April 2013 Galaxy Update

Galaxy Updates

Welcome to the April 2013 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

ballaxy Galaxy public server

ballaxy hosts the BALL (Biochemical Algorithms Library) Project tools, i.e. computer aided drug design and molecular modelling based on protein and ligand structure data. It is tailored to handle structural molecular data (pdb, mol, mol2, hin, xyz, smiles) and to offer tools for modelling tasks like chemical shift prediction "NightShift" or optimal bond order assignment of ligands "BOA Constructor". A login is required and everybody can create a login, but there is no guarantee how long any data will be preserved. ballaxy is supported by the groups of Hans-Peter Lenhof (Saarland University, Saarbrücken, Germany), Oliver Kohlbacher (University of Tübingen, Germany), and Andreas Hildebrandt (University of Mainz, Germany).

South Green Galaxy public server

South Green Galaxy is a part of the South Green Bioinformatics Platform (SGBP), "a bioinformatics platform applied to the genomic resource analysis of southern and Mediterranean plants." It supports many custom tools and data sources relevant to plants. It also has a 10 MB storage quota for anonymous users. Account creation is restricted to those with an active collaboration and that work on southern and Mediterranean plants. South Green Galaxy is sponsored by CIRAD, IRD (Institut de recherche pour le développement), Bioversity International, INRA, Montpellier SupAgro

These servers join the growing list of public Galaxy servers.

New Papers

There are several things to report in the New Papers arena. First, the process we used to synchronise the Galaxy CiteULike group with it's Mendeley mirror broke, and has not been fixed yet. Mendeley dropped support for automatic synchronization with CiteULike at the end of February and so no updates have been pushed to Mendeley since then. We are looking for processes that are not too labor / manual intervention intensive. We are also reviewing our general use of CiteULike and Mendeley. If you have any suggestions, please [send them to us](mailto:outreach AT galaxyproject DOT org).

Second several new tags were added, most of them attached to papers with the methods tag, and indicating (if the paper indicates) where the analysis was run.

usemain: Analysis run on Main
usepublic: Analysis run on other public Galaxy servers
useprivate: Analysis run on private Galaxy servers
usecloud: Analysis run on cloud based Galaxy servers
cloud: Papers that emphasize or are about cloud deployments

We will likely back-annotate papers with these new tags from the beginning of 2013, but not prior to that.

Finally, 32 new papers were added to the Galaxy CiteULike Group in March, including these which might be of general interest to the Galaxy community.

There are now over 900 papers in the Galaxy CiteULike Group.

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

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.


2013 Galaxy Community Conference (GCC2013)
   The deadline for submitting oral presentation abstracts is 12 April.   

The 2013 Galaxy Community Conference (GCC2013) will be held 30 June through July 2 in Oslo Norway, at the University of Oslo.

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, keynotes, lightning talks and breakouts, all about high-throughput biology and the tools that support it. The conference also includes a Training Day for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics.

Registration, Talk/Poster Submission Open

Early registration and paper and poster abstract submission are open.

2013 Galaxy Community Conference (GCC2013) Training Day

Register early and save up to 75% off regular registration costs. Early registration is very affordable, with combined registration (Training Day + main meeting) starting at ~ €95 for post-docs and students. Registering early also assures you a spot in the Training Day workshops you want to attend. Once a session becomes full, it will be closed to new registrations. Early registration closes 24 May.

Abstract submission for both oral presentations and posters is also open. Abstract submission for oral presentations closes 12 April, and poster abstract submission closes 3 May. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.


There are still several sponsorships still available. Please contact the Organizers if your organization would like to help sponsor this event.

Galaxy at GMOD 2013, Biocuration 2013 and TGAC

Biocuration 2013
Introduction to Galaxy Workshop @ TGAC
GMOD 2013

Galaxy will have a presence at both the [GMOD 2013](http://gmod.org/wiki/April 2013 GMOD Meeting) and Biocuration 2013. Both are being held in Cambridge, UK in early April. If you are interested in either community, then it would be great to see you there.

There is also a Galaxy Workshop at The Genome Analysis Centre in nearby Norwich, UK on 11 April, the day after Biocuration ends.

Other Upcoming Events

See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on these and other events.


