Foundation skills for HPC in computational biomolecular research - BioExcel Summer School
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Date:
Monday 3 - Friday 7 July 2017Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Friday 13 January 2017Application deadline:
Friday 28 April 2017Participation:
Open application with selectionContact:
Charlotte PeartonRegistration fee:
£0Registration closed
Overview
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.
Audience
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.
Outcomes
After this course you will be able to or have acquired:
-
Confidently navigate through the file structure and operating system of the computer.
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Working knowledge of linux, including basic command line operations
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Obtain & submit data from/to a range of external sources
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Compile, install and test software
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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.
Programme
| 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 |
All |
| 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 | ||
In association with
How to apply
In order to be considered for a place on this course, applicants must do the following:
1. Complete the online application form.
2. Submit a WORD document to cpearton@ebi.ac.uk containing a short biography, including your work history and a description of your current research interests (maximum of 300 words total)-on/before Friday 28 April 2017 - 12:00 GMT.
3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.
Further details will be provided on your confirmation email after completing the online form.
Incomplete applications will NOT be considered. Please read through the following guidance document for further information on how to complete your application.
Registration for the course is free. Attendees need to cover their own travel and accommodation expenses.
BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary please indicate this during the application process. Eligibility criteria and conditions for travel grants are available here.
Application deadline
28 April 2017
Number of places
25 places
Organisers
Vera Matser - University of Cambridge
Adam Carter - University of Edinburgh
Lee Larcombe - Amphimatic
Arno Proeme - University of Edinburgh
Mohamed Alibi - EMBL-EBI, UK
Brett McClintock
Trainers
Lee Larcombe - Amphimatic
Mohamed Alibi - EMBL-EBI, UK
Vera Matser - EMBL-EBI, UK
Arno Proeme - University of Edinburgh
Brett McClintock - EMBL-EBI, UK
Csaba Halmagyi - EMBL-EBI, UK