Ensembl API Workshop
Organizers: |
Nirav Merchant, Fiona McCarthy, 411 |
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Local Point of Contact: |
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Trainers: |
Bert Overduin, Ph.D. |
Date: |
January 23, 2013 |
Location: |
Roy Drachman A119 (College of Pharmacy) - see Building 202 (east) on campus map, just east of Keating Building |
Online Registration: |
http://www.iplantcollaborative.org/forms/registration-form-ensemble-browser-and-api-workshops-january-22-23-2013 |
Flyer: |
Workshop Description
The Ensembl project (http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly vertebrate, genome sequences.
This 1/2-day workshop is aimed at researchers and developers interested in exploring Ensembl beyond the browser.
Ensembl uses MySQL relational databases to store its information. A comprehensive set of Application Programming Interfaces (APIs) serve as a middle-layer between underlying database schemes and more specific application programmes. The APIs aim to encapsulate the database layout by providing efficient high-level access to data tables and isolate applications from data layout changes.
The workshop covers the Ensembl Core database and API. The database schema and the API design as well as its most important objects and their methods will be presented. Short presentations will be interspersed by hands-on exercises to put the learned into practice.
Ensembl Core databases and API
The set of species-specific Ensembl Core databases stores genome sequences and most of the annotation information. This includes the gene, transcript and protein models as annotated by the Ensembl automated genome analysis and annotation pipeline as well as assembly information, cDNA and protein alignments, external references and e.g. markers and repeat regions. The Core API also forms the basis for the Variation, Compara and Regulation APIs, that can be used retrieve variation, comparative genomics and regulation data from Ensembl, respectively.
Prerequisites
1. To attend this workshop participants should have a working knowledge of Perl and molecular biology / genetics. Participants without Ensembl knowledge are encouraged to also attend the Browser workshop.
2. Please test your iPlant credentials to ensure you have access. You can log-in from user.iplantcollaborative.org, click the button "iPlant Login"
- Once authenticated, click the "My Services" link
- Under "My Services" please ensure you have access to: Atmosphere, Discovery Environment, iPlant Data Store. You can also request access to other services here
- If you have account problems, please email support@iplantcollaborative.org
3. Please check your email and this wiki prior to the workshop, as this is the way we will communicate any important changes.
4. Please check this software requirement list and install the necessary software: Software Requirements
- Please contact your system administrator if you do not have permission to install software on your computer.
Workshop Agenda (Tentative)
Time |
Topic |
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08:00 – 08:15 |
Introduction to Ensembl |
08:15 – 10:00 |
Core database and API hands-on |
10:00 – 10:15 |
Break |
10:15 – 12:00 |
Core database and API hands-on |
Attendee List (20 max)
Name |
Research Area |
|
---|---|---|
Alexander Tchourbanov |
alexander@big.ac.cn |
Computational Biology |
Alexander Ochoa |
alexocho@email.arizona.edu |
Genetics and Nucleic Acids |
Robert Fitak |
rfitak@email.arizona.edu |
Genetics and Nucleic Acids |
John McMullen |
jgm2@email.arizona.edu |
Genetics and Nucleic Acids |
Lipsa Das |
lipsadas@email.arizona.edu |
Cancer Biology |
Kim Yong |
kyong@u.arizona.edu |
Molecular Biosciences |
J. Cesar Ignacio-Espinoza |
igancioe@email.arizona.edu |
Ecological Studies |
Liwen Lai |
liwen7@gmail.com |
Genetics and Nucleic Acids |
George Watts |
gwatts@azcc.arizona.edu |
Genetics and Nucleic Acids |
Mana Ohkura |
manabanana@email.arizona.edu |
Molecular Biosciences |
Laurel Johnstone |
laureljo@email.arizona.edu |
Genetics and Nucleic Acids |
Fiona McCarathy |
fionamcc@email.arizona.edu |
Ag omics tools and research |
Nirav Merchant |
nirav@email.arizona.edu |
Computation Research, Genomics |
Susan Miller |
sjmiller@email.arizona.edu |
Modern Analysis |
Eun-Hae Kim |
eunhaek@email.arizona.edu |
Biological and Critical Systems |
Patricia Stock CANCELLED |
spstock@email.arizona.edu |
Prokaryote-Eukaryote Symbioses |
Luis Rivera |
lrivera@cals.arizona.edu |
Bioinformatics |
Jianwei Zhang CANCELLED |
jzhang@cals.arizona.edu |
Plant Biology |
Kapeel Chougule |
kapeelc@gmail.com |
Computer and Computation Research |
Samendra Sherchan |
samendrasherchan@email.arizona.edu |
Env Biology |
Andy Lenards |
lenards@iplantcollaborative.org |
Computer and Computation Research |
Wait List |
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Kalpana Algotar |
kalgotar@asu.edu |
Software Development |