Date Topic/Event Venue/Location Contact
April 5-6 2013 GMOD Meeting Cambridge, United Kingdom, immediately prior to Biocuration 2013 Dave Clements
April 7-8 BOSC/Broad Interoperability Hackathon Cambridge, Massachusetts, United States Brad Chapman
April 7-10 GO Galaxy Workshop Biocuration 2013, Cambridge, United Kingdom Dave Clements, Suzanna Lewis
April 9-11 Workshop: Integrated Research Data Management for Next Gen Sequencing Analysis Using Galaxy and Globus Online Software-as-a-Service BioIT World, Boston, Massachusetts, United States Ravi K. Madduri, Alex R. Paciorkowski, Vas Vasiliadis
Talk: Integrated Research Data management and Analysis in NGS using Globus Online, Galaxy and Amazon Web Services Ravi K. Madduri
April 10 Introduction to Galaxy Boot Camp UC Davis Bioinformatics Core Davis, California, United States Nikhil Joshi
April 11 Introduction to RNASeq Boot Camp Nikhil Joshi
April 11 Introduction to Galaxy Workshop The Genome Analysis Centre, Norwich, United Kingdom Dave Clements
May 14-16 Tutorial: Exploring and Enabling Biomedical Data Analysis with Galaxy Great Lakes Bioinformatics Conference (GLBIO) 2013, Pittsburgh, Pennsylvania, United States Anton Nekrutenko
May 16-17 Galaxy Workflows for Bioinformatics Analysis, and
Workshop 1A – Galaxy Workflows for Bioinformatics Analysis
Workshop in Next-Generation Sequence Analysis and Metabolomics (WiNGS), UNC-Charlotte, North Carolina, United States James Taylor
May 28-31 A Genomics Virtual Lab for Cancer Research Bio-IT World Asia, Singapore Dominique Gorse
Next-Gen Sequencing Analysis Using GigaGalaxy Tin-Lap Lee
Open Source and Web-Based Analysis of NGS Data Using Galaxy at the Center for Research Informatics University of Chicago Jorge Andrade
June 6-7 Informatics on High Throughput Sequencing Data Workshop Toronto, Ontario, Cananda Francis Ouellette
June 8-11 WS08: Biomedical Data Analysis with Galaxy Workshop at European Human Genetics Conference (ESHG2013), Paris, France Anton Nekrutenko, Enis Afgan
June 13-14 Genomics and Epigenomics with Deep Sequencing, the 24th CDB Meeting RIKEN, CDB, Kobe, Japan Anton Nekrutenko
June 30 - July 2 2013 Galaxy Community Conference (GCC2013) University of Oslo, Oslo, Norway Organizers



March 2013 Meetup

Slides and the screencast from the March GalaxyAdmins Meetup are now available [Hailiang "Leon" Mei](mailto:hailiang DOT mei AT nbic DOT nl) spoke on NBIC Galaxy deployment at SURFsara's HPC cloud. NBIC Galaxy (Andromeda) was migrated to a HPC cloud hosted by Surfsara in September 2012. Leon discussed the setup of this HPC cloud and the architecture of NBIC Galaxy and shared their experiences installing the NBIC Galaxy using the Cloudman scripts. The presentation finished with a list of issues and our possible future plans. Dan Blankenberg also discussed the new Galaxy release process, and the upcoming Data Manager enhancements.

GalaxyAdmins Future Directions

The GalaxyAdmins group is coming up on it's one year anniversary (coinciding with GCC2013) and this is a good opportunity to discuss what the future of the group should be. If you are interested, please join the discussion on this email thread.

Some starting topics for discussion are on the GalaxyAdmins Future Directions page. These include

  • What should the group's goals and activities be?
  • What type of leadership structure should the group have, and how should it be selected?

The discussion, however, is wide open to any topic relevant to the group. If you have any opinions or suggestions please reply to the group. Anyone with an interest in the group is encouraged to post.

Once the discussion settles, we will summarize the discussion on the wiki page and suggest an action plan for making those things happen.

Galaxy Distributions

tool shed

April 1, 2013 Distribution

Tool Shed Contributions

Galaxy Tool Shed
  • ctcf_analysis: computationally predict CTCF sites for a nucleotide sequence
  • interproscan_to_excel: Convert interproscan raw or xml output to an Excel file
  • snpeff_cds_report: Get transcripts from Ensembl for snpEff variants and report coding changes
  • mmuff: Missense Mutation and Frameshift Finder Workflow

Other News