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Technology Track

Presentations

Session Chairs

Hagit Shatkay, University of Delaware, United States
Dominic Clark, Pistoia Alliance, Inc, United Kingdom

Schedule subject to change
Tuesday, July 23rd
10:20 AM-10:40 AM
EMBL-EBI Tools as a Service
  • Fabio Madeira, EMBL-EBI, United Kingdom

Presentation Overview: Show

The EMBL-EBI Job Dispatcher framework (https://www.ebi.ac.uk/services) provides free access to Bioinformatics tools and related data via a web browser and via Web Services. In this talk, I would like to demonstrate the ‘Tools as a service’ capabilities of the framework and how to integrate these services into analysis workflows.

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10:40 AM-11:00 AM
EBI Search API – Looking for more
  • Young mi Park, EMBL-EBI, United Kingdom

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EBI Search, a search engine allowing access to data available from EMBL-EBI, provides extended search and results features in addition to text searching; These include bi-directional cross-reference searching, finding similar entries (faceting and more-like-this) and searching applied on sequences analysis results, which will be on the agenda of the talk.

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11:00 AM-11:20 AM
RNAcentral: a hub of information for non-coding RNA sequences
  • Blake Sweeney, European Molecular Biology Laboratory, United Kingdom

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In this talk we will demonstrate using the RNAcentral database to explore non-coding RNA sequences. We will focus on examining a genomic region for ncRNA, searching for ncRNA sequences by name, and finding ncRNA sequences similar to novel sequences. This talk is aimed at anyone interested in ncRNA data

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11:20 AM-11:40 AM
Protein services, tools and visual components enabling integration and interpretation of the UniProt Knowledgebase (UniProtKB)
  • Andrew Nightingale, EMBL-EBI, United Kingdom

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We will present updates to UniProt including integration of clinically relevant data within new tools and services on the UniProt website and as programmatic services to facilitate the integration of the UniProtKB into users’ analysis pipelines. We will also introduce a collection of portable web components to visualise protein knowledge.

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11:40 AM-12:40 PM
IT Infrastructure for AI and Analytics in medicine and research
  • Ulrich Walter, IBM Deutschland GmbH, Germany

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In this session we will discuss the infrastructure and requirements for buliding the data pipeline for AI and analytics in context of use cases in bio medicine and R&D.

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2:00 PM-2:20 PM
Storage Systems that Support Tomorrow's Life Science Applications Today
  • David Hiatt, WekaIO, United States

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Research has become increasingly complex and compute intensive. While new tools and analytical processes such as artificial intelligence (AI) and deep hold great promise, they stress the supporting IT infrastructure. Learn how today's storage systems leverage software to deliver the performance, scale, and cost efficiencies for tomorrow's life sciences applications.

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2:20 PM-2:40 PM
The CPTAC Data Browser: A New Generation of Data Visualization Tools from the Clinical Proteomic Tumor Analysis Consortium
  • Anna Calinawan, Icahn School of Medicine at Mount Sinai, United States

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The CPTAC Data Browser: A New Generation of Data Visualization Tools from the Clinical Proteomic Tumor Analysis Consortium

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2:40 PM-3:00 PM
BioThings API: Promoting Best-practices via a Biomedical API Development Ecosystem
  • Chunlei Wu, The Scripps Research Institute, United States

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The demonstration will be focusing on the utility of our core BioThings APIs (targeting bioinformaticians and researchers as the API users); and the set of Biomedical API development tools like BioThings SDK, BioThings Studio and BioThings Explorer (targeting API developers).

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3:00 PM-4:00 PM
Big Data Meets Drug Target Discovery
  • Robert Gentleman, 23andMe, United States

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23andMe is a company is built on science. We make evidence-based decisions. In a world where health is poorly understood, we use data to better understand wellness and disease. We bring science to our customers and help them use it in meaningful ways. In 2015 we began a Therapeutics division (https://therapeutics.23andme.com/) to use our genotype and phenotype data to help develop new therapies for diseases and conditions with serious unmet medical need. In this talk I will discuss how we use our large genotype and phenotype data base to drive the discovery of novel therapeutics. I will show some examples where we find known targets to exemplify the approach. I will discuss how different ethnicities and founder populations can provide us with novel insights. I will discuss some of the challenges in going from a genetic signal to a drug target.

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4:40 PM-5:40 PM
Towards a production-ready solution for reproducible articles
  • Emmy Tsang, eLife, United Kingdom

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In this session, we will showcase eLife’s first computationally reproducible article as part of the Reproducible Document Stack (RDS) project. We will demonstrate how researchers can create reproducible articles with Stencila Desktop, an open-source, user-friendly manuscript editor, and outline our plans to develop RDS into a scalable, production-ready solution.

