Technology Track Accepted Presentations

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


TT01 Biomolecular sequence analysis with Jalview and JPred4
Date: Monday, July 13: 10:10 am - 11:10 amRoom: Wicklow Hall 2B

Presenting Author: Geoffrey Barton, Division of Computational Biology, College of Life Sciences, University of Dundee, United Kingdom

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The updated Jpred4 protein secondary structure prediction service has enhanced result visualisations, and a REST API for high-throughput analysis. The Jalview multiple sequence alignment workbench now supports linked cDNA/Protein analysis, integration with UCSF Chimera and the PDBe query services for 3D structure discovery.

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TT02 BioJS 2.0: more flexible, modular, open web biological visualization
Date: Monday, July 13: 11:40 am - 12:00 pmRoom: Wicklow Hall 2B

Presenting Author: Manuel Corpas, TGAC, United Kingdom

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We present BioJS 2.0, the newly updated BioJavaScript library for visualisation of biological data. Since our upgrade we now have adopted NPM, browserify and other JavaScript technologies to give BioJS that interactive look and feel we all recognise in modern web applications.

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TT03 The European Variation Archive
Date: Monday, July 13: 12:00 pm - 12:20 pmRoom: Wicklow Hall 2B

Presenting Author: Francisco Lopez-Domingo, EMBL-European Bioinformatics Institute, United Kingdom

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The European Variation Archive (EVA) is a genetic variation resource covering variants of any type across species and populations, including both germline and cancer genomes. EVA is an open access Big Data provider that enables users to efficiently retrieve relevant information from its knowledge-base. Current implementation consists of a HTML5 web-interface and a NoSQL backend

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TT04 Sensitive and fast homology searches with HMMER via the Web
Date: Monday, July 13: 12:20 pm - 12:40 pmRoom: Wicklow Hall 2B

Presenting Author: Robert Finn, EMBL-EBI, United Kingdom

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Homology searches allow the transfer of data between sequences. The HMMER website (http://www.ebi.ac.uk/Tools/hmmer) provides fast, accurate and sensitive searches. Through the synergistic coupling of algorithmic developments, hardware and intuitive data visualizations, large sequence databases can be searched and the results analyzed and filtered in close to real-time.

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TT05 The Universal Protein Resource (UniProt): New Development on Proteomes, Variation and Proteomics
Date: Monday, July 13: 2:00 pm - 2:20 pmRoom: Wicklow Hall 2B

Presenting Author: Benoit Bely, European Bioinformatics Institute, United Kingdom

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The demonstration will present how to use the Proteomes portal on UniProt.org to find data about non-redundant and redundant proteomes.
It will also demonstrate the content and use of proteomics and variation data in UniProt.

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TT06 ProDomAs; A Web Server for Assigning Protein Domains using Neural Network
Date: Monday, July 13: 2:20 pm - 2:40 pmRoom: Wicklow Hall 2B

Presenting Author: Changiz Eslahchi, Institute for Research in Fundamental Sciences (IPM), School of Biological Science, Iran

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ProDomAs web server implements a novel automatic algorithm for assigning structural domains of a protein chain. Results show that ProDomAs outperforms other automatic methods. This web server can be used to decompose and visualize structural domains in 1D and 3D representations and is available at http://bs.ipm.ir/softwares/prodomas.

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TT07 Multiple Sequence Alignment using Clustal Omega
Date: Monday, July 13: 2:40 pm - 3:00 pmRoom: Wicklow Hall 2B

Presenting Author: Fabian Sievers, University College Dublin, Ireland

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Clustal Omega is a Multiple Sequence Alignment program that can
align virtually any number of protein sequences and nucleotide
sequences of comparable length. It uses Hidden Markov Models to
align individual sequences and profiles. Clustal Omega is faster than
high accuracy aligners and more accurate than faster aligners, as
measured on protein structure derived benchmarks

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TT08 20 years of CATH: new methods to predict the structure and function of novel protein sequences
Date: Monday, July 13: 3:30 pm - 3:50 pmRoom: Wicklow Hall 2B

Presenting Author: Ian Sillitoe, University College London (UCL), United Kingdom

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New tools in CATH: predicting protein function from sequence, investigating evolution of structural domains, accessing representative datasets and bleeding-edge annotations.

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TT09 Phyre2: Protein modeling and analysis made easy
Date: Monday, July 13: 3:50 pm - 4:10 pmRoom: Wicklow Hall 2B

Presenting Author: Mark Wass, Imperial College London, United Kingdom

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The Phyre2 web portal is used by over 40,000 researchers and provides rapid, accurate 3D modeling of a protein sequence with an intuitive and easy-to-use interface for exploring results. The demonstration will provide an overview of the range of tools available in Phyre2

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TT10 Aquaria: Simplifying discovery and insight from protein structures
Date: Monday, July 13: 4:10 pm - 4:30 pmRoom: Wicklow Hall 2B

Presenting Author: Seán O'Donoghue, CSIRO & Garvan, Australia

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This Tech Track talk will present Aquaria (http://aquaria.ws), a new web resource that streamlines and simplifies the generation of insight from protein structures. The talk will outline how Aquaria can be used, both by biologists (via its web-based user interface) as well as bioinformaticians (via its API).

