMBOSS is a mature package of software tools developed for the molecular biology community. We have made a major effort to add new features and applications for this release. EMBOSS 6.4.0 includes ontologies, taxonomy, automated access to public data resources, a new query language and new data types.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT24: Peter Rice - EMBOSS: New developments and extended data access
TOP

TT25Monday, July 18: 2:30 p.m. - 2:55 p.m.
PredictProtein sequence analysis in the cloud

Room: J565

Presenting Author: Guy Yachdav, Technical University Munich

Abstract:
In this technology track we report the
release of a new freely available protein feature prediction machine image for high-throughput cloud computing and includes the most popular prediction methods from our group, including PredictProtein. We will show how to use the image and some of the methods integrated.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT25: Guy Yachdav - PredictProtein sequence analysis in the cloud
TOP

TT26Monday, July 18: 2:30 p.m. - 2:55 p.m.
Become an Expert User of the RCSB Protein Data Bank Website and Web Services

Room: Lounge 1

Presenting Author: Peter Rose, University of California San Diego

Abstract:
We will demonstrate the latest features of the redesigned RCSB PDB website and provide tips how to effectively use the website and web services. Focus will be on query refinement, data export, sequence and structural neighbors, and programmatic access of data through web services and web widgets.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT26: Peter Rose - Become an Expert User of the RCSB Protein Data Bank Website and Web Services
TOP

TT27Monday, July 18: 3:00 p.m. - 3:25 p.m.
The Spanish National Bioinformatics Institute (INB)

Room: J241

Presenting Author: Allan Orozco, Spanish National Bioinformatics Institute

Abstract:
Our main goal with the Technology Track will cover aspects related to the bioinformatics tools, systems, desktop applications, data bases, web services and bioinformatics methods developed by the INB (Spanish National Bioinformatics Institute) and used by biologists and bioinformatics that work in areas that require complex data.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT27: Allan Orozco - The Spanish National Bioinformatics Institute (INB)
TOP

TT28Monday, July 18: 3:00 p.m. - 3:25 p.m.
HHblits: Lightning-fast iterative sequence searching by HMM-HMM comparison

Room: J565

Presenting Author: Michael Remmert, Gene Center Munich

Abstract:
HHblits is the first iterative search method based on pairwise comparison of profile Hidden Markov Madols (HMMs). Using a very fast profile-profile based prefilter it achieves better runtimes than the frequently-used methods PSI-BLAST and HMMER3 and greatly improves upon these methods in terms of sensitivity/selectivity and alignment quality.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT28: Michael Remmert - HHblits: Lightning-fast iterative sequence searching by HMM-HMM comparison
TOP

TT29Monday, July 18: 3:00 p.m. - 3:25 p.m.
ENCODE Genome-Wide Data on the UCSC Genome Browser

Room: Lounge 1

Presenting Author: Melissa Cline, UCSC

Abstract:
The ENCODE data on the UCSC Genome Browser is a rich resource for bioinformatics research, with experimental designs that promote integrative, cross-species analysis. This presentation covers the types of ENCODE data, how to obtain the data you want efficiently, and relevant Genome Browser functionality that simplifies ENCODE data analysis.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT29: Melissa Cline - ENCODE Genome-Wide Data on the UCSC Genome Browser
TOP

TT30Monday, July 18: 3:30 p.m. - 3:55 p.m.
Using the EMBL-EBI services through the JDispatcher framework

Room: J241

Presenting Author: Mickael Goujon, EMBL-EBI

Abstract:
The JDispatcher framework has been developed to encourage users to consume a broad range of analytical services provided by the EMBL-EBI. It focuses on improving accessibility and user experience for both the scientist and the software developer. It offers some unique features to assist the users during the results analysis.

