Welcome to the March 2016 Galactic News, a summary of what is going on in the Galaxy community.

If you have anything to include in the next News, please send it to [Galaxy Outreach](mailto:outreach AT galaxyproject DOT org).

GCC2016

GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. This will be the 7th annual gathering of the Galaxy community, and we are expecting over 200 participants again this year. The 2016 Galaxy Community Conference includes 2 days of hackathons, 2 days of training, and a two day meeting featuring accepted presentations, keynotes, poster sessions, the new Visualization Showcase and Software Demo sessions, lightning talks, birds-of-a-feather meetups, and plenty of networking.

GCC2016 Early Registration

Early registration for GCC2016 is now open. Registration costs depend on which events you register for, your career stage & affiliation, and when you register. Early bird registration ends May 20 and is up to 40% less than regular registration rates. Early bird registration starts at less than $45 / day for students and postdocs, and at $65 / day for other attendees from non-profits.

You can also sign up for conference housing during registration.

You are strongly encouraged to review the training and housing options before beginning the registration process.

GCC2016 Abstract Submission Deadlines!

The deadline for oral presentation abstracts is March 25, 2016. Abstracts will be reviewed and submitters will be notified of acceptance status no later than April 11, 2016.

Poster and Demo abstract submission closes May 20, 2016 (or earlier depending on poster space availability). Poster and demo submissions are reviewed on a rolling basis, and submitters will be notified of acceptance status no later than two weeks after the abstract is submitted. You may submit similar content for oral presentations, posters, and demos.

Topics should be of interest to those working in high-throughput data analysis and research. Presentations that are Galaxy-centric are encouraged, but not required. Please see the abstracts page for full details.

Scholarships: International application deadline is March 20

We are pleased to offer scholarships for the 2016 Galaxy Community Conference, being held in Bloomington, Indiana, United States, June 25-29. Scholarships are available to students and post-docs in historically under-represented groups, and to those from or based in Low and Lower-Middle Income Economies, as defined by the World Bank. If this describes you or one of your students then we hope to receive an application.

Scholarships cover registration and lodging during the GCC Meeting, and for any Training or Hackathon events the applicant chooses to attend. Scholarships do not cover travel or other expenses. The application deadline is May 1 for members of historically underrepresented groups and March 20 for those from Low and Lower-Middle Income Economies.

See the full announcement for details.

Sponsors

We are pleased to announce that BioTeam will again be a sponsor for this annual event. BioTeam is a professional services and products company at the intersection of science and information technology. BioTeam solves analytics, big data and scientific computing challenges for organizations by mapping the right technologies to their unique scientific needs. BioTeam has a well-established history of providing forward-thinking solutions to the Life Sciences.

The BioTeam Appliance Galaxy Edition is a push-button solution that let’s researchers get up and running quickly with Galaxy. The Galaxy Appliance comes preinstalled with a production instance of Galaxy, bioinformatics tools, and reference datasets. This powerful system is specifically configured for computationally intensive scientific workloads. Most importantly, the Galaxy Appliance is an open system so researchers can install whatever tools they need and use the server as their own high-performance informatics infrastructure along side Galaxy. BioTeam provides ongoing support for the Galaxy Appliance, enabling researchers to minimize their IT burden. The Galaxy Appliance is used by researchers around the world for metagenomic, ChIP-Seq, RNA-Seq analysis and more. For more information: http://bioteam.net/bioteam-appliance/galaxy-edition/

This is the fourth year in a row that BioTeam has been a GCC Sponsor.

We continue to seek other sponsors as well and offer a wide range of sponsorship plans. If your organization is interested in having a presence at GCC2016, please contact the GCC2016 Exec for more information.

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New Papers

54 new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in February, bringing the total number of papers to over 3000. Highlights from last month include:

• MetaPalette: A $k$-mer painting approach for metagenomic taxonomic profiling and quantification of novel strain variation David Koslicki, Daniel Falush, arXiv:1602.05328 [q-bio.GN] (17 Feb 2016)
• Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads by Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Éric Rivals, Claire Lemaitre, Vincent Miele, Gustavo Sacomoto, Camille Marchet, Bastien Cazaux, Amal Zine El Aabidine, Leena Salmela, Susete Alves-Carvalho, Alexan Andrieux, Raluca Uricaru and Pierre Peterlongo, GigaScience, Vol. 5, No. 1. (11 February 2016), doi:10.1186/s13742-015-0105-2
• Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression Menno van der Voort, Marcel Kempenaar, Marc van Driel, Jos M. Raaijmakers, Rodrigo Mendes, Ecology Letters (January 2016), pp. n/a-n/a, doi:10.1111/ele.12567
• RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data Audrey M. Michel, James P. A. Mullan, Vimalkumar Velayudhan, Patrick B. F. O'Connor, Claire A. Donohue, Pavel V. Baranov, RNA Biology (29 January 2016), pp. 00-00, doi:10.1080/15476286.2016.1141862

