Technology Track Schedule

Attention Conference Presenters - please review the Speaker Information Page available here.


TT01 Monitoring, analyzing, and exploring Ion Torrent™ NGS data with Torrent Suite™ Software and Torrent Variant Caller
Date: Sunday, July 13: 10:30 a.m. - 11:25 a.m.Room: 309

Presenting author: Darryl Leon, Thermo Fisher Scientific, United States

Session Chair: Dominic Clark

Presentation Overview: Show/Hide
An overview and demonstration of Torrent Suite™ Software (TSS 4.2) will be provided.
TSS 4.2 is a web-based tool for monitoring Ion Torrent sequencing runs and analyzing sequencing results. In addition, a review of the Torrent Variant Caller will be presented.

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TT02 Computational biology careers at Pfizer R&D
Date: Sunday, July 13: 11:30 a.m. - 12:25 p.m.Room: 309

Presenting author: Enoch Huang, Pfizer R&D, United States

Session Chair: Dominic Clark

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What does computational biology look like in a drug discovery setting? How can the application of computational methods lead to improved target selection, patient stratification, and ultimately increased success rates in the clinic? We present a brief overview of computational biology at Pfizer and two research vignettes.

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TT03 Interactive Visual Analysis with Galaxy Charts
Date: Sunday, July 13: 3:05 p.m. - 3:30 p.m.Room: 309

Presenting author: Aysam Guerler, Johns Hopkins University, United States

Session Chair: Andrew Cowley

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Galaxy Charts is a novel visual analysis environment for the web-based genomic analysis platform Galaxy. We will demonstrate how to quickly visualize tabular results with customizable bar diagrams, pie charts, scatterplots and others from within Galaxy.

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TT04 KeyPathwayMiner - Extracting relevant pathways by combining OMICS data and biological networks
Date: Sunday, July 13: 3:35 p.m. - 4:00 p.m.Room: 309

Presenting author: Alexander Junge, University of Southern Denmark, Denmark

Session Chair: Andrew Cowley

Presentation Overview: Show/Hide
In our presentation, we introduce the latest version of KeyPathwayMiner.
A software framework for extracting novel-pathways
given a biological network and a series of case-control studies from
one or multiple OMICS datasets. We will go through the different steps: data import, parameter settings, visualization and analyzing the results.

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TT05 Synapse: Software infrastructure for collaborative reproducible research
Date: Sunday, July 13: 4:05 p.m. - 4:30 p.m.Room: 309

Presenting author: Abhishek Pratap, SAGE Bionetworks, United States

Session Chair: Andrew Cowley

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Synapse (www.synapse.org) is a free and open source informatics platform for data-driven collaborative research. Built from the ground up for a rich data sharing experience, Synapse provides tools for versioning, annotating data combined with provenance tracking and fine grained access control. We will demo these features with real examples.

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TT06 BioJS: an open source standard for biological visualization
Date: Sunday, July 13: 4:35 p.m. - 5:00 p.m.Room: 306

Presenting author: Guy Yachdav, ROSTLAB, Germany

Session Chair: TBD

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The talk will present the Bio Javascript project - a repository for biological information representation tools, its current status and future roadmap. The talk will also describe how BioJS components are used in the PredictProtein meta server.

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TT07 PAGIT: Post Assembly Genome Improvement Toolkit
Date: Sunday, July 13: 4:35 p.m. - 5:00 p.m.Room: 309

Presenting author: Thomas Otto, Wellcome Trust Sanger Institute, United Kingdom

Session Chair: Andrew Cowley

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For the vast majority of NGS genome projects, the resources are simply not available to manually generate high-quality annotated sequences, and consequently many genomes remain as poor-quality drafts. To overcome that problem we have produced several tools (REAPR, ICORN and PAGIT) to automatically improve Illumina and PacBio assemblies.

