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 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.  

Applications for spring / summer 2023 closed on Monday 27th February.  The next round of courses will take place in September-October 2023 and applications will open in June 2023. Future course applications will be announced on this web page and through our course mailing list. All courses are in person in the Conference Room in the Weatherall Institute for Molecular Medicine. 

To receive the latest information about courses and application dates please subscribe to our mailing list by emailing obds-announce-subscribe@maillist.ox.ac.uk

Summer 2023 Courses

Genomics on the Linux command line (Introductory course)

• One week - 24/04/2023-28/04/2023, 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 management with Conda
• High Performance Computing with Slurm
• Processing genomic data (RNAseq) on the command line
• Version control with Git and GitHub

Python programming and data science (requires basic knowledge of Linux command line and Conda)

• Ten days over 3 weeks 02/05/2023-17/05/2022, 9.30am-4pm
• Cost: £2000
• Concepts of programming
• Python syntax and data structures
• Writing algorithms, functions and scripts
• Processing genomic data using Python scripts
• Data science in Python - Jupyter Lab, Numpy & Pandas
• Plotting in Python - Matplotlib and Seaborn
• Introduction to machine learning in Python - Scikit-learn
• Classification, dimensionality reduction and clustering

R for data science and genomics (requires basic knowledge of Linux command line)

• Two weeks 05/06/2023-16/06/2023, 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 19/06/2023-23/06/2023, 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 

Autumn 2023 Courses

Courses available:

• Genomics on the Linux command line (Introductory course - 1 week)
• R for data science and genomics (Introductory course - 2 weeks)
• Introduction to single-cell RNAseq data analysis using R (requires familiarity with R programming, Tidyverse, ggplot and Bioconductor) (1 week)

Provisional dates:

• 25/09/2023 - 20/10/2023

Funded Places / Bursaries

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.

Please carefully consider the eligibility criteria for different bursaries before applying. If you apply for bursaries your application will be considered separately for each bursary and if you are selected funding will be offered regardless of whether you have also applied for a self-funded place.