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Technology Track Presentations

TT01: Systems biology verification project: crowdsourcing computational method benchmarking, results verification, and in depth peer review - Past, present, and future.
Room: Terrace 1
Date: Saturday, July 22: 2:00 pm - 2:55 pm

Presenting Author: Stephanie Boue, sbv IMPROVER - Philip Morris International, Switzerland

Chair: Henning Hermjakob, EMBL-EBI

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The presentation will summarize past, present, and future activities from an industry-sponsored project, sbv IMPROVER, aiming at (i) unbiased benchmarking of computational methods relevant to systems biology and precision medicine, (ii) fostering scientific transparency of industry-funded research, and (iii) encouraging independent in depth peer review of scientific results.

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TT02: Dockstore: reproducible bioinformatics workflows in the cloud
Room: Terrace 1
Date: Saturday, July 22: 3:00 pm - 3:55 pm

Presenting Author: Marc Fiume, Global Alliance for Genomics & Health, Canada

Chair: Henning Hermjakob, EMBL-EBI

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We demonstrate Dockstore (https://dockstore.org), an open, crowd-sourced repository of bioinformatics workflows and its seamless integration with DNAstack (https://dnastack.com), a cloud-based platform for storage, bioinformatics workflow execution, and sharing. Together, the services provide a simple way of finding and executing reproducible workflows on private datasets in the cloud.

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TT03: Supporting highly scalable scientific data analysis with Galaxy
Room: Terrace 1
Date: Saturday, July 22: 4:30 pm - 4:50 pm

Presenting Author: James Taylor, Johns Hopkins University, United States

Chair: Dominic Clark, EMBL-EBI

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We will describe a variety of recent developments in Galaxy, a framework for supporting large scale analysis, to enable much larger scale analyses, to improve usability and user experience, and to support new user communities.

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TT04: Phyre2: Protein modeling and analysis made easy
Room: Terrace 1
Date: Saturday, July 22: 4:50 pm - 5:10 pm

Presenting Author: Michael Sternberg, Imperial College London, United Kingdom

Chair: Dominic Clark, EMBL-EBI

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The Phyre2 web portal provides rapid, accurate 3D modeling of a protein sequence and an easy-to-use interface for exploring results (www.sbg.bio.ic.ac.uk/~phyre2/ ). The demonstration will present the theory behind Phyre2 and illustrate the typical results and their interpretation.

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TT05: Recent Developments in the Pathway Tools Software and BioCyc Databases
Room: Terrace 1
Date: Saturday, July 22: 5:15 pm - 5:35 pm

Presenting Author: Peter Karp, SRI International, United States

Chair: Dominic Clark, EMBL-EBI

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Pathway Tools is a system for computational genomics, metabolic
pathway informatics, and regulatory informatics. New are an omics
dashboard for visual interpretation of gene-expression data, a system
for notifying scientists of database updates in their interest areas,
and a tool for searching for metabolic routes across communities of
organisms.

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TT06: GeneHancer-enriched VarElect: non-coding variant interpretation tool for genome sequencing
Room: Terrace 1
Date: Saturday, July 22: 5:35 pm - 5:55 pm

Presenting Author: Simon Fishilevich, Weizmann Institute of Science, Israel

Chair: Dominic Clark, EMBL-EBI

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Disease interpretation of non-coding genomic variants represents a major challenge. We will demonstrate how the combination of GeneHancer, our novel database of distant-acting enhancers and their target genes, along with VarElect, our NGS phenotyper, can leverage the GeneCards Suite’s knowledgebase to decipher unsolved cases of genetic disease.

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TT07: GenomeSpace: Open source interoperability platform with crowd-sourced analysis recipes
Room: Terrace 1
Date: Sunday, July 23: 10:00 am - 10:20 am

Presenting Author: Ted Liefeld, The University of California San Diego, United States

Chair: Dominic Clark, EMBL-EBI

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The GenomeSpace Recipe Resource is an online repository of analysis “recipes”, which are short, standalone guides for accomplishing common bioinformatics analysis tasks in GenomeSpace using 2-3 tools or data resources. Here, we show how researchers can use GenomeSpace to combine the capabilities of multiple bioinformatics tools in several research scenarios.

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TT08: The GenePattern Notebook Environment
Room: Terrace 1
Date: Sunday, July 23: 10:20 am - 10:40 am

Presenting Author: Michael Reich, UCSD, United States

Chair: Dominic Clark, EMBL-EBI

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GenePattern Notebook allows researchers to embed the hundreds of bioinformatics methods available in GenePattern into a Jupyter notebook, without the need to write code. Researchers create complete research narratives using formatted text, graphics, data, and executable analyses in a familiar notebook format. An online resource is freely available at https://www.genepattern-notebook.org.

