Cellular Genetics Informatics
Cellular Genetics
Our Services
- 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
- 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 still growing and there will be new positions available in 2020-2021, please check the Sanger vacancies website for more information or contact Vladimir Kiselev 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. Please contact Vladimir Kiselev for further information. For apprenticeship information please check the dedicated Sanger website.
Core team

Dr Maria Keays
Senior Software Developer

Simon Murray
Bioinformatics Apprentice

Dr Alexander Predeus
Principal Bioinformatician

Martin Prete
Senior Software Developer

Ola Tarkowska, MSc. Eng
Senior Software Engineer

Vasyl Vaskivskyi
Bioinformatician

Dr Stijn van Dongen
Senior Software Developer
Previous team members

Miss Tanya Bayzetinova
Student Placement

Batuhan Cakir
Visiting Scientist

Mr Ruben Chazarra Gil
Visiting Scientist

Anton Khodak
Senior Software Developer