November 2012 Galaxy Update
Welcome to the November 2012 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.
These papers may be of interest to the Galaxy community:
- "Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing," Nikolaus Obholzer, Ian A. Swinburne, Evan Schwab, Alex V. Nechiporuk, Teresa Nicolson, Sean G. Megason; Development (10 October 2012)
→ The MegaMapper package is implemented in Galaxy and is available as a VirtualBox VM and an Amazon AMI.
- "CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences," Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, Oliver Hobert, Genetics (10 October 2012)
- "G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes," Danielle Lemay, William Martin, Angie Hinrichs, Monique Rijnkels, J. German, Ian Korf, Katherine Pollard, BMC Bioinformatics, Vol. 13, No. 1. (28 September 2012), 253
- "Creating re-usable tools from scripts: The Galaxy Tool Factory," Ross Lazarus, Antony Kaspi, Mark Ziemann, The Galaxy Team, Bioinformatics (28 September 2012)
These papers were among 44 papers added to the Galaxy CiteULike group since the last Galaxy Update.
And, there are now 500 papers in the Galaxy CiteULike Group.
New Trello Issue Board
The Galaxy project has a new issue tracking system, implemented with Trello. To report an issue, fill out the form at *http://galaxyproject.org/trello''' and submit (use markdown for formatting, if desired). You can also ''comment on and vote for issues directly on the Trello issue board itself.
The same guidelines for creating issues used previously apply here as well - report software issues and change requests, but get support and ask questions on the mailing list.
All open galaxy-central bitbucket issues were imported and, though they still need to be sorted out, comments/voting on them are more than welcome. Our hope is that this issue tracker will be a more effective community interface than the Bitbucket issues were, with the voting features and simpler visibility.
- Computational Biologist @ the Harvard Stem Cell Institute's (HSCI)Center for Stem Cell Bioinformatics
- Bioinformatician/Statistician opening at EMBL Heidelberg, Germany
- offre CDD INRA Versailles - developpement chaine de traitements RnaSeq sous Galaxy - France Genomique
- The Galaxy Project is hiring post-docs @ Penn State and Emory
Got a Galaxy-related opening? Send it to firstname.lastname@example.org and we'll put it in the Galaxy News feed and include it in next month's update.
Upcoming Events and Deadlines
There are November application, poster, and paper deadlines for
- ICG & Bio-IT APAC 2012 abstract and poster deadlines (Oct 31 and Nov 15)
- Next Generation Sequencing Workshop application deadline (U Adelaide, Nov 2)
- Rocky 2012 early registration deadline (Nov 8)
- ISCB-Asai/SCCG 2012 early registration deadline (Nov 12)
November conferences include ASHG 2012 (with 2 Galaxy workshops), Personal Genomes @ CSHL, NETTAB 2012, and ICG & Bio-IT APAC 2012. Course and workshops include The Genome Access Course at CSHL (includes Galaxy), NGS workshops at Queensland and Adelaide, and Generation and Analysis of NGS data workshop @ Ghent.
See the Galaxy Events Google Calendar for details on these and other events.
Tool Shed Contributions
Several new repositories were added to the Galaxy Tool Shed in September.
cloudmap_variant_discovery_mapping: Map a mutation using in silico bulk segregant linkage analysis using variants that are already present in the mutant strain of interest.
riboPicker: Easy identification and removal of rRNA-like sequences
picard: Wrappers for the Picard SAM/BAM manipulation tools.
nebula: Tools suite for ChIP-seq data analysis tools from the Nebula Galaxy server.
sparql_galaxy: Execute an SPARQL query against an OWL ontology
cluster3: A Wrapper for the Cluster3.0 program, which implements "the most commonly used clustering methods for gene expression data analysis."
The October 23, 2012 distribution includes an important security fix; integration with a new Trello Issue Board; Tool Shed direct updates; API fixes, tuneups, and brand-new methods to control libraries; multiple Admin changes enable better access to user data to solve problems; and updates to the Visualization tool set cover Trackster, Circster, and the new Scatter Plot tool.
The October 5, 2012 distribution included migrating BWA to the Galaxy Main Tool Shed, accessible tool versions in the UI, and new exit code features enable clearer experimental tracking and ease reproducibility. This release also includes Visualization updates, a new admin tool for PostgreSQL dataset cleanup, and improvements in API, Workflow, and Security components.
- Phylogenies! Hacking! Tucson in January! And, hopefully Galaxy too. If you are interested in coding, phylogenies, and tool integration please take a look at the Phylotastic Hackathon Announcement. Apply by November 16.
- Slides for all 11 talks at 1st Swiss Galaxy Day are now available online.
- Slides for 5 other Galaxy related events in October are also now available.
- workflow-to-galaxy (0.3.4) @ RubyGems.org: Acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool (
- American Internet Services (AIS) unveils Life Sciences SaaS, featuring Galaxy
- The Tool Shed Wiki wiki has been re-written with a new, cleaner presentation. And check out all the new features!