• Denis Bienroth, Murdoch Children's Research Institute, Australia
• Mirana Ramialison 

We present a novel data analysis and visualization framework called VR-Omics with interactive functionalities using either virtual reality or a common desktop solution for 3D visualisation for spatial transcriptomics datasets. VR-Omics supports all common spatial transcriptomics detection methods from sequencing to imaging-based patforms.

• David Yuan

The European Nucleotide Archive (ENA) at EMBL-EBI is one of the largest and long-standing public databases along with partner resources at NCBI and DDBJ forming the International Nucleotide Sequence Database Collaboration. ENA serves the bioinformatics community worldwide via the submission, processing, archiving and distribution of sequencing data. Supported data types cover from raw reads, through alignments and assemblies to functional annotation, enriched with contextual information relating to samples and experimental configurations. Since its inception in early 1980s, ENA has evolved into a comprehensive sequence data coordination platform with applications to specific scientific domains. Since 2020, EMBL-EBI has created and maintained services that build on the ENA data coordination platform such as Pathogens Portal and the COVID-19 Data Portal; ENA has helped these initiatives analysing millions of SARS-CoV-2 genomes systematically.

The volume of data in ENA has seen steady growth, at around 35% year over year for the last five years, and is projected to to exceed 150 PB by 2027. To sustain ENA in the face of ever increasing sequencing data volumes we present three technical goals:

1. To increase operational performance in most valuable areas
2. To improve and simplify systems to ensure sustainability
3. To tailor ENA services to fit modern sequencing analysis workflows

In support of these goals, we are taking steps to improve ENA to serve the bioinformatics community better with higher efficiency, and we are undertaking a programme of user outreach to establish closer collaboration with our user community and to better understand the data generation and analytical workflows that make use of ENA services. This includes workflows such as pipelines for SARS-CoV-2 analysis and metagenomic sequence assembly built by users around ENA.

In addition to highlighting the technical challenges that operating at such a large scale brings, we also present ENA services in the context of two specific analysis workflows, illustrating how ENA can be used as a data management platform to support scientific drivers. In particular, we use the Pathogen Analysis System to showcase some of the more familiar ENA features and how to apply them to analyse millions of SARS-CoV-2 genomes in a streaming mode. We also describe how metagenomics workflows can be well integrated with ENA.

1. Burgin, Josephine et al. “The European Nucleotide Archive in 2022.” Nucleic acids research vol. 51,D1 (2023): D121-D125. https://doi.org/10.1093/nar/gkac1051
2. Rahman, Nadim et al. “Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses” Biorxiv (2023): https://www.biorxiv.org/content/10.1101/2023.04.19.537514v2

• Howard Baek, Fred Hutchinson Cancer Center
• Elizabeth Humphries, Fred Hutchinson Cancer Center
• Sean Finan, Boston Children’s Hospital and Harvard Medical School

This presentation will have two parts. The first will be an introduction to genomics related resources from our
training network, followed by a demonstration of the tool suite pVACtools (pVACtools.org), and the tools MIRA and CODAL for integrating analysis of ATAC and RNAseq data.

• Howard Baek

This presentation will have two parts. The first will be an introduction to data handling related resources from our training network followed by a demonstration of two clinical tools that help researchers work with clinical records, DeepPhe (https://deepphe.github.io/) and EMERSE (https://project-emerse.org).

• Qian Liu

Here we present an R/Bioconductor toolset (Rcwl, RcwlPipelines, ReUseData) to assist researchers with efficient management and analysis of large genomic data. The toolset employs workflow infrastructure, containerization strategy, and Conda environment, enabling users to implement reproducible and streamlined data analysis within a unified R environment across different computing environments.

• Jessica Miller

The Open Science movement has been evolving rapidly in recent years, and the Royal Society has been a driving force in its development and wider adoption. Jessica Miller from Royal Society’s publishing team will discuss the Open Science initiatives, its associated successes and challenges, and the future opportunities. 

• Jon Jiang, MemVerge Inc., United States

WaveRider is a novel framework that dynamically adapts RAM and CPU core allocation for bioinformatics workloads in the cloud. Using MemVerge's SnapSHOT technology, it monitors resource consumption and resizes instances on-demand. WaveRider reduces costs by 24%-28% and prevents Out-of-Memory issues, offering a more cost-efficient and flexible solution for cloud-based bioinformatics pipelines.

