February 2013 Galaxy Update

Welcome to the February 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 Public Galaxy Servers

The Yeoman Galaxy Server runs the SAskatchewan PHosphorylation Internet REsource (SAPHIRE). This tool by the University of Saskatchewan Bioinformatics Research Group allows you to predict phosphorylation sites in soybean proteins, and will be expanded to other plants in the near future. See also "Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights," by Brett Trost, Anthony Kusalik, Bioinformatics (22 January 2013)

Note: The Yeoman Galaxy server is no longer running. From Brett Trost:

While our server did originally use Galaxy, I later found development and maintenance to be easier using a custom-designed web server rather than using Galaxy.

Brett further explained that this was partly because the lab's skill set made setting up their own custom solution easier.

Pathogen Portal supports comparative analysis of host response to pathogens. It provides an RNA-Seq pipeline to characterize the transcriptome of all NIAID Bioinformatic Resource Center (BRC) pathogens and their key hosts. It can analyze transcriptome data for genomes stored at EuPathDB, PATRIC, and VectorBase. The pipeline is built on Galaxy. Galaxy has been modified to simplify RNA-Seq analysis for informatics-naïve, biologically focused users and provide a guided experience to quality control of read data, read mapping, assembling transcripts, estimating gene expression values, and doing differential expression analysis. See "Database resources for the tuberculosis community" by Lew, et al.

OPPL-Galaxy is a set of functions that can be executed over OWL ontologies with the aim of facilitating the use of semantic activities within Galaxy Bioinformatics workflows. Additional NCBO-Galaxy tools provide Galaxy users with the functionality of the NCBO BioPortal services. See "OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows" by by Aranguren, et al.

These servers join the growing list of public Galaxy servers.

New Papers

These papers may be of interest to the Galaxy community. The first three describe the Public Galaxy servers listed above.

• "Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights," by Brett Trost, Anthony Kusalik, Bioinformatics (22 January 2013)
• "Database resources for the tuberculosis community," by Lew, et al., Tuberculosis (January 2013)
• "OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows," by Aranguren, et al., Journal of Biomedical Semantics, Vol. 4, No. 1. (2013), 2
• "A genome-wide view of mutation rate co-variation using multivariate analyses," by Ananda, et al., Genome Biology, Vol. 12, No. 3. (22 March 2011), R27

There are now over 830 papers in the Galaxy CiteULike Group.

Who's Hiring

The Galaxy is expanding! Please help it grow.

• The Galaxy Project is hiring software engineers and post-docs! at both Emory and Penn State.
• Poste d’ingénieur bio-informaticien en métagénomique au Laboratoire d’Analyses Bioinformatiques en Génomique et Métabolisme (LABGeM)
• Offre de stage M2 PRO, Mathématique, Informatique et Génome (MIG) est une unité de l'INRA de Jouy-en-Josas
• Engineer position in bioinformatics: structural polymorphism analysis from NGS data @ UMR de Génétique Végétale, INRA-Université Paris Sud-CNRS

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 Voting Closes 11 February

Thanks to everyone who nominated topics for the 2013 Galaxy Community Conference (GCC2013) Training Day. These nominations were compiled into a ballot which you can vote on until 11 February. If you might attend the GCC2013 Training Day then please review the possible topics and then vote for your top 3 choices. Your votes will determine not only the topics that are offered, but also which topics should be offered more than once, assigned to which rooms, and which ones should not be scheduled at the same time. Your vote matters.

About the GCC2013 Training Day:

The 2013 Galaxy Community Conference (GCC2013) will start on 30 June with a Training Day featuring 4 parallel tracks, each with three workshops (each of which are two hours long) for a total of twelve sessions. There will be at least one complete track (3 consecutive workshops) about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. 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.

Once voting closes on 11 February, we will contact possible instructors and publish a Training Day schedule before registration opens on 22 February.

Registration, Talk & Poster Submission Opens 22 February

Early Registration, and talk and poster abstract submission all open 22 February. Watch the mailing lists and this wiki for details.

Sponsorships

In addition to the sponsors that we announced in January, we are pleased to announce that GigaScience Journal, a BioMed Central open access journal, is a Silver Sponsor of GCC2013.

Two companies have also stepped forward to be the sole Platinum Sponsor and one of the two Gold Sponsors. We hope to announce them later this month.

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

A GalaxyAdmins Meetup was held on January 16, 2013. John Chilton of the Minnesota Supercomputing Institute presented "Deploying Production Galaxy Environments on OpenStack with CloudBioLinux and CloudMan." Greg Von Kuster of the Galaxy Team gave an update on recent Tool Shed enhancements. Slides and a screencast are now available.

The next GalaxyAdmins meetup will be Wednesday, March 20th

Other Upcoming Events and Deadlines

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

Events

Deadlines

• February 1: Metagenomics: From the Bench to Data Analysis, EMBO Practical Course Application & Abstract Deadline
• February 1: PAG Asia 2013 Poster Abstract deadline
• February 11: GCC2013 Training Day Topic voting closes
• February 15: European Human Genetics Conference 2013 (ESHG 2013) Abstract Deadline
• February 15: Next NGS Challenge Conference Abstract Deadline
• February 22: Biology of Genomes Abstract deadline
• February 25: Biocuration 2013 Early Registration Deadline
• February 28: ESEB Congress 2013 Abstract Deadline
• March 1: Analyzing Next-Generation Sequencing Data Course Application Deadline
• March 1: ISMB/ECCB 2013 Highlight Papers Deadline
• March 1: Next NGS Challenge Conference Poster Deadline

Galaxy Distributions

January 11, 2013 Galaxy Distribution

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r a4113cc1cb5e

Tool Shed Contributions

• flexbar:: flexible barcode and adapter removal
• proteomics_datatypes, xtandem, mascot, tpp_prohets, omssa, msgfplus: All new proteomics-related repositories, all from Ira Cooke
• custom_amplicon_alignment: align amplicons using primers for high accuracy
• file_to_ftp: Copy Datasets from history to FTP
• s_mart: manage your RNA-Seq and ChIP-Seq data. Produce many different plots to visualize data
• bamedit, idr_package, macs2, peakranger & spp_package: all from modENCODE
• differential_expression_analysis_pipeline_for_rnaseq_data: perform differential expression analysis on two different conditions.

Other News

• Video of Peter Li's ICG7 talk on GigDB and Galaxy is now online. Galaxy content starts 68 minutes in.
• IIHG Bioinformatics Short Course downloadable PDFs cover Galaxy Intro and File formats, NGS Intro, Galaxy Basics, and Reproducibility and Collaboration within Galaxy
• How to launch your own copy of a customized modENCODE Galaxy on Amazon Web Services
• The Galaxy service pilot in CSIRO poster.
• Exome-Seq example added to the NGS in Galaxy tutorial from Center for Health Bioinformatics at the Harvard School of Public Health
• RNA-seq Analysis in Galaxy tutorial published by BaRC, Whitehead Institute
• Performing de novo assemblies using the NBIC Galaxy instance, part of de novo Assembly from NGS Data Course at NBIC released
• Slides and tutorials from Galaxy NGS training held at Roscoff are now available, and most (maybe all) are in English
• galaxy-vm-launcher absorbed into CloudBioLinux.