April 2012 Galaxy Update

Galaxy Updates

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:

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

Please Help!  Yes you!
The Galaxy is expanding! Please help it grow. 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
April 2012 GMOD Meeting   Informatics on High Throughput Sequencing Data Workshop Next-gen Sequencing in Evolutionary Biology Course ISMB 2012

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

Date Topic/Event Venue/Location Contact
April 4-5 NBIC NGS Exome Sequencing & Variant Calling course
Including a session on Read Mapping and Variant Calling with Galaxy
Radboud UMC, Nijmegen Hailiang "Leon" Mei
April 5-6 April 2012 GMOD Meeting
Including a Galaxy Workshop on evening of April 5
Washington DC, immediately following Biocuration 2012 Dave Clements
April 24-26 Leveraging SaaS for Next-Gen Sequencing: Case Study with the Galaxy Community
Pre-Conference Workshop
Bio-IT World, Boston, Massachusetts, United States Ravi Madduri, Elizabeth Bartom
June 6-8 Dynamically Scalable, Accessible Analysis with Galaxy Cloud Bio-IT World Asia, Singapore James Taylor
June 11-12 Informatics on High Throughput Sequencing Data Workshop Toronto, Ontario, Canada Francis Ouellette
June 11-19 Next-gen Sequencing in Evolutionary Biology Course US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States Sergei Kosakovsky Pond
July 11 Reproducible workflows for next generation sequencing analysis Nowgen, University of Manchester, United Kingdom Tom Hancocks
July 13-17 Bioinformatics Software Interoperability SIG (BSI-SIG) ISMB 2012, Long Beach, California, United States Anton Nekrutenko
July 25-27 2012 Galaxy Community Conference
Early registration and abstract submission are now open.
Chicago, Illinois, United States Dave Clements

GCC2012 Update

2012 Galaxy Community Conference

Training Day

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:

Other News

New non-wiki documentation

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.