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TT11 Illumina BaseSpace® Apps - Accelerating Bioinformatics Analysis with Easy, Accurate, and Efficient tools for Next Generation Sequencing Data
Date: Tuesday, July 14: 10:10 am - 11:10 amRoom: Wicklow Hall 2A

Presenting Author: Raymond Tecotzky, Illumina, United States

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We will show an overview and then a rapid, real-time demonstration of several apps to demonstrate the power of state of the art informatics analysis of genomic nextgen sequencing data and the compelling results of those analyses.
:-)

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TT12 A comparison of predicted promoters between hg19 and hg38 reference genomes
Date: Tuesday, July 14: 10:10 am - 10:30 amRoom: Wicklow Hall 2B

Presenting Author: Alexander Kaplun, QIAGEN Bioinformatics, United States

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We will discuss the results of the comparison of the virtually calculated promoters between the hg19 and hg38 reference genomes along with insights gained regarding the distribution of regulatory features such as known transcription factor binding sites, ChIP fragments and DNAse I hypersensitivity sites.

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TT13 "Bringing structure to biology" on a device near you
Date: Tuesday, July 14: 10:30 am - 10:50 amRoom: Wicklow Hall 2B

Presenting Author: Swanand Gore, EMBL-EBI, United Kingdom

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We present significant enhancements to macromolecular structure representation at PDBe (http://pdbe.org):

- REST API with interactive documentation (http://pdbe.org/api)

- Responsive webpages with concise representation of key data features including biological assemblies; domain mappings; function; literature; experiment and validation (e.g. http://pdbe.org/2qk9)

- Search interface with a powerful auto-suggestion and faceted presentation of results
(http://www.ebi.ac.uk/pdbe/entry/search/index)

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TT14 A tale of ice and fire: Stability and change in bioinformatics framework services at EMBL-EBI
Date: Tuesday, July 14: 11:40 am - 12:00 pmRoom: The Liffey A

Presenting Author: Andrew Cowley, EMBL-EBI, United Kingdom

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We will describe recent changes to the Job Dispatcher framework and EBI Search engine at EMBL-EBI, highlighting the need to maintain compatibility while also adding new features and retiring depreciated services.

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TT15 Chipster VM - comprehensive package of NGS data analysis tools and reference data, with an intuitive GUI
Date: Tuesday, July 14: 11:40 am - 12:00 pmRoom: Wicklow Hall 2A

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

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Chipster is free, open source software for analyzing high-throughput data. It is available as a ready-to-run virtual machine containing a comprehensive collection of analysis tools and reference data. Users can save workflows and visualize data interactively with a GUI. This talk covers Chipster from users’ and administrators’ point of view.

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TT16 What’s new in the Galaxy (Project)?
Date: Tuesday, July 14: 12:00 pm - 12:20 pmRoom: The Liffey A

Presenting Author: Dave Clements, Galaxy Project, Johns Hopkins University, United States

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An update on the Galaxy Project, a free and open- source data integration and analysis platform for life science research (http://galaxyproject.org). This talk will highlight recent and upcoming work in multi-sample analysis, user interface improvements, tool usage and definition updates, using Docker for tool integration, and integration with interactive environments.

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TT17 XEML Interactive Designer, Metadata Management Tool for Genotypes, Environmental Conditions and Sampling Strategy
Date: Tuesday, July 14: 12:00 pm - 12:20 pmRoom: Wicklow Hall 2A

Presenting Author: Benjamin Dartigues, BioInformatics Center of Bordeaux (CBIB), France

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XEML-Lab Designer, a metadata capture workflow enabling the intuitive design of experiments is back. Originally designed to facilitate sharing of environmental data related to experiments, the new version is now available for all standard platforms. This presentation summarizes all available functionalities as well as the downstream data integration analysis.

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TT18 RiboGalaxy: a platform for the alignment, analysis and visualization of ribo-seq data.
Date: Tuesday, July 14: 12:20 pm - 12:40 pmRoom: The Liffey A

Presenting Author: Audrey Michel, University College Cork, Ireland

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We will present RiboGalaxy (http://ribogalaxy.ucc.ie/), a freely
available Galaxy-based web server specifically tailored for pre-processing, aligning and analysing ribo-seq data with the visualisation functionality provided by GWIPS-viz (http://gwips.ucc.ie).
We will demonstrate how users
can pre-process, align and analyse their ribo-seq data with the tools and workflows hosted on RiboGalaxy.

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TT19 @Note2 – open-source computational tools for biomedical text mining
Date: Tuesday, July 14: 12:20 pm - 12:40 pmRoom: Wicklow Hall 2A

Presenting Author: Miguel Rocha, Universidade do Minho, Portugal

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The @Note2 project (http://www.anote-project.org) provides a number of user-friendly open-source computational tools for biomedical text mining, including tools for information retrieval and publication management, named entity recognition and relationship extraction, and a manual curation environment for annotating documents. This demonstration will present the main @Note functionalities and technological features.

