September 2012 Galaxy Update
Welcome to the September 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:
"Next-generation sequencing data interpretation: enhancing reproducibility and accessibility", by Nekrutenko & Taylor, Nature Reviews Genetics, 13, 667-672 (September 2012)
"IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis", by Merelli, Viti, Milanesi, BMC Bioinformatics, Vol. 13, No. Suppl 14. (2011), S5
"Data Mining as a Discovery Tool for Imprinted Genes Genomic Imprinting", by Chelsea Brideau, Paul Soloway, Methods in Molecular Biology, Vol. 925 (2012)
Three new publicly accessible Galaxy servers were added to the Public Galaxy Servers page in August:
|Server||Purpose / Community||Other Comments||Restrictions||Sponsor|
|IBDsite||a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis||CNR-ITB|
|NCBO and OPPL Galaxy||The NCBO-Galaxy tools provide Galaxy users with the functionality of the NCBO BioPortal services. OPPL-Galaxy is a set of functions that can be executed over OWL ontologies with the aim of facilitating the use of semantic activities within Galaxy Bioinformatics workflows.||See "NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform," by Giménez, et al., presented at ICBO2012; and "OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL" by Aranguren, et al.||Universidad de Murcia|
|PopGenIE||The Populus Genome Integrative Explorer Galaxy instance.||Storage quotas||Plant Physiology, University of Umeå|
There are September application, poster, and paper deadlines for
September events include Galaxy workshops and talks in South Africa, the Automated and reproducible analysis of NGS data (ARANGS12), Beyond the Genome 2012, and ICG Americas 2012.
See the Galaxy Events Google Calendar for details on these and other events.
The 1st Swiss Galaxy Workshop will be held October 3-4 in Bern, and is aimed at Galaxy administrators and users alike. We also welcome participants who are using other workflow management systems, and tool developers who are looking for such systems to offer their tools to a wider audience.
We would like to discuss the status of the Galaxy project, new developments, interface to other systems, extensions and best practice in reproducible research.
The workshop is part of the SyBIT Tech Day series.
A new mailing list has been launched, specifically for the French Galaxy Community:
This list is intended to communicate and share our experiences with Galaxy in France. The official language of this list is French. See the list announcement, list archive and list subscription page for more. Postings to the list will be integrated into Galaxy search.
Several new repositories were added to the Galaxy Tool Shed in August.
sambamba_filterFlexible filtering of BAM/SAM
ncbi_blast_plustblastx, blastn, blastp, blastx, BLAST XML → tabular, and tblastn
kmersvmuse a Support Vector Machine (SVM) with k-mer sequence features (kmer-SVM) to identify predictive combinations of short TF binding sites which determine the tissue specificity of these genomic assays.
The most recent Galaxy distribution was released on July 20, 2012.
- blend4j - a Java library for interacting with the API.
- Two new tutorials from Paul-Michael Agapow:
- Ntino Krampis BioTechniques interview on doing bioinformatics on the cloud, including CloudMan.
- Jeremy Goecks updated his RNA-seq Analysis Exercise Galaxy Page to cover quality control through CuffDiff: paired-end data, iGenomes gtf, answer key, and bonus resources
- Slides and videos for the Iowa Initiative in Human Genetics Bioinformatics Course
- A few summaries of the recent 2012 Galaxy Community Conference (GCC2012) have been posted online: