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Fri 27 Oct 2017
09:30 - 13:30

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

Provided by: Bioinformatics


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Biological data analysis using InterMine

Fri 27 Oct 2017

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.

The InterMine web interface offers sophisticated query and visualisation tools, as well as comprehensive web services for bioinformaticians. Genomic and proteomic data within InterMine databases includes pathways, gene expression, interactions, sequence variants, GWAS, regulatory data and protein expression.

Part 1 (2.5 - 3 hours) will introduce participants to all aspects of the user interface, starting with some simple exercises and building up to more complex analysis encompassing several analysis tools and comparative analysis across organisms. No previous experience is necessary for this part of the workshop.

Part 2 (1 hour) will focus on the InterMine API and introduce running InterMine searches through Python and Perl scripts. While complete beginners are welcome, some basic knowledge of perl, and/or python would be an advantage. The InterMine R package will also be introduced. Those not interested in this part of the workshop are welcome to leave or there will be a more advanced exercise using the web interface available as an alternative.

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 aimed at bench biologists and bioinformaticians who need to analyse their own data against large biological datasets, or who need to search against several biological datasets to gain knowledge of a gene/gene set, biological process or function. 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. See www.intermine.org for a comprehensive list of InterMine databases.
  • 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 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

No previous experience of InterMine databases is required.
Some knowledge of perl or python would be an advantage for Part 2 of the workshop.

Sessions

Number of sessions: 1

# Date Time Venue Trainer
1 Fri 27 Oct   09:30 - 13:30 09:30 - 13:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site map Rachel Lyne
Topics covered

The following features of the InterMine web interface will be covered:

  • Search interfaces and advanced query builder
  • Automated analysis of sets, e.g gene sets, including enrichment statistics
  • Analysis workflows
  • Tools for cross-organism analysis between InterMine databases.
  • Web services
Objectives

By the end of the workshop, researchers will know how to use the InterMine interface and will have gained an understanding of how data can be passed between tools to create an analysis pipeline. Those participating in part 2 will have knowledge of the range of InterMine web services available, how to automatically generate code from the web interface and how to customise this code to run user-defined searches across the data.

Format

Presentations, demonstrations and practicals

Registration fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, 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 days

Frequency

A number of times per year

Theme
Databases and Services

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