Summer School in Bioinformatics

Date:

 Monday 25 Friday 29 June 2018

Venue: 

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

Application opens: 

Thursday December 14 2017

Application deadline: 

Tuesday March 13 2018

Participation: 

Open application with selection

Registration fee: 

£670

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 year’s projects are as follows:

Proteomics (data analysis and functional interpretation)

In this project, you will work with real-life proteomics data from clinical tumour samples. Your task will be to analyse the proteomics data and interpret the results using the Open Targets Platform, enabling you to review them in a wider context.

Networks and pathways

This project will explore ‘omics data in the larger context of biological systems.  You will use gene expression databases to explore the results of RNA-seq analyses 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.

Wrangling structural data

In this project you will explore the structural data available within the Protein Data Bank. You will assess structures of interest by utilising other biological databases, statistical methods and molecular visualisation tools. You will investigate various aspects of these macromolecules, such as sequence and structural similarity, Pfam domains, function and bound ligands.

Functional annotation of proteins

Enzymatic activity is one of the important functions of proteins in an organism. Enzymes are classified using hierarchical “EC numbers”. In this project, you will use computational approaches to predict the enzymatic activities of a protein.

Phylogenetics

You will investigate a dataset of viral sequences, and use various phylogenetic analyses to draw conclusions about the evolutionary history of the taxon and its geographic spread.

Analysis of pathways in metabolic networks

You will work with an example model metabolic pathway from the BioModels database, and learn how to carry out computational analyses to find common patterns in the networks. These might include computing feasible pathways through the network, and minimal reactions to knock out specific metabolic functions - along with visualisation and exploration to gain important insight into the results.

Curation of systems models in BioModels

Recently, mathematical modelling approaches have become increasingly common in cell biology research. Such a quantitative approach supports cell signalling and cancer research by helping to elucidate mechanisms and provide predictions that can be validated.  Current trends suggest that many experimental researchers use mathematical models and simulations to emphasise the validity of their hypothesis and often present them as the last figure of their publications. In this project, you will learn to use simulation software like COPASI to encode simple mathematical models from recent publications and reproduce the simulation results. You will curate mathematical models available in BioModels.

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.

Syllabus, tools and resources

During this course you will learn about:

  • Bioinformatics as a science

  • Designing bioinformatics studies

  • Data management and reproducibility

  • Basic tools and resources for bioinformatics

The exact range of resources and tools covered will vary by project; 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 25 June 2018
10:00 – 10:30 Registration and tea/coffee  
10:30 – 11:30 Welcome and introduction Alexandra Holinski and Andrew Cowley
11:30 – 12:30 The science of bioinformatics Alex Bateman
12:30 – 14:00 Lunch + poster session  
14:00 – 15:00 The bioinformatics one way mirror: when “not-true” is not false Bill Pearson
15:00 – 16:30 Activity (including coffee/tea break) Alexandra Holinski and Andrew Cowley
16:30 – 17:50 Data Management Andrew Cowley and Melissa Burke
17:50 – 18:00 Bedroom-check-in  
18:00 – 19:00 Networking-drinks  
19:00 Evening meal @ Hinxton Hall  
Day 2 - Tuesday 26 June 2018
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 + poster session  
14:00 – 15:00 Data visualisation Niki Karamanis
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 27 June 2018
09:00 - 10:30 Group work  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group work  
12:00 - 12:30 Mini tutorial Pablo Porras
12:30 - 13:30 Lunch  
13:30 - 14:30 Keynote lecture 1
Zamin Iqbal
14:30 - 15:00 Tea/coffee break  
15:00 - 15:30 Group projects 2 minute interim report  
15:30 - 18:00 Group work
 
19:00 Evening meal @ Hinxton Hall  
Day 4 - Thursday 28 June 2018
09:00 - 10:30 Group work  
10:30 - 11:00 Tea/coffee break  
11:00 - 12:00 Group work  
12:00 - 12:30 Mini tutorial Lee Larcombe
12:30 - 13:30 Lunch  
13:30 - 14:30 Keynote lecture 2
Velislava Petrova
14:30 - 15:00 Tea/coffee break  
15:00 - 18:00 Group work  
19:00 Evening meal @ Hinxton Hall  
Day 5 - Friday 29 June 2018
09:00 – 10:30 Preparation of group presentations  
10:30 – 11:00 Tea/coffee break  
11:00 – 12:00 Group presentation  
12:00 – 13:00 Lunch  
13:00 – 14:00 Group presentation  
14:00 – 15:00 Award ceremony, course feedback and wrap up  
15:30 Bus to train station