The new papers were tagged with:

#	Tag		#	Tag		#	Tag		#	Tag
2	Cloud		3	Other		-	Shared		4	UseMain
1	HowTo		1	Project		3	Tools		9	UsePublic
5	IsGalaxy		5	RefPublic		-	UseCloud		-	Visualization
29	Methods		-	Reproducibility		3	UseLocal		11	Workbench

The Galaxy CiteULike group surpassed 3000 pubs in February. 49% of them use Galaxy in their methods.

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Events

March 7-8: Online IUC Contribution Fest - RADSeq Tools and Workflows

A remote Contribution Fest will be held 7th and 8th of March for developers to work on Galaxy RADSeq tools.

RADSeq is a cheap sequencing technology that is used by many resource-limited groups who would benefit a lot from easy-to-use galaxy tools. Indeed there has been quite some interest in analyzing RADSeq with Galaxy. Currently there is a wrapper for stacks and little more to help with RAD specific analysis (though many other galaxy tools are useful with RADs - bwa, cap3, gatk, velvet, ...).

If you are interested in participating in the hackathon but not interested in actual tool development - we will assemble a list of smaller, manageable Python and JavaScript tasks to work on and certainly documentation is a chronically lacking for collections so we could use help there and no actual coding would be required.

We encourage ideas or advice about how to organize this so please let us know. A core group will be available on IRC all day and we will have google hangouts across those days to organize, answer questions, and report progress.

We will do our best to coordinate and make this hackathon a nice and productive experience and we would like to especially focus on working reasonable hours and discourage overnighters.

All forms of contribution are welcome!

GMOD Meeting, June 30 - July 1

The 2016 GMOD meeting will be held immediately following GCC2016 and in the same venue as GCC2016. http://gmod.org/wiki/|GMOD is a consortium of open-source software project, including Galaxy, that address common challenges with biological data. Other projects in the GMOD consortium include

• Tripal: A web front end for Chado databases. Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
• JBrowse: A client-side genome browser and successor to the venerable http://gmod.org/wiki/GBrowse. JBrowse as a Galaxy Tool was presented by Helena Rasche at GCC2015. Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
• MAKER: A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces. A MAKER-Galaxy by Agriculture and Agri-Food Canada was presented at ISMB 2014.
• InterMine and BioMart: These are both popular data sources that are integrated with Galaxy.

Early bird registration ends May 21. For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract. Note: GCC2016 and GMOD have separate event registration, but are sharing housing - you won't even have to change rooms.

Galaxy in Google Summer of Code

We are delighted to announce that Galaxy will be participating in Google Summer of Code this year, along with http://gmod.org/wiki/|GMOD and Reactome, as part of the Open Genome Informatics initiative.

The current list of project ideas is on this project ideas page. There is a bit more time to firm up and add new project ideas. It is also possible for students to suggest their own ideas and we will try hard to find them a mentor. If you add (or have) new ideas to the proposal, please let our GSoC coordinators Robin Haw, Scott Cain, and Marc Gillespie know.

Between now and 13 March, would-be student participants will start to discuss application ideas with this group. Please let Robin know if you have any questions about GSoC.

February GalaxyAdmins Slides & Video

Slides and video from the February 2016 GalaxyAdmins meetup are now available.

