ELIXIR at the ISMB/ECCB, 21-25 July 2019

ELIXIR is proud to be a sponsor of this year’s ISMB/ECCB Conference, 21-25 July 2019. ELIXIR will be present at booths 23 and 24.

There will be a number of opportunities to engage with ELIXIR throughout the conference. The information below summarises our contributions to the programme and outlines the Tracks and COSIs.

Should you need additional details then please contact Melissa Balzano, ELIXIR Events Officer: melissa.balzano[at]elixir-europe[dot]org, +44 (0)1223 494305.


The ELIXIR::GA4GH Strategic Partnership

Timing Monday 22 July 2019, 10:15 am - 12:40 pm
Speakers Gary Saunders (ELIXIR Hub) and Jonathan Tedds (ELIXIR Hub)
Track This session describes the complementary activities carried out by both organisations in order to establish and implement a suite of interoperable standards and tools to overcome the technical and regulatory hurdles to aid genomic data-sharing (GA4GH on an international scale, ELIXIR predominantly on a European scale).
Description Large cohorts, with potentially millions of participants, are needed to understand the genetic and molecular signatures of diseases, and they provide a cornerstone for the creation of personalised treatments. The ELIXIR::GA4GH Strategic Partnership will facilitate the responsible sharing of these sensitive data across Europe in order to help create virtual cohorts with tens of millions of participants. In this session we will describe the complimentary activities that are carried out by both organisations with a focus on secure data archival, federated data discoverability, authorised data access, and distributed data analysis.

ELIXIR Beacons: Federating Data Discoverability

Timing Monday 22 July 2019, 2:00 pm - 4:00 pm
Speakers Gary Saunders (ELIXIR Hub) and Frederic Haziza (ELIXIR-ES)
Track This workshop will demonstrate the Beacon API, a data discovery protocol that allows users to determine the presence or absence of a particular allele in a dataset, without disclosing any further data differentiating the individuals it contains.
Description The ELIXIR Beacons project is a Driver Project of the Global Alliance for Genomics and Health that provides a simple way to federate data discoverability. The ELIXIR Beacons protocol can allows any variation data back end to be connected to the ELIXIR Beacons network which can then be queried to ask questions like 'does this dataset have any information about allele 'X' at position 'Y' in the genome?'. This workshop will show how recent extensions to the Beacon API has extended its functionality by adding support for additional types of genomic variants and improved metadata support. Additionally we will also demonstrate the accompanying ELIXIR Beacon reference implementation which utilises risk mitigation strategies by integrating the ELIXIR Authorization and Authentication Infrastructure (AAI), demonstrating to data owners how to light Beacons at different tiers of data access: open, registered, or controlled.

Bioschemas and 4OSS: recommendations on metadata for tools

Timing Monday 22 July 2019, 4:40 pm - 6:00 pm
Speakers Kenneth McLeod (ELIXIR UK) and Leyla Garcia (ELIXIR Hub)
Track Learn what Bioschemas and 4 simple recommendations for open source software (4OSS) are about and how to use them to add metadata to your research software and get more visibility.
Description This tutorial aims to introduce Bioschemas and 4OSS so research software become more findable (mainly) but also interoperable and reusable. Bioschemas is a community initiative based on schema.org aiming to facilitate the adoption of structured metadata in Life Science web pages in order to improve findability and interoperability. 4OSS comprises 4 key recommendations to improve quality of open source research software. Both of them support elements aligned with the Findable, Accessible, Interoperable and Reusable (FAIR) principles. During this session, participants will become familiar with Bioschemas and 4OSS and will learn how to use them in order to annotate (open) research software with metadata.

Scalable Plant Research in Cloud Environments (COSI)

Timing Wednesday July 24, 10:15 am - 6:00 pm

Introduction to the ELIXIR plant community
Frederik Coppens, VIP, Belgium

Plant Phenotyping infrastructure: Breeding API & MIAPPE
Cyril Pommier, INRA, France

(Plant) Data Resources at EBI
Bruno Contreras-Moreira

Cloud Computing and Free Available Academic Clouds
Pablo Moreno, EMBL-EBI, UK

Overview of CyVerse tools and services: introduction to data/metadata management and sharing with CyVerse
Jason Williams, Assistant Director, External Collaborations Lead, CyVerse

Introduction to Galaxy and the European Galaxy community
Anika Erxleben, University of Freiburg, Germany

A PhenoMeNal Workflow to Study the Metabolites Variation in Bryophytes across Seasons
Kristian Peters, Leibniz Institute of Plant Biochemistry, Germany

FAIRly maintain and publish research data with e!DAL (electronic Data Archive Library)
Björn Grüning, University of Freiburg, Germany

Overview of tools and container infrastructure
Olivier Sallou (tbc)

Genome annotation with Galaxy


This session will give participants an introduction to what is needed to use and create cloud-enabled bioinformatics pipelines. Speakers from several projects that are already using cloud computing to solve plant related research questions will be featured. Based on their hands-on experience, speakers will showcase usage of cloud computing in their projects, including bottlenecks and learned best practices. We will introduce participants to usage of established as well as emerging data repositories and standards. The focus will be on accessing and using these resources for FAIR data management strategies and integrative analysis leveraging the power and scalability of cloud computing, with a particular emphasis on resources created by the ELIXIR Galaxy working group, and by the larger ELIXIR community.

At the end of the session participants will be able to leverage cloud computing and data resources for their research questions according to best practices, using established production platforms.

More information https://www.iscb.org/ismbeccb2019/3748#sst02