June 2014 Galaxy Update

Galaxy Updates

Welcome to the June 2014 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.

Galaxy-User Being Retired June 6

Galaxy Biostar
Join the conversation! Learn how here.

The Galaxy Biostar online forum was launched April 23 as a replacement for the Galaxy-User mailing list.
During the past 5 weeks, Galaxy Biostar has been wildly successful with over 125 active threads, more than 5 times the number of active threads on Galaxy-user in the 5 weeks before the switch. Galaxy-User has remained open during the transition, but now it's time to retire it. All new posting to Galaxy-User will be stopped on Friday, June 6, some 101 months, and 8,100 postings after it was launched. All those postings will remain available both in Galaxy Biostar (where they have been imported), and in the online list archives. Thanks for making Galaxy Biostar, and Galaxy-User before it, such a great resource. # Events ## GCC2014: June 30 - July 2, Baltimore
GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2014) will start one month from today, June 30, and run through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States.

Registration Closes June 6

Registration closes the month. Registering now saves 100% of late registration fees. When you register you can also reserve lodging at Charles Commons, a very affordable housing option in the same building as the conference.

Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There are 5 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 15 sessions and over 37 hours of workshop material.

Abstracts and Program

The program has been published and all titles and abstracts for accepted talks, are now online. Accepted poster abstracts will posted within a week.

The conference is still accepting late abstract submissions. These will be considered as cancellations occur and space frees up (and we have always had a few cancellations).

Sponsorships and Exhibitors

Penguin Computing

We are happy to have Penguin Computing as a GCC2014 Silver Sponsor. Penguin, like all Platinum, Gold, and Silver Sponsors will have a table at GCC2104.

There are still Silver and Bronze sponsorships available for the GCC2014 and Giga sponsorships for the Hackathon. Please contact the Organizers if your organization would like to help sponsor these events.

In 2014 we are also adding non-sponsor exhibit spaces in addition to the sponsor exhibits. This will significantly increase the size of the exhibit floor. Please contact the Organizers if your organization would like to have an exhibit space at GCC2014.

Galaxy Hackathon at GCC2014

GCC2014 Hackathon

The very first Galaxy Project Hackathon will take place at Johns Hopkins immediately preceding GCC2014 from starting June 28th.

Do you have a feature you've always wanted to implement? Just want to hack on Galaxy (or CloudMan!) with other folks? The Galaxy Hackathon will be a great opportunity to meet and work closely with other community and Galaxy Team members over the course of three days, culminating in some really great improvements and new features to show off at the Galaxy Community Conference afterward.

Participation in the hackathon itself is completely free, but there's limited space so if you're interested and would like to participate please go ahead and book both your lodging and hackathon seat at EventBrite. Register now. As of this writing there are only 11 spots left.

To help organize ideas and people into more concrete projects, we've also set up a hackathon-specific Trello board that we'd love for everyone to go ahead and start using it. The board is public and open to commentary and voting, but to create new cards you’ll need to be added as a member so please note the instructions on the board for that.

Amazon Web Services

Finally, we are happy to have Amazon Web Services on board as the Cloud Infrastructure sponsor for the GCC2014 Hackathon!

Other Events

There are at least 13 other Galaxy related events in the next two months in Thailand, Canada, France, the United States, Italy, the Netherlands, Australia, and Brazil. Also see the Galaxy Events Google Calendar for details on other events of interest to the community.


ABiMS Informatics on High Throughput Sequencing Data Workshop  62nd ASMS Conference on Mass Spectrometry and Allied Topics Using Galaxy for Analysis of High Throughput Sequence Data @ UC Davis Bioinformatics Core   Analisi dati Next Generation Sequencing in Galaxy   GCC2014 registration ends June 6 
Date Topic/Event Venue/Location Contact
June 2-3 Open (and Big) Data – the next challenge 1st Asian Conference on Open Access Scholarly Publishing, Bangkok, Thailand Scott Edmunds
June 9-10 Informatics on High Throughput Sequencing Data Workshop Toronto, Canada Francis Ouellette
June 10 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 11 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 11-12 Galaxy RNAseq de novo/avec référence & cleaning Formation en Bioinformatique Plateforme ABiMS, Station Biologique de Roscoff, France
June 15-19 62nd ASMS Conference on Mass Spectrometry and Allied Topics
Including at least 5 workshop/talk/posters
Baltimore, Maryland, United States See presenter list
June 16 Initiation à l’utilisation de Galaxy Cycle "Bioinformatique par la pratique" 2014, INRA Jouy-en-Josas, France Véronique Martin, Sophie Schbath
June 17 Analyse primaire de données issues de séquenceurs nouvelle génération sous Galaxy
June 16-20 Using Galaxy for Analysis of High Throughput Sequence Data
Workshop is full; can join the waiting list.
UC Davis, California, United States UC Davis Bioinformatics Training
June 18-20 Analisi dati Next Generation Sequencing in Galaxy Presidio Ospedaliero San Giovanni di Dio, Cagliari, Italy CRS4 Segreteria
June 23-34 Galaxy : initiation à la phylogénie Formation en Bioinformatique Plateforme ABiMS, Station Biologique de Roscoff, France Christophe Caron
June 28-30 Galaxy Hackathon Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States Organizers
June 30 -
July 2
2014 Galaxy Community Conference (GCC2014) Organizers
July 7-9 NBIC/BioSB RNA- seq data analysis course Leiden, the Netherlands NBIC/BioSB
July 10 An Introduction to Galaxy with the Genomics Virtual Lab Post-GSA 2014 Workshop, Sydney, Australia Mark Crowe
July 28 - August 1 Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform University of São Paulo (USP), São Paulo, Brazil Dave Clements

New Papers

49 papers were added to the Galaxy CiteULike Group in May. Some papers that may be particularly interesting to the Galaxy community:

The new papers were tagged in many different areas:

# Tag    # Tag    # Tag    # Tag
4 Cloud - Project 7 Tools 2 UsePublic
1 HowTo 1 RefPublic - UseCloud 1 Visualization
2 IsGalaxy 3 Reproducibility 2 UseLocal 14 Workbench
21 Methods 1 Shared 10 UseMain

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.


New Public Servers

One new public Galaxy servers was added to the published list in May:

deepTools

deepTools Galaxy Server


Galaxy Distributions

The most recent Galaxy Distribution was released on April 14, 2014.

BioBlend 0.4.3 was released on April 11, 2014.

The most recent version of CloudMan was released in January 2014.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   
Describe your instance now


One new deployment description was added in May: deepTools The Community Log Board and Deployment Catalog Galaxy community hubs* were launched last your. If you have a Galaxy deployment, or experience you want to share then please publish them.

Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

In no particular order:

Tools

Datatypes

Workflows

Packages

Tool Updates:

Other News

usegalaxy.org offline May 31, 2014

usegalaxy.org will be down 2014/05/31

Access to all TACC-based resources and services, including usegalaxy.org and the Galaxy Project Test Server, will be unavailable from 9 a.m. to 5 p.m., central US time, on Saturday, May 24 31, 2014. TACC staff will be performing an upgrade to the networking infrastructure. During this time, jobs will continue to run.

During this time you are encouraged to use any of the 60+ public Galaxy servers.