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<<div(left)>>
||<class="th"> # ||<class="th"> Tag ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/methods|methods]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/workflow|workflow]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/other|other]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/shared|shared]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/howto|howto]] ||
||<)> X || [[http://www.citeulike.org/group/16008/tag/project|project]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/reproducibility|reproducibility]] ||
||<)> x || [[http://www.citeulike.org/group/16008/tag/tools|tools]] ||
<<div>>
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 * paper 1. <<div(left)>>
||<class="th"> # ||<class="th"> Tag ||
||<)> 21 || [[http://www.citeulike.org/group/16008/tag/methods|methods]] ||
||<)> 11 || [[http://www.citeulike.org/group/16008/tag/workflow|workflow]] ||
||<)> 6 || [[http://www.citeulike.org/group/16008/tag/other|other]] ||
||<)> 7 || [[http://www.citeulike.org/group/16008/tag/tools|tools]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/shared|shared]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/project|project]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/isgalaxy|isgalaxy]] ||
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/howto|howto]] ||
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/reproducibility|reproducibility]] ||
<<div>>
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These papers were among [[http://www.citeulike.org/group/16008/library|xx papers added to the Galaxy CiteULike group]] since the last [[GalaxyUpdates|Galaxy Update]] (for a total of xxx papers in the last xxx months). The new papers are spread [[http://www.citeulike.org/group/16008/tags|across x categories]].  * "[[http://dx.doi.org/10.1242/dev.083931|Rapid positional cloning of zebrafish mutations by linkage and homozygosity mapping using whole-genome sequencing]]," Nikolaus Obholzer, Ian A. Swinburne, Evan Schwab, Alex V. Nechiporuk, Teresa Nicolson, Sean G. Megason; ''[[http://dev.biologists.org/|Development]]'' (10 October 2012) <<BR>>
 &rarr; ''The [[http://bit.ly/QupZs1|MegaMapper]] package is implemented in Galaxy and [[http://bit.ly/QupZs1|is available as a VirtualBox VM and an Amazon AMI]].''<<BR>><<BR>>

 * "[[http://dx.doi.org/10.1534/genetics.112.144204|CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences]]," Gregory Minevich, Danny S. Park, [[Dan|Daniel Blankenberg]], Richard J. Poole, Oliver Hobert, ''[[http://www.genetics.org/|Genetics]]'' (10 October 2012)<<BR>><<BR>>

 * "[[http://dx.doi.org/10.1186/1471-2105-13-253|G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes]]," Danielle Lemay, William Martin, Angie Hinrichs, Monique Rijnkels, J. German, Ian Korf, Katherine Pollard, ''[[http://www.biomedcentral.com/bmcbioinformatics/|BMC Bioinformatics]]'', Vol. 13, No. 1. (28 September 2012), 253<<BR>><<BR>>

 * "[[http://dx.doi.org/10.1093/bioinformatics/bts573|Creating re-usable tools from scripts: The Galaxy Tool Factory]]," [[fubar|Ross Lazarus]], Antony Kaspi, Mark Ziemann, [[GalaxyTeam|The Galaxy Team]], ''[[http://bioinformatics.oxfordjournals.org/|Bioinformatics]]'' (28 September 2012)

These papers were among [[http://www.citeulike.org/group/16008/library|44 papers added to the Galaxy CiteULike group]] since the last [[GalaxyUpdates|Galaxy Update]].

'''And, there are now 500 papers in the [[http://www.citeulike.org/group/16008/library|Galaxy CiteULike Group]].'''
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== New Trello Issue Board ==

The Galaxy project has a [[http://bit.ly/gxyissues|new issue tracking system]], implemented with [[http://trello.com|Trello]]. ''To report an issue'', fill out the form at '''http://galaxyproject.org/trello''' and submit (use markdown for formatting, if desired). You can also ''comment on and vote for issues directly'' on the [[http://bit.ly/gxyissues|Trello issue board]] itself.

The same guidelines for creating issues used previously apply here as well - report software issues and change requests, but get support and ask questions on the mailing list: [[http://dev.lists.galaxyproject.org/|galaxy-dev@bx.psu.edu]].

All open [[https://bitbucket.org/galaxy/galaxy-central|galaxy-central bitbucket issues]] were imported and, though they still need to be sorted out, comments/voting on them are more than welcome. Our hope is that this issue tracker will be a more effective community interface than the ''Bitbucket'' issues were, with the voting features and simpler visibility.

[[http://usegalaxy.org|{{attachment:Images/NewsGraphics/2012_10_23_trello-inbox.png|2012_10_23_trello-inbox|width="900"}}]]
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 * [[http://bit.ly/R2ZJoW|Computational Biologist]] @ the [[http://www.hsci.harvard.edu/|Harvard Stem Cell Institute's (HSCI)]][[http://www.hsci.harvard.edu/research/center-stem-cell-bioinformatics|Center for Stem Cell Bioinformatics]]
 * [[http://bit.ly/X7Hl30|Bioinformatician/Statistician opening]] at EMBL Heidelberg, Germany
 * [[http://bit.ly/TKoV9h|offre CDD INRA Versailles]] - developpement chaine de traitements !RnaSeq sous Galaxy - France Genomique
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 * [[http://bit.ly/TKoV9h|offre CDD INRA Versailles]] - developpement chaine de traitements !RnaSeq sous Galaxy - France Genomique
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[[http://www.ashg.org/2012meeting/pages/workshops.shtml|{{attachment:Images/Logos/ASHG2012Logo.png|ASHG 2012|height="100"}}]] [[http://www.ashg.org/2012meeting/pages/workshops.shtml|{{attachment:Images/Logos/ASHG2012Logo.png|ASHG 2012|height="100"}}]]&nbsp;
[[http://meetings.cshl.edu/courses13.html|{{attachment:Images/Logos/CSHLLogo.jpg|CSHL|height="100"}}]]
[[http://www.intlpag.org/|{{attachment:Images/Logos/PAGLogo114.png|Plant and Animal Genome (PAG 2013)}}]]
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 * [[http://www.iscb.org/rocky2012|Rocky 2012]] (deadline October 4)
 * [[http://www.nbic.nl/bbc2012|BeNeLux Bioinformatics Conference 2012 ]] (deadline October 22)
 * ICG & Bio-IT APAC 2012 abstract and poster deadlines (Oct 31 and Nov 15)
 * Next Generation Sequencing Workshop application deadline (U Adelaide, Nov 2)
 * Rocky 2012 early registration deadline (Nov 8)
 * ISCB-Asai/SCCG 2012 early registration deadline (Nov 12)
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November events include the ... November conferences include ASHG 2012 (with 2 Galaxy workshops), Personal Genomes @ CSHL, NETTAB 2012, and ICG & Bio-IT APAC 2012. Course and workshops include The Genome Access Course at CSHL (includes Galaxy), NGS workshops at Queensland and Adelaide, and Generation and Analysis of NGS data workshop @ Ghent.
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||<class="th"> October 31 - November 6 || ''[[http://meetings.cshl.edu/courses/c-ecg12.shtml|Computaional & Comparative Genomics Course]]'' || [[http://www.cshl.edu/|Cold Spring Harbor Laboratory]], New York, United States || [[http://www.cs.virginia.edu/brochure/profs/pearson.html|William Pearson]], [[JamesTaylor|James Taylor]] ||
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||<class="th" style="text-align:center" |2>November 6-10 ||''[[http://www.ashg.org/2012meeting/pages/workshops.shtml#9|Galaxy 101: Data Integration, Analysis and Sharing]]'' ||<style="text-align:center" |2>'''[[http://www.ashg.org/2012meeting/|American Society of Human Genetics (ASHG)]]''', San Francisco, California, United States ||<style="text-align:center" |2>[[JenniferJackson|Jennifer Jackson]], [[JeremyGoecks|Jeremy Goecks]] ||
||''[[http://www.ashg.org/2012meeting/pages/workshops.shtml#12|Working with High-Throughput Data and Data Visualization]]'' ||
||<class="th" style="text-align:center" |2>November 6-10 ||''[[http://www.ashg.org/2012meeting/pages/workshops.shtml#9|Galaxy 101: Data Integration, Analysis and Sharing]]''<<div(indent red)>>Sold out<<div>> ||<style="text-align:center" |2>'''[[http://www.ashg.org/2012meeting/|American Society of Human Genetics (ASHG)]]''', San Francisco, California, United States ||<style="text-align:center" |2>[[JenniferJackson|Jennifer Jackson]], [[JeremyGoecks|Jeremy Goecks]] ||
||''[[http://www.ashg.org/2012meeting/pages/workshops.shtml#12|Working with High-Throughput Data and Data Visualization]]''<<div(indent red)>