July 2012 Galaxy Update
Welcome to the July 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.
"Using Cloud Computing Infrastructure with CloudBioLinux, CloudMan, and Galaxy", by Enis Afgan, Brad Chapman, Margita Jadan, Vedran Franke, James Taylor, Current Protocols in Bioinformatics. 2012 June: Unit 11.9.
"Using Galaxy to Perform Large-Scale Interactive Data Analyses", by Jennifer Hillman-Jackson, Dave Clements, Daniel Blankenberg, James Taylor, Anton Nekrutenko, Galaxy Team, Current Protocols in Bioinformatics. 2012 June: Unit 10.5.
These papers were among 31 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 348 papers in the last ~16 months). The new papers are spread across 8 categories.
The 2012 Galaxy Community Conference (GCC2012) will be held July 25-27, in Chicago. Register by July 18 to avoid paying late registration rates. Register well before July 18, if you are planning on attending the GCC2012 Training Day. Training Day has limited space and will likely sell out before the entire conference does.
There are July (and June 30!) application and registration deadlines for
- the Galaxy Workshops in South Africa (deadline: June 30) and the South African Genetics & Bioinformatics Society Conference (deadline July 1)
- Systems Bioinformatics Workshop (deadline: June 30)
- GMOD Summer School (deadline: July 9)
- GCC2012 (deadline: July 18)
- and eScience 2012, Beyond the Genome, BioVis, ISCB-Asia, and the CSHL Advanced Sequencing Technologies and Applications, and Computational and Comparative Genomics courses.
See the Galaxy Events Google Calendar for details on these and other events.
Several new repositories were added to the Galaxy Tool Shed in June.
- CGA Tools - Complete Genomics' CGA Tools is now available.
qiime1_3_0- Extension of jjohnson's
qiimerepository, intended as an extension of that work. Only tools verified working in Galaxy with Qiime 1.3.0 documentation included.
upload_local_file- Add data to histories without having to upload them through the network.
svdetect- Detect genomic structural variations from paired-end and mate-pair sequencing data
pcr_markers- Tools for design of PCR-based Markers from Variant Data
sickle- A windowed adaptive trimming tool for FASTQ files using quality
scythe- A very simple adapter trimmer
protk- Identify Peptides and Proteins from tandem Mass Spec data
The most recent Galaxy distribution was released on May 11, 2012.
A new version of CloudMan was Released in June.
Several new videos, screencasts, and tutorials were posted:
- OpenHelix Video Tip of the Week: Visualizing the Galaxy
- Using PhyloTastic Tools inside Galaxy, by Rutger Vos
- Getting Started with the CloudMan Platform Using BioCloudCentral, by Enis Afgan
- Using Galaxy for NGS Analysis, by Luce Skrabanek
- RNA-Seq Course v1.0 documentation, by UC Davis Bioinformatics Professional Training Program
- Cloud Computing for Bioinformatics (using AWS and Galaxy, but not using CloudMan), by UC Davis Bioinformatics Professional Training Program
- Genomic Resequencing Variant Detection and Interpretation in a Diagnostic Context Hands on workshop: Next generation sequence data analysis, by Hailiang (Leon) Mei, Jeroen Laros
Several new and updated genomes were added to Galaxy Main in June:
- bosTau4, bosTau6, bosTauMd3, canFam2, ce10, gorGor3, mm9, mm10, panTro3, rn4,