Ensembl Browser and REST API workshops: Multi-Omics data analysis using Ensembl resources, Big Data & Artificial Intelligence Course, Amity University

Date:

 Tuesday 24 Thursday 26 September 2019

Venue: 

Amity University - Amity Road, Sector 125, Noida,  Uttar Pradesh,  201313, India

Application opens: 

Tuesday 13 August 2019

Application deadline: 

Friday 20 September 2019

Participation: 

First come, first served

Registration fee: 

PhD Students - ₹3000. Staff Scientists - ₹5000

Course Overview

The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.

The browser workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users. 

The REST API workshop is aimed at researchers and developers interested in exploring Ensembl beyond the website. The workshop covers how to use the Ensembl REST APIs, including understanding the major endpoints and how to write Python/Perl/R scripts to call them.


Feedback from previous courses: "There are probably quite few people out there who all assume that Ensembl today is the same as it was years ago. It is not. With many new features and datasets incorporated/interlinked, it offers data exploration like never before. This course was a very useful update on what Ensembl has become" Browser workshop, CRUK, April 2016

"Very useful workshop, certainly one of the most informative and useful I have attended. Delivered by someone who was extremely familiar with the website and its capabilities, not someone who had used it a couple of times and proclaimed themselves to be an expert." Browser workshop, Cardiff, March 2014

If you think you'd like to host a similar course at your institute, you can find out more on the Ensembl workshops page.

Audience

The browser course on 24th September is aimed at wet-lab researchers and bioinformaticians.

The optional REST API courses on the 25th/26th September are aimed at bioinformaticians and wet-lab biologists who can program in Python or R and have attended the browser course.

Learning outcomes

After the browser course, participants should be able to:

  • view genomic regions and manipulate the view to add features they are interested in.
  • explore information about genes and their sequences, and gene data in bulk using BioMart.
  • analyse genomic variants and associated phenotypes and their own variation data using the VEP.
  • view homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.

After the REST API course 

participants should be able to:

  • Synthesise the data types accessible through the Ensembl REST API
  • Understand the methods in the Ensembl REST API
  • Navigate the Ensembl REST API documentation to find available methods
  • Write Python/R scripts to access data via the Ensembl REST API

Programme

Ensembl Browser workshop:

Morning: Introduction to Ensembl and Ensembl genes. Viewing genes and locations in the browser. Data export with BioMart.

Afternoon: The afternoon sessions depend on the participants' interest. We can cover genetic variation, comparative genomics and gene regulation, depending on what you express an interest in when you register.

Ensembl REST API workshop:

09:30-10:00    Overview of the Ensembl REST API
10:00-11:00    Accessing GET queries with the Ensembl REST API
11:00-11:20    Tea/Coffee Break    
11:20-12:30    Decoding json and chaining REST queries together
12:30-13.15    Lunch
13:15-14:30    Accessing POST queries with the Ensembl REST API
14:30-15:00    Rate limiting