Presentation PDF: Download PDF

TOP

TT31Monday, July 18: 3:30 p.m. - 3:55 p.m.
Chipster 2.0: User-friendly NGS data analysis software with interactive genome browser

Room: J565

Presenting Author: Eija Korpelainen, CSC - IT Center for Science

Abstract:
The open source software Chipster (http://chipster.csc.fi/) enables biologists to analyze and visualize NGS data and construct workflows. Tools cover quality control, preprocessing, alignment, normalization, differential expression, peak calling, motif discovery and pathway analysis. Reads and results can be viewed interactively in their genomic context with the in-built genome browser.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT31: Eija Korpelainen - Chipster 2.0: User-friendly NGS data analysis software with interactive genome browser
TOP

TT32Monday, July 18: 3:30 p.m. - 3:55 p.m.
GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens

Room: Lounge 1

Presenting Author: Esther Schmidt, German Cancer Research Center (DKFZ)

Abstract:
RNA interference (RNAi) allows systematic screening for loss-of-function phenotypes on a genome-wide scale, providing a rich source of functional annotation. The GenomeRNAi database (www.genomernai.org) holds RNAi-induced phenotype data from published screens for human and drosophila. Data on RNAi reagents are provided, as well as phenotype download options and GBrowse visualization.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT32: Esther Schmidt - GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens
TOP

TT33Monday, July 18: 4:00 p.m. - 4:25 p.m.
EBI Search: a new way to explore biology

Room: J241

Presenting Author: Mickael Goujon, EMBL-EBI

Abstract:
The European Bioinformatics Institute provides free and unrestricted access to vast resources of biomolecular data. In order to improve accessibility and usability large-scale user experience testing (UX analysis) was used to review and improve the institute’s search service and make it simpler for users to explore these data.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT33: Mickael Goujon - EBI Search: a new way to explore biology
TOP

TT34Monday, July 18: 4:00 p.m. - 4:25 p.m.
Introduction to National Center for Biomedical Ontology (NCBO) Technology

Room: J565

Presenting Author: Ray Fergerson, Stanford University

Abstract:
Ontologies are increasingly used to integrate heterogeneous information sources. NCBO provides a public repository for biomedical ontologies and tools to use them to annotate text and to search biomedical datasets. This demo is an overview of current and planned NCBO technology, covering the BioPortal application, Web services, and widgets.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT34: Ray Fergerson - Introduction to National Center for Biomedical Ontology (NCBO) Technology
TOP

TT35Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
TT35 re-scheduled to: Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
GenoCAD: A Web-Based Open Source Application to Design Synthetic DNA Molecules

Room: Lounge 1

Presenting Author: Jean Peccoud, Virginia Tech

Abstract:
GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT35: Jean Peccoud - GenoCAD: A Web-Based Open Source Application to Design Synthetic DNA Molecules
TOP

TT36Tuesday, July 19: 10:45 a.m. - 11:10 a.m.
Overview of The Universal Protein Resource (UniProt)

Room: J241

Presenting Author: Benoit Bely, The European Bioinformatics Institute

Abstract:
1. A description of UniProt, including new developments.
2. Accessing UniProt using simple query syntax, including helpful suggestions and hints.
3. Exploration of sequence similarity searches, alignments and ID mapping tools.
4. Accessing UniProt data programmatically.

This demonstration is intended to be interactive and user participation and feedback is welcomed.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT36: Benoit Bely - Overview of The Universal Protein Resource (UniProt)
TOP

TT37Tuesday, July 19: 10:45 a.m. - 11:10 a.m.
NGS Best Practices through Galaxy: Cloud-based variant discovery with visual analytics

Room: J565

Presenting Author: Daniel Blankenberg, Penn State University

Abstract:
Here, we present a collection of Galaxy workflows for the discovery of variants in re-sequencing studies. In addition to highlighting a new set of polymorphism discovery workflows, our demonstration will be performed in the Amazon Cloud and will utilize a newly implemented visual analytics framework.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT37: Daniel Blankenberg - NGS Best Practices through Galaxy: Cloud-based variant discovery with visual analytics Show Comments
TOP

TT38Tuesday, July 19: 10:45 a.m. - 11:10 a.m.
New Interactive Approach to the Visual Analysis of Protein Structure and Function

Room: Lounge 1

Presenting Author: Nadezhda Doncheva, Max Planck Institute for Informatics

Abstract:
Residue interaction networks derived from protein structures are very useful for understanding the structural and functional roles of residues. Therefore, we developed the software RINalyzer that offers novel visual analytics tools and supports the simultaneous viewing and exploration of a residue network in 2D and the corresponding 3D protein structure.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT38: Nadezhda Doncheva - New Interactive Approach to the Visual Analysis of Protein Structure and Function
TOP

TT39Tuesday, July 19: 11:15 a.m. - 11:40 a.m.
RaptorX: an integrated web server for protein sequence-structure alignment and protein structure prediction

