Scientific platforms

Image: Genome Research Limited

Scientific Platforms
Science at scale

Scientists at the Wellcome Trust Sanger Institute and EMBL-EBI are supported by their state-of-the-art research tools and scientific platforms that operate at scale.

Sequencing
Sequencing

The Wellcome Trust Institute has one of the largest DNA sequencing facilities in the world and is currently capable of producing more than 1700 terabases (1700 x 10 12 bp) of DNA sequence per year. Thanks to the latest Illumina hardware and bespoke in-house developed software, this is one of the most accurate and efficient sequencing facilities in the world.

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Big data processing & analysis: EMBL-EBI
Big data processing & analysis:
EMBL-EBI

EMBL-EBI makes open access biological research data sets available. These are used extensively across the world by more than five million researchers in academia and industry. Some 18.5 million requests for data are made on a daily basis to EMBL-EBI’s websites. Analysing this data has become a bottleneck for life-science research and EMBL-EBI provides facilities to enable this work.

The Embassy Cloud provides private, secure, virtual machine-based workspaces within the EMBL-EBI infrastructure, in which clients can make optimal use of their own customised workflows, applications and datasets.

Embassy Cloud “tenants” have direct access to the EMBL-EBI data, services and compute. This is a practical and cost-effective alternative to replicating services and downloading vast public datasets locally. Tenants can access their workspace from anywhere in the world, reducing the need for capital investments in hardware and related operational costs.

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Big data processing & analysis: Wellcome Trust Sanger Institute
Big data processing & analysis:
Wellcome Trust Sanger Institute

The data output from the Wellcome Trust Sanger Institute is increasing all the time and the Institute has developed new technologies for storing and accessing the data. The iRODS (Integrated Rule-Orientated Data System) is a tool that is accessible to all for the management and distribution of sequence data.

The Institute has also developed more efficient data-storage formats that, like all the Institute’s software tools, are made available to the research community on an open-access basis.

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Data storage
Data storage

The Wellcome Genome Campus has a world-class supercomputing environment, providing the best production platforms and services. Between the Wellcome Trust Sanger Institute and EMBL-EBI, there are several high performance compute clusters with may thousands of CPU cores. Data is served to researchers around the world, daily.

Storage is around 42 petabytes at the Wellcome Trust Sanger Institute and around 100 petabytes at EMBL-EBI. As genomics research expands, so do the data storage and access requirements of researchers. We are adding more storage and greater processing power all the time, to meet these demands.

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Single cell genomics
Single cell genomics

The single cell genomics facility can deliver thousands of single cell genomes, transcriptomes, and epigenomes, every day. This gives hugely valuable information about the state of a particular cell at a particular time, which supports research into general cell biology as well as applied cancer, immunology, and infectious disease research.

The facility employs microfluidic systems, acoustic dispensing, conventional flow sorting of single cells, and liquid handling robots. These technologies are complemented by a fully automated sample handing, quality control, and library preparation pipeline.

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Cellular generation & phenotyping
Cellular generation & phenotyping

The Cellular Generation and Phenotyping core facility provides central cell biology support, in particular to scale-up and automate existing protocols. The facility has expertise in cell derivation from primary tissue, induced pluripotent stem cell derivation, cellular differentiation, phenotypic assays, and end point analysis. In addition to providing enhanced skills to research groups, the facility attracts funding for research in its own right and also carries out contract work.

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Stem cell informatics
Stem cell informatics

Stem Cell Informatics develops custom laboratory information systems (LIMS) and computational research tools high-throughput laboratory analysis of human stem cells.

The team has also developed WGE, a highly interactive, web-based visual tool that employs an embedded genome browser and database to assist scientists in designing genome editing strategies using the CRISPR/Cas9 system.

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Genome editing
Genome editing

The Wellcome Genome Campus is one of the first places in the world where it is possible to routinely use the latest Crispr-cas9 genome editing technology.

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Molecular cytogenetics
Molecular cytogenetics

The molecular cytogenetics facility offers a range of FISH (fluorescence in situ hybridisation) services for the study of whole chromosomes. Services include: physical assignment of BACs, fosmids, transgenes, cDNA clones onto metaphase chromosomes; high-resolution mapping and gap sizing by fibre-FISH with single-molecule DNA fibres and extended chromatin fibres; karyotyping by combined M-FISH and inverted DAPI-banding; validation of structural and copy number variations; and multi-directional chromosome painting.

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Cytometry
Cytometry

The Cytometry Core Facility provides state of art instrumentation together with assistance in running samples, data analysis and experimental design, in order to measure cell characteristics. Sorting is also provided as a service application. The facility supports a range of flow cytometric techniques and currently has six cytometers with a variety of possible applications.

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Model pipelines
Animal model pipelines

This facility provides and characterises knock-out mice for large scale research projects. They also provide and care for mice, zebrafish, rats and frogs that are used in research studies by scientists all over the world.

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Achievements and uniqueness
Achievements and uniqueness

The Wellcome Genome Campus is unique in the world as the largest concentration of genomics knowledge and facilities. In this environment, ideas flourish to become world-changing discoveries that are applied to real-world problems.

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