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Oxford Biomedical Data Science Training Programme

The Oxford Biomedical Data Science Training Programme delivers training in the skills and methods required for the analysis and interpretation of large-scale biomedical datasets, particularly genomic and functional genomic data.

The OBDS programme was established in 2018 with funding from Wellcome, the Cancer Research UK Oxford Centre and the NIHR Oxford Biomedical Research Centre. To date the programme has trained over 100 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 Autumn 2022, we are offering four short courses:

1. Genomics on the Linux command line (Introductory course)

  • One week - 19/09/2022-23/09/2022, 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

2. Python programming and data science (Introductory course)

  • 2 weeks 26/09/2022-07/10/2022, 9.30am-4pm Monday-Friday
  • 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

3. R for data science and genomics (Introductory course)

  • Two weeks 10/10/2022-21/10/2022, 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

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

  • One week 24/10/2022-28/10/2022, 9.30am-4pm Monday-Friday *date changed
  • 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

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).

Applications for Autumn 2022 closed on Monday18th July. Applications for courses in January / February 2023 will open in September 2022. Courses will be run in person in the WIMM Conference Room.

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