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TT20 Zegami: Software for high throughput image exploration
Date: Tuesday, July 14: 2:00 pm - 2:20 pmRoom: Liffey Hall 2

Presenting Author: Stephen Taylor, Computational Biology Research Group, United Kingdom

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We have developed a tool called Zegami which has the ability to display thousands of images, movies, stacked images or even 3D objects in a web browser. From here you can search, sort, filter and group based on the image associated metadata. The software is free for academic use.

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TT21 Publishing with Genomics, Proteomics & Bioinformatics
Date: Tuesday, July 14: 2:00 pm - 2:40 pmRoom: Wicklow Hall 2A

Presenting Author: Jialei Xie, Genomics, Proteomics & Bioinformatics, China

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The open-access journal Genomics, Proteomics & Bioinformatics (GPB) is the official journal of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. GPB publishes high-quality articles in omics and bioinformatics worldwide in various article types. GPB has been indexed in PubMed/MEDLINE, Chemical Abstracts, Scopus, etc.

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TT22 Secure, Scalable and Cost Effective Computing for Large Scale Genomics Analysis on Amazon Web Services
Date: Tuesday, July 14: 2:00 pm - 3:00 pmRoom: Wicklow Hall 2B

Presenting Author: Angel Pizarro, Amazon Web Services, United States

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Scalability, security, and low costs make cloud computing attractive for genomic sequencing data analysis and storage. We will discuss how researchers are using Amazon Web Services (AWS) to create scalable, performant, collaborative, and cost effective solutions for genomics, health, and big-data workflows. Come learn about how AWS can help your research.

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TT23 CIViC: Crowdsourcing the Clinical Interpretation of Variants in Cancer
Date: Tuesday, July 14: 2:20 pm - 2:40 pmRoom: Liffey Hall 2

Presenting Author: Malachi Griffith, The Genome Institute, Washington University School of Medicine, United States

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Interpreting the clinical relevance of cancer variants is a significant bottleneck in clinical cancer sequencing pipelines, delaying the adoption of precision medicine. To this end, we present CIViC (www.civicdb.org) a crowd sourcing interface for the clinical interpretation of variants in cancer.

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TT24 WebChemistry: a platform for the detection, validation, comparison, and characterization of structural patterns in biomacromolecules
Date: Tuesday, July 14: 2:40 pm - 3:00 pmRoom: Liffey Hall 2

Presenting Author: David Sehnal, CEITEC - Central European Institute of Technology, Czech Republic

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We present the WebChemistry platform, a set of tools for in silico analysis of structural bioinformatics data. The tools give the user the ability to detect, validate, compare, and characterize any pattern of interest (such as binding and catalytic sites, sequences, or channels) and are freely accessible at http://ncbr.muni.cz/WebChemistry.

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TT25 Realising the Infrastructure for Systems Biology Europe
Date: Tuesday, July 14: 2:40 pm - 3:00 pmRoom: Wicklow Hall 2A

Presenting Author: Carole Goble, University of Manchestor, United Kingdom

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ISBE will offer European researchers easy access to state-of-the-art facilities, data, models, and training by interconnecting national systems biology centres and making their collective expertise, resources and services readily available.

This is improve biological data and model standardisation across difference laboratories, makig them more combinable and re-usable.

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TT26 FAIRDOM: FAIR Data and Model Mangement in Systems Biology
Date: Tuesday, July 14: 3:30 pm - 3:50 pmRoom: Wicklow Hall 2A

Presenting Author: Natalie Stanford and Carole Goble, University of Manchester, Netherlands

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FAIRDOM (http://fair-dom.org/) enables the systems biology community to produce Findable, Accessible, Interoperable and Reproducible Data, Operating procedures and Models. Heterogeneous data and models from systems investigations can be aggregated and interlinked in the central FAIRDOMHub, for stewardship and publication, or in a local FAIRDOM instance, for collaboration and sharing.

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TT27 Bioinformatics Cloud Services for Life Sciences
Date: Tuesday, July 14: 3:50 pm - 4:10 pmRoom: Wicklow Hall 2A

Presenting Author: Christophe Blanchet, French Institute of Bioinformatics - IFB, France

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The French Institute of Bioinformatics (IFB), ELIXIR French node, aims to provide scientists with bioinformatics services relying on the required computing and storage capacities while providing a user-friendly and easily adjustable solution. A selection of bioinformatics software and pipelines have been integrated as turnkey cloud services, now available to scientists.

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TT28 GenomeSpace: An environment for frictionless bioinformatics
Date: Tuesday, July 14: 4:10 pm - 4:30 pmRoom: Wicklow Hall 2A

Presenting Author: Sara Garamszegi, The Broad Institute of Harvard and MIT, United States

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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 client-side tools. GenomeSpace supports cloud-based storage, handles file format compatibility issues automatically, and enables reproducibility of multi-tool analyses.

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