Cellular Genetics Informatics

Cellular Genetics

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.

About us

We provide informatics support for the Human Cell AtlasHuman Induced Pluripotent Stem Cell Initiative and Human BioMolecular Atlas Program. We work with large amounts of single-cell RNA sequencing and microscopy imaging data.

More information about our group is available in our Travel Guide.

Our Services

Our team:

  • provides comprehensive bioinformatics support for the Cellular Genetics programme
  • develops and supports single-cell Nextflow analysis pipelines for various experimental protocols, including 10X, Smartseq2, scATACseq, TraCeR/BraCeR, CITEseq, inDrop.
    All of our pipelines have full HPC (LSF) and OpenStack Cloud integrations
  • enables data sharing with external collaborators
  • facilitates data submission to ArrayExpress
  • maintains and supports the programme’s Jupyter Hub dedicated for the data secondary analysis. We provide software support and a set of standard analysis notebooks, including Seurat, scanpy, single cell data integration notebooks
  • enables data access for external collaborators via Jupyter Hub
  • develops 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
  • develops and supports the Cellular Genetics Imaging portal which allows the users to both run the imaging analysis pipelines and visualise their results
  • develops GPU-accelerated imaging pipelines
  • deploys bespoke and the publication supporting websites containing models and concise data visualisations
  • organises workshops for the users on different topics, including 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
  • Front End: Javascript, React
  • Interactive Analysis Environments: Jupyter Hub
  • Pipelines runners: Nextflow
  • Secondary Analysis: R, python, C, bash
  • Imaging: Omero, Bio-Formats, Fiji, cellprofiler, StarFish

Positions available

Our team is growing, please check the Sanger vacancies website for more information.

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.

Our people

Core team

Photo of Dr Maria Keays

Dr Maria Keays

Senior Software Developer

Photo of Simon Murray

Simon Murray

Bioinformatics Apprentice

Photo of Dr Alexander Predeus

Dr Alexander Predeus

Principal Bioinformatician

Photo of Martin Prete

Martin Prete

Senior Software Developer

Photo of Vasyl Vaskivskyi

Vasyl Vaskivskyi

Bioinformatician

Photo of Dr Stijn van Dongen

Dr Stijn van Dongen

Senior Software Developer

Previous team members

Photo of Miss Tanya Bayzetinova

Miss Tanya Bayzetinova

Student Placement

Photo of Batuhan Cakir

Batuhan Cakir

Visiting Scientist

Photo of Mr Ruben Chazarra Gil

Mr Ruben Chazarra Gil

Visiting Scientist

Photo of Anton Khodak

Anton Khodak

Senior Software Developer

Photo of Dr Vladimir Kiselev

Dr Vladimir Kiselev

Cellular Genetics Informatics Team Leader

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