skip to content
 

Intermine

 

Description

InterMine is a freely available open-source data warehouse built specifically for the integration and analysis of complex biological data.

These are two half day courses organised to run alongside each other.

User Interface Course

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafishHymenoptera, Planaria, and more recently human.

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 a powerful web service API, with multiple language bindings including Python and R.

This course will focus on the InterMine web interface and 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. 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 (a comprehensive list of InterMine databases is available here.)

API Course

InterMine-based data analysis platforms are available for many organisms including mouse, rat, budding yeast, plants (over 87 plant genomes), nematodes, fly, zebrafish, Hymenoptera, Planaria, and more recently human.

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 a powerful web service API, with multiple language bindings including Python and R.

This course will focus on programmatic access to InterMine through the API and InterMine searches will be done using Python 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 (a comprehensive list of InterMine databases is available here.

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.

 

Prerequisites

User Interface Course

  • 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.
  • This course is for researchers from a broad biological background as the techniques learned can be applied to any InterMine database, covering a diverse range of organisms and biological data.
  • No previous experience of InterMine databases is required.

API Course

  • This course is aimed at bench biologists and bioinformaticians who are interested in large scale and/or automated analysis of their own or existing data against large biological datasets, or who are interested in graphs and other visualisations of data generated through an InterMine search.
  • The course is also suitable for anyone wanting to know what an API is and how the ability to access data programmatically could help them in their research.
  • This course is for researchers from a broad biological background as the techniques learned can be applied to any InterMine database, covering a diverse range of organisms and biological data.
  • No previous experience of InterMine databases is required.
  • Some basic knowledge of python and R would be an advantage but it is not required.
  • The automatic code generation feature of InterMine means that the programming side is accessible to beginners. However, researchers with programming experience would also benefit from this event, learning how the InterMine API can be applied to the biological techniques taught.

 

For additional information on the User Interface Course, follow this link.

For additional information for the API Course, follow this link.

 

Subject: