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Tue 17 Nov 2020
13:00 - 16:00

Venue: Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter)

Provided by: Bioinformatics


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Biological data analysis using the InterMine API (Online)
PrerequisitesNew

Tue 17 Nov 2020

Description

PLEASE NOTE The Bioinformatics Team are presently teaching as many courses live online. We aim to simulate the classroom experience as closely as possible, with opportunities for one-to-one discussion with tutors and a focus on interactivity throughout.

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

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.

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
  • 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.
  • 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
  • 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.
Sessions

Number of sessions: 1

# Date Time Venue Trainers
1 Tue 17 Nov   13:00 - 16:00 13:00 - 16:00 Bioinformatics Training Facility - Online LIVE Training (Time Zone = BST in Summer, GMT in Winter) D. Butano,  Kevin Herald Reierskog,  Rachel Lyne
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

This is subject to change in line with the online training schedule.

Day 1 Topics
Session 1 InterMine APIs Overview
Session 2 Hands-on code along in Python
Session 3 Advanced exercises & InterMineR
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

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