March 2012 Galaxy Update
Welcome to the March 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.
New Papers
There were 28 papers added to the Galaxy CiteULike group since the last Galaxy Update. The new papers were spread across 5 categories.
| # | Tag | # | Tag | |
|---|---|---|---|---|
| 15 | methods | 2 | howto | |
| 7 | other | 2 | workflow | |
| 3 | isgalaxy |
Who's Hiring
- The Galaxy Project is hiring post-docs and software engineers at Emory and Penn State.
- Bioinformatics Analyst @ U Virgina Bioinformatics Core
- Bioinformatician / Sr. Database Developer @ GigaScience / BGI Hong Kong
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 March application deadlines for a Next-gen Sequencing in Evolutionary Biology course at NESCent; Bio-Linux, and Advanced RNA-Seq and ChIP-Seq Data Analysis courses at Hinxton; Next Generation Sequencing Data Analysis at EMBL Heidelberg; Bioinformatics and Comparative Genome Analyses in Naples; Statistical Analysis of Genomic Data at CSHL; abstract deadlines for BITS 2012 and Information Visualization in BioMedical Informatics (IVBI 2012); and early registration deadlines for the April GMOD Meeting and Copenhagenomics.
See the Galaxy Events Google Calendar for details on these and other events.
Events
GCC2012 Update
- The 2012 Galaxy Community Conference (GCC2012) will be held July 25-27, in Chicago.
- The conference will feature two full days of presentations and discussions.
- Abstract submission opened February 13, and will [close April 16](/src/events/gcc2012/Key Dates/index.md).
-
A whole day of training has been added, and topics set:
- Early registration will open any day now and close June 11.
Tool Shed Contributions
At least 8 new repositories were added to the Galaxy Tool Shed in February, including
- CREST (Clipping REveals STructure): maps somatic structural variation in cancer genomes
- MACS 1.4 ChIP-Seq peak calling (Main has 1.3)
- java_genomics_toolkit: NGS, especially WIG transformations (add/log/Z-score/etc) and visualization (KMeans/heatmaps)
- mrFAST and mrsFAST: map Illumina short reads to reference assemblies; fast and memory-efficient
- mrCaNaVaR: Read depth analysis method to characterize segmental duplications & predict absolute copy numbers
- SCALCE: Compression of FASTQ files
Other News
New non-wiki documentation
- Tutorial: Using the UCSC Genome Browser and Galaxy to study regulatory sequence evolution in Drosophila, by Casey Berman
- Notes on installing Galaxy by Paul-Michael Agapow
Galaxy-Announce now the default for new users on Main
Newly registered users on Main, the Galaxy project's public server, who check "Subscribe to a mailing list" at registration time, are now subscribed to the moderated and low-volume Galaxy-Announce mailing list, instead of the high-volume, and sometimes overwhelming Galaxy-User list. This change was also made in the Galaxy source.