• James McCafferty, Wellcome Sanger Institute, United Kingdom

The Wellcome Sanger Institute in Cambridge UK is a world-leader in genomics research. My role as Chief Information Officer includes responsibility for our core informatics and data management. This presentation will outline the current setup and work underway at the Sanger, demonstrating how informatics and data management are key to our current and future scientific endeavours. I will outline the main elements of our new Informatics Strategy. This aims to build a world-class informatics capability to support our science. I’ll also outline our Data Management Strategy. We have over 90PB of genomics-related data, so managing and getting best value from our data is critical to our science. Finally, I’ll highlight some future directions in better exploiting technology to improve how we do science generally. The ‘Digital Transformation of our Science’ is a vision that sees all our scientists suitably trained and equipped to exploit next-generation digital infrastructure and techniques, to improve all aspects of their science.

• Patricia Carvajal-López, EMBL-EBI, United Kingdom
• Marta Lloret-Llinares, EMBL-EBI, United Kingdom
• Cath Brooksbank, EMBL-EBI, United Kingdom

Bioinformatics core facilities (BCF) play an essential role in enabling research in life sciences. As deep learning and high-throughput sequencing methodologies are increasingly applied to analyse molecular data, there is a growing need for highly specialised services from BCFs and their supporting teams.

As BCF scientists transition from entry level to managerial roles there are some tools that partially describe the competencies they require as they progress through this career. The ISCB bioinformatics competency framework, published at the EMBL-EBI Competency Hub (https://competency.ebi.ac.uk), is one of them. However, the current version of the framework (V3) does not reflect the competency proficiency needed by BCF scientists as they progress in their careers. The Curriculum Task Force of the ISCB Education Committee continues to work on providing updated frameworks for bioinformatics core competencies. Nonetheless, the current stage of analysing the competencies related to career progression of BCF scientists requires the active participation of this community of practice.

The effort of developing a well-defined competency framework along with training for this community will be essential to support career progression of BCF specialists who, in return, enable research and development within the life sciences.

• Kübra Narcı, Deutsches Krebsforschungszentrum, Germany
• Florian Heyl, Deutsches Krebsforschungszentrum, Germany
• Christian Mertes, Technical University Munich, Germany
• Paul Menges, Deutsches Krebsforschungszentrum, Germany
• Luiz Gadelha, Deutsches Krebsforschungszentrum, Germany
• Vangelis Theodorakis, Technical University Munich, Germany
• Daniel Huebschmann, Deutsches Krebsforschungszentrum, Germany
• Ivo Buchhalter, Deutsches Krebsforschungszentrum, Germany

With increasing numbers of human omics data, there is an urgent need for adequate resources for data sharing while also standardizing and harmonizing data processing. Within the federated European Genome-Phenome Archive (EGA), the German Human Genome-Phenome Archive (GHGA) strives to provide (i) the necessary secure IT-infrastructure for Germany, (ii) an ethico-legal framework to handle omics data in a data-protection-compliant but open and FAIR manner, (iii) harmonized metadata schema, and (iv) standardized workflows to process the incoming omics data uniformly.
GHGA is aiming to be more than an archive. GHGA will build on cloud computing infrastructures managed in a network of data generators. Researchers will have controlled access to raw and processed sequence data using recognized GA4GH-compliant NGS workflows. For this, GHGA is working with the nf-core community to co-develop and standardize bioinformatics workflows for data analysis, benchmarking, statistical analysis, and visualizations. Besides, continuous integration and deployment to test and benchmark workflows, synthetic and experimental datasets will be applied to guarantee the high quality of workflows. Finally, by delivering on IT infrastructure and the aforementioned goals, an ethico-legal framework, metadata schemas, and standardized and reproducible workflows, GHGA will enable cross-project analysis and promote new collaborations and research projects.

• Ayesha Iqbal, Max Planck Institute for Biology of Ageing, Germany
• Camila Duitama Gonzalez, Institut Pasteur, France
• Franziska Metge, Radboud University Medical Center, Netherlands
• Yun Wang, Max Planck Institute for Biology of Ageing, Germany
• Jorge Boucas, Max Planck Institute for Biology of Ageing, Germany

Flaski is a flask-dash collection of interactive web apps for data analysis and visualisation in life sciences with session management and versioning. Flaski current range of apps includes general purpose plotting (eg. scatter plots, heatmaps), data rich apps (eg. RNAseq database), machine learning (eg. PCA, t-SNE), and submission forms for backend jobs (eg. RNAseq, AlphaFold). App-to-app communication ensures easy maintenance and use of general apps across the stack. Flaski is built upon interactions between code experienced and non-experienced users for which sessions created over the web interface can be downloaded and further worked on in python as a standard plotly object and vice-versa. Flaski is responsive, depending on your data size it will work well on your desktop display down to your mobile phone. Flaski is open source under the MIT license and can be used without restrictions under https://flaski.age.mpg.de.

• Francisco Javier Lopez, Genomics England, United Kingdom
• Adrianto Wirawan, Genomics England, United Kingdom
• Augusto Rendon, Genomics England, United Kingdom

Building WGS analysis pipelines to support a national-scale clinical service is not a trivial task. In an academic / research environment, developers will typically focus on creating functional and reproducible workflows. Resources are typically limited and once the project is finished, results are published and in most cases that is the end of the journey. Developing WGS analysis pipelines fit for clinical-service purpose possesses some critical challenges imposed by requirements such as service sustainability, contractual Turn Around Times, evolving with new technology paradigms, team growth, strict regulation, among others. Genomics England is a company wholly owned by the Department of Health and Social Care of the United Kingdom. Upon successful completion of the 100k Genomes project, GEL started a transformation process to support the Genomic Medicine Service for the NHS. It has been a challenging task for Genomics England’s pipelines to address the additional clinical-service requirements mentioned above. Although great progress has been made, some of these challenges still impact our activities. In this presentation we will walk through the learnings from 8+ years of experience developing WGS analysis pipelines with a national-scale clinical purpose.

• Hua Li
• Meeta Mistry
• Jenny Drnevich, University of Illinois Urbana-Champaign, United States of America
• Ellis Patrick
• Ayushi Agrawal, The J. David Gladstone Institutes, United States of America

Panel topics may include:
- current challenges with spatial data
- platform pros and cons or experiences
- best practices or things that worked
- tools for data analysis, integration, visualization
- strategies for finding time/resources to spend on development of new approaches

Attendees will break into small groups to discuss topics from lightning talks and panel.

One representative from each group will summarize key points from breakout group discussion.