skip to primary navigationskip to content
 

Biological data analysis using InterMine

Intermine

 

Description

InterMine is a freely available data warehouse and analysis software 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.

 

Trainers

Rachel Lyne, University of Cambridge

 

Audience and Prerequisites

  • 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. 

 

Syllabus, Tools and Resources

 

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

 

Learning 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.

 

Links

Book Here

Intermine website

Filed under: