Cellular Genetics Informatics | Cellular Genetics

Cellular Genetics Informatics | Cellular Genetics

Cellular Genetics Informatics

Cellular Genetics Informatics Team

Our Research and Approach

Our team provides efficient access to cutting-edge Bioinformatics and Imaging analysis methods for Cellular Genetics programme, which leads and is involved in a number of world-class research initiatives including the Human Cell AtlasHuman Induced Pluripotent Stem Cell Initiative and Human BioMolecular Atlas Program. More information about our group is available in our Travel Guide

Our Services

  • Development and support of single-cell analysis pipelines for various experimental protocols, such as 10X, Smartseq2, scATACseq, CITEseq, inDrop etc.
  • 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.
  • 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.
  • Deployment of the publication supporting websites containing concise data visualisations.
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Our Development Stack

Our development stack is based on the Sanger’s High Performance Compute architecture (thousands of cores orchestrated by LSF) and the Sanger’s OpenStack Flexible Compute Architecture (private OpenStack cloud with thousands of cores orchestrated by Kubernetes) and consists of the following items (more information is in our GitHub organisation):

  • Back End: Docker, Singularity, Kubernetes, Terraform, Ansible
  • Front End: React, Javascript
  • Pipelines: Nextflow, CWL
  • Secondary Analysis: R, python, C, bash

Positions available!

Our team is still growing and there will be new positions available in 2019-2020, 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.

People

Kiselev, Vladimir
Dr Vladimir Kiselev
Group Leader

     

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Alumni

Research Programmes and Faciltites

Partners and Funders

Within Sanger, we work closely with the following groups:
Internal Partners