Our team maintains both hardware and software infrastructure to support the research in microbial genomics. To ensure the reproducibility and traceability of our experiments, we have a dedicated sequencing output archival system based on the IRIDA platform, we maintain a Galaxy Instance (and we added several tools to the Galaxy Toolshed), and a private cloud based on OpenNebula through our infrastructure.

Our team is composed of experience senior scientists, with experience in infrastructure management, software development, data analysis and microbial genomics and microbiome analysis.

Our team has organised several hackathons in the past, and we are always happy to engage with other bioinformaticians from all over the world. We provide several training opportunities to scientists based at the Quadram Institute and occasionally we deliver training and workshops abroad.

Training

The Core Bioinformatics team is committed to support the bioinformatic and data science needs of the institute through a variety of training activities. Our goal is to foster a collaborative environment, open for everyone and in particular supportive of researchers or students interested to start their bioinformatic journey.

Through a diverse range of training activities, the we create a dynamic and skilled community of researchers equipped to tackle the complex data challenges in modern microbiology.

Internal workshops and data science group meetings

We organise regular internal workshops and group meetings to promote computational knowledge sharing and skill development within the institute. Among these activities is our Data Science Club, which brings together all data science actors once a month and serves as a forum for discussing new methodologies, sharing best practices, and exploring bioinformatics tools.

We rely on a combination of formal presentations, to explore major concepts, and hands-on sessions to allow participants to gain practical knowledge, and we thrive to make our workshop inclusive for all and welcoming for beginners.

Workshops with international experts

To ensure Quadram Institute researchers and students have access to the most up-to-date computational resources and tools, we regularly organise workshops featuring international experts. In 2024, we have hosted workshops on Anvi’o, a powerful platform for the analysis and visualisation of ‘omics datasets, and OMA, a method and database for inferring orthologs among complete genomes.

These workshops bring world-class experts to the Quadram Institute, providing our researchers with direct access to the developers and power users of critical bioinformatics tools. Through a combination of lectures, demonstrations, and hands-on sessions, these workshops enable our researchers to quickly adopt and effectively utilise state-of-the-art computational methods in their work. This initiative not only enhances our technical capabilities but also fosters valuable connections with leading figures in the field of bioinformatics.

Hackathons and code-hacking sessions

The Core Bioinformatics team is involved in the organisation of internal and international hackathons, aiming to tackle specific computational challenges and promote collaborative coding. As an example, we hosted in 2024 a local session for the nf-core hackathon, an international event focused on developing and improving Nextflow pipelines for bioinformatics.

These intensive, short-term events bring together researchers, developers, and bioinformaticians to work on targeted computational challenges. They provide an excellent opportunity for researchers and students to engage in computational projects, learn new skills, and contribute to open-source projects that benefit the wider scientific community.

Infrastructure

Hardware

Based on the Norwich Research Park, our institute has a modern computing infrastructure providing both an High Performance Computing cluster (HPC) and a private on-premises Cloud.

In 2024 we refurbished our systems in a collaborative effort between the Core BioInformatics group and NBI Research Computing thanks to the £1.5 million BBSRC award for research infrastructure, improving the capacity of both the open-source OpenNebula cloud platform and the SLURM-based HPC cluster.

The advanced setup features diverse, powerful nodes, including ten 84-core Genoa processors with 512GB RAM each, three 192-core Genoa processors with 1.5TB RAM each, and three 128-core Milan processors boasting 4TB RAM each. This configuration provides 2,436 CPU cores and 36.5TB of RAM.

Additionally, the infrastructure incorporates multiple NVIDIA A100 and L40S GPUs, significantly boosting AI and machine learning capabilities. The system is backed by a robust Ceph storage solution, offering 100TB of usable storage for virtual machines.

This second-generation cloud significantly enhances the institute’s capacity for computational microbiology and bioinformatics research while bolstering its capabilities in AI applications for bioscience. The advanced infrastructure solidifies the Quadram Institute’s position as a world-class research institute in microbial genomics projects and paves the way for cutting-edge research.

Platforms

To ensure long term storage of raw sequencing datasets, we maintain an instance of IRIDA (The Integrated Rapid Infectious Disease Analysis), that provides a centralised dataset storage and metadata management, access to automated pipelines and APIs to retrieve datasets from the command line, from the web browser or from Galaxy.

We maintain a Galaxy instance, with all the tools needed for microbial genomics analysis, and seamlessly integrated with other platforms.

Our researchers can spin up a Virtual Machine from our private cloud using a web interface, and each VM has access to the datasets stored in the HPC.