Summer School in Bioinformatics

Date:

 Monday 26 Friday 30 June 2017

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Sunday January 01 2017

Application deadline: 

Tuesday March 14 2017

Participation: 

Open application with selection

Contact: 

Lucy Criddle

Registration fee: 

£670.00

Registration closed

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Overview

This course provides an introduction to the use of bioinformatics in biological research, giving participants guidance for using bioinformatics in their work whilst also providing hands-on training in tools and resources appropriate to their research.

Participants will initially be introduced to bioinformatics theory and practice, including best practices for undertaking bioinformatics analysis, data management and reproducibility. To enable specific exploration of resources in their particular field of interest, 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.

The course includes training and mentoring provided by experts from EMBL-EBI and external institutes.

Group projects

A major element of this course is a group project, where participants will be placed in small groups to work together on a challenge set by trainers from EMBL-EBI data resource and research teams.  This allows people to explore the bioinformatics tools and resources available in their area of interest and to apply these to a set problem, providing them with hands-on experience of relevance to their own research. 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.

Groups are mentored by the trainers who set the initial challenge, but active participation from all group members is expected.  Groups are pre-organised before the course, and all group members will be sent some short “homework” in preparation for their project work prior to the start of the course.

The basic outline of the projects on offer this year are given below.  In your application you should indicate your first and second choice of project, based on your judgement of which would benefit your research most.  Not all projects may be offered, final decisions on which projects will be run during the course will be made based on the number of applicants per project.

This years projects are as follows:

Structural biology and functional prediction: You will investigate and predict the functions of uncharacterised proteins, using PDBe’s search interface. In doing so you will develop a workflow and access PDBe programmatically via an API.

De novo assembly and annotation: You will assemble and annotate the genome of a strain of Escherichia coli. You will compare the results to known genomes to discover why this strain of the mostly harmless bacteria turned out to be deadly.

Networks and pathways: This project is focused on placing 'omics data in the larger context of biological systems.  You will look at gene expression databases to explore the results of the analysis of RNA-seq data and use Cytoscape to visualise that data in protein-interaction networks and to perform functional enrichment analysis in order to gain insight into system-level trends.

Phylogenetics: You will be investigating a dataset of viral sequences, and using various phylogenetic analyses to draw conclusions about the evolutionary history of the taxon and its geographic spread.

Metabolomics: Characterisation of the physiological variations of the metabolome in biofluids is critical to understand human physiology and to avoid confounding effects in cohort studies. In this project you will work through setting up a simple analysis pipeline going from raw data to data matrix, ending with some simple statistical analysis. The focus will be on urine samples from 184 volunteers that were analysed by reversed-phase ultrahigh performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (LTQ-Orbitrap).  

Genomic Variation Project: Explore the results of SNP-calling using web-based resources such as Ensembl Variant Effect Predictor. You will investigate the functions of the genes/proteins that contain SNPs and compare your results to existing genomic variation data using bioinformatics tools and databases. This project will give you the skills to critically evaluate genetic variation data to form evidence-based hypotheses.

Chemogenomics: This project will involve target identification and validation for a given disease utilising data from OpenTargets, ChEMBL for target-ligand pairs, SureChembl for patent data, KNIME for data analysis and PDB for study of protein-ligand interactions.

Audience

This course is aimed at individuals working across biological sciences who have little or no experience in bioinformatics. Applicants are expected to be at an early stage of using bioinformatics in their research with the need to develop their skills and knowledge further. No previous knowledge of programming / coding is required for this course.

Syllabus, tools and resources

During this course you will learn about:

  • Bioinformatics as a science

  • Designing bioinformatic studies

  • Data management and reproducibility

  • Basic tools and resources for bioinformatics


Please note that 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.

Outcomes

After this course you 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

Programme

Time Topic Trainer
Day 1 - Monday 26 June 2017
10:00 - 10:30 Registration and tea/coffee  
10:30 - 11:30 Welcome and introduction Laura Emery
11:30 - 12:30 Study Design for Bioinformatics Alex Bateman
12:30 - 13:30 Lunch  
13:30 - 14:30 The bioinformatics one-way mirror: when "not-true” is not false Bill Pearson
14:30 - 15:00 Activity Laura Emery
15:00 - 15:30 Tea/coffee break  
15:30 - 17:30 Data management Amy Tang
17:30 - 17:50 Discussion  
17:50 - 18:00 Bedroom check-in  
18:00 - 19:00 Networking drinks  
19:00 Evening meal @ Hinxton Hall  
Day 2 - Tuesday 27 June 2017
09:00 - 10:30 Introduction to EBI resources and web services Andrew Cowley and Melissa Burke
10:30 - 11:00 Tea/coffee break  
11:00 - 12:30 Introduction to sequence searching Bill Pearson
12:30 - 14:00 Lunch  
14:00 - 15:00 Data integration case studies Denise Carvalho-Silva and Yasset Perez-Riverol
15:00 - 15:30 Tea/coffee break  
15:30 - 16:00 Intro to group projects Sarah Morgan
16:00 - 17:30 Meet your mentors  
17:30 - 18:00 Discussion  
19:00 Evening meal @ Hinxton Hall  
Day 3 - Wednesday 28 June 2017
09:00 - 10:30 Group work day 2  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group work day 2 cont...  
12:00 - 12:30 Optional mini tutorial: Networks Pablo Porras
12:30 - 13:30 Lunch -  
13:30 - 14:30 Keynote lecture 1 (Kendrew Lecture Theatre) Evangelia Petsalaki, EMBL-EBI
14:30 - 15:00 Tea/coffee break  
15:00 - 15:30 Group projects 2 minute interim report  
15:30 - 18:00 Group work day 2 cont...  
19:00 Evening meal @ Hinxton Hall  
Day 4 - Thursday 29 June 2017
09:00 - 10:30 Group work day 3  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group work day 3 cont...   
12:00 - 12:30 Optional mini tutorial: Data integration Lee Larcombe
12:30 - 13:30 Lunch  
13:30 - 14:30 Keynote lecture 2 (Kendrew Lecture Theatre) Zam Iqbal, EMBL-EBI
14:30 - 15:00 Tea/coffee break  
15:30 - 18:00 Group work day 3 cont...  
19:00 Evening meal @ Hinxton Hall  
Day 5 - 
09:00 - 10:30 Preparation of group presentations  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group presentations  
12:00 - 13:00 Lunch  
13:00 - 14:00  Group presentations cont...  
14:00 - 15:00 Award Ceremony  
15:30 - 16:00 Course feedback and wrap up  
13:30 End of course