National Institute of Plant Genome Research
Digital India     
 
International Workshop on
NGS data analysis and Ensembl resources (NGS-Ensembl)
July 9 - 12, 2019
Organized by

Sub – Distributed Information Center (Sub - DIC)
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067
And
Ensembl Team, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
Funded By
Department of Biotechnology

Ministry of Science and Technology, Government of India, New Delhi

View Workshop Brochure 


List of Selected Candidate
About This Workshop :

The Sub-DIC facility at NIPGR periodically organizes trainings/workshops/symposiums/ seminars in Bioinformatics. These workshops offer short courses useful for understanding the developments in different aspects of Bioinformatics. We aim to provide exposure and hands on intensive training in systems Biology, Bioinformatics applications in agriculture, genomics and proteomics.

This time we are organising a four days International Workshop on Next Generation Sequencing (NGS) data analysis and Ensembl resources (NGS-Ensembl). This is a collaborate effort between NIPGR and Ensembl team.
This workshop have two components:-
  1. NIPGR Component: Next Generation Sequencing (NGS) data analysis.
  2. Ensembl Component: Ensembl Browser and REST API workshop Link for Details
Browser Workshop

This one-day browser workshop consists different modules and tools demonstration, followed by exercises, as listed below
  • Introduction to Ensembl: origin, goals and organisation of the Ensembl project

  • Genebuild: how are Ensembl gene and transcripts predictions made?

  • Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions

  • Variation: SNPs and other polymorphisms, haplotypes, linkage disequilibrium, structural variants like CNVs

  • Regulation: Sequences that may be involved in gene regulation, and integration of ENCODE data

  • Data export with BioMart: retrieving genomic information using a web interface (no programming required).

Learning outcomes

At the end of 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 Variant Effect Predictor (VEP).

  • View homologous genes and genomic regions, functional elements involved in gene regulation and their activity in different cell types.
REST API Workshop

The Ensembl REST API allows language agnostic programmatic access to Ensembl data. The Ensembl project provides a comprehensive and integrated source of annotation of various genome sequences. 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 scripts to call them.
Learning outcomes

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 scripts to access data via the Ensembl REST API
Workshop Timing: 9.30 a.m. to 5.30 p.m.

Important Dates:
  • February 25, 2019: Registration Open.
  • April 15, 2019: Last Date of Submission of Application Form.
  • April 30, 2019: List of selected candidates available online.
  • May 15, 2019: Last date for confirmation of attendance by selected candidates.
How to Apply: Please Email the complete Application form including the abstract enlisting research interests and how this workshop would be beneficial to you at workshop@nipgr.ac.in latest by April 15, 2019.

Registration Details: The registration fee for the workshop is 10,000/- per participant (for regular) and 7,000/- (for students).

Registration fee includes:
  • Participation in the workshop.
  • Tea/coffee breaks and lunch for all days of the workshop.
  • Certificate for successful completion.
  • Workshop Kit including stationery and personalized I-Card.
  • Proceedings of the workshop.
  • Online Access to all the training material.

Important Notes:

  1. ............if any
Number of Participants: The total number of selected participants is limited to 30.
*********************
IEWGDD 2019
*********************
[NATIONAL INSTITUTE OF PLANT GENOME RESEARCH]
New Delhi
Training Code: [NIPGR- __]
Title: International Ensembl Workshop on Genomics and Database development
Date: 9th July to 12th July 2019
Duration:4 Days
Subject Area: Ensembl genome browser and REST API training, NGS data analysis, and database development
Objectives: To train the researchers on Ensembl genome browser and REST APIs, NGS data analysis, and database development
Contents: To use of tools in Ensembl Genome, Bioinformatics & Database development
Methodology:Lectures, Demonstration and Hands-on Sessions
Level of Participants:Plant/Animal researchers from Academia / Industry
Prerequisites:--------------------
Number of participants:30
Expected date of announcement: ---------------------
Boarding and lodging arrangements etc.:Participants have to arrange their own accommodation
Registration FeeWithout Accommodation
India/ SAARC Countries/ Other Countries Regular delegates: ---------/-
Students: ---------/-
Contact Address:
Dr. Jitendra Thakur (jthakur@nipgr.ac.in)
Dr. Shailesh Kumar (shailesh@nipgr.ac.in)
Phone: 011-26735108
Fax: 011-26741658
E-mail: bic@nipgr.ac.in
Web-Address: http://www.nipgr.ac.in
**************************************************************************************************************
IEWGDD 2019 Schedule
**************************************************************************************************************
DAY 1
08:00-08:30 Registration
08:30-08:40 Welcome address by Dr. Shailesh, NIPGR
08:40-09:00 Lamp Lightning 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
11:00-12:30 Genes and transcript annotation
12:30-13:00 Variation data and the VEP*
13:00-13:30 Lunch Break
13:30-15:00 Regulatory data*
15:30-16:00 Tea/Coffee Break
16:00-17:30 BioMart
DAY 2
09:30-10:30 Comparative Genomics*
10:30-11:00 Tea/Coffee Break
11:00-11:30 Overview of the Ensembl REST API
11:30-12:00 Accessing GET queries with the Ensembl REST API
12:00-13:00 Decoding json and chaining REST queries together -1
13:00-14:00 Lunch Break
13:00-14:00 Decoding json and chaining REST queries together -2
14:00- 15:00 Accessing POST queries with the Ensembl REST API
15:00-15:30 Tea/Coffee Break
15:30-16:00 Rate-limiting
16:00-17:15 Lecture by Dr. Shailesh Kumar
DAY 3
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
09:30-10:30 Database development with PERL, MySQL and PHP (Hands-on session) (Indian speaker) - I
10:30-10:45 Tea/Coffee Break
10:45-13:15 Database development with PERL, MySQL and PHP (Hands-on session) (Indian speaker) - II
13:15-14:00 Lunch
14:00-15:30 Bioconductor Packages for NGS data analysis (Hands-on session) (Indian speaker)
15:30-16:00 Tea/Coffee Break
16:00-17:30 TextMining of PubMed using pubmed.mineR (Hands-on session) (Indian speaker)