International Workshop on NGS data analysis and Ensembl resources, New Delhi, 9-12 July 2019

Date:

 Tuesday 9 Friday 12 July 2019

Venue: 

National Institute of Plant Genome Research - Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi,  Delhi,  110067, India

Application opens: 

Friday 01 March 2019

Application deadline: 

Monday 15 April 2019

Participation: 

Open application with selection

Registration fee: 

INR 10,000; INR 7,000 for students

Course Overview

This workshop has two components:
Ensembl Component: Ensembl Browser and REST API workshop by Dr. Astrid Gall (Ensembl trainer).
NIPGR Component: Next Generation Sequencing (NGS) data analysis, Basic Linux, Perl, R and database development.

Ensembl component: Browser workshop

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 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. 

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.

Ensembl component: REST API workshop

This 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 scripts to call them.
Feedback from previous courses: "Wish I had taken the course long time ago. Didn't know before how good and powerful APIs are!" API workshop, EMBL-EBI, January 2016

"I really enjoyed the course, and the ENSEMBL API will become a very relevant part of my toolset." API workshop, Cambridge, December 2013

NIPGR Component: 

  • Basics Linux, Perl, and R programming with ggplots.
  • Whole genome assembly and annotations of microbes.
  • Variation detection by whole genome sequencing.
  • Whole transcriptome data analysis.
  • Bioconductor Packages for NGS data analysis
  • TextMining of PubMed using pubmed.mineR
  • Database development with PERL, MySQL and PHP

Audience

Researchers from academia/industry, both wet-lab researchers and bioinformaticians.

Prerequisites: Some programming skills (Python, R or Perl) and a free Microsoft Account.

Learning outcomes

Ensembl browser workshop

After this 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.

Ensembl REST API workshop

After this 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 scripts to access data via the Ensembl REST API

Programme

DAY 1
By Dr. Astrid Gall (Ensembl Trainer) for 30 Participants
08:00-08:30  Registration 
08:30-08:40  Welcome address by Dr. Jitendra Thakur, NIPGR 
08:40-09:00  Lamp Lightning (Director, NIPGR and Ensembl staff) and Introduction 
09:00-10:30  Introduction to Ensembl and the Region in Detail View 
10:30-11:00  Tea/Coffee Break and Photo Session 
11:00-12:00  Genes and transcript annotation 
12:00-13:00  Variation data and the VEP, Regulatory data or Comparative Genomics*
13:00-14:00 Lunch Break 
14:00-15:00  Variation data and the VEP, Regulatory data or Comparative Genomics* 
15:00-15:30  Tea/Coffee Break 
15:30-17:00  BioMart, Further Ensembl resources and Summary
DAY 2
By Dr. Astrid Gall (Ensembl Trainer) for 15 Participants (Batch-1)
09:30-10:00  Overview of the Ensembl REST API 
10:00-10:30  Accessing GET queries with the Ensembl REST API 
10:30-11:00 Tea/Coffee Break 
11:00-13:00  Decoding json and chaining REST queries together 
13:00-14:00 Lunch Break 
14:00-15:00  Accessing POST queries with the Ensembl REST API 
15:00-15:30  Rate-limiting 
15:30- 16:00 Tea/Coffee Break 
16:00-17:15 Lecture by Dr. Shailesh Kumar 
NGS Session (By Indian Speakers for 15 Participants, Batch-2)
09:00-10:30  Introduction to Linux command line (Hands-on session) (Indian speaker) 
10:30-11:00  Tea/Coffee Break 
11:00-13:00  Introduction to NGS Data Analysis (Hands-on session) (Indian speaker) 
13:00-14:00  Lunch 
14:00-15:30  RNA-Seq data analysis (Hands-on session) (Indian speaker) 
15:30-16:00  Tea/Coffee Break 
16:00-17:30  Variant annotation and Variant Filtration with Whole Genome Sequencing datasets (Hands-on session) (Indian speaker) 
DAY 3
By Dr. Astrid Gall (Ensembl Trainer) for 15 Participants (Batch-2)
09:30-10:00  Overview of the Ensembl REST API 
10:00-10:30  Accessing GET queries with the Ensembl REST API 
10:30-11:00 Tea/Coffee Break 
11:00-13:00  Decoding json and chaining REST queries together 
13:00-14:00 Lunch Break 
14:00-15:00  Accessing POST queries with the Ensembl REST API 
15:00-15:30  Rate-limiting 
15:30- 16:00 Tea/Coffee Break 
16:00-17:15 Lecture by Dr. Shailesh Kumar 
NGS Session (By Indian Speakers for 15 Participants, Batch-1)
09:00-10:30  Introduction to Linux command line (Hands-on session) (Indian speaker) 
10:30-11:00  Tea/Coffee Break 
11:00-13:00  Introduction to NGS Data Analysis (Hands-on session) (Indian speaker) 
13:00-14:00  Lunch 
14:00-15:30  RNA-Seq data analysis (Hands-on session) (Indian speaker) 
15:30-16:00  Tea/Coffee Break 
16:00-17:30  Variant annotation and Variant Filtration with Whole Genome Sequencing datasets (Hands-on session) (Indian speaker) 
DAY 4
NGS Session (By Indian Speakers for 30 Participants)
09:30-10:30  Database development with PERL, MySQL and PHP (Hands-on session) by Dr. Shailesh Kumar, NIPGR, New Delhi - I 
10:30-10:45  Tea/Coffee Break 
10:45-13:15  Database development with PERL, MySQL and PHP (Hands-on session) by Dr. Shailesh Kumar, NIPGR, New Delhi - II 
13:15-14:00  Lunch 
14:00-15:30  Bioconductor Packages for NGS data analysis (Hands-on session) by Dr. S. Ramachandran, CSIR-IGIB, New Delhi 
15:30-16:00  Tea/Coffee Break 
16:00-17:30  TextMining of PubMed using pubmed.mineR (Hands-on session) by Dr. S. Ramachandran, CSIR-IGIB, New Delhi