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Wednesday, July 24th
10:20 AM-10:40 AM
PDFigCapX and FigSplit - a Pipeline for Extracting Figures, SubFigures and Captions from Biomedical Publications: Supporting Bio-Curation and Discovery
  • Hagit Shatkay, University of Delaware, United States
  • Pengyuan Li, University of Delaware, United States

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Figures and captions convey essential information in biomedical publications. We introduce an effective pipeline, comprising two systems, toward curation-support of published figures: PDFigCapX for identifying and extracting figures and captions from publications, and FigSplit for splitting extracted compound multi-panel images into their constituent subfigures.

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10:40 AM-11:00 AM
Phyre, PhyreRisk and Missense3D: Modelling protein structure and the impact of missense variants
  • Michael Sternberg, Imperial College London, United Kingdom

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We present:

Phyre2 – a web-server to predict protein structure from sequence (http://www.sbg.bio.ic.ac.uk/phyre2 )

PhyreRisk – a dynamic database mapping variants onto experimental and Phyre-predicted structures( http://phyrerisk.bc.ic.ac.uk )

Missense3D – a web server that reports the structural impact of a missense variant on experimental and predicted structures http://www.sbg.bio.ic.ac.uk/~missense3d/ )

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11:00 AM-11:20 AM
Isabl - An open-source patient-centric framework for scalable bioinformatics operations
  • Juan S Medina, Memorial Sloan Kettering Cancer Center, United States

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Isabl is a plug-and-play open-source framework for scalable bioinformatics operations designed to support automated processing and management of NGS assets and their metadata. Isabl's patient centric model enables advanced integrations with multinomial data types and linkage to institutional information systems such as clinical databases and visualization interfaces.

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11:20 AM-11:40 AM
MISO LIMS : managing information for sequencing operations
  • Morgan Taschuk, Ontario Institute for Cancer Research, Canada

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MISO is a laboratory information management system designed for eukaryotic sequencing operations, supporting many different -omic sequencing protocols, long and short reads, and microarrays. Prioritizing accuracy, simplified data entry, and metadata integrity, MISO incorporates a wide feature set useful for facilities to track their lab workflows in great detail.

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11:40 AM-12:40 PM
Bioinformatics and Exploratory Data Analysis in Pharmaceutical Industry. Applications to drug research and development.
  • Daniel Marbach, Roche Innovation Center Basel, Switzerland
  • Jitao David Zhang, Roche Innovation Center Basel, F. Hoffmann-La-Roche AG,, Switzerland
  • Fabian Birzele, F. Hoffmann-La Roche Ltd., Switzerland

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It takes many years from studying diseases and presuming suitable targets to finally filing a drug for approval by health authorities. In this talk, we will describe the “daily life” of bioinformaticians in Roche and how all steps along the development chain are driven by data.

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2:00 PM-3:00 PM
The geneXplain platform for bioinformatic and systems biology analysis
  • Philip Stegmaier, geneXplain GmbH, Germany

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The geneXplain platform is an online toolbox and workflow management system for a broad range of bioinformatic and systems biology
applications that has been used in a number of studies. This demonstration introduces data management and analysis capabilities of the platform
highlighting its utility for network analysis and drug discovery.

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3:00 PM-4:00 PM
Fairspace
  • Kees van Bochove, The Hyve, Netherlands

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Fairspace, a new open source project from The Hyve, helps organizations quickly stand up a FAIR compliant metadata, data governance and auditing layer over existing storage and applications. Fairspace is developed in collaboration with Institut Curie (Paris), and aims to contribute to the growing open source ecosystem around FAIR Data.

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4:40 PM-5:00 PM
SWISS-MODEL: homology modelling of protein structures and complexes
  • Gerardo Tauriello, SIB Swiss Institute of Bioinformatics, Basel & University of Basel, Switzerland

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SWISS-MODEL (swissmodel.expasy.org) is a state-of-the-art computational protein structure modelling workbench with a user-friendly web interface. This talk will present the fully automated SWISS-MODEL workflow to predict high-quality three-dimensional structures of proteins and complexes in their most likely quaternary structure starting from the respective amino acid sequences.

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5:00 PM-5:20 PM
GeneWeaver.org: A RESTful service for multi-species data integration in functional genomics
  • Elissa J Chesler, The Jackson Laboratory, United States

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Advances to the GeneWeaver software system for the integration, analysis and visualization of genomics data across species will be presented, including its redevelopment as a suite of RESTful API services. Applications in interpretation of human genetics and navigation of heterogeneous network graphs of multi-species data will be presented.

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5:20 PM-5:40 PM
CATH: tools and datasets to analyse protein structure, sequence and function
  • Ian Sillitoe, UCL, United Kingdom

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An update on the tools, methods and datasets available from the CATH protein structure classification database, including the latest developments on clustering functional families (FunFams) within hugely populated evolutionary superfamilies.