January 2013 Galaxy Update

Welcome to the January 2013 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

#	Tag
35	methods
21	workbench
2	isgalaxy
2	shared
1	other
1	tools
1	reproducibility

These papers may be of interest to the Galaxy community:

• "The ChIP-seq-Defined Networks of Bcl-3 Gene Binding Support Its Required Role in Skeletal Muscle Atrophy", by Robert W. Jackman, Chia-Ling Wu, Susan C. Kandarian, PLoS ONE Vol. 7, No. 12 → Uses Cistrome & Nebula Galaxy Servers

There are now 599 papers in the Galaxy CiteULike Group.

Who's Hiring

• The Galaxy Project is hiring!

  • Post-docs at Penn State University (Nekrutenko Lab)
  • Post-docs and Software Engineers at Emory University (Taylor Lab)
• GenePeeks is hiring a Computational Geneticist and a Tools Programmer.
• offre de stage pour un stage de 6 mois (Master2) dans l'équipe Bioinformatique de Syngenta Seeds à Toulouse
• Two Galaxy focused internships are open at EMBL Heidelberg.
• Engineer position in bioinformatics: structural polymorphism analysis from NGS data @ UMR de Génétique Végétale, INRA-Université Paris Sud-CNRS
• Offre de stage M2 PRO, Mathématique, Informatique et Génome (MIG) est une unité de l'INRA de Jouy-en-Josas

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.

GCC2013

Training Day Topic Nominations

Nominations are now open for Training Day topics for the 2013 Galaxy Community Conference (GCC2013). GCC2013 will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions.

Any topic of interest to the Galaxy Community can be nominated. See what's been nominated so far (and what was offered at GCC2012). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like.

Topic nomination closes 11 January.

Sponsorships

Please join us in thanking Molecular Life Science at the University of Oslo, The Research Council of Norway, Functional Genomics and Elixer for hosting and funding the 2013 Galaxy Community Conference.

We are also pleased to announce 'Amazon Web Services as the GCC2013 Training Day Sponsor. There are still several sponsorships still available. Please contact the Organizers if your organization would like to help sponsor this event.

January GalaxyAdmins Web Meetup

The next GalaxyAdmins Meetup will be Wednesday, January 16, 2013 at 10am US central time. John Chilton of the Minnesota Supercomputing Institute will cover "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan."

Please join us.

Other Upcoming Events and Deadlines

See the Galaxy Events Google Calendar for details on these and other events.

Events

Deadlines

• January 7: ISMB/ECCB 2013 Proceedings Deadline
• January 10: Genomic Standards Council Meeting (GSC 15) Early Registration Deadline
• January 11: GCC2013 Training Day Topic Nominations close
• January 14: Great Lakes Bioinformatics Conference 2013 (GLBIO) Paper/Presentation deadline
• January 15: PAG Asia 2013 Early Registration deadline
• January 30: Genomic Standards Council Meeting (GSC 15) Registration Deadline
• January 31: Biocuration 2013 Presentation and Poster Deadline
• February 1: Metagenomics: From the Bench to Data Analysis, EMBO Practical Course Application & Abstract Deadline
• February 1: PAG Asia 2013 Poster deadline

New Galaxy Distributions

Dec 20, 2012 Distribution

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 36ad8aa7b922

Dec 3, 2012 Distribution

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r f364d992270c

Tool Shed Contributions

It was a banner month for Galaxy Tool Shed contributions:

• snp_annotation: Split vcf file, variant effect predictor, protseq, netphos, mitoprot, conservation, gpi & join results.

• Two Bismark repositories were created:

  • methylation_analysis_bismark:

    • Bismark: bisulfite mapper, methylation caller;
    • Methylation Extractor: methylation information for individual cytosines;
    • Methylation by region: create a bedgrapgh with methylation percentages aggregated by region;
    • Differential Methylation: comparison of two samples' methylation by region

  • bismark:

    • Methylation extractor
    • Bisulfite mapper (bowtie)
    • Bisulfite mapper (bottie2)
• bedtools_annotate: Annotate the depth X breadth of coverage of features from multiple files
• add_value, change_case, condense_characters, convert_characters, cut_columns, merge_cols, remove_beginning, show_beginning, show_tail, trimmer, : All moved from distribution to tool shed.
• assessing_target_enrichment: Workflows to compute coverage on targeted regions when using hybrid-capture
• matrix_normalization: Normalization tool for matrix formatted data
• plot_distribution: plot distribution of numeric data in table format (either single data column or entire matrix)
• bamedit: Merging, splitting, filtering, and QC of BAM files
• macs2: Model-based Analysis of ChIP-Seq
• peakranger: multi-purpose, ultrafast ChIP Seq peak caller
• spp_phantompeak: SPP cross-correlation analysis package

• These protein tools were contributed by the Galaxy-P project:

  • pride_biomart: Fetch data from PRIDE's BioMart server.
  • dbbuilder: Download protein databases from common sources.
  • msconvert: Tool wrappers for the msconvert application distributed as part of Proteowizard.
  • ProteinPilot: Tools for working with ProteinPilot.
  • decoyfasta: Transproteomic pipeline decoyFASTA tool.
  • ms2preproc: Tool wrapper for ms2preproc.
  • digestdb: Tool wrapper for transproteomic pipeline application digestdb.
  • openms: Tool wrappers for various applications that contained in the OpenMS suite.
  • mzxml2search: Use MzXML2Search to convert peak lists.
• seq2hla: HLA typing from RNA-Seq sequence reads
• snp_annotation: Split vcf file, variant effect predictor, protseq, netphos, mitoprot, conservation, gpi and join result files.
• trim_galaore: Wrapper script that makes use of the publicly available adapter trimming tool Cutadapt and FastQC for optional quality control once the trimming process has completed.

Other News

• Slides from 4 Galaxy Related Talks at the Workflows and the Cloud for Reproducible Bioinformatics workshop at ISCB-Asia are available on the wiki. Slides for all talks are at GigaScience's SlideShare account.
• Bio-Linux 7 "includes the popular Galaxy bioinformatics environment pre-configured and running on the desktop, with the most common tools ready to use out-of-the box."
• workflow-to-galaxy (0.3.5): This Ruby Gem acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (.xml and .rb files).
• Milos Pjanic blog: How to change file attributes in workflows in Galaxy