Bioinformatics Summer School

This popular computational course is run jointly with EMBL-EBI and will
provide an introduction to the use of bioinformatics in biological
research using publicly available data resources and tools. Participants
will initially be introduced to bioinformatics theory and practice.

To enable the specific exploration of resources, in a particular
field of interest, participants will actively take part in a
project; working with others to conduct bioinformatics based research to
explore biological questions. This group project is a major element of
the course; participants will be placed into groups according to their
scientific area of interest and relevance to available projects. The
bioinformatics resources, available in their area of interest, will be
explored and applied to a set problem. The group work will culminate in a
presentation session involving all participants on the final day of the
course, giving an opportunity for wider discussion on the benefits and
challenges of working with biological data.

This course is aimed at individuals working in biological disciplines who
have little or no experience in bioinformatics. Applicants are expected
to be beginning bioinformatics related projects or need to use such
approaches in their work.

Please note: The course will not cover aspects of
computer programming or in-depth data analysis; there will be no
opportunity for you to analyse your own data during this course.

Learning outcomes
Following course completion participants should be able to:

• Discuss applications of bioinformatics in biological research
• Browse, search, and retrieve biological data from public repositories
• Use appropriate bioinformatics tools to explore biological data
• Comprehend some ways biological data can be stored, organised and interconverted

The Bioinformatics Summer School 2016 will start at
approximately 10.00 on Monday 13 June and close at approximately 14.30 on
Friday 17 June 2016.

This is a residential summer school. All students are requested to stay
onsite for the full duration to benefit fully from discussions and
interactions with the faculty and other students. The programme will
include training and mentoring provided by experts from EMBL-EBI and
external institutes.

Course topics

• Issues in bioinformatics
• Designing bioinformatics studies
• Databases
• Tools

Group projects
Participants will be divided into focused groups to work on a small
project set by EMBL-EBI resource and research staff, ending in a
presentation from each group on the final day of the course. In your
application you should indicate which of the following projects would
most benefit your research:

• De novo assembly and annotation: Participants will assemble and annotate the genome of a strain of Escherichia coli. Compare the results to known genomes to discover why this strain, of mainly harmless bacteria, turned out to be deadly.
• Phylogenetics: Investigation of a dataset of viral sequences and the use of various phylogenetic analyses to draw conclusions about the evolutionary history of the taxon and its geographic spread.
• RNA-Seq and networks: This project will investigate expression changes, associated with glioblastoma, using expression data obtained from normal and tumour tissue. The focus of this project will be how expression levels are different in cancer.
• Structural biology and functional prediction: Investigation and prediction of the functions of uncharacterised proteins, using PDBe’s search interface. As part of the project you will develop a workflow and access PDBe programmatically via an API.
• Chemogenomics: This project will involve target-ligand pairs, SureChembl for patent disease data, KNIME for data analysis and PDB for study of protein-ligand interactions. Some docking calculations may be performed to determine potential ligands for the identified target

During the application process you will be required to select which of
the above projects would benefit your research most. Additional
alternative projects may be made available if high interest is shown in a
particular area of research not currently reflect above. This can be
detailed in “other” during the application process.

A draft programme will be available shortly.

Course instructors
Sarah Morgan EMBL-EBI, UK
Laura Emery EMBL-EBI, UK
William Pearson University of Virginia, USA
Tom Hancocks EMBL-EBI

Keynote lecture
Julian Rayner Wellcome Trust Sanger Institute, UK

Confirmed tutors
Andrew Cowley EMBL-EBI, UK
William Pearson University of Virginia, USA
Pedro Beltrao EMBL-EBI, UK

Event organiser
Lucy Criddle Wellcome Genome Campus, UK

Fees

The fees include accommodation, meals and lectures for the duration of
the Bioinformatics Summer School 2016. The fee will be requested once
acceptance is confirmed.

Accommodation
This is a residential summer school. All participants will stay at The
Wellcome Genome Campus Conference Centre, Hinxton, Cambridge, for the
nights of 13, 14, 15 and 16 June 2016.

If you wish to book onsite accommodation either side of the summer
school/course dates, please contact the Conference
Centre directly.

Applications
Application deadline: Closed

Places on this summer school are limited to 30 students and will be
awarded on merit. Applicants should be PhD students currently engaged in
relevant research and will be required to complete an online application
form.
The selection process will take place in March 2016

The following will need to be provided:

• Qualifications and justification for attendance
• A list of relevant publications
• A scientific outline of current research
• Supervisor’s details: your supervisor will then receive an e-mail requesting a supporting statement to complete your application.

Please note: Applications cannot be considered without a
supervisor’s supporting statement.

Travel visas
Please contact the event organiser if you require a letter to support a
travel visa application, once your application has been successful. Note
that letters will be provided to confirmed attendee only.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website:
www.ukba.homeoffice.gov.uk/visas-immigration/
Information for general visitors and business visitors:
www.ukba.homeoffice.gov.uk/visas-immigration/visiting/business/business-activities/