May 2012 Galaxy Update
Welcome to the May 2012 edition of Galaxy Update, a monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.
GCC2012: Just 3 Months Away!
- The 2012 Galaxy Community Conference (GCC2012) will be held July 25-27, in Chicago.
- Early registration is now open. The early registration deadline is June 11.
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- Has less capacity than the 2 days of the main meeting, and
- So far, everyone who has registered for the main meeting has also registered for the Training Day.
- Cheap, non-shared rooms in the James Stuckel Towers on the UIC campus (and adjacent to the conference venue) are going fast.
- Did we mention that Early registration is now open?
Training Day: We Need Your Help!
GCC2012 Training Day needs your help! We are adding several new sessions to the GCC2012 Training Day that will cover how to use Galaxy to perform several common kinds of analysis, such as ChIP-Seq, RNA-Seq, Metagenomics, and others. However, before we can to do that, we need your input on which topics there is the most interest in!
If you are planning on or are interested in attending GCC2012, please take 2 minutes to tell us which topics you are interested in. We will use your feedback to set the Training Day schedule.
Also, if you are interested in presenting a topic, especially a "how to use Galaxy" topic, then we strongly encourage you to also nominate yourself (or, hey someone else!) on the survey as well. Please provide your feedback no later than May 11.
| Give up your input! |
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Galaxy Tour de France 2012
We are pleased to announce the Galaxy Tour de France 2012, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in Perpignan, Lyon and Paris. Each day will feature a Galaxy for Biologists workshop in the morning, and a Galaxy for Developers workshop in the afternoon. All workshops will be taught by Galaxy Team members Nate Coroar, Anton Nekrutenko and James Taylor.
Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible. See Galaxy Tour de France 2012 for details and links.
New Public Server: Nebula
Nebula is a web service provided by Institut Curie and powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data. Many thanks to Institut Curie for making Nebula publicly available.
New Papers
This paper may be of interest to the Galaxy community:
Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis, by Kun H. Liu, Matthew McCormack, Jen Sheen, Plant Methods 2012, 8:12
| This open access article includes a detailed recipe describing how Galaxy was used in their analysis. This paper was among 31 papers added to the Galaxy CiteULike group since the last Galaxy Update. The new papers were spread across 5 categories. |
# | Tag | # | Tag | |
|---|---|---|---|---|---|
| 19 | methods | 1 | howto | ||
| 6 | other | 6 | workflow | ||
| 2 | shared |
Who's Hiring
- The Galaxy Project is hiring post-docs and software engineers @ Emory and Penn State.
- Internship @ EMBL Heidelberg building an emBASE-Galaxy Bridge
- Computational Biologist, Harvard School of Public Health
- Bioinformatics Analyst @ U Virginia
- [Bioinformaticians @ FDA](http://gmod.org/wiki/News/Bioinformaticians @ FDA)
Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.
Upcoming Events and Deadlines
Deadlines
There are May application deadlines for the Informatics on High Throughput Sequencing Data Workshop, and abstract and poster deadlines for SciPy and EuroSciPy (May 1!), SocBiN Bioinformatics 2012, and InCoB.
See the Galaxy Events Google Calendar for details on these and other events.
Events
Tool Shed Contributions
At least 7 new repositories were added to the Galaxy Tool Shed in April, including
- head_and_tail, cdf_plot, venn, and matrix_visualization
- BEAST (Bayesian Evolutionary Analysis Sampling Trees): Bayesian MCMC analysis of molecular sequences.
- rtg_investigator: Mapping and Analysis Software for NGS Platforms Roche, Illumina and Complete Genomics; software from Real Time Genomics.
- filter_on_md: Filter mapped reads on MD tag string in SAM files.
Distribution
The most recent distribution was on March 12, 2012. Look for a new one this month.