Ensembl Browser Workshop
Organizers: |
Nirav Merchant, Fiona McCarthy, 411 |
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Local Point of Contact: |
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Trainers: |
Bert Overduin, Vertebrate Genomics Team, EMBL, Wellcome Trust Genome Campus |
Date: |
January 22, 2013 |
Location: |
Keating 103 |
Online Registration: |
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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 |
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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 |
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 |