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Mon 16 Sep - Tue 17 Sep 2019
09:30, ...

Venue: Bioinformatics Training Room, Craik-Marshall Building, Downing Site

Provided by: Bioinformatics


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Bioinformatics for Principal Investigators
Updated

Mon 16 Sep - Tue 17 Sep 2019

Description

The aim of this workshop is to provide principal investigators with an introduction to the challenges of working with biological data and to the best practices, and tools, needed to perform bioinformatics research effectively and reproducibly.

On day 1, we will cover the importance of experimental design, discuss the challenges associated with (i) the analysis of high-throughput sequencing data (utilising RNA-seq as a working example) and (ii) the application of machine learning algorithms, as well as issues relating to reusability and reproducibility.

On day 2, we will put into practice concepts from day 1, running a RNA-seq data analysis pipeline, going from raw reads through differential expression analysis and the interpretation of downstream analysis results. Challenges encountered at each step of the analytical pipeline will be discussed. Please note that day 2 is optional.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book or register your interest by linking here.

Target audience
  • Principal Investigators from the University of Cambridge, Affiliated Institutions and other external Institutions, who are using or planning to use bioinformatics in their research
  • Please be aware that these courses are only free for registered University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here.
  • Further details regarding eligibility criteria are available here
Sessions

Number of sessions: 2

# Date Time Venue Trainers
1 Mon 16 Sep   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Nicholas Luscombe,  Simon Andrews,  Dr I.I. Mohorianu,  Dr A.J. Enright,  Dr Florian Markowetz,  Andrew Smith
2 Tue 17 Sep   09:30 - 17:00 * 09:30 - 17:00 * Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Dr A.J. Enright
* Optional session.
Topics covered

Bioinformatics

Objectives

After this course you should be able to:

  • Define the opportunities and challenges of bioinformatics use in research
  • Identify your team needs in terms of bioinformatics skills needed to process biological data effectively
  • Implement reproducible and reusable methods in biomedical research
  • Evaluate RNA-seq analysis pipelines (day 2)
Aims

During this course you will learn about:

  • How experimental design and quality assessment affect downstream analysis
  • Challenges associated with the analysis of high-throughput data and the usage of popular machine learning algorithms
  • Best practices for working with data reproducibly
  • How to analyse RNA-seq data (day 2)
Format

Presentations, demonstrations

Timetable

Day 1 Topics Speaker
9:30 - 10:15 Using bioinformatics in research - what to do and what not to do Nicholas Luscombe, Francis Crick Institute
10:15 - 10:30 Tea/Coffee Break
10:30 - 11:30 Using bioinformatics in research - the importance of planning Simon Andrews, Babraham Institute
11:30 - 12:30 Challenges of working with RNA-seq data Anton Enright, Dept. of Pathology, Univ. of Cambridge
12:30 - 13:30 Lunch (not provided)
13:30 - 14:30 Challenges of Machine learning Irina Mohorianu, Stem Cell Institute, Univ. of Cambridge
14:30 - 15:30 Reproducibility in bioinformatics research Florian Markowetz, CRUK
15:30 - 15:45 Tea/Coffee Break
15:45 - 16:15 ELIXIR: The European Research Infrastructure for Life-Science Data Andrew Smith, ELIXIR Hub
16:15 - 17:30 Panel discussion: How to get started All
Day 2
9:30 - 10:30 RNA-seq data - QC and alignment Anton Enright, Dept. of Pathology, Univ. of Cambridge
10:30 - 10:45 Tea/Coffee Break
10:45 - 12:30 RNA-seq data - DE analysis Anton Enright, Dept. of Pathology, Univ. of Cambridge
12:30 - 13:30 Lunch (not provided)
13:30 - 15:30 Downstream analysis Anton Enright, Dept. of Pathology, Univ. of Cambridge
15:30 - 15:45 Tea/Coffee Break
15:45 - 17:00 Downstream analysis Anton Enright, Dept. of Pathology, Univ. of Cambridge
Registration fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

2

Frequency

Twice a year

Theme
Specialized Training

Booking / availability