• Mitchell Shiell, Ontario Institute of Cancer Research (OICR), Canada
• Jon Eubank, Ontario Institute of Cancer Research (OICR), Canada
• Justin Richardsson, Ontario Institute of Cancer Research (OICR), Canada
• Brandon Chan, Ontario Institute of Cancer Research (OICR), Canada
• Puneet Bajwa, contact@overture.bio, Canada
• Robin Haw, contact@overture.bio, Canada
• Christina Yung, contact@overture.bio, Canada
• Lincoln Stien, Ontario Institute of Cancer Research (OICR), Canada
• Melanie Courtot, Ontario Institute of Cancer Research (OICR), Canada

Overture is a collection of modular software components that build into scalable genomics data management systems. In this talk, we discuss how Overture can help achieve FAIR data goals and demonstrate its core software components: Song, Score, Maestro, Arranger and Ego. 

• Filippo Utro, IBM, United States

This talk will present several distinct initiatives by IBM Research focused on multi-omics analysis with the unified goal of accelerating disease and drug discovery. I will cover a range of open-source tools and give you our perspective on Foundation Models and Quantum technology’s future use in life science.

• Nicola Bordin

CATH provides a comprehensive database for classifying protein structures based on evolutionarily related features. The recent availability of over 800 million protein models from AlphaFold and ESMFold has significant implications for CATH. This Technology Track presents CATH-AlphaFlow and ChainSaw to analyse and classify the models efficiently and robustly.

• Philippe Youkharibache, NCI/NIH, USA
• Jiyao Wang, NCBI/NLM/NIH, USA

iCn3D is an open source web-based software developed initially at the NIH to allow scientists from different backgrounds to perform and share 3D visualizations and structural analyses over the Internet. Its unique link sharing mechanism enables collaborative research, scientific education and 3D publishing.

• Frederic Cazals

This talk will present a recently developed library providing a comprehensive software instrument
to tackle the complex challenges currently faced in structural bioinformatics. The presentation will also feature
several live demos.

• Nikolina Nakic

Targets supported with genetic evidence are twice as more likely to achieve clinical success. How can we further improve those odds? This talk will illustrate how we are de-risking early drug discovery by integrating genetics with biological insights enabled by technical advances in omics and functional genomics.

• Judith Zaugg

Phenotypic variation (including disease) across individuals has two main sources: genetic variation, and variation in environmental exposures. In the past decades the field made tremendous advances in mapping common genetic variants to complex traits and diseases. Yet, the majority of these disease-associated variants lie in the non-coding part of the genome, which makes is very difficult to understand the underlying molecular mechanisms. For the environmental impact on complex phenotypes, we still know very little, yet epigenetics may play a significant role. Our vision is to mechanistically understand how non-coding genetic variants affect gene regulation, how they interplay with epigenetic processes, and how these interplay impacts cellular signaling and cell-cell interactions. In this talk I will present our most recent work on cell-type specific and enhancer-mediated regulatory networks that integrate environmental signaling with genetic and epigenetic variation. I will show applications of our predictive models to investigate aging of bone marrow niche and the immune system. Overall, our integrative approach with a focus on gene regulation provides a powerful tool to gain mechanistic insights into complex biological processes including disease mechanisms.

• Francisco Azuaje, Genomics England, UK

This presentation will overview advances, challenges, and opportunities for enabling biomedical research through AI using different data types. The latter includes omics, natural language, and clinical imaging. It will illustrate impact and lessons from ongoing health care and research initiatives at Genomics England and elsewhere.

• Julio Saez-Rodriguez

Multi-omics technologies, and in particular those with single-cell and spatial resolution, provide unique opportunities to identify deregulated intra- and inter-cellular processes in disease that can be potential therapeutic targets. I will present recent methods and applications towards this end by leveraging existing knowledge of the underlying mechanisms.

• Enoch Huang, Pfizer, USA
• Tuan Le, Pfizer, Germany
• Joe Salens, Pfizer, USA
• Andreas Steffen, Pfizer, Germany

In this presentation, we delve into how we develop computational methods for different stages of the drug discovery pipeline. Examples will include finding promising starting points derived from integrative analysis of chemical proteomics data, generating and optimising small molecules using machine learning, and characterizing late-stage biologics like gene therapy.

• Janet Piñero

We will introduce DISGENET plus, a platform to leverage the knowledge of disease genomics to support drug development and precision medicine applications. We will showcase different functionalities of the platform that include a web interface, a REST API, and an R package.

• José Carbonell-Caballero

PerMedCoE, a newly established European Center of Excellence in personalized medicine, focuses on refactoring and enhancing scalability to deliver a powerful HPC framework to translate omics analyses into practical cellular models. In this presentation, we will summarize the main strategies we are following to achieve such a challenging goal.

• Manali Ghosh, St. Jude Children's Research Hospital, United States

Whether you are graduating soon or early in your degree, it is never too soon to think about your next career step. Dr. Manali Ghosh, a postdoc recruiter, will provide general information regarding what to look for when searching for a postdoc position, in addition to information specific to St. Jude.