April 2012 Galaxy Update
Welcome to the April 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
This paper may be of interest to the Galaxy community:
- Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field and Karen Nelson , "Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community." BMC Bioinformatics 2012, 13:42
These were among 28 papers added to the Galaxy CiteULike group since the last Galaxy Update. The new papers were spread across 6 categories.
| # | Tag | # | Tag | |
|---|---|---|---|---|
| 9 | methods | 1 | howto | |
| 14 | other | 2 | workflow | |
| 1 | repeoducibility | 2 | shared |
Who's Hiring
- The Galaxy Project is hiring post-docs and software engineers at Emory and Penn State.
- Computational Biologist, Harvard School of Public Health
- Computational Genomics Specialists, Smithsonian Institution, Washington, DC
- Bioinformatician @ U Edinburgh
- Bioinformatics Analyst @ U Virginia
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 April application deadlines for EMBL-EBI Summer Bioinformatics School and Plant Bioinformatics Course; abstract deadlines for InCoB, DILS, BOSC, ISMB Tech Track, and GCC2012; and an early registration deadline for BITS.
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 abstract submission deadline is April 16.
- Early registration is now open.
- The conference will feature two full days of presentations and discussions.
- A whole day of training is also scheduled
Tool Shed Contributions
At least 15 new repositories were added to the Galaxy Tool Shed since the last Galaxy Update, including
- EMBER: analysis technique for inferring the genes regulated by transcription factor.
- hmmer: hmmscan/hmmsearch as one tool, plus hmmpress
- RNA SEQ by Expectation Maximization (RSEM).
- FastqMcf from ea-utils: remove barcodes and primers, filter and clip.
- Augustus: eukaryotic gene prediction.
- sed_wrapper: Get the power of Unix sed in Galaxy
- antiSMASH: antibiotics and secondary metabolite analysis shell
- snp_mapping_using_wgs: Map mutation by plotting recombination frequency from crossing to a polymorphic strain
- ems_variant_density_mapping Map mutation by linkage to regions of high mutation density using WGS data
- bcftools_view: Convert BCF → VCF
- check_snpeff_candidates: Mark up snpEff output file with matches to a gene candidate list
- match: search for occurrences of a short motif, allowing mismatches
- sharplab_interval_analysis: align 2 interval sets, find overlaps, calculate and plot coverage
- sharplab_seq_motif: DREME, SRA → FASTQ, FIMO → BED, FASTA → Markov Model, reverse complements, and more.
- mtls_analysis: Functions to analyze and compare multiple ChIP-seq experiments
New Distribution
There has been one Galaxy distribution in the past month. The most recent release (March 12), includes these highlights:
- Emboss tools and datatypes moving from the Galaxy distribution to the Galaxy's Main Tool Shed in the NEXT release. Read more about the upcoming tool migrations...
- Galaxy tool XML configuration, managing tool panel layout, and Galaxy tool versions.
- RNA-Seq Tools: Added CuffMerge version 1.0.0, Updated TopHat default parameters
- External Display Apps: Added RViewer, Updated IGV
- Now visualize ENCODE "peak" datatype tracks in the Galaxy Track Browser (aka Trackster)
- Multiple Workflow updates including enhancements to input dataset options, display modes, and sharing.
- CloudMan now offers preliminary support for OpenNebula cloud type and a larger default tools volume (10GB vs old 2GB).
Other News
New non-wiki documentation
- Analyzing epigenome data in context of genome evolution and human diseases, by Feuerbach, et al.
- Analyzing Complete Genomics masterVar File through Galaxy, by Complete Genomics (only viewable in Adobe Reader)
HTTPS is now the default for Main
The Galaxy Project's public server (usegalaxy.org, "Main") now uses HTTPS, the encrypted version of HTTP for all communication.
New Style for Main
Have you noticed? usegalaxy.org has a new style.
Galaxy is participating in the 2012 Google Summer of Code
The Galaxy Project is participating in the 2012 Google Summer of Code as part of the "Genome Informatics* group. See the group's page if you are interested in participating.