Ensembl tutorial signup

Workshop Evaluation Form: BROKEN http://genome-test.gi.ucsc.edu/~kate/ensemblEvaluation.doc

On January 28, Bert Overduin from Ensembl will be on campus presenting an all-day hands-on workshop covering the Ensembl tools. The time and place are:

E2 506 (lab across from CBSE office) 9:30am - 5pm (with possible overflow till 6pm) After-workshop dinner with Bert at the Palomar for interested folks

The standard workshop course description is reproduced below: Workshop description
Or, in WORD doc format: BROKEN http://genome-test.gi.ucsc.edu/~kate/ensemblWorkshop.doc

The workshop is will be held in E2 conference room 506. It will begin at 9:30 a.m. and will end at 5pm, with an additional hour available for overflow questions and topics. Attendees should bring their own laptop (if this is a problem for you, contact kate).

Bert is requesting input for tailoring the course to the audience here.

Please let us know if you would like to attend by adding your name to this page in the appropriate section. If you have any suggestions for material you would like covered in the workshop, write that down as well.

Attending

Browser staff

• Kate
• Brian
• Brooke
• Fan
• Ann
• Rachel
• Hiram - how would a user load a set of genes from a gff file and do intersections of that with the ensembl gene set ? What types of intersections are available ? What does the gene history display look like for a particular gene ?
• Galt
• Donna - I would like to hear about areas of functionality that Ensembl offers but UCSC doesn't (could be useful in referring mailing list users), also areas in which Ensembl offers a more comprehensive solution than UCSC.
• Angie
• Kayla
• Bob
• Markd
• Kent

• Sofie (Haussler wet lab staff)

Post-docs & grads

• Ting Wang (Haussler post-doc)
• David Greenberg (Haussler wet lab)
• Jason Underwood (Haussler wet lab)
• Kord Kober (Evolutionary Bio)
• Lauren Lui (Haussler rotation)
• Pinal Kanabar (Stuartlab : I will be able to attend only morning session)
• Sol Katzman (Haussler wet lab)

Workshop description

Browsing Genes and Genomes with Ensembl

Dr. Bert Overduin European Bioinformatics Institute

The Ensembl project (http://www.ensembl.org) provides a comprehensive and integrated source of annotation of, mainly chordate, 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 workshop consists of the following modules. Most modules consist of a presentation, 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.

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 mining with BioMart: retrieving datasets using the data mining tool BioMart Evaluating genes and transcripts: how are Ensembl gene and transcripts predictions made? Comparative genomics and proteomics: orthologues, protein families, whole genome alignments and syntenic regions OR Variations: SNPs, haplotypes, linkage disquilibrium

The only prerequisite for this workshop is general knowledge of molecular biology / genomics and a familiarity with web browsers.

Note: As Ensembl focuses on chordates, it contains few genomes of lower animals and none of plants or prokaryotes (for available genomes, please have a look at http://www.ensembl.org).

Requirements

- Computer room with a pc for each participant (30 is the maximum number of participants) - Each pc should have a (reasonably fast) internet connection and an internet browser installed (preferably FireFox, although Internet Explorer will also do) - Pc for the instructor that is connected to a projector, has an internet connection and has MS PowerPoint installed

Costs

For academic institutions the course is free of charge. However, travel, accommodation and subsistence costs of the instructor should be reimbursed by the host. It would be appreciated if the host arranges for accommodation.

Certificates

We don't usually make and give out certificates of attendance to participants of the workshop ourselves. However, if the host wants to do this, this is fine by us and our instructor would be happy to sign the certificates!