- 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
Organiser:
Enquiries:
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.