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:-

• Ensembl Component: Ensembl Browser and REST API workshop (Link for Details)
• 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:

• Participants will need to have some programming skills (Python, R or Perl).
• Participants will need to have a free Microsoft Account.
• Participant should bring own laptop.

Number of Participants: The total number of selected participants is limited to 30.

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NGS-Ensembl
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[NATIONAL INSTITUTE OF PLANT GENOME RESEARCH]
New Delhi

NGS-Ensembl Schedule