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Instructor-led course

Provided by: Bioinformatics


This course has 1 scheduled run. To book a place, please choose your preferred date:


Wed 19 Jun 2019

Events available

Biological data analysis using the InterMine API
PrerequisitesNew


Description

InterMine is a freely available data integration and analysis system that has been used to create a suite of databases for the analysis of large and complex biological data sets.

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants, nematodes, fly, zebrafish and more recently human. See here for a comprehensive list of InterMine databases. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression.

InterMine provides sophisticated query and visualisation tools both through a web interface and an extensive API; this course will focus on programmatic access to InterMine through its API and on running InterMine searches using Python, Perl and R scripts. The exercises will mainly use the fly, human and mouse databases, but the course is applicable to anyone working with data for which an InterMine database is available.

This event is organised alongside a half day course on Biological data analysis using the InterMine User Interface. More information on this event are available here.

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 Interest by linking here.

Target audience
  • The course is suitable for anyone wanting to know how the InterMine API works and how accessing InterMine data programmatically could help them in their research
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals
  • 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
Prerequisites
  • Some basic knowledge of Perl and/or Python and/or R would be an advantage.
  • No previous experience of InterMine databases is required.
Objectives

By the end of the workshop, researchers will know how to use the InterMine interface to auto-generate code for use with the API and how this can be extended to do more in depth analysis such as generating visualisations and applying enrichment statistics to gene sets.

Aims

During this course you will learn about the following InterMine API features:

  • Running queries against diverse omics data across a range of organisms
  • Applying enrichment statistics to a gene list to identify over-represented terms (such as Gene Ontology and pathway terms and publications).
  • Using set operations to analyse gene sets.
  • Generating visualisations of key biological data (such as expression graphs and enrichment results)
Format

Presentations, demonstrations and practicals

Timetable

Day 1 Topics
Session 1 Introduction - what is an API and why might we use one?
Session 2 Hands-on code along
Session 3 Advanced exercises: producing figures and data visualisations
Session 4 Exercises - use cases and questions
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

0.5

Frequency

A number of times per year

Related courses
Theme
Databases and Services

Events available