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TT09: Using Online Classes to Flip Bioinformatics Classrooms
Room: Terrace 1
Date: Sunday, July 23: 10:40 am - 11:00 am

Presenting Author: Niema Moshiri, University of California, San Diego, United States

Chair: Dominic Clark, EMBL-EBI

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Educational psychologists agree that traditional one-to-many lectures are minimally effective for student learning. We will discuss how our interactive text helps implement flipped and fully-adaptive bioinformatics courses that force students to "invent" classical bioinformatics concepts (i.e., active learning) rather than introducing these concepts in a lecture (i.e., passive learning).

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TT10: Computational Antibody Design Software and Database
Room: Terrace 1
Date: Sunday, July 23: 11:10 am - 11:30 am

Presenting Author: Konrad Krawczyk, Oxford University Department of Statistics, United Kingdom

Chair: Dominic Clark, EMBL-EBI

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We demonstrate SAbDab/SAbPred computational tools for facilitating antibody engineering. The software has been developed at Oxford University and encompasses an auto-updating database of antibody structures and rapid, accurate antibody modeling and prediction tools. The software is available for installation in academic and non-academic organizations.

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TT11: Combine Your Data with Functional Annotations from UniProt Using Protein Services
Room: Terrace 1
Date: Sunday, July 23: 11:30 am - 11:50 am

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

Chair: Dominic Clark, EMBL-EBI

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We will present the different services available in the Proteins API, demonstrate how they can be used interactively using the genomic coordinates service to retrieve UniProt protein annotation and compare this to the information available from BED files. The demonstration will lead onto how the services are used within ProtVista.

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TT12: Using CATH-Gene3D to predict the structure and function of novel protein sequences and examine the impacts of genetic variations
Room: Terrace 1
Date: Sunday, July 23: 11:50 am - 12:10 pm

Presenting Author: Christine Orengo, University College London, United Kingdom

Chair: Dominic Clark, EMBL-EBI

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CATH classifies 3D-structures from the Protein Databank (PDB) into superfamilies of protein domains that are related by evolution. This talk will provide an overview of the data, tools and visualisations and how functional site data can provide insights into the interpretation of diseases associated with mutations in human.

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TT13: Reference open source infrastructure for FAIR Research Data Management in academic hospitals
Room: Terrace 1
Date: Sunday, July 23: 2:00 pm - 2:55 pm

Presenting Author: Kees van Bochove, The Hyve, Netherlands

Chair: Kees van Bochove, The Hyve

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Many academic hospitals today are organizing data governance across clinic and research groups, to achieve precision medicine goals. This talk provides real-life examples of how open source tools such as iRODS, Arvados, i2b2/tranSMART and Jupyter can be combined to achieve FAIR data management from source EHR to research analysis results.

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TT14: Genomics, Proteomics & Bioinformatics (GPB) --- a rising journal in the field
Room: Terrace 1
Date: Sunday, July 23: 3:00 pm - 3:55 pm

Presenting Author: Yuxia Jiao, Genomics, Proteomics & Bioinformatics, China

Chair: Kees van Bochove, The Hyve

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Genomics, Proteomics & Bioinformatics (GPB) is one of ISCB’s Journals of Interest. As the official journal of Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China, GPB is hosted by Elsevier as a gold open-access journal and publishes high-quality articles on omics and bioinformatics worldwide.

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TT15: Pathway Studio Use Case: A disease-centric analysis of Pre-Eclampsia
Room: Terrace 1
Date: Monday, July 24: 10:00 am - 10:55 am

Presenting Author: Chris Cheadle, Elsevier Inc, United States

Chair: Rob Finn, EMBL-EBI

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Presented as part of the “Elsevier in the Classroom “ model curriculum series, this interactive hands-on session is designed to move the new user through some of the basic Pathway Studio software capabilities on a click-by-click basis.

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TT16: Lay out your manuscripts, theses and reports like a pro with LaTeX for Biologists
Room: Terrace 1
Date: Monday, July 24: 11:00 am - 11:55 am

Presenting Author: John Lees-Miller, Overleaf, United States

Chair: Rob Finn, EMBL-EBI

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Learn how to get started with Overleaf and run step-by-step through everything you’ll need to create and publish an article. You will also learn how to share your documents with your collaborators, and how the integrated commenting system can be used to allow others to give quick feedback. 

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TT17: Jalview and the Dundee Resource for Sequence Analysis and Structure Prediction
Room: Terrace 1
Date: Monday, July 24: 12:10 pm - 12:30 pm

Presenting Author: Geoffrey Barton, University of Dundee, United Kingdom

Chair: Rob Finn, EMBL-EBI

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Jalview and The Dundee Resource for Sequence Analysis and Structure Prediction are ELIXIR-UK Tools and Data resources for biological sequence analyis. We will present JPred4, JABAWS 2.2, and Jalview 2.10.2, and highlight new Jalview capabilities, including visualisation and analysis of genomic variants on 3D structure.

