Welcome to the CompBioMed Training Portal
One of the objectives of our Centre of Excellence is to train future generations of scientists within the field of computational biomedicine, by running training courses on topics such as HPC use, software engineering and algorithm design, as well as training medical practitioners in the basic medical and clinical contexts of HPC simulation (see CompBioMed Training Plan).
This Portal aims to be a sustainable open-access educational and training resource for Computational Biomedicine, including HPC, and it displays:
- the past and upcoming training events organised within the CompBioMed project
- the training material developed for each course (course slides, code examples, exercises, video recording)
- the training courses offered by our partners that are relevant for the CompBioMed user community
Training events
Other trainings
- PATC: Short course on HPC-based Computational Biomedicine [Online, 15-18 February 2022]
- MPI and OpenMP in Scientific Software Development [Amsterdam (NL)/Online, 9-11 June 2021]
- Sensitive Data Management and EUDAT Services [Online, 29 March 2021]
University education
CompBioMed University Education is an experimental-computational workflow in molecularly-based medicine that can be delivered to medical students, to science and engineering students, or as part of a bespoke training programme to familiarise trainees with genome-based computational biomedicine using state-of-the-art experimental and computational resources.
The course involves a combination of field work, wet laboratory-based experimental work, taught lectures, supervised workshops, small group tutorial sessions, and data analysis using high performance computing. Participants purify microbial genomic DNA from environmental samples and use conserved regions of the gene encoding the 16S bacterial ribosomal RNA for amplification of genomic microbial DNA. This DNA is sequenced using Illumina Next Generation Sequencing on an iSeq-100 machine and a bioinformatics pipeline is used on the raw data to understand microbial diversity by performing microbiome analysis on HPC.
CompBioMed has delivered this course at UCL every year since 2017-2018, and an expanded version of the course has been used since 2017-2018 for a third year undergraduate research project for students taking Molecular Biosciences degrees (MSc/BSc Biochemistry and BSc Molecular Biology) at UCL.
From 2020-2021 an expanded version is offered medical students at the University of Sheffield (USFD), in collaboration with UCL, USFD and associate partner Alces Flight.
We aim to give the course to medical students at Universidad Pompeu Fabra (UPF), University of Amsterdam, and the University of Oxford.
USFD and UPF are developing HPC-based courses in cardiovascular and in neuromusculoskeletal research, alongside Associate Partner Dassault Systèmes for delivery to MSc Bioengineering students.
If you are a trainer who would like to run this programme in your institution, CompBioMed can provide expert resources in the form of protocols and instructor and/or computational support: please let us know about your interest!
If you are a student and wish to follow this training programme, please feel welcome to get in touch too!
Training repository
Click the button above for a repository of CompBioMed’s past, present, and future training materials and courses, as well as the training courses offered by our partners that are relevant to the CompBioMed user community.