Oxford Biomedical Data Science Training Programme

The OBDS programme was established in 2017 with funding from Wellcome, the Cancer Research UK Oxford Centre and the NIHR Oxford Biomedical Research Centre. To date the programme has trained over 150 biomedical researchers, who have benefited from the course in different ways (see testimonials).

This unique programme runs three times per year, with timings aligned to the University of Oxford terms. The programme delivers  face-to-face online lectures, tutorials and group exercises. Our multi-week format and small group size enable us to go step-by-step through real world scenarios from setting up software environments to processing data and visualisation of results. The interactive format encourages participants to lead group exercises; quickly building the confidence and resilience required for independent work.  

In January/February 2023, we are offering three short courses. All courses are in person in the Conference Room in the Weatherall Institute for Molecular Medicine.    

Genomics on the Linux command line (Introductory course)

• One week - 23/01/2023-27/01/2023, 9.30am-4pm Monday-Friday
• Cost: £1000
• Navigating the Linux command line
• Editing and processing files in Linux
• Configuring the Linux terminal and SSH
• Software managment with Conda
• High Performamce Computing with Slurm
• Processing genomic data (RNAseq) on the command line

R for data science and genomics (Introductory course)

• Two weeks 30/01/2023-10/02/2023, 9.30am-4pm Monday-Friday
• Cost: £2000
• Programming in R
• Tidyverse and ggplot2
• Statistics in R
• Introduction to Bioconductor
• RNAseq differential expression using DESeq2
• Pathways: over-representation and gene set enrichment analysis

Introduction to single-cell RNAseq data analysis using R (requires familiarity with R programming, Tidyverse, ggplot and Bioconductor)

• One week 20/02/2023-24/02/2023, 9.30am-4pm Monday-Friday
• Cost: £1000
• Data processing with CellRanger
• Single-cell RNAseq data analysis using Seurat​​
• Single-cell RNAseq data analysis using Bioconductor
• Investigating cell doublets and ambient RNA
• Introduction to data integration using Seurat 

Funded Places

The Cancer Research UK Oxford Centre offers two fully funded places on each course. To be considered for CRUK funding, research projects must be cancer research focused and applicants must be CRUK Oxford Centre members (you can sign up here). CRUK funding will be allocated by representatives of the Centre Management Group on the basis of both application quality and fit with Centre strategy (details of which can be found here).

Through the Ling Felce Award, the CAMS-Oxford Institute (NDM) has funding available to promote excellence in cross-disciplinary studies. Funding priority will be given to applicants affiliated with the CAMS-Oxford Institute and those nearing the end of their studies or contract. For more information please contact the CAMS-Oxford Institute Training Programmes Coordinator. 

The Oxford Biomedical Research Centre (BRC) offers one fully funded training place on each course. To be considered for BRC funded places, projects must fall within the remit of the NIHR, which funds research for patient benefit. Applications will only be considered from candidates working on human samples. Priority will be given to applicants in research groups affiliated with BRC Themes. Details of all BRC Themes are available on the Oxford BRC website.

Applications for winter 2023 open at 9am on Monday 10th October and close at 12pm on Monday 31st October.

Online application form: https://oxford.onlinesurveys.ac.uk/obds-winter-2023-applications