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Mon 16 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 User Interface (Online)
BeginnersUpdated

Mon 16 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.

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.)

This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event is 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
  • 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.
  • 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.

Sessions

Number of sessions: 1

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

Aims

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

  • Search interfaces and advanced query builder: running queries against diverse omics data
  • Analysis of sets, e.g gene sets, including enrichment statistics and set operations
  • Analysis workflows
  • Tools for cross-organism analysis between InterMine databases.
  • Visualisations of key biological data (such as expression graphs and interaction networks)
Format

Presentations, demonstrations and practicals

Timetable

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

Day 1 Topics
Session 1 Introduction to InterMine
Session 2 Walk through interface with hands-on exercises
Session 3 Workflows
Session 4 BlueGenes Interface demo
Session 5 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

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