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TT08 Ceci n’est pas une pipe. An open standard for reproducible genomics pipelines
Date: Monday, July 14: 10:30 a.m. - 11:25 a.m.Room: 306

Presenting author: Nebojsa Tijanic, Seven Bridges Genomics, United States

Session Chair: Rodrigo Lopez

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We have developed an open protocol and a set of open source tools that enables researchers to share analysis pipelines in a fully reproducible manner. Bioinformatics tools are packaged in docker container images along with a formal description of their inputs and outputs; these tools can then be chained together to create pipeline description files

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TT09 Using D2P2 the Database of Disordered Protein Predictions
Date: Monday, July 14: 10:30 a.m. - 10:55 a.m.Room: 309

Presenting author: Matt Oates, University of Bristol, United Kingdom

Session Chair: Dr. Jim Procter

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D2P2 is a collection of disordered protein predictions for a large library of complete proteomes. In this talk common scientific use cases of the website, along with how to integrate our data with your own software will be demonstrated. Some knowledge of programming could be helpful but is not required.

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TT10 Pathview: an R/Bioconductor package for pathway-based data integration and visualization
Date: Monday, July 14: 11:00 a.m. - 11:25 a.m.Room: 309

Presenting author: Weijun Luo, UNC Charlotte, United States

Session Chair: Dr. Jim Procter

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We will describe the overall design of Pathview, including functional modules, user interface and data flow. Three main features will be covered with real examples: 1) two graphic styles: KEGG view and Graphviz view; 2) strong support for data integration; 3) easy to automate and integrate into functional analysis pipelines.

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TT11 Application of HGMD database within a typical variant analysis pipeline, and the unique challenges of annotating pharmacogenomic variants
Date: Monday, July 14: 11:30 a.m. - 11:55 p.m.Room: 306

Presenting author: Jennifer Hogan, BIOBASE, United States

Session Chair: Rodrigo Lopez

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Advances in next generation sequencing have opened the door to using it as a powerful tool in the diagnostic process for patients suffering from rare inherited or de novo disease. In this presentation we will discuss the application of HGMD database within a typical variant analysis pipeline, and the unique challenges of annotating pharmacogenomic variants.

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TT12 The DOE Systems Biology Knowledgebase (KBase): Progress towards a system for collaborative and reproducible inference and modeling of biological function
Date: Monday, July 14: 11:30 a.m. - 11:55 p.m.Room: 309

Presenting author: Robert Cottingham, DOE Systems Biology Knowledgebase (KBase), United States

Session Chair: Dr. Jim Procter

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KBase is an extensible bioinformatics platform that enables researchers to collaboratively generate, share and test hypotheses with large-scale models of metabolic and regulatory behavior of microbes, plants and communities. This presentation summarizes the analysis capabilities and data in KBase, and discusses how developers can use the API and contribute software.

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TT13 When silent mutations scream: revisiting annotation of regulatory elements
Date: Monday, July 14: 12:00 p.m. - 12:25 p.m.Room: 306

Presenting author: Alexander Kaplun, BIOBASE, United States

Session Chair: Rodrigo Lopez

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We will discuss the important role that regulatory elements can play in pathological processes and in modulating the severity of inherited and denovo genetic disorders.

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TT14 Sequencing and Genomic Analysis Onsite and in the Cloud,
Date: Monday, July 14: 12:00 p.m. - 12:25 p.m.Room: 309

Presenting author: Raymond Tecotzky, Illumina, United States

Session Chair: Dr. Desmond Higgins/Dr. Jim Procter

Presentation Overview: Show/Hide
Genomics research promises to revolutionize public and human health. Yet, extracting meaningful information from an enormous collection of sequence data is at risk without the development of new and scalable bioinformatics approaches. Illumina’s genomics cloud platform delivers a suite of industry-leading analysis tools, ensures secure data storage, and simplifies collaboration with integrated, push-button sharing.

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TT15 Some Research Topics at the AIST Computational Biology Research Center in Japan
Date: Monday, July 14: 2:10 p.m. - 2:35 p.m.Room: 310

Presenting author: Paul Horton, AIST Computational Biology Research Center, Japan

Session Chair: Andrew Cowley/Dr. William Pearson

Presentation Overview: Show/Hide
I will give an overview of some ongoing projects, including NGS read and genome alignment, protein sequence analysis, novel techniques to infer combinatorial regulatory factors and others. I hope that delegates curious about Japan will come and hear about what is going on at our center in Tokyo!

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TT16 Elastic-R: Connecting the dots of scientific computing, from the pi to the clouds.
Date: Monday, July 14: 2:10 p.m. - 2:35 p.m.Room: 309

Presenting author: Karim Chine, Cloud Era Limited, United Kingdom

Session Chair: Dr. Desmond Higgins/Dr. Jim Procter

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Elastic-R is a virtual data science platform enabling everyone to use cloud computing seamlessly and work with R, python and many other data analysis tools in a productive and collaborative way. Elastic-R takes care transparently of security, resources creation and management, connectivity and sharing and leverages all available compute facilities.

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TT17 Privacy Preserving Search in Bioinformatics
Date: Monday, July 14: 2:40 p.m. - 3:05 p.m.Room: 310

Presenting author: Kana Shimizu, AIST Computational Biology Research Center, Japan

Session Chair: Andrew Cowley/Dr. William Pearson

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We develop privacy preserving search systems enabling users to search remote databases with guaranteed privacy. In this talk we will describe a chemical compound search system which achieves both computational efficiency and strong security. We will also introduce a pilot study for searching allele information from genomic databases.

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TT18 Protein and RNA alignment and analysis with Jalview 2.8.2 and JABA 2.1
Date: Monday, July 14: 2:40 p.m. - 3:05 p.m.Room: 309

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

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We will describe the most recent updates to Jalview and JABAWS that allow the comparison of RNA and Protein secondary structure predictions with secondary structure patterns observed in 3D structure. We will also discuss future development plans, including ENSEMBL integration, phylogenic analysis and state of the art sequence database searches.

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TT19 the khmer project: cloud-based raw sequencing analysis on a budget
Date: Monday, July 14: 3:10 p.m. - 3:35 p.m.Room: 310

Presenting author: Michael Crusoe, Michigan State University, United States

Session Chair: Andrew Cowley/Dr. William Pearson

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Using real datasets we will show you how to analyze short-read nucleotide sequencing data using a rented, on-demand, and well-priced cloud computer. The khmer project provides a IPython Notebook compatible interface to powerful yet memory efficient algorithms to improve genome, metagenome, and transcriptome assembly. All software presented is open source.

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TT20 Hyper-plexed biomarker imaging using the MultiOmyx platform enables novel systems biology insights for the diagnosis and treatment of disease
Date: Monday, July 14: 3:10 p.m. - 4:05 p.m.Room: 309

Presenting author: Brion Sarachan, GE Global Research, United States

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We describe a novel multiomic, hyper-plexed tissue analyses platform, MultiOmyx, which enables the quantitative analysis of ~60 protein and nucleic acid biomarkers at subcellular level in the same, intact tissue section. Novel image analysis and computational biology algorithms and visualization tools enable new systems biology discoveries.

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TT21 Garuda: Fly to the future of biology
Date: Monday, July 14: 3:40 p.m. - 4:05 p.m.Room: 310

Presenting author: Hiroaki Kitano, The Systems Biology Institute, Japan

Additional authors:
Samik Ghosh, The Systems Biology Institute, Japan
Hiroaki Kitano, RIKEN Center for Integrative Medical Sciences, Japan


Session Chair: Andrew Cowley/Dr. William Pearson

Presentation Overview: Show/Hide
A key challenge in analyzing biomedical data is the ability to discover the right computational tools for a specific analysis and navigate through them.
Garuda provides programming interfaces to connect software as gadgets, explore them through the gateway and operate them through the dashboard, supported by a global alliance

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TT22 BaseSpace® Onsite - Bioinformatics Platform,
Date: Tuesday, July 15: 10:30 a.m. - 10:55 a.m.Room: 313

Presenting author: Raymond Tecotzky, Illumina, United States

Session Chair: Dr. William Pearson

Presentation Overview: Show/Hide
Genomics research promises to revolutionize public and human health. Yet, extracting meaningful information from an enormous collection of sequence data is at risk without the development of new and scalable bioinformatics approaches. Illumina’s genomics cloud platform delivers a suite of industry-leading analysis tools, ensures secure data storage, and simplifies collaboration with integrated, push-button sharing.

Presentation PDF: Download Abstract

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TT23 The EMBL-EBI Job Dispatcher framework for bioinformatic applications
Date: Tuesday, July 15: 10:30 a.m. - 10:55 a.m.Room: 309

Presenting author: Weizhong Li, EMBL-EBI, United Kingdom

Session Chair: Rodrigo Lopez

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The EMBL-EBI Job Dispatcher is a framework designed to manage the running of bioinformatic applications via web and Web Services interfaces catering for a global range of users. Recent improvements include a broader range of tools, faster and higher job capacity and an increased number of genomic and protein databases.

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TT24 From the Ground to the Cloud in 25 minutes: Building a Customized Galaxy Analysis Server Using Only a Web Browser
Date: Tuesday, July 15: 11:00 a.m. - 11:25 a.m.Room: 313

Presenting author: Daniel Blankenberg, Galaxy Team / Penn State, United States

Session Chair: Dr. William Pearson

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Here, we demonstrate just how easy it is to run your own customized Galaxy. We will launch a private Galaxy instance, download and install required tools and dependencies, acquire and build reference datasets and indexes, and perform a computationally intensive analysis.

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TT25 A reputation-based web application (sbv IMPROVER Network Verification Challenge) that facilitates collaboration on biological network models
Date: Tuesday, July 15: 11:00 a.m. - 11:55 p.m.Room: 309

Presenting author: Julia Hoeng, PMI R&D, Switzerland

Additional authors:
Anselmo Di Fabio, ADS, United States


Session Chair: Rodrigo Lopez

Presentation Overview: Show/Hide
This presentation will discuss the crowd-verification approach that allowed domain experts from 60 institutions across 12 countries to visualize/expand 34 networks, and is currently being used to investigate smarter solutions to complement peer review and verify networks that are suitable for drug discovery, toxicological and mechanistic research in respiratory diseases.

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TT26 Persephone. A Very Fast Multi-Genome Browser
Date: Tuesday, July 15: 11:30 a.m. - 12:25 p.m.Room: 313

Presenting author: Maxim Troukhan, Ceres, Inc., United States

Session Chair: Dr. William Pearson

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A fast genome browser, called Persephone(TM), visualizes genomic data of different types: genetic maps, genomic sequences, gene models, QTLs, RNA-seq, synteny, SNPs, etc. Its main focus is speed and low memory footprint. It is capable of showing 10 million SNPs in 10 seconds in a smooth, intuitive way.

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TT27 Bioinformatics and Computer Biology Systems design applied to Medical Molecular Nanobiotechnology
Date: Tuesday, July 15: 12:00 p.m. - 12:25 p.m.Room: 309

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

Session Chair: Dr. Jim Procter/Dr. William Pearson

Presentation Overview: Show/Hide
The demostration will show several prototypes in Bioinformatics and Data Bases on Molecular Medical Nanobiotechnology through CloudBiolinux functionality (Hadoop and Map Reduce) working at the Biocomputing “Nelly” Cluster, located in University of Costa Rica, Central America (Global replicator of Galaxy Web Services (University of Pennsylvania, USA)).

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TT28 Recent Developments in the Pathway Tools Software and BioCyc Databases **New schedule time**
Date: Sunday, July 13: 11:30 a.m - 11:55 amRoom: 306

Presenting author: Peter Karp, SRI International, United States

Session Chair: Jason Ernst

Presentation Overview: Show/Hide
Pathway Tools facilitates creation of databases integrating genomic,
metabolic, and regulatory information in support of metabolic modeling
and omics analysis. It now accomodates gene-knockout and Phenotype
Microarray data, and has a new route searching tool for metabolic
networks. BioCyc consists of 3,500 Pathway/Genome Databases for
sequenced organisms.

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TT29 Scaling Galaxy: Preparing for Those Next Few Orders of Magnitude
Date: Tuesday, July 15: 2:00 p.m. - 2:25 p.m.Room: 310

Presenting author: John Chilton, Galaxy Project, United States

Session Chair: Dr. Lonnie Welch

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The pace of data generation continues to increase. This enables new questions, but also brings challenges in managing, integrating, and analyzing these datasets. We will discuss what the Galaxy Project is doing and planning to do to leverage Galaxy’s existing platform to support these new, larger and more complex analyses.

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TT30 UniProt: New website and latest developments
Date: Tuesday, July 15: 2:00 p.m. - 2:25 p.m.Room: 309

Presenting author: Sangya Pundir, EMBL-European Bioinformatics Institute, United Kingdom

Session Chair: Dr. Jim Procter/Dr. William Pearson

Presentation Overview: Show/Hide
The demonstration will cover: 


1. A description of UniProt
2. New UniProt beta site, functionalities and design
3. Accessing UniProt using simple query syntax
4. Proteomes querying and retrieval
5. Sequence similarity searches, alignments and ID mapping tools provided

This demonstration will also encourage user interaction and feedback.

