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 (NIPGR), 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 


Final List of Selected Candidates

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 collaborative effort between NIPGR and Ensembl team.
This workshop have two components:-
  1. Ensembl Component: Ensembl Browser and REST API workshop (Link for Details)
  2. NIPGR Component: Next Generation Sequencing (NGS) data analysis, Basic Linux, Perl, R and database development.
Ensembl Component
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
NIPGR Component (Hands on training)
  • 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
Workshop Details
Workshop Dates: July 9 - 12, 2019

Workshop Timing: 9.30 a.m. to 5.30 p.m.

Important Dates:
  • March 01, 2019: Registration Open.
  • April 15, 2019: Last Date of Submission of Application Form.
  • April 25, 2019: List of selected candidates available online with waiting list.
  • May 15, 2019: Last date for received Demand Draft (DD) of Registration fee.
  • May 30, 2019: Second list of selected candidates.
How to Apply: Please email the complete application form at workshop@nipgr.ac.in by April 15, 2019. The selected participants will be intimated by Email or Website by April 25, 2019. Selected candidates will be required to register by paying the necessary registration fees by post (e.g. Demand Draft) on or before May 15, 2019. The fee is payble by Demand Draft (DD) from any nationalized bank in favour of the "Director, National Institute of Plant Genome Research" payble at New Delhi.

Please send the Demand Draft (DD) to the address given below.              
Dr. Shailesh Kumar, Laboratory #202,
National Institute of Plant Genome Research (NIPGR),
Aruna Asaf Ali Marg, P.O. Box No. 10531
New Delhi 110067


Please email us at workshop@nipgr.ac.in for any questions and concern.

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. Participants will need to have some programming skills (Python, R or Perl).
  2. Participants will need to have a free Microsoft Account.
  3. Participant should bring own laptop.
Number of Participants: The total number of selected participants is limited to 30.

*********************
NGS-Ensembl
*********************
[NATIONAL INSTITUTE OF PLANT GENOME RESEARCH]
New Delhi
Training Code: [NIPGR-2019]
Title: International Workshop on NGS data analysis and Ensembl resources (NGS-Ensembl)
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:Some programming skills (Python, R or Perl) and a free Microsoft Account
Number of participants:30
Expected date of announcement: February 27, 2019
Boarding and lodging arrangements etc.:Participants have to arrange their own accommodation
Registration FeeWithout Accommodation
India/ SAARC Countries/ Other Countries Regular delegates: 10,000/-
Students: 7000/-
Contact Address:
workshop@nipgr.ac.in
Phone: 011-26735108
Fax: 011-26741658
E-mail: workshop@nipgr.ac.in
Web-Address: http://www.nipgr.ac.in

**************************************************************************************************************
NGS-Ensembl Schedule
**************************************************************************************************************
DAY 1
By Ensembl Trainer for 30 Participents
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 Ensembl Trainer for 15 Participents (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 Participents, 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 Ensembl Trainer for 15 Participents (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 Participents, 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 Participents)
09:00-09:45 Next-generation Molecular Breeding for Crop Improvement (Lecture) by Dr. Swarup Parida, NIPGR, New Delhi
09:45-10:30 Transcriptomic insights into the plant structure and function (Lecture) by Dr. Aashish Ranjan, NIPGR, New Delhi
10:30-11:00 Tea/Coffee Break
11:00-12:00 Database and web-server development for drug discovery (Lecture) by Prof. G P S Raghava, IIIT-D, New Delhi
12:00-13:00 NGS, Genomics, Application and Challenges(Lecture) by Dr. Debasis Chattopadhyay, NIPGR, New Delhi
13:00-14:00 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