Comprehensive Bioinformatics support for the programme users.
Development and support of single-cell Nextflow analysis pipelines for various experimental protocols, such as 10X, Smartseq2, scATACseq, TraCeR/BraCeR, CITEseq, inDrop etc. All of our pipelines have full HPC (LSF) and OpenStack Cloud integrations.
Data sharing with external collaborators.
Data submission to ArrayExpress.
Maintenance and support of the programme's Jupyter Hub dedicated for the data secondary analysis. We provide software support and a set of standard analysis notebooks, such as Seurat, scanpy, single cell data integration notebooks etc.
Data access for external collaborators via Jupyter Hub.
Development of the programme's internal Web portal which includes a multiuser sample tracker, ability for the users to run our pipelines from the web and integration with our Jupyter Hub.
Development and support of the programme's Imaging portal which allows the users to both run the imaging analysis pipelines and visualise their results.
Organisation of workshops for the users on different topics, such as Git, Jupyter Notebooks, Docker/Cloud, Rstudio/Shiny, Nextflow.
Illustrator: Christina Usher
Our Software/Analysis Stack
We run our pipelines and perform analysis on the Sanger’s High Performance Compute cluster (thousands of cores orchestrated by LSF) and the Sanger’s OpenStack Flexible Compute environment (private OpenStack cloud with thousands of cores orchestrated by Kubernetes). We use the following software/analysis stack (more information is in our GitHub organisation):
Back End: Kubernetes, Docker, Singularity, Terraform, Ansible
We have an excellent experience with student internships and apprenticeships. We welcome students with their own funding (with a possibility of topping it up) to work on both infrastructure and research projects. Please contact Vladimir Kiselev for further information. For apprenticeship information please check the dedicated Sanger website.
We explore the consequences of genome variation on human cell biology, and thus gene function in health and disease. We conduct large-scale systematic screens to discover the impact of naturally-occurring and engineered genome mutations in human iPS cells, their differentiated derivatives, and other cell types.
Partners and Funders
Within Sanger, we work closely with the following groups:
Gene expression involves the transformation of genetic information encoded in DNA sequence into a gene product, such as a protein. Regulation of gene expression is a fundamentally important process in biology because controlling the timing, location and level of gene expression is critical for the gene product to function correctly. The majority of mutations that alter disease risk for most common diseases are thought affect gene regulation, although how these mutations actually function is not well understood in most cases. Our group uses a combination of statistical and experimental approaches to map mutations that affect gene regulation in humans.
The Hemberg group is interested in developing quantitative models of gene expression. Our approach is theoretical and we strive to develop novel mathematical models as well as computational tools that can be used by other researchers.
Our Informatics support team is responsible for both developing and providing scale out scientific compute platforms that can both meet todays scientific challenges but also provide support and development as new and potentially disruptive technologies arise.
We measure, model, and modulate cell state. We use genome engineering and synthetic biology to create cell lines that can be employed for CRISPR/Cas9-based genetic screening and high throughput cell biology assays. We develop probabilistic models as well as software tools to accurately analyse the readouts.
We use cutting edge single cell genomics technologies and computational methods to understand genes, proteins and cells in human health and disease. We have a long-standing interest in understanding global principles of gene regulation, protein interactions and have a particular interest in immunity.