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TT31 Using HPC techniques to accelerate NGS workflows
Date: Tuesday, July 15: 2:30 p.m. - 2:55 p.m.Room: 313

Presenting author: Pierre Carrier, Cray, Inc., United States

Session Chair: Dr. Desmond Higgins

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High Performance Computing technology and methodologies offer many opportunities to eliminate performance bottlenecks in many components of NGS workflows. We will use trinityRNASeq to illustrate some examples of optimizations that enable efficient scaling to thousands of processors, and discuss with the attendees about bottlenecks they encounter in their NGS workflows.

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TT32 GenomeSpace: An Environment for Frictionless Bioinformatics
Date: Tuesday, July 15: 2:30 p.m. - 2:55 p.m.Room: 310

Presenting author: Ted Liefeld, Broad Institute, United States

Session Chair: Dr. Lonnie Welch

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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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TT33 Alignments with Annotations
Date: Tuesday, July 15: 2:30 p.m. - 2:55 p.m.Room: 309

Presenting author: William Pearson, U. of Virginia School of Medicine, United States

Session Chair: Dr. Jim Procter/Dr. William Pearson

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The FASTA programs can incorporate functional site annotations, variation data, and domain boundaries, potentially modifying the similarity score. Variant annotation allows the alignment score to improve; the domain annotation strategy partitions the alignment score across the annotated domains, reducing the problem of homologous over-extension.

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TT34 GTFAR: Genome and Transcriptome Free Analysis of RNA
Date: Tuesday, July 15: 3:00 p.m. - 3:25 p.m.Room: 313

Presenting author: Tade Souaiaia, University of Southern California, United States

Session Chair: Dr. Desmond Higgins

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The Genome and Transcriptome Free Analysis of RNA pipeline provides users with a software package
to analyze RNA-seq data without an accompying reference transcriptome/genome. While also
capable of providing reference based align-and-count estimation of gene expression, GTFAR
clusters reads to identify differently expressed sequences with homology to multiple organisms.

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TT35 geWorkbench-Web: An integrated web interface to a multitude of bioinformatics tools
Date: Tuesday, July 15: 3:00 p.m. - 3:25 p.m.Room: 310

Presenting author: Aris Floratos, Columbia University, United States

Session Chair: Dr. Lonnie Welch

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In this talk we present geWorkbench-Web, a new, web-enabled version of geWorkbench (genomics Workbench), the the bioinformatics platform of the National Center for the Multiscale Analysis of Genomic and Cellular Networks. geWorkbench-Web provides access to an integrated suite of tools for the analysis and visualization of data from a wide range of genomics domains.

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TT36 Lynx: A REST based platform for annotations and systems analysis of multi-gene disorders
Date: Tuesday, July 15: 3:00 p.m. - 3:25 p.m.Room: 309

Presenting author: Dinanath Sulakhe, Computation Institute / University of Chicago, United States

Session Chair: Dr. Jim Procter/Dr. William Pearson

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We will demonstrate the Lynx Platform, its web application interface and comprehensive web services (http://lynx.ci.uchicago.edu) and describe its design and service-oriented architecture. We will also showcase how Lynx can be used for the downstream analysis of NGS data, expression data, and others.

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TT37 Construct, analyze and interpret the network using biomedical knowledge in VisANT
Date: Tuesday, July 15: 3:30 p.m. - 3:55 p.m.Room: 313

Presenting author: zhenjun Hu, Bioinformatics Program, Boston University, United States

Session Chair: Dr. Desmond Higgins

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VisANT is a software platform for visually building and analyzing networks of relations among and between biological entities. Here we focus on the illustration of the built-in functionalities that use integrated biomedical knowledge, such as disease, drugs and Gene Ontology to aid the network construction, analysis and interpretation.

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TT38 Cellular Phenotype Database with…
Date: Tuesday, July 15: 3:30 p.m. - 3:55 p.m.Room: 310

Presenting author: Catherine Kirsanova, EMBL-European Bioinformatics Institute, United Kingdom

Session Chair: Dr. Lonnie Welch

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Full title is «Cellular Phenotype Database with Ontology assisted data browsing».

I will show the ontology assisted data browsing along with the major principles of data aggregation in EBI's Cellular Phenotype Database, including demonstration of some generic ideas how to organize diverse data for better browsing and querying.

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