Cookies on this website

We use cookies to ensure that we give you the best experience on our website. If you click 'Accept all cookies' we'll assume that you are happy to receive all cookies and you won't see this message again. If you click 'Reject all non-essential cookies' only necessary cookies providing core functionality such as security, network management, and accessibility will be enabled. Click 'Find out more' for information on how to change your cookie settings.

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 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 190 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 Autumn 2023 open are now closed.  Applications for courses in January-March 2024 will open in October 2023.

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

 

AUTUMN 2023 COURSES

In September - October 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 - 11/09/2023-15/09/2023, 9.30am-4pm Monday-Friday
  • 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

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

  • Nine days over three weeks
  • 18/09/2023-20/09/2023, 9.30am-4pm Monday-Wednesday
  • 25/09/2023-27/09/2023, 9.30am-4pm Monday-Wednesday
  • 03/10/2023-05/10/2023, 9.30am-4pm Tuesday-Thursday
  • Programming in R
  • Tidyverse and ggplot2
  • 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)

  • Six days over two weeks:
  • 09/10/2023-11/10/2023, 9.30am-4pm Monday-Wednesday
  • 16/10/2023-18/10/2023, 9.30am-4pm Monday-Wednesday
  • Data processing with CellRanger
  • Single-cell RNAseq data analysis using Seurat​
  • Introduction to data integration using Seurat 
  • Single-cell RNAseq data analysis using Bioconductor
  • Investigating cell doublets and ambient RNA

 

Winter 2024 Courses

 

Genomics on the Linux command line (Introductory course)

  • One week - 15/01/2024-19/01/2024, 9.30am-4pm Monday-Friday
  • University of Oxford staff and postgraduate students £1000 (external applicants £2000 exc VAT)
  • 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 (Introductory course)

  • 6 days over 2 weeks (22/01/2024-24/01/2024, 29/01/2024-31/01/2024) 9.30am-4pm Monday-Wednesday
  • University of Oxford staff and postgraduate students £1000 (external applicants £2000 exc VAT)
  • Basic programming concepts - variables, iteration and conditionals
  • Code organisation - scripts and functions
  • Writing biological algorithms
  • Reading and writing files
  • Python data science - Matrices and Data frames with Numpy and Pandas
  • Plotting in Python - Matplotlib and Seaborn

R for data science and genomics 

  • Prerequisites: basic knowledge of Linux command line (ls, cd, pwd, cp, ln, rm)
  • Nine days over three weeks  (19/02/2024-21/02/2024, 26/02/2024-28/02/2024, 04/03/2024-06/03/2024) 9.30am-4pm Monday-Wednesday
  • Cost: £2000 (External applicants £4000 exc VAT)
  • Programming in R
  • Tidyverse and ggplot2
  • 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

  • Prerequisites: familiarity with R programming, Tidyverse, ggplot2 and Bioconductor)
  • Six days over two weeks (11/03/2024-13/01/2024, 18/03/2024-20/03/2024), 9.30am-4pm Monday-Friday
  • Cost: £1200 (external applicants £2400 exc VAT)
  • Data processing with CellRanger
  • Single-cell RNAseq data analysis using Seurat​​
  • Introduction to data integration using Seurat 
  • Single-cell RNAseq data analysis using Bioconductor
  • Investigating cell doublets and ambient RNA in Bioconductor

 

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.