Foundation skills for HPC in computational biomolecular research - BioExcel Summer School


 Monday 3 Friday 7 July 2017


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Friday 13 January 2017

Application deadline: 

Friday 28 April 2017


Open application with selection


Charlotte Pearton

Registration fee: 


Registration closed


This 5-day BioExcel Summer School will use project-based learning to empower life scientists to get the most out of using computers. Using example problems and challenges that life-scientists will come across in their day-to-day work, e.g. obtaining data, installing software, cleaning data, analysing data, this course will help participants gain the foundational computational skills needed to move into the domain of high-end computing.


The course is a primer for people who want to start using High Performance Computing (HPC) but find the concept quite daunting and lack the needed computational skills. This summer school is project-based, formal classroom teaching will be kept to a minimum. No prerequisites are required for this course. Participants from any career stage are welcome to apply for this course.

Syllabus, tools and resources

The summer school will explore concepts such as computer architecture, hardware and software requirements, operating system, file structure, non-trivial software installation, using linux commands, automating tasks using the unix shell, software documentation & best practice.


After this course you will be able to or have acquired:

  • Confidently navigate through the file structure and operating system of the computer.

  • Working knowledge of linux, including basic command line operations

  • Obtain & submit data from/to a range of external sources

  • Compile, install and test software

  • Read and modify scripts


 What will this course not do?

  • This course will not teach you how to programme, though you would be much better prepared after this course to start a self-taught course

  • This is not a course on HPC computing but will teach you the foundational skills and concepts that you need to start learning about HPC computing. A full course “Introduction to HPC computing for life-scientists” will be organised in autumn 2017 or early 2018.


Time Topic Trainer
Day 1 - Monday 3rd July
10:00 - 11:00 Introduction to EBI and BioExcel Vera Matser
11:00 - 12:00 Course expectations and user stories  All
12:00 - 13:00 Lunch  
13:00 - 15:00 The computational roadmap; from your local machine to clusters and HPC


15:00 - 15:30 Break  
15:30 - 17:30 Introduction to project work (Project 0)

Vera Matser

Lee Larcombe

18:30 - 20:00 Evening meal (at Welcome Trust Conference Centre)  
Day 2 - Tuesday 4th July
09:00 - 09:30 Summary of Day 1 and introduction to concepts of Day 2 using the computational route map  All
09:30 - 12:30 Project 1  
12:30 - 13:30 Lunch  
13:30 - 14:00 Visit to the computing facility  
14:00 - 17:30 Project 2   
18:00 - 20:00 Evening meal (Red Lion, Hinxton)  
Day 3 - Wednesday 5th July
09:00 - 09:30 Summary of Day 2 and introduction to concepts of Day 3 using the computational route map  All
09:30 - 12:30 Project 3  
12:30 - 13:30 Lunch  
13:30 - 16:30 Project 4  
16:30 - 21:00 Free evening in Cambridge (bus provided)  
Day 4 - Thursday 6th July
09:00 - 09:30 Summary of Day 3 and introduction to concepts of Day 4 using the computational route map  All
09:30 - 12:30 Project 5  
12:30 - 13:30 Lunch  
13:30 - 17:30 Project 6  
18:00 - 20:00 Evening meal (Welcome Trust Conference Centre)  
Day 5 - Friday 7 July
09:00 - 09:30 Summary of Day 4 using the computational route map  All
09:30 - 13:00 Introduction to HPC computing Arno Proeme
13:00 - 14:00 Course feedback and wrap up Vera Matser
  Lunch vouchers will be provided - End of course