Room: J241

Presenting Author: Jinbo Xu, Toyota Tech Inst at Chicago

Abstract:
RaptorX is a well-known software package for protein modeling and has been consistently ranked very top in the past several CASP events. We will demonstrate how to use RaptorX as an analytic and visualization tool to align protein sequences and structures and to predict 3D structures of a protein sequence.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT39: Jinbo Xu - RaptorX: an integrated web server for protein sequence-structure alignment and protein structure prediction
TOP

TT40Tuesday, July 19: 11:15 a.m. - 11:40 a.m.
YABI: A sophisticated Internet-based cross–omics analytic environment

Room: J565

Presenting Author: Matthew Bellgard, Murdoch University

Abstract:
We will describe the design and features of YABI, a sophisticated bioinformatics system that enables transparent access to supercomputing infrastructure, flexible analysis workflow creation/reuse and support of external workflow environments. Yabi is available at http://ccg.murdoch.edu.au/yabi/.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT40: Matthew Bellgard - YABI: A sophisticated Internet-based cross–omics analytic environment Show Comments
TOP

TT41Tuesday, July 19: 11:15 a.m. - 11:40 a.m.
Clustal Omega for Protein Multiple Sequence Alignment

Room: Lounge 1

Presenting Author: Desmond Higgins, Conway Institute

Abstract:
Clustal Omega is a high capacity high accuracy protein multiple alignment package. It is one of the most accurate aligners, based on standard benchmark datasets and it can routinely align 100,000 or more sequences on a single processor. This demonstration will give an overview of its features.

Presentation PDF: Download PDF

TOP

TT42Tuesday, July 19: 11:45 a.m. - 12:10 p.m.
Introducing InterProScan 5

Room: J241

Presenting Author: Craig McAnulla, EMBL-EBI

Abstract:
InterProScan is used extensively for automated sequence analysis of protein and genomic sequence data. Completely re-written, InterProScan is a flexible application designed to be easy to install and use. We will describe the benefits of the new system for biologists, bioinformaticians and bioinformatics service providers.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT42: Craig McAnulla - Introducing InterProScan 5
TOP

TT43Tuesday, July 19: 11:45 a.m. - 12:10 p.m.
EDAM ontology and BioXSD: The unifying semantics and syntax for bioinformatics tools

Room: J565

Presenting Author: Matus Kalas, University of Bergen

Abstract:
The EDAM (EMBRACE Data And Methods) ontology and the BioXSD XML Schema will contribute to more efficient integration of bioinformatics tools and resources into analytical workflows. EDAM is an ontology of bioinformatics operations, types of data, formats, and topics. BioXSD is a common format for sequences, alignments, and feature annotations.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT43: Matus Kalas - EDAM ontology and BioXSD: The unifying semantics and syntax for bioinformatics tools
TOP

TT44Tuesday, July 19: 11:45 a.m. - 12:40 p.m.
Killer App Award

Room: Lounge 1

Presenting Author: Seán O'Donoghue, EMBL
Syed  Asad Rahman, EBI 
Sirisha  Gollapudi, University of Leicester 
Joanna M. Kasprzak, Adam Mickiewicz University 


Abstract:

The ISMB 'Killer App Award' (http://killerapp.iscb.org/2011.html) will be awarded for the individual or team with a tool or system judged to be of most practical benefit to biochemists and/or molecular biologists. To be eligible, a system or tool must be fully functional, and must be presented at the ISMB conference as a poster. Three finalists have been chosen and invited to give a short talk about their application during the Killer App session. The winner will be announced in the closing ceremony, and will receive a certificate from the ISMB/ISCB plus an Apple iPad. The three finalists are:

ECBlast: a novel tool for searching similar enzymes based on chemical knowledge" by Syed Asad Rahman, Franz Fenninger, Gillleain Torrence, Lorenzo Baldacci, Nimish Gopal, Gemma L Holliday, and Janet M Thornton.

GWAS Central: a database for the integration and comparative interrogation of genome-wide association study datasets" by Robert C. Free, Robert K. Hastings, Tim Beck, Sirisha Gollapudi, Gudmundur A. Thorisson, and Anthony J. Brookes.

PyRy3D: a tool for modeling of large macromolecular complexes" by Joanna M. Kasprzak, Wojciech Potrzebowski, Mateusz Dobrychłop and Janusz M. Bujnicki.



Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT44: Seán O'Donoghue - Killer App Award
TOP

TT45Tuesday, July 19: 12:15 p.m. - 12:40 p.m.
CAMERA: Metagenomic Resources and Tools

Room: J241

Presenting Author: Shulei Sun, University of California, San Diego

Abstract:
CAMERA provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology. Its computational resources include rich and distinctive bioinformatics tools and a flexible collaborative workflow environment that makes it possible for researchers to analyze large and complex sequencing data generated by NGS technology.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT45: Shulei Sun - CAMERA: Metagenomic Resources and Tools
TOP

TT46Tuesday, July 19: 12:15 p.m. - 12:40 p.m.
Knowledge-driven QTL analysis and network-based candidate gene discovery with Ondex

Room: J565

Presenting Author: Keywan Hassani-Pak, Rothamsted Research

Abstract:
Integrative and automated tools are required for analyzing QTL and selecting candidate genes. We introduce a knowledge-driven approach based on the Ondex (www.ondex.org) framework for data integration and network visualization. We present a web-based tool which links classical genetics views with modern network views to explain functional candidacy of genes.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT46: Keywan Hassani-Pak - Knowledge-driven QTL analysis and network-based candidate gene discovery with Ondex
TOP

TT47Tuesday, July 19: 2:30 p.m. - 2:55 p.m.
SORF, a web application for heterogeneous data management and visualisation

Room: Hall F2

Presenting Author: Fady Mohareb, The Bioinformatics Group - Cranfield University

Abstract:
SORF is a web application for heterogeneous data management and visualisation, compatible with a wide variety of experimental data formats. This demonstration will guide the attendants through the procedures of defining a new experiment, uploading experimental datasets, as well as an overview of the visualisation tools the system currently provides.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT47: Fady Mohareb - SORF, a web application for heterogeneous data management and visualisation
TOP

TT48Tuesday, July 19: 2:30 p.m. - 2:55 p.m.
Oqtans: A Galaxy-integrated workflow for Quantitative Transcriptome Analysis from NGS data

Room: J241

Presenting Author: Géraldine Jean and Sebastian J. Schultheiss, Friedrich Miescher Laboratory of Max Planck Society

Abstract:
We demonstrate how a complete quantitative RNA-seq analysis can be performed easily and effectively in <20 minutes with our Machine-Learning-powered workflow. It's integrated in the easy-to-use Galaxy framework and is accessible locally or in the cloud (http://galaxy.fml.mpg.de). We developed a modular toolsuite that performs better or as well as the state-of-the-art for short-read alignments, transcript identification/quantification and differential expression analysis.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT48: Géraldine Jean and Sebastian J. Schultheiss - Oqtans: A Galaxy-integrated workflow for Quantitative Transcriptome Analysis from NGS data
TOP

TT49Tuesday, July 19: 2:30 p.m. - 2:55 p.m.
NCBO Web Services and Development of Semantic Applications

Room: J565

Presenting Author: Patricia Whetzel, Stanford University / National Center for Biomedical Ontology

Abstract:
Ontologies provide domain knowledge to drive data integration and information retrieval. The National Center for Biomedical Ontology provides a suite of ontology-based Web services for the development of semantically aware software applications. This presentation will provide an overview of these Web services and their use within software applications.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT49: Patricia Whetzel - NCBO Web Services and Development of Semantic Applications
TOP

TT50 Withdrawn Tuesday, July 19: 2:30 p.m. - 2:55 p.m.
OncoPortal, a data management and analysis framework for cancer research

Room: Lounge 1

Presenting Author: Arek Kasprzyk, Ontario Institute for Cancer Research

Abstract:
To address the needs of the increasingly-collaborative field of cancer research, we are creating OncoPortal. Based on the BioMart software, OncoPortal is a set of tools that allows cancer research projects to quickly and easily allow users to access their data, analyse them, and integrate them with external annotation sources.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT50: Arek Kasprzyk - OncoPortal, a data management and analysis framework for cancer research
TOP

TT51Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
Recent Developments in the Pathway Tools Software and BioCyc Databases

Room: Hall F2

Presenting Author: Peter Karp, SRI International

Abstract:
Recent developments include growth of the BioCyc database collection
to 1,100 genomes, the ability of Pathway Tools to automatically
generate flux-balance models from its Pathway/Genome databases in a
manner that drastically reduces model-development time, and
upgrading of the web metabolic map diagram.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT51: Peter Karp - Recent Developments in the Pathway Tools Software and BioCyc Databases
TOP

