September 2013 Galaxy Update

Galaxy Updates

Welcome to the September 2013 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.


New Public Servers

A record five new servers joined the list of over 40 publicly accessible Galaxy servers in August.

Galaxy-P

Galaxy-P

Galaxy-P is a multiple 'omics' data analysis platform with particular emphasis on mass spectrometry based proteomics. Galaxy-P is developed at the University of Minnesota, deployed at the Minnesota Supercomputing Institute. Pending imminent hardware upgrades, usegalaxyp.org is running with fairly limited computational resources and on disk that is not backed up. Galaxy-P is under active development - things will break and things will change, so your patience is requested.

You can also install your own copy of Galaxy-P, either locally or in the cloud, and Galaxy-P has a User guide (web, pdf)

GWIS

GWIS

NICTA Bioinformatics' Genome-wide Interaction Search (GWIS) for multivariate GWAS analysis cuts the computational time for analyzing all pairs of SNP interactions in genome-wide association studies (GWAS) from months to minutes on commodity computers. Any non-commercial user can request an account via email.

See

Martin Luther University Halle-Wittenberg

Martin Luther University Halle-Wittenberg

Martin Luther University Halle-Wittenberg's Galaxy server provides implementations of tools developed by the groups of Bioinformatics and Pattern Recognition and/or Bioinformatics in collaboration with internal and external partners.

  • CRISPRer is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers.
  • TALgetter allows you to scan input sequences for putative target sites of a given TAL (transcription activator-like) effector as typically expressed by many Xanthomonas bacteria.
  • TALgetterLong allows you to scan input sequences for putative target sites of a given TAL (transcription activator-like) effector as typically expressed by many Xanthomonas bacteria in large input data, but lacks some of the features of TALgetter (e.g., computation of empirical p-values).
  • TALENoffer is a tool for predicting off-targets of TAL effector nucleases (TALENs).
  • Dimont (beta) is a universal tool for de-novo motif discovery. Dimont has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

MBAC Metabiome Portal

MBAC Metabiome Portal

The MBAC Metabiome Portal is a flexible and customizable webserver that simplifies control, usage, access, and analysis of microbiome, metabolome, and immunome data (the Metabiome). The Portal uses a relational database management system and distributed analytical resources and includes several tools such as sequence clustering, filtering sequencing artifacts, taxonomic analysis, and functional annotation.

Users access the MBAC Metabiome Portal through a Galaxy based web browser to perform individual and group analysis and share their results. Programming support is also available to configure and run customized pipelines. Users can view a demo of the Metabiome Database here.

ZBIT Bioinformatics Toolbox

ZBIT Bioinformatics Toolbox

The ZBIT Bioinformatics Toolbox enables public access to these bioinformatics tools developed at Department of Cognitive Systems at the University of Tübingen of our bioinformatics tools.

  • TFpredict: Identification and structural characterization of transcription factors
  • SABINE: Prediction of the binding specificity of transcription factors
  • SBML2LaTeX: Conversion of SBML files into human-readable reports
  • BioPAX2SBML: Conversion of BioPAX format to SBML qual
  • SBMLsqueezer: Generate kinetic rate equations for biochemical networks
  • EDISA: Extracting biclusters from multiple time-series of gene expression profiles
  • ModuleMaster: Finding cis-regulatory modules using promoter analysis and microarray expression data regression.

New Papers

# Tag    # Tag    # Tag
- Cloud - RefPublic 2 UseLocal
- HowTo - Reproducibility 5 UseMain
1 IsGalaxy 4 Shared 1 UsePublic
18 Methods 3 Tools - Visualization
1 Project - UseCloud 8 Workbench

30 new papers were added to the Galaxy CiteULike Group in August. This paper may be particularly interesting to the Galaxy community:


2014 Galaxy Training Survey

Take the Galaxy training survey

Help guide Galaxy's 2014 training efforts by taking the Galaxy Training Survey! Please take a few minutes to let us know what you would like to see offered, and where you would like training to be held.


Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.


Events

RNA-Seq Workshop: From Pipette to P-value! @ UC Davis Bioinformatics Core The Genomic Bioinformatics Workshop Individualizing Medicine Conference   Beyond the Genome   Analisi dati Next Generation Sequencing in Galaxy: exome, RNA-Seq, metagenomica   Galaxy Training Days
See the Galaxy Events Google Calendar for details on these and other events.
Date Topic/Event Venue/Location Contact
September 9-11 RNA-Seq Workshop: From Pipette to P-value! UC Davis Bioinformatics Core Davis, California, United States Email
September 28 - October 1 Galaxy Workshop The Genomic Bioinformatics Workshop, Sydney, Australia Ross Lazarus, Dan Blankenberg
September 30 - October 2 TBA, part of the Cancer Care session Individualizing Medicine Conference, Mayo Clinic, Rochester, Minnesota, United States James Taylor
October 1-3 Galaxy Beyond the Genome 2013,San Francisco, California, United States Jeremy Goecks
October 7-8 TBD NGS & Bioinformatics Summit Europe, Berlin, Germany Anton Nektutenko
Using Galaxy to Provide a NGS Analysis Platform Hans-Rudolf Hotz
October 8-11 Analisi dati Next Generation Sequencing in Galaxy: exome, RNA-Seq, metagenomica CRS4, Loc. Pixinamanna, Pula CA, Italy Paolo Uva
October 9-11 Galaxy Training Days GenoToul bioinformatics facility, INRA, Toulouse Auzeville, France Sarah Maman
October 22-26 Introduction to Integrative Analysis with GenomeSpace ASHG 2013, Boston, Massachusetts, United States Michael Reich
High Throughput Data Analysis and Visualization with Galaxy' Anton Nekrutenko, Jennifer Jackson
January 11-15 Plant and Animal Genome XXII (PAG 2014) San Diego, California, United States Dave Clements
January 16-17 2014 GMOD Meeting San Diego, California, United States Dave Clements

# Galaxy Distributions ## Aug 12, 2013 Galaxy Distribution Highlights: Upgrades to Data Manager including improved installation actions Visualization Framework tunings, plus updates to Phyloviz, Scatterplot, and Trackster Workflows include new reproducibility controls and editing features Multiple Tool Shed enhancements, features, and tunings * Plus additional updates to the UI, Admin and Core, and API, an important Security Fix reminder, and Bug Fixes http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist http://galaxy-dist.readthedocs.org new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg update release_2013.08.12
CloudMan

CloudMan Release

A new version of CloudMan was released in July.


Tool Shed Contributions

Galaxy Tool Shed

Other News