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Ensembl Browser Workshop

Ensembl Browser Workshop

Organizers:

Nirav Merchant, Fiona McCarthy, 411

Local Point of Contact:

Nirav Merchant

Trainers:

Bert Overduin, Vertebrate Genomics Team, EMBL, Wellcome Trust Genome Campus

Date:

January 22, 2013
9 AM - 5 PM

Location:

Keating 103

Online Registration:

http://www.iplantcollaborative.org/forms/registration-form-ensemble-browser-and-api-workshops-january-22-23-2013

Flyer:

downloadable flyer

Workshop Description

The Ensembl project (http://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 lots of hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. The workshop is primarily targeted at wetlab researchers.

The following modules will be covered:

Module

Description

Introduction to Ensembl:

origin, goals and organization of the Ensembl project

Worked example:

guided tour of the most important pages of the Ensembl website

Data retrieval with BioMart:

retrieving complex / large datasets using the data retrieval tool BioMart

Comparative genomics:

orthologues and paralogues, protein families, whole genome alignments and syntenic regions

Variation:

sequence variants, structural variants, Variant Effect Predictor

Custom annotation:

uploading / attaching your own data (BED, GFF, BAM, VCF files) to Ensembl

Most modules consist of a presentation and demo, followed by the opportunity to do exercises.

Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl.

Note: Most examples and exercises in the workshop will be focused on human as this is by far the most richly annotated species. However, most of what is taught in the workshop can be applied to other species in the Ensembl browser (http://www.ensembl.org), as well as to the species in the Ensembl and Ensembl Genomes browsers that contain genomes of invertebrates, protists, plants, fungi and bacteria (http://www.ensemblgenomes.org).

Prerequisites

The only prerequisite for this workshop is general knowledge of molecular biology / genomics and a familiarity with web browsers.
Those who register for this workshop are requested to fill out this questionnaire: http://www.surveymonkey.com/s/G65Y2C2

Workshop Agenda (Tentative)

Time

Topic

09:00 – 09:30

Introduction to Ensembl

09:30 – 10:30

Worked example

10:30 – 10:45

Break

10:45 – 11:15

Hands-on exercises

11:15 – 11:30

BioMart

11:30 – 12:00

Hands-on exercises

12:00 – 13:00

Lunch Break

13:00 – 13:30

Comparative genomics

13:30 – 14:45

Hands-on exercises

14:45 – 15:00

Break

15:00 – 15:45

Hands-on exercises

15:45 – 16:00

Custom annotation

16:00 – 16:30

Hands-on exercises

16:30 – 17:00

Wrap-up, questions and answers

Attendee List (40 max)

Name

Email

Research Area

Alexander Tchourbanov

alexander@big.ac.cn

Computational Biology

Ming-Min Lee

mingmail@email.arizona.edu

Genetics and Nucleic Acids

Kalpana Algotar

kalgotar@asu.edu

Software Development

Natalia Ignatenko

nai@email.arizona.edu

Cell Biology

Amit Algotar

algotar@email.arizona.edu

Cancer Biology

Alexander Ochoa

alexocho@email.arizona.edu

Genetics and Nucleic Acids

Robert Fitak

rfitak@email.arizona.edu

Genetics and Nucleic Acids

Eva Nichols

ekn@email.arizona.edu

Cell Biology

Amanda Cooksey

amcooksey@email.arizona.edu

Genetics and Nucleic Acids

Lipsa Das

lipsadas@email.arizona.edu

Cancer Biology

Kim Yong

kyong@u.arizona.edu

Molecular Biosciences

Liwen Lai

liwen7@gmail.com

Genetics and Nucleic Acids

George Watts

gwatts@azcc.arizona.edu

Genetics and Nucleic Acids

Tanya Renner CANCELLED

tanyrenner@email.arizona.edu

Evolutionary Biology

Mana Ohkura

manabanana@email.arizona.edu

Molecular Biosciences

Megan Phifer-Rixey

mrixey@email.arizona.edu

Genetics and Nucleic Acids

Laurel Johnstone

laureljo@email.arizona.edu

Genetics and Nucleic Acids

Richard Lapoint

rlapoint@email.arizona.edu

Systematic and Population Biology

Fiona McCarathy

fionamcc@email.arizona.edu

Ag omics tools and research

Nirav Merchant

nirav@email.arizona.edu

Computation Research, Genomics

Andrew Gloss

agloss@email.arizona.edu

Genetics and Nucleic Acids

Susan Miller

sjmiller@email.arizona.edu

Modern Analysis

Hillary Mehl CANCELLED

hillary.l.mehl@gmail.com

Plant Biology

Ann Danowitz

danowitz@cals.arizona.edu

Computer Systems Architecture

Eun-Hae Kim

eunhaek@email.arizona.edu

Biological and Critical Systems

Patricia Stock

spstock@email.arizona.edu

Prokaryote-Eukaryote Symbioses

Luis Rivera

lrivera@cals.arizona.edu

Bioinformatics

Jianwei Zhang

jzhang@cals.arizona.edu

Plant Biology

Kapeel Chougule CANCELLED

kapeelc@gmail.com

Computer and Computation Research

Samendra Sherchan

samendrasherchan@email.arizona.edu

Env Biology

Andy Lenards

lenards@iplantcollaborative.org

Computer and Computation Research