June 2012 Galaxy Update
Welcome to the June 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.
GWIPS-viz features tools for the analysis of protein synthesis. GWIPS-viz is part of the Genome Wide Information on Protein Synthesis using ribosome profiling project, and is in early development. At present it includes tools for motif searches and visualization:
- MEME - Multiple Em for Motif Elicitation
- FIMO - Find Individual Motif Occurrences
- Sequence Logo generator for fasta (e.g. Clustal alignments)
- CodonLogo generator for fasta (e.g. Clustal alignments)
Many thanks to the LAboratory of Post-Transcriptional control and bioInformatics (LAPTI) at University College Cork for making this Galaxy server publicly accessible.
|Early registration ends June 11!|
- The 2012 Galaxy Community Conference (GCC2012) will be held July 25-27, in Chicago.
- Three new topics have been added to the GCC2012 Training Day:
- The GCC2012 Training Day
- Cheap rooms in the James Stuckel Towers on the UIC campus (and adjacent to the conference venue) are going fast.
- A draft schedule for all 3 days of the conference has been published. This includes 12 Training Day sessions on 10 different topics, and over 25 presentations by Galaxy Community and Galaxy Team members.
These papers may be of interest to the Galaxy community:
- Identifying elemental genomic track types and representing them uniformly, Sveinung Gundersen, Matus Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Sandve, BMC Bioinformatics, Vol. 12, No. 1. (30 December 2011), 494
- CodonLogo: A sequence logo based viewer for codon patterns, Virag Sharma, David P. Murphy, Gregory Provan, Pavel V. Baranov, Bioinformatics (17 May 2012)
- Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support, Mohamed Abouelhoda, Shadi Issa, Moustafa Ghanem, BMC Bioinformatics, Vol. 13, No. 1. (2012), 77
- CADDSuite - a workflow-enabled suite of open-source tools for drug discovery, Oliver Kohlbacher, Journal of Cheminformatics, Vol. 4, No. Suppl 1. (2012), O2
These papers were among 32 papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of 317 papers in the last ~15 months). The new papers were spread across 7 categories, including the new tools category.
There are June application and early registration deadlines for GCC2012, ISMB 2012, SciPy, and the Winter School in Mathematical and Computational Biology, and an abstract deadline for ASHG 2012. It's also a big month for conferences and courses, including Arthropod Genomics, Bio-IT World Asia (James Taylor will be speaking), SocBIN, Next-gen sequencing in evolutionary biology Course at NESCent (Sergei Kosakovsky-Pond will cover Galaxy), Informatics on High Throughput Sequencing Data Workshop (Francis Ouellette will cover Galaxy), Copenhagenomics, SMBE 2012, and, ESHG 2012, to name just a few.
See the Galaxy Events Google Calendar for details on these and other events.
|June 6-8||Dynamically Scalable, Accessible Analysis with Galaxy Cloud||Bio-IT World Asia, Singapore||James Taylor|
|June 11-12||Informatics on High Throughput Sequencing Data Workshop||Toronto, Ontario, Canada||Francis Ouellette|
|June 11-19||Next-gen Sequencing in Evolutionary Biology Course||US National Evolutionary Synthesis Center (NESCent), Durham, North Carolina, United States||Sergei Kosakovsky Pond|
|June 26||Galaxy: un environnement d'analyses bioinformatiques||l'Institut de Biologie de Lille, France||Sophie Gallina|
|July 11||Reproducible workflows for next generation sequencing analysis||Nowgen, University of Manchester, United Kingdom||Tom Hancocks|
|July 13-17|| ISMB 2012 and BOSC 2012
Five presentaitons, one SIG, one Codefest, and counting
Early registration ends June 1
|Long Beach, California, United States||Galaxy Outreach|
|July 25-27|| 2012 Galaxy Community Conference
Early registration ends June 11.
|University of Illinois Chicago, United States||Dave Clements|
These new repositories
deseq_hts- version 1.6.1 of the DESeq
fastqdump- convert SRA to FASTQ
iassembler- assemble Sanger and/or Roche-454 EST data into contigs
were created, and the
java_genomics_toolkit repositories were updated in the Galaxy Tool Shed in May.
A new Galaxy distribution was released on May 11, 2012.
- 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.
- GalaxyCzars a discussion group for Galaxy community members who are responsible for large Galaxy installations has been started. Their first conference call will be this month.
- Want to know how other sites are implementing their Galaxy installations? See the GalaxyCzars survey results.
- Galaxy Main was down for a little over a day. Watch the Galaxy News for an explanation.