Date: Monday 3 – Friday 7 July 2017
Venue: European Bioinformatics Institute (EMBL-EBI) – Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
Application opens: Friday January 13 2017
Application deadline: Friday April 28 2017
Participation: Open application with selection
Contact: Charlotte Pearton
Registration fee: £0, participants will need to cover their own accommodation and transport cost
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 the travel grants are available here.
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.
Learning Outcomes
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.
Programme
– subject to slight change
| Time | Topic | Trainer |
| Day 1 – Monday 3rd July 2017 | ||
| 10:00 – 11:00 | Introduction to EBI & BioExcel | Vera Matser |
| 11:00 – 11:30 | Course expectations | Vera Matser |
| 11:30 – 12:00 | User stories | |
| 12:00 – 13:00 | Lunch | |
| 13:00 – 15:00 | The computational roadmap; from your local machine to clusters and HPC | TBC |
| 15:00 – 15:30 | Break | |
| 15:30 – 17:30 | Introduction to project work | All |
| 18:00 – 20:00 | Dinner @ (exact time and venue tbc) | |
| Day 2 – Tuesday 4th July 2017 | ||
| 9:00 – 9:30 | Summary of Day 1 and introduction to concepts of day 2 using the computational route map | |
| 9:30 – 12:30 | Project 1 | All |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 16:30 | Project 2 | All |
| 16:30 – 17:30 | Keynote 1 | |
| 18:00 – 20:00 | Dinner @ (exact time and venue tbc) | |
| Day 3 – Wednesday 5th July 2017 | ||
| 9:00 – 9:30 | Summary of Day 2 and introduction to concepts of day 3 using the computational route map | |
| 9:30 – 12:30 | Project 3 | All |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 16:30 | Project 4 | All |
| 16:30 – 17:30 | Keynote 2 (TBC) | |
| 18:00 – 20:00 | Dinner @ (exact time and venue tbc) | |
| Day 4 – Thursday 6th July 2017 | ||
| 9:00 – 9:30 | Summary of Day 3 and introduction to concepts of day 4 using the computational route map | |
| 9:30 – 12:30 | Project 5 | All |
| 12:30 – 13:30 | Lunch | |
| 13:30 – 17:30 | Project 6 | All |
| 18:00 – 20:00 | Dinner @ (exact time and venue tbc) | |
| Day 5 – Friday 7th July 2017 | ||
| 9:00 – 9:30 | Summary of Day 4 using the computational route map | |
| 9:30 – 13:00 | Introduction to HPC computing | Adam Carter |
| 13:00 – 14:00 | Course wrap-up | Vera Matser |
| Lunch vouchers will be provided | ||
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 (via EMBL-EBI website).
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. Please read the BioExcelTravelGrant for the BioExcel travel grant.
Organisers & Trainers
Lee Larcombe, NexaSTEM
Mohamed Alibi, EMBL-EBI
Brett McClintock, EMBL-EBI
Csaba Halmagyi, EMBL-EBI
Vera Matser, BioExcel (EMBL-EBI)
Arno Proeme, BioExcel (University of Edinburgh, EPCC)
Adam Carter, BioExcel (University of Edinburgh, EPCC)
