Cellular Genetics Informatics
- 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.
- Development of GPU-accelerated imaging pipelines.
- Deployment of bespoke and the publication supporting websites containing models and concise data visualisations.
- 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
- Interactive Analysis Environments: Jupyter Hub
- Pipelines runners: Nextflow
- Secondary Analysis: R, python, C, bash
- Imaging: Omero, Bio-Formats, Fiji, cellprofiler, StarFish
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.
Dr Vladimir Kiselev
Cellular Genetics Informatics Team Leader
I am leading the Cellular Genetics Informatics team. Our team provides efficient access to cutting-edge analysis methods, environments and pipelines for Cellular Genetics programme, which leads and is involved in a number of world-class research initiatives including the Human Cell Atlas, Human Induced Pluripotent Stem Cell Initiative and Human BioMolecular Atlas Program. We work with large amounts of single-cell RNA sequencing and microscopy imaging data.
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