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TT18: BioSamples - a solution for sample meta data storage and query
Room: Terrace 1
Date: Monday, July 24: 2:00 pm - 2:20 pm

Presenting Author: Luca Cherubin, European Bioinformatics Institute, United Kingdom

Chair: Dominic Clark, EMBL-EBI

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The talk will focus on what the BioSamples database is and the main purpose behind it. We will describe how users interact with BioSamples as a hub linking sample information with data spanning multiple resources

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TT19: easyGWAS: A cloud-based platform for comparing the results of genome-wide association studies
Room: Terrace 1
Date: Monday, July 24: 2:20 pm - 2:40 pm

Presenting Author: Damian Roqueiro, ETH Zurich, Switzerland

Chair: Dominic Clark, EMBL-EBI

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We will present different use cases to illustrate the full functionality of easyGWAS. Firstly, users will be guided through steps to upload genotype and phenotype data onto the platform. Secondly, different analysis methods will be presented. Finally, the results of the analyses will be visualised, compared and shared with others.

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TT20: Expression Atlas: A platform for integrating and displaying expression data
Room: Terrace 1
Date: Monday, July 24: 2:40 pm - 3:00 pm

Presenting Author: Alfonso Munoz-Pomer Fuentes, European Bioinformatics Institute, United Kingdom

Chair: Dominic Clark, EMBL-EBI

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Expression Atlas is a web-service that collects, annotates, re-analyses and displays gene expression data. With over 3,000 experiments, we include landmark studies, such as GTEx. Using Experimental Factor Ontology (EFO) annotations, we enable ontology-expansion based search. Our data visualisation is also accessible from other sites through an embeddable reusable widget.

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TT21: Pancancer analysis using MethylMix 2.0.
Room: Terrace 1
Date: Monday, July 24: 3:05 pm - 3:25 pm

Presenting Author: Kevin Brennan, Stanford University, United States

Chair: Dominic Clark, EMBL-EBI

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We will present MethylMix 2.0, a recent update to our algorithm that uses beta mixture modules to identify DNA methylation-deregulated genes. We will demonstrate the utility of MethylMix by applying it for cancer subtyping and in a pancancer analysis of The Cancer Genome Atlas (TCGA).

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TT23: Overview of a suite of tools and training material for implementing FAIR data principles
Room: Terrace 1
Date: Tuesday, July 25: 10:00 am - 10:20 am

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

Chair: Edgardo Ferran, EMBL-EBI

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In the context of global endorsement of principles to make data findable, accessible, interoperable and reusable by humans and computers, we present standards-based tools, architecture, and training material that help communities implement FAIR principles for their data sources, demonstrated by application in areas ranging from rare diseases to plant breeding.

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TT24: Galaxy Interactive Environments: Combining the computational power of Galaxy with the analytical flexibility of Jupyter
Room: Terrace 1
Date: Tuesday, July 25: 10:20 am - 10:40 am

Presenting Author: Anton Nekrutenko, The Pennsylvania State University, United States

Chair: Edgardo Ferran, EMBL-EBI

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In many analysis scenarios a researcher wants to perform an exploratory analysis of results obtained within Galaxy to verify an observation or test a hypothesis. Combining Galaxy with environments such as Jupyter creates an extremely powerful platform fully encompassing the "raw data-to-publication'' pathway and making it reproducible.

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TT25: Bringing Innovations in Systems and Analytics to the Bedside: Design of the CompGen Machine
Room: Terrace 1
Date: Tuesday, July 25: 10:40 am - 11:00 am

Presenting Author: Subho Banereje, Uniersity of Illinois at Urbana Champaign, United States

Chair: Edgardo Ferran, EMBL-EBI

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We present the CompGen machine, a research computing system built at the UIUC to integrate the analysis of omics, medical sensor, and electronic health record data to provide more precise, personalized and data-driven therapeutics. We demonstrate the efficacy of the machine on several important healthcare problems.

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TT26: Aquaria - Simplifying discovery and insight from protein structures
Room: Terrace 1
Date: Tuesday, July 25: 11:10 am - 11:30 am

Presenting Author: Sean O'Donoghue, Garvan Institute Of Medical Research, Australia

Chair: Edgardo Ferran, EMBL-EBI

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Aquaria (http://aquaria.ws) is a web resource that simplifies the process of gleaning insight from >100 million protein structure models. This talk overviews Aquaria’s features, highlighting (1) browsing to find related structures, (2) adding user-defined sequence feature, and (3) use of crowd-sourcing to improve visualization of uncertainty and depth perception.

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TT27: The LiteMol suite – interactive web-based visualization of large-scale macromolecular structure data
Room: Terrace 1
Date: Tuesday, July 25: 11:30 am - 11:50 am

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

Chair: Edgardo Ferran, EMBL-EBI

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LiteMol suite is a unique combination of data delivery services CoordinateServer and DensityServer, efficient compression BinaryCIF format, and a lightweight 3D molecular viewer. The solution enables near-instant delivery and display of models, experimental data, and annotations of arbitrary size. It is available free of charge at https://www.litemol.org.

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