Biological data analysis using InterMine (User Interface) BeginnersUpdated
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. See here for a comprehensive list of InterMine databases.
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.
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.
This event is organised alongside a half day course on Biological data analysis using the InterMine API. More information on this event are available here.
The training room is located on the first floor and there is currently no wheelchair or level access available to this level.
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.
- 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.
- 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
No previous experience of InterMine databases is required.
Number of sessions: 1
| # | Date | Time | Venue | Trainer | |
|---|---|---|---|---|---|
| 1 | Wed 19 Jun 2019 09:30 - 12:30 | 09:30 - 12:30 | Bioinformatics Training Room, Craik-Marshall Building | map | Rachel Lyne |
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.
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
- Automated 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)
Presentations, demonstrations and practicals
| Day 1 | Topics |
| Session 1 | Introduction to InterMine |
| Session 2 | Walk through interface with hands-on exercises: Keyword search and report pages, Lists - analysing gene sets, Template searches, Advanced searches using the query builder, Region search |
| Session 3 | Analysis workflows |
| Session 4 | Exercises - use-cases and questions |
- 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
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