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 * {{{nebula}}}: Tools suite for ChIP-seq data analysis tools from the [[http://nebula.curie.fr|Nebula Galaxy server]].
 * {{{sparql_galaxy}}}: Execute an SPARQL query against an OWL ontology
 * {{{cluster3}}}: A Wrapper for the [[http://bonsai.hgc.jp/Xmdehoon/software/cluster/software.htm|Cluster3.0 program]], which implements "the most commonly used clustering methods for gene expression data analysis."

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November 2012 Galaxy Update

Galaxy Updates

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.


New Papers

These papers may be of interest to the Galaxy community:

These papers were among xx papers added to the Galaxy CiteULike group since the last Galaxy Update (for a total of xxx papers in the last xxx months). The new papers are spread across x categories.


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.

Upcoming Events and Deadlines

ASHG 2012  CSHL Plant and Animal Genome (PAG 2013)

Deadlines

https://www.google.com/calendar/embed?src=mq93blfvdoosh5unpmivu4kh1c%40group.calendar.google.com

There are November application, poster, and paper deadlines for

November events include the ...

See the Galaxy Events Google Calendar for details on these and other events.

Events

Date

Topic/Event

Venue/Location

Contact

October 31 - November 6

Computaional & Comparative Genomics Course

Cold Spring Harbor Laboratory, New York, United States

William Pearson, James Taylor

October 28 - November 2

Genomic Virtual Laboratory Workshop

eResearch Australasia, Sydney, Australia

Enis Afgan

November 6-10

Galaxy 101: Data Integration, Analysis and Sharing

Sold out

American Society of Human Genetics (ASHG), San Francisco, California, United States

Jennifer Jackson, Jeremy Goecks

Working with High-Throughput Data and Data Visualization

Sold out

November 12-14

The Genome Access Course

Cold Spring Harbor Laboratory, New York, United States

Assaf Gordon

November 13-15

Analyse des données RNA-seq et ChIP-seq (séquençage haut-débit), à l'aide d'outils orientés vers un public de biologistes

PRABI (Pôle Rhône-Alpes de Bioinformatique), Doua de l'Université Claude Bernard - Lyon, Lyon, France

Guy Perrière

January 12-16

Plant and Animal Genome (PAG 2013)

San Diego, California, United States

Dave Clements

March 2-5

W6: Community Resource Solutions to Analyzing Large Genomic Data Sets

ABRF 2013
Palm Springs, California, United States

Dave Clements

June 30 - July 2

2013 Galaxy Community Conference (GCC2013)

University of Oslo, Oslo, Norway

Galaxy Outreach

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."

New Distribution

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.

Other News