Complete News Brief

Highlights:

• Emboss tools and datatypes have now moved from the Galaxy distribution to the Galaxy Main Tool Shed.

• Tool Integration Tests, Custom Tool Panel Configuration, and Configurable Tool Output Locations.

• Improved Multiprocess Job Handling and Enhanced OpenID Support.

• GATK version 1.4, FreeBayes, Updated Megablast using NCBI BLAST+, Trinity, WormBase 2, and IGB external display.

• Trackster upgrades include strand coloring, interval datatype support, and tabix indexing (fast!!).

• Updated User Interface, Workflow-API upgrades, and Custom UCSC Display.

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 17d57db9a7c0

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

The email post "Interested in speaking with other institutions deploying Galaxy locally?" by Ann Black-Ziegelbein generated a huge amount of interest. Ann proposed a bi-monthly conference call to discuss the broader issues of doing Galaxy deployments.

The resulting community, now dubbed GalaxyCzars, welcomes anyone who cares about Galaxy deployments and wants to share their experience, or learn from others. If that describes you, please help us get started by taking this short survey. This will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public on the GalaxyCzars and Capacity Planning pages.

Dave Clements (channeling Ann Black-Ziegelbein)

The May 2012 Galaxy Update is now available. Galaxy Update is a (mostly) 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.

Highlights:

• GCC2012 Just 3 Months Away!

  • Training Day needs your input!

• Galaxy Tour de France 2012: This Month!

• A new public server: Nebula for ChIP-Seq

• 31 New Papers

• Open Positions at six different institutions

• Upcoming Events and Deadlines

• Tool Shed Contributions

If you have anything you would like to see in the June Galaxy Update, please let me know.

Dave Clements

We are pleased to announce the Galaxy Tour de France 2012, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in Perpignan, Lyon and Paris. Each day will feature a Galaxy for Biologists workshop in the morning, and a Galaxy for Developers workshop in the afternoon. All workshops will be taught by Galaxy Team members Nate Coroar, Anton Nekrutenko and James Taylor.

Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible.

The Tour is generously sponsored and hosted by the Laboratoire de Biologie Intégrative des Organismes Marins, the Laboratoire Biométrie et Biologie Evolutive, and the Inserm - Mines ParisTech - Institut Curie - Bioinformatics and Computational Systems Biology of Cancer. Further support for the workshops is provided by an Amazon Web Services (AWS) Education Grant.

Dave Clements

The April 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complements the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

• 28 New Papers

• Open Positions at six different institutions

• Upcoming Events and Deadlines

• GCC2012 Update, including early registration is open, and abstract submission closes April 16.

• Tool Shed Contributions

If you have anything you would like to see in the May Galaxy Update, please let me know.

Dave Clements

We are pleased to announce that early registration for the 2012 Galaxy Community Conference (GCC2012) is now open. GCC2012 will be held July 25-27, at the UIC Forum, in Chicago, Illinois. The conference will feature two full days of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training this year, featuring 3 parallel tracks with four workshops each, covering seven different topics.

The Galaxy Community Conference is for:

• Sequencing core facility staff
• Bioinformatics core staff
• Bioinformatics tool and workflow developers
• Bioinformatics focused principal investigators and researchers
• Data producers
• Power bioinformatics users

This event will help you with integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology.

Registration is very affordable this year, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11.

Conference lodging can also be booked. Low-cost rooms have been reserved on the UIC campus. You can also stay at the official conference hotel, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early, if you would like to stay in either.

Finally, abstract submission is also open, from now through April 16. Abstracts on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts page for details.

Looking forward to seeing you in Chicago!

Dave Clements on behalf of the GCC2012 Organizing Committee

Complete News Brief

Highlights:

• Emboss tools and datatypes moving from the Galaxy distribution to the Galaxy's Main Tool Shed in the NEXT release. Read more about the upcoming tool migrations...

• Galaxy tool XML configuration, managing tool panel layout, and Galaxy tool versions.

• RNA-Seq Tools: Added CuffMerge version 1.0.0, Updated TopHat default parameters

• External Display Apps: Added RViewer, Updated IGV

• Now visualize ENCODE "peak" datatype tracks in the Galaxy Track Browser (aka Trackster)

• Multiple Workflow updates including enhancements to input dataset options, display modes, and sharing.

• CloudMan now offers preliminary support for OpenNebula cloud type and a larger default tools volume (10GB vs old 2GB).

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 40f1816d6857

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

The March 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complements the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

• 28 New Papers

• Open Positions at four different institutions

• Upcoming Events and Deadlines

• GCC2012 Update, including

  • Abstract submission is open.
  • Training Day topics are set.

• Tool Shed Contributions

If you have anything you would like to see in the April Galaxy Update, please let me know.

Dave Clements

Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring.

Software Engineers and
Post-Docs at Emory

The Taylor Lab in the Biology and Mathematics & Computer Science at Emory University is looking for software engineers and postdoctoral scholars to work on the Galaxy Project.

We are seeking software engineers with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting for full details.

Postdoctoral applicants should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement for full details.

Post-Docs at Penn State

The Nekrutenko Lab at the Huck Institutes of Life Sciences at Penn State is seeking highly opinionated and biologically inclined Postdoctoral researchers within the Galaxy Project to develop best practices for analysis of next-generation sequencing data in all areas of Life Sciences where NGS is used. Successful candidates will join a vibrant research group at the Center for Comparative Genomics and Bioinformatics at Penn State University.

Please send your CV to <jobs AT galaxyproject DOT org>.

We have an opening for a Bioinformatics Analyst at the University of Virginia Bioinformatics Core. The analyst will work with other core staff on grant-funded and chargeback-based projects to manage and analyze large-scale datasets produced by next-generation sequencing. In addition to what's listed in the job announcement, the ideal candidate will have both Galaxy experience and next-gen sequencing expertise.

Stephen Turner
Director

GigaScience Journal and BGI Hong Kong are hiring a Bioinformatician/Senior Database Developer. This Hong Kong based position will be responsible for developing and managing BGI’s public and private databases, and will include working with a team at the Chinese University of Hong Kong integrating these resources with Galaxy software and the BGI cloud.

See the job posting for more responsibilities, qualifications, and contact information. We are in a bit of a hurry for this particular position (although some more software focused positions are likely to come up later in the year), so if you are interested or have any questions about the role please contact: editorial@gigasciencejournal.com.

Scott Edmunds
Editor, GigaScience

Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (GCC2012). Submissions on any topics of interest to the Galaxy community are encouraged. Areas of interest include, but are not limited to:

• Best practices for local Galaxy installation and management
• Integrating tools and/or data sources into the Galaxy framework
• Deploying galaxy on different infrastructures
• Compelling or novel uses of Galaxy for biomedical analysis

See the GCC2011 program for an idea of the breadth of topics that are covered. Oral presentations will be approximately 15-20 minutes long, including time for question and answer. There will also be an opportunity for lightning talks, which will be solicited at the meeting. The submission deadline is April 16. See the GCC2012 Abstracts page for more details and how to submit.

GCC2012 will be held, July 25-27 in Chicago, Illinois, United States. GCC2012 will run for two full days, and be preceded by a full day of training workshops. If you are a bioinformatics tool developer, data provider, workflow developer, power bioinformatics user, sequencing or bioinformatics core staff, or a data and analysis archival specialist, then GCC2012 is for you. Registration will open in March.

GCC2012 is hosted by the University of Illinois at Chicago, the University of Illinois at Urbana-Champaign, and the Computation Institute.

Dave Clements