Technology Track Schedule


TT01 - Jalview and JABAWS in 2013: extensible open source sequence analysis
Date: Sunday, July 21: 10:30 a.m. - 10:55 a.m.Room: Hall 9

Presenting author: James Procter, University of Dundee, United Kingdom

Session Chair: Geoff Barton

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We will demonstrate the latest developments and discuss the future plans for Jalview, a platform for interactive Protein and RNA alignment, analysis and annotation, and JABAWS, an easy-to-install server that provides sequence alignment and analysis services. Both are open source, and their core development is supported by the UK's BBSRC.

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TT02 - GRANATUM: a social collaborative working space semantically interlinking biomedical researchers, knowledge and data for the design and execution of in-silico models and experiments in cancer chemoprevention
Date: Sunday, July 21: 10:30 a.m. - 10:55 a.m.Room: Hall 10

Presenting author: Vasilis Promponas, University of Cyprus, Cyprus

Session Chair: Dominic Clark

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We will describe the design and features of GRANATUM, a user-friendly system that enables biomedical researchers to socially collaborate, exchange knowledge and data, as well as develop/save/execute/share virtual screening scientific workflows within an integrated environment. GRANATUM is available at http://www.granatum.org/.

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TT03 - NDEx - An Information Commons for Biological Networks
Date: Sunday, July 21: 11:00 a.m. - 11:25 a.m.Room: Hall 9

Presenting author: Dexter Pratt, Cytoscape Consortium, United States

Session Chair: Geoff Barton

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A prototype of the NDEx (Network Data Exchange) website from the Cytoscape Consortium will be demonstrated. NDEx is an open-source, web-based software system to enable individuals, groups, and software applications to share, store, manipulate, and publish biological network knowledge.

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TT04 - The SeqAn C++ library as SDK for efficient genome analysis
Date: Sunday, July 21: 11:00 a.m. - 11:25 a.m.Room: Hall 10

Presenting author: Knut Reinert, FU Berlin, Germany

Session Chair: Dominic Clark

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SeqAn is an open-source C++ library (BSD license) that contains many efficient data structures and algorithms for sequence analysis. It supports parallelization (multi-core and accelerators) and easy integration into workflow engines such as KNIME. SeqAn is used as SDK at several institutions among them the NY genome center.

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TT05 - Opening Up Pharmacological Space: The Open PHACTS API
Date: Sunday, July 21: 11:30 a.m. - 11:55 p.m.Room: Hall 9

Presenting author: Chris Evelo, Maastricht University, Netherlands

Session Chair: Geoff Barton

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This demonstration will show how the Open PHACTS API can be used to interrogate a large collection of integrated biomedical databases. The system is based on semantic technology and can benefit a wide range of use cases, from data mining/scientific discovery through to supporting mobile and desktop applications.

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TT06 - Integration of heterogeneous -Seq and -Omics datasets :Ongoing Research and Development Projects at CLC bio
Date: Sunday, July 21: 11:30 a.m. - 12:25 p.m.Room: Hall 10

Presenting author: Michael Lappe, CLC bio, Denmark

Session Chair: Dominic Clark

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A discussion of which features might have the biggest impact on coping with the complexity of current biological data. The focus will be on providing users with a unified view on integrated data from heterogeneous sources across different levels of resolution.

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TT07 - XworX – A cloud enabled analysis platform for experimentalists in genomic research
Date: Sunday, July 21: 12:00 p.m. - 12:25 p.m.Room: Hall 9

Presenting author: Albert Kriegner, AIT Austrian Institute of Technology, Austria

Session Chair: Geoff Barton

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We present XworX, a workflow based cloud enabled software framework for an unlimited range of bioinformatics tasks - from simple assay design, elaborate analyses to print-ready reports. XworX provides automated data logging and enables easy workflow generation for routine tasks. It has a growing “Appstore” with currently ~500 Apps. XworX is freely available on http://www.xworx.org

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TT08 - DRIMust: a web server for Discovering Rank Imbalanced Motifs Using Suffix Trees
Date: Sunday, July 21: 2:10 p.m. - 2:35 p.m.Room: Hall 9

Presenting author: Limor Leibovich, Technion, Israel

Session Chair: Rodrigo Lopez

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Sequence elements of DNA, RNA and proteins are involved in mediating molecular recognition events. We present a new web application, freely accessible through the website: http://drimust.technion.ac.il for de-novo motif discovery. Comparing it to other state-of-the-art tools demonstrated significant advantage in accuracy of results as well as in short running times.