TT52Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
eSysbio - an online system for interdisciplinary life science research

Room: J241

Presenting Author: Pål Puntervoll, Uni Research

Abstract:
eSysbio provides a virtual workspace for project-oriented data sharing and analyses. Researchers get instant access to remote Web service tools and R-script/packages through automatically generated web-based graphical user interfaces. Workflows can be manually constructed from the services and R-scripts, and the history of the composite analysis is recorded.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT52: Pål Puntervoll - eSysbio - an online system for interdisciplinary life science research
TOP

TT53Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
Interfacing with Industry: The EMBL-EBI Industry Programme and SME Forum

Room: J565

Presenting Author: Dominic Clark, EMBL-EBI

Abstract:
This presentation will provide an overview and demonstration of some of the means by which the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) interacts with industry stakeholders, who already comprise a significant and growing proportion of EMBL-EBI’s user base.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT53: Dominic Clark - Interfacing with Industry: The EMBL-EBI Industry Programme and SME Forum
TOP

TT54Tuesday, July 19: 3:00 p.m. - 3:25 p.m.
BioMart: A data federation framework for large collaborative projects

Room: Lounge 1

Presenting Author: Junjun Zhang, Ontario Institute for Cancer Research

Abstract:
To manage the data generated by large, collaborative biological projects, we have created BioMart data federation system. BioMart seamlessly presents geographically-disparate data sources in a single access point, thereby enabling the creation of distributed, databases ideally suited for presenting the complex data generated by multi-institution projects.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT54: Junjun Zhang - BioMart: A data federation framework for large collaborative projects
TOP

TT55Tuesday, July 19: 3:30 p.m. - 3:55 p.m.
Database on Potential “Antibiotics” From Flowering Plants

Room: Hall F2

Presenting Author: Rajarajan Swaminathan, Presidency College (Aut)

Abstract:
The database provides details about phytochemical compounds whose potential antimicrobial activities have been experimentally verified by in vitro/in vivo/clinical trials with feisty details if any and provides instant access via the www.bifcpresidency.tn.gov.in.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT55: Rajarajan Swaminathan - Database on Potential “Antibiotics” From Flowering Plants
TOP

TT56Tuesday, July 19: 3:30 p.m. - 3:55 p.m.
Jalview 2.7

Room: J241

Presenting Author: Geoffrey Barton, University of Dundee

Abstract:
Jalview 2.7 is the latest version of this freely available, and widely used Java based multiple sequence alignment, annotation, visualization and editing tool. In this technology track presentation, we will give a tour of its core strengths, and how they will be developed in the future.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT56: Geoffrey Barton - Jalview 2.7
TOP

TT57Tuesday, July 19: 3:30 p.m. - 3:55 p.m.
The International Society for Biocuration and the efforts of its members

Room: J565

Presenting Author: Claire O'Donovan, EMBL - EBI

Abstract:
In this technical track, I would like to introduce the participants to the International Society for Biocuration and report on the diverse and valuable work of its members around the world as well as highlighting the potential careers in this field.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT57: Claire O'Donovan - The International Society for Biocuration and the efforts of its members
TOP

TT58Tuesday, July 19: 4:00 p.m. - 4:25 p.m.
KeyPathwayMiner - Detecting case-specific biological pathways by using expression data

Room: Hall F2

Presenting Author: Nicolas Alcaraz, Max Planck Institute for Informatics

Abstract:
We introduce KeyPathwayMiner, a tool that allows for extracting and visualizing active
key-pathways in a given series of gene expression studies. We detect sub-networks where most genes are differentially expressed in a particular disease. KeyPathwayMiner
identifies maximal connected sub-graphs where all but k nodes are differentially
expressed in all but l cases.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT58: Nicolas Alcaraz - KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
TOP

TT59Tuesday, July 19: 4:00 p.m. - 4:25 p.m.
The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool

Room: J241

Presenting Author: Jeremy Goecks, Emory University

Abstract:
The Galaxy Track Browser (GTB) is a Web-based genome browser integrated into the Galaxy platform. GTB leverages the Galaxy platform to combine data visualization and data analysis, enabling users to (a) specify parameters and run tools to produce and visualize new data and (b) dynamically filter visualized data.

Presentation PDF: Download PDF

ISMB/ECCB 2011 Blog
TT59: Jeremy Goecks - The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool
TOP