Upcoming Events

There are many upcoming events in the next few months. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date	Topic/Event	Venue/Location	Contact
March 7-8	IUC Contribution Fest - RADSeq Tools and Workflows	Online	IUC
March 15	Initiation à l’utilisation de Galaxy	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
March 16	Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
March 17	Traitement bioinformatique des données RNA-Seq sous Galaxy	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
March 29	Introduction à l'analyse de données RNAseq sous Galaxy	Galaxy User Group Grand Ouest (GUGGO), Rennes, France	Yvan Le Bras
April 6	Approaches for the Integration of Visual and Computational Analysis of Biomedical Data	BioIT World 2016, Boston, Massachusetts, United States	Nils Gehlenborg
April 22-26	Workshop on Galaxy: Practical Course	SolBio International Conference 2016, Riviera Maya, México	Oswaldo Trelles
May 11-13	NGS & Cancer : Analyses RNA-Seq	Paris, France	Cancéropôle Île-de-France
May 23-24	Analyse statistique de données RNA-Seq sous Galaxy -Recherche des régions d'intérêt différentiellement exprimées	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
May 30	Initiation à l’utilisation de Galaxy	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
May 31	Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy	Part of Le cycle "Bioinformatique par la pratique" 2016, Jouy-en-Josas, France	Formation Migale
June 9-10	Informatics on High-throughput Sequencing Data	Montreal, Quebec, Canada	Francis Ouellette
June 13-17	Using Galaxy For Analysis of High Throughput Sequence Data	Davis, California, United States	UC Davis Bioinformatics Training Program
June 25-29	2016 Galaxy Community Conference (GCC2016)	Indiana University, Bloomington, Indiana, United States	Organizers
June 30 - July 1	GMOD Meeting	Indiana University, Bloomington, Indiana, United States	Scott Cain

Designates a training event offered by GTN member(s)

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Who's Hiring

The Galaxy is expanding! Please help it grow.

• Bioinformatics Web Application Developer-Biology, Washington University in St. Louis, Missouri, United States
• Software developer and Post-docs, Gehlenborg Lab, Harvard Medical School, Boston, Massachusetts, United States
• Postdoctoral Research Positions, Molecular and Cellular Biology Department at Baylor College of Medicine, Houston, Texas, United States
• Bioinformaticist, Johns Hopkins University Applied Physics Laboratory (APL)
• Software Engineer, Oregon Health Sciences University, Portland, Oregon, United States

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.

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New Public Galaxy Servers

Three new publicly accessible Galaxy servers were listed in February:

BISTRO

• Link:

  • BISTRO Galaxy

• Domain/Purpose:

  • Taxonomic studies of environmental microbial communities

• Comments:

  • Publishes the PipeAlign workflow and supporting tools. These tools include ballast, RASCAL, LEON, and MACSIMS.

• User Support:

  • Email support

• Quotas:

  • Supports anonymous access and creation of user logins.

• Sponsor(s):

  • This instance of Galaxy is managed by the BISTRO platform.

MiModD NacreousMap

• Link:

  • MiModD NacreousMap

• Domain/Purpose:

  • This server exposes the NacreousMap mapping/plotting tool of MiModD for users of MiModD who do not want to install the required dependencies (R and rpy2) for graphical output from this tool on their local system. MiModD is a comprehensive software package for the identification and annotation of mutations in the genomes of model organisms from whole-genome sequencing (WGS) data.

• Comments:

  • CloudMap users can replot data produced with the Hawaiian Variant Mapping tool using the NacreousMap engine to obtain optimized (much smaller files that display faster) plots.
  • To install the complete MiModD package for use as a command line tool or for integration into any local Galaxy follow the installation instructions in the MiModD User Guide.

• User Support:

  • MiModD User Guide
  • MiModD Google Group

• Quotas:

  • The quota for anonymous usage is 50MB, registered users have 250MB available.
  • You can analyze/plot data in VCF format or the "Per variant report" format generated by local runs of the MiModD NacreousMap tool. The latter has the advantage of being up to 20 times smaller than the corresponding VCF file.

• Sponsor(s):

  • The Baumeister Laboratory at the Institute for Biology 3 of the Albert-Ludwig University in Freiburg/Breisgau, Germany.

NIOO-KNAW PhyloProfiler

• Link:

  • NIOO-KHAN Public Galaxy Server featuring PhyloPofiler

• Domain/Purpose:

  • PhyloProfiler consists of several filtering and reporting options for analyzing PhyloChip data consisting of OTUs with hybridization scores (HybScores).

• Comments:

  • See Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression by van der Voort, et al., in Ecology Letters doi: 10.1111/ele.12567

• User Support:

  • See the Galaxy PhyloChip analysis pipeline PhyloProfiler User’s Manual

• Quotas:

  • Anonymous access is supported.

• Sponsor(s):

  • BRS group of the Netherlands Bioinformatics Centre (NBIC) in collaboration with the Laboratory of Phytopathology of the Wageningen University/NIOO-KNAW.

Releases

Galaxy v16.01

The Galaxy Committers team is pleased to announce the January 2016 (v16.01) release of Galaxy.

Galaxy administrators should also be aware of the