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TT09 - Understanding Cancer Genomes Using Galaxy
Date: Sunday, July 21: 2:10 p.m. - 2:35 p.m.Room: Hall 10

Presenting author: Jeremy Goecks, Emory University, United States

Session Chair: Dominic Clark

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We will demonstrate how Galaxy can be used to analyze high-throughput/next-generation sequence data from primary cancer tumors. We will show pipelines/workflows for performing small variant discovery, differential gene expression, and eQTL analysis. Finally, we will show visual analysis tools for refining variant discovery and visualizing gene fusions.

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TT10 - Verification of Systems Biology Research in the Age of Collaborative-Competition
Date: Sunday, July 21: 2:40 p.m. - 3:35 p.m.Room: Hall 9

Presenting author: Raquel Norel, sbv IMPROVER, Switzerland

Session Chair: Rodrigo Lopez

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sbv IMPROVER stands for systems biology verification and Industrial Methodology for Process Verification in Reaserch. It is a robust methodology that verifies systems biology approaches using double-blind performance assessment and applies the wisdom of crowds to solve scientific challenges. The project includes scientists from Philip Morris International and IBM Research.

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TT11 - MobiDB: a comprehensive database of intrinsic protein disorder annotations
Date: Sunday, July 21: 2:40 p.m. - 3:05 p.m.Room: Hall 10

Presenting author: Tomás Di Domenico, University of Padua, Italy

Session Chair: Dominic Clark

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The demonstration will consist on a presentation of MobiDB, explaining the current situation of intrinsic protein disorder annotations and why it motivated the development of this new resource. We will then proceed to demonstrate the software live, while encouraging feedback by attendees in regard to usability, features, etc.

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TT12 - Expression Atlas
Date: Sunday, July 21: 3:10 p.m. - 3:35 p.m.Room: Hall 10

Presenting author: Jan Taubert, EMBL-EBI, United Kingdom

Session Chair: Dominic Clark

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The Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress, servicing queries for condition-specific gene expression patterns and exploratory searches for biologically interesting genes. We demonstrate current developments supporting the analysis of baseline and differential omics experiments.

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TT13 - Enabling biologists to analyze NGS data: update on the open source Chipster software
Date: Sunday, July 21: 3:40 p.m. - 4:05 p.m.Room: Hall 9

Presenting author: Eija Korpelainen, CSC - IT Center for Science, Finland

Session Chair: Rodrigo Lopez

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Chipster (http://chipster.csc.fi) provides a unified, biologist-friendly interface to over 120 analysis tools including FastQC, PRINSEQ, TagCleaner, SAMtools, BEDtools, Bowtie, BWA, TopHat, HTSeq, Cufflinks, edgeR, DESeq, DEXSeq, MACS and F-Seq. Its built-in genome browser allows seamless viewing of reads and results. Chipster is open source and available as a virtual machine.

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TT14 - BioGPS and MyGene.info: organizing online and gene-centric information
Date: Sunday, July 21: 3:40 p.m. - 4:05 p.m.Room: Hall 10

Presenting author: Chunlei Wu, The Scripps Research Institute, United States

Session Chair: Dominic Clark

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BioGPS (http://biogps.org) is a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. It allows users to access known gene-centric resources, as well as to discover new resources. For developers, we provide MyGene.info (http://mygene.info) web services for programmatic access to gene-centric data.

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TT15 - KeyPathwayMiner - Extracting disease-specific pathways by combining OMICS data and biological networks
Date: Monday, July 22: 10:30 a.m. - 10:55 a.m.Room: Hall 9

Presenting author: Jan Baumbach, University of Southern Denmark, Denmark

Session Chair: Rodrigo Lopez

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We present KeyPathwayMiner 4.0, a set of integrated methods for extracting and visualizing expressed key-networks where most genes are dysregulated due to specific diseases, treatments or perturbations. We will investigate Huntington’s disease and colorectal cancer by connecting the human interactome with gene expression data and genome-wide methylation profiles, respectively.

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TT16 - Taverna Online - with metagenomic examples
Date: Monday, July 22: 10:30 a.m. - 10:55 a.m.Room: Hall 10

Presenting author: Alan Williams, University of Manchester, United Kingdom

Session Chair: Christophe Blanchet

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The demonstration will showcase Taverna Online - a web-based environment for the creation, editing and execution of workflows. Metagenomics will be used as the testcase.

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TT17 - New Tools and Visualization Features at the RCSB Protein Data Bank
Date: Monday, July 22: 11:00 a.m. - 11:25 a.m.Room: Hall 9

Presenting author: Peter Rose, University of California, San Diego, United States

Session Chair: Rodrigo Lopez

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We will demonstrate the latest features of the RCSB PDB website including the representation of peptide-like molecules and quaternary structure, protein feature view, new views of search results, and our RCSB PDB Mobile app for iPhone/iPad/Android.

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TT18 - BioCANET: Data integration technological platform for bioinformatics studies in biodiversity and biomedicine in Central America
Date: Monday, July 22: 11:00 a.m. - 11:25 a.m.Room: Hall 10

Presenting author: Allan Orozco, School of Medicine, University of Costa Rica, Costa Rica

Session Chair: Christophe Blanchet

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BiocaNET is a bioinformatics platform of the UCR (University of Costa Rica) composed of seven nodes and a central node, whose main mission is to provide support and development services in bioinformatics in the different areas of biodiversity, omics and molecular medicine in Central America.

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TT19 - Latest Advances in Bioinformatics Computing
Date: Monday, July 22: 11:30 a.m. - 12:25 p.m.Room: Hall 9

Presenting author: George Vacek, Convey Computer, United States

Session Chair: Rodrigo Lopez

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Convey’s Hybrid-Core server delivers extremely high-performance for genomic data analysis workflows including reference mapping, de novo assembly, functional annotation, variant analysis and RNA expression profiling. Comparative performance for a range of bioinformatics application workflows will be presented, including the Broad’s variant analysis workflow and hybrid assembly using PacBio reads.

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TT20 - Cellular Phenotype Database — first release and submission pipeline
Date: Monday, July 22: 11:30 a.m. - 11:55 p.m.Room: Hall 10

Presenting author: Katerina Kirsanova, EMBL-EBI, United Kingdom

Session Chair: Christophe Blanchet

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The Cellular Phenotype database is built using MongoDB, that allows extremely fast quering and data flexibility. Leveraging on its power, we are building an infrastructure for data integration that will enable the development of new algorithm for data analysis as well as improving our understanding of how cellular systems function.

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TT21 - Weaving a Web of Federated Queries: Using SPARQL to Query BioPortal and the Gene Expression Atlas
Date: Monday, July 22: 12:00 p.m. - 12:25 p.m.Room: Hall 10

Presenting author: James Malone, NCBO, United States

Session Chair: Christophe Blanchet

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Ontologies provide domain knowledge to drive data integration and information retrieval. The NCBO BioPortal SPARQL endpoint, containing 300 ontologies and 9.8M term mappings, enables query expansion via federated queries. This presentation will demo queries of the BioPortal SPARQL endpoint, the Gene Expression Atlas and federated queries using both repositories.

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TT22 - GenomeRNAi: A Phenotype Database for Large-scale RNAi Screens
Date: Monday, July 22: 2:10 p.m. - 2:35 p.m.Room: Hall 9

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

Session Chair: Rodrigo Lopez

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

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TT23 - GenomeSpace: An environment for frictionless bioinformatics
Date: Monday, July 22: 2:10 p.m. - 2:35 p.m.Room: Hall 10

Presenting author: Michael Reich, Broad Institute, United States

Session Chair: Christophe Blanchet

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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 desktop software. GenomeSpace supports cloud-based storage, automates file format conversion, and continually expands the community of participating tools.

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TT24 - Europe PubMed Central: enabling use of the life science literature
Date: Monday, July 22: 2:40 p.m. - 3:05 p.m.Room: Hall 9

Presenting author: Jo McEntyre, EMBL-EBI, United Kingdom

Session Chair: Johannes Soedling

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Europe PubMed Central is a database of life science research articles and abstracts, including PubMed (http://europepmc.org). Recently, we have developed several new features, including RESTful web services, data citation alerts, and mechanisms for text and data miners to link results to articles in Europe PubMed Central.

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TT25 - Genomic Applications: De Novo Assemblers Parallelization and Code Optimization
Date: Monday, July 22: 2:40 p.m. - 3:35 p.m.Room: Hall 10

Presenting author: Carlos Sosa, Cray Inc, United States

Session Chair: Christophe Blanchet

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Next-Generation Sequencing (NGS) technology generates reads of short segments of genomic data increasingly fast and inexpensively when compared to the rate that this data can be analyzed, shifting the genomic analysis bottleneck from chemistry done in the laboratory to a computational string manipulation problem, well suited for High-Performance Computing (HPC).

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TT26 - Overview of The Universal Protein Resource (UniProt)
Date: Monday, July 22: 3:10 p.m. - 3:35 p.m.Room: Hall 9

Presenting author: Hermann Zellner, European Bioinformatics Institute, United Kingdom

Session Chair: Johannes Soedling

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UniProt is the most comprehensive catalogue of protein sequences and functional annotation.

The Demonstration will cover:
1. A description of UniProt
2. New developments, functionalities and design
3. Accessing UniProt using simple query syntax. The user will be presented with helpful suggestions and hints.
4. Exploration of sequence similarity

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TT27 - GeneWeaver: Building Context-Driven Similarity on Empirically-defined Functional Genomics Relationships
Date: Monday, July 22: 3:40 p.m. - 4:05 p.m.Room: Hall 9

Presenting author: Elissa Chesler, The Jackson Laboratory, United States

Session Chair: Johannes Soedling

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We will demonstrate advances in GeneWeaver.org, a web-accessible database and set of biclique enumeration analysis tools designed for knowledge discovery in heterogeneous life science data. GeneWeaver is designed around a highly curated data repository and an ability to dynamically integrate user data against this backdrop of functionally annotated gene sets.

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TT28 - GWIS: free online exhaustive search for bivariate interactions in GWAS
Date: Monday, July 22: 3:40 p.m. - 4:05 p.m.Room: Hall 10

Presenting author: David Rawlinson, National ICT Australia, Australia

Session Chair: Christophe Blanchet

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In 2012 we presented GWIS, our fast method for exhaustive bivariate epistasis detection in GWAS data. Following recent publication of our methods, we now present a GWIS webserver, free for research use, and also discuss recent extensions to our methods, including the prospect of exhaustive 3rd-order analysis.

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TT29 - Using Genome3D's structural insights to learn about your protein
Date: Tuesday, July 23: 10:30 a.m. - 10:55 a.m.Room: Hall 9

Presenting author: Christine Orengo, UCL, United Kingdom

Session Chair: Dominic Clark

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Genome3D is a collaborative project that unites key UK-based protein structure resources to provide unique insights into sequence–structure–function relationships. It presents annotations
from leading structure prediction algorithms (DomSerf, FUGUE, Gene3D, pDomTHREADER, Phyre and SUPERFAMILY) based on the leading protein domain classifications (CATH and
SCOP).

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TT30 - MOLE 2.0: Improved Approach for Analysis of Biomacromolecular Channels and Pores
Date: Tuesday, July 23: 11:00 a.m. - 11:25 a.m.Room: Hall 9

Presenting author: Lukáš Pravda, Central European Institute of Technology, Czech Republic

Session Chair: Dominic Clark

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Shape of biomacromolecular channels and pores influence protein’s behavior and substrate specificity.
Here we demonstrate Mole 2.0 a highly customizable tool designed for both swift and accurate substrate/product access/egress channel detection and characterization. Novel GUI enables user ‘one click’ approach data analysis even on large biomacromolecules such as ribosomal subunits.

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TT31 - DNASkittle Genome Browser
Date: Tuesday, July 23: 11:30 a.m. - 12:25 p.m.Room: Hall 9

Presenting author: Josiah Seaman, DNASkittle, United States

Session Chair: Dominic Clark

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Presenting a new kind of genome browser that uses data visualization from the primary sequence to enable open-ended pattern recognition. DNASkittle can be used for general characterization of a genetic sequence and discovering new genome elements that are not recognized by existing algorithms.

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TT32 - NVBIO: efficient sequence analysis on GPUs
Date: Tuesday, July 23: 2:10 p.m. - 3:05 p.m.Room: Hall 9

Presenting author: Jacopo Pantaleoni, NVIDIA, Germany

Session Chair: Rodrigo Lopez

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Because of the inherently parallel and high-throughput nature, NVIDIA GPUs are a natural fit for the data-intensive computing required in bioinformatics applications. NVBIO is a flexible sequence analysis library developed by NVIDIA from the ground-up to exploit GPU’s superior computing capabilities and offer a breakthrough in performance and energy efficiency.

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TT33 - BiBiCloud: a Cloud-Based Server for Big Data Bioinformatics
Date: Tuesday, July 23: 3:10 p.m. - 3:35 p.m.Room: Hall 9

Presenting author: Alexander Sczyrba, Bielefeld University, Germany

Session Chair: Rodrigo Lopez

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Utilizing cloud compute grid environments is a non-trivial task even for computer experts. Our BiBiCloud framework supports developers in setting up both a web application framework and server environment, as well as integrating cloud-based grid compute resources. We will present the BiBiCloud framework with a typical analysis pipeline.

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TT34 - Technology for sharing methods and data of computational experiments in a digital era
Date: Tuesday, July 23: 3:40 p.m. - 4:05 p.m.Room: ICC Lounge 81

Presenting author: Marco Roos, Leiden University Medical Center, Netherlands

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For scientists who use digital technologies to perform biological research, we present advances in tools and guidelines that enable methods and results to be structured and exposed in machine-readable and interoperable formats. We present Research Objects (http://ResearchObject.org) and Nanopublications (http://Nanopub.org) as tools for digital preservation, acknowledgement, sharing, and reproducibility.

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TT35 - XXmotif: A powerful algorithm and web server for de-novo motif discovery in nucleotide sequences
Date: Tuesday, July 23: 3:40 p.m. - 4:05 p.m.Room: Hall 10

Presenting author: Johannes Soeding, Gene Center, LMU Munich, Germany

Session Chair: Johannes Soedling

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XXmotif is the first de-novo motif discovery tool that directly optimizes the statistical significance of enrichment for PWMs. On ChIP-chip/seq, miRNA knock-down, and co-expression datasets, XXmotif improves upon state-of-the-art tools in numbers and quality of correctly identified motifs. We will demonstrate both web server and command-line tool usage (http://xxmotif.genzentrum.lmu.de).

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TT36 - MutAid - A NGS based integrated and user-friendly mutation screening and decision support system for human molecular diagnostics
Date: Tuesday, July 23: 3:40 p.m. - 4:05 p.m.Room: Hall 9

Presenting author: Ram Vinay PANDEY, Austrian Institute of Technology, Austria

Session Chair: Rodrigo Lopez

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We have developed a NGS based mutation screening and decision support system called MutAid, aiming to make high throughput technology a routine mutation screening tool for non-expert clinician. Currently MutAid supports mutation screening via multiplexed, individual and target re-sequencing or whole exome sequence data analysis generated from Illumina, 454, iontorrent along with Sanger sequencing validation.

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