• Event
  • Scientific training

Earlham Institute summer school on bioinformatics

The course will provide an overview of bioinformatics from sequence searching, expression data, through to protein-protein interactions, including an overview of common databases, tools and tasks.

Start date:

25 July 2016

End date:

29 July 2016

Time:

12h00 - 13h30

Venue:

Earlham Institute

Registration deadline:

20 May 2016

Cost:

£300

About the event.

What is the workshop about?

The course will provide an overview of bioinformatics from sequence searching, expression data, through to protein-protein interactions. You will receive an overview of common databases, tools and tasks, learn why, when and how to use the command line, and will finish with a session in groups focussed on answering a biological question using the tools learned over the course. The course comprises conceptual lectures, hands on exercises, and group activities. It also provides ample opportunities to interact with expert trainers, motivated researchers and your fellow trainees.
 

What will I learn?

  • Basic understanding of when it is important to use the command line, plus learning some basic skills
  • Overview of databases for raw DNA sequences, reference sequences and protein sequences
  • Sequence retrieval tools, genome databases and gene prediction
  • Multiple sequence alignments tools
  • Understand what an ontology is, and how it is used
  • Be familiar with the Gene Ontology and the analyses it supports
  • Know how to search and use the Gene Ontology in your project
  • Overview of protein-protein interaction (PPI) networks, experimental methods to detect PPIs, tools and applications to visualise and analyse PPIs.
  • Insight into the basic biological mechanisms of transcription-factor (TF) mediated gene expression, databases containing experimentally verified TF- target information and various tools and resources available to reconstruct de novo the transcriptional regulatory networks of non-model organisms.
  • Browse the UniProt database in detail, learning about its structure and the type of data it contains
  • Understand how to browse, query and retrieve data from the Expression Atlas
  • Understand the data flow from ArrayExpress database and how we control the quality of data sets in the Atlas

Target Audience:

This course is aimed primarily at PhD students and early career postdocs. You will ideally have a project in the near immediate future or still in the early stages of development related to the subject matter of this course. You will be new to the area of bioinformatics and want to get a feel for the range of tools available for analysis of your data. The selection committee will be looking at the overlap between the applicants’ expectations from the course and what the course will be delivering, coupled with the timely application of skills learned during the course to their research.

Programme.

Day 1 - 25 July 2016

Time

Topic

12:00 - 13:00

Registration and lunch

13:00 - 13:15

Welcome

13:15 - 14:30

Flash presentations from delegates and trainers

14:30 - 15:00

Coffee break

15:00 - 17:00

Databases and tools(NCBI, EBI, SIB) Hands on exercise: Mapping types of data to databases and tools

Day 2 - 26 July 2016

Time

Topic

09:00 - 10:30

Sequence searching

10:30 - 11:00

Coffee break

11:00 - 12:30

Part 2: Multiple alignments

12:30 - 13:30

Lunch

13:30 - 14:30

Part 1: Multiple alignments

14:30 - 15:30

Why do we need to know about the command line and Linux?

15:30 - 16:00

Coffee break

16:00 - 17:30

Hands-on exercises: Linux & basic computing concepts

Day 3 - 27 July 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 10:30

Exploring expression data

10:30 - 11:00

Coffee break

11:00 - 12:30

Exploring expression data

12:30 - 13:30

Lunch

13:30 - 15:00

Exploring Protein Sequence and Functional Information with UniProt

15:00 - 15:30

Coffee break

15:30 - 17:00

Exploring Protein Sequence and Functional Information with UniProt

Day 4 - 28 July 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 10:30

Ontologies for life sciences: examples from the Gene Ontology (Pt 1)

10:30 - 11:00

Coffee break

11:00 - 12:30

Ontologies for life sciences: examples from the Gene Ontology (Pt 2)

12:30 - 13:30

Lunch

13:30 - 15:00

Protein-Protein Interactions and Pathways: SignalLink and more (Pt 1)

15:00 - 15:30

Coffee break

15:30 - 17:00

Protein-Protein Interactions and Pathways: SignalLink and more (Pt 2)

Day 5 - 29 July 2016

Time

Topic

08:30 - 09:00

Morning coffee

09:00 - 09:15

The question...

09:15 - 10:30

Using what you have learnt, go and explore

10:30 - 11:00

Coffee break

11:00 - 12:30

Share your thinking and results. Wrap up and feedback time.

12:30 - 13:30

Lunch and departure

Fees and accommodation.

£300.00 which is inclusive of lunch and refreshments, course dinner and course materials.
Accommodation and transport from/to hotel to EI will be available as an optional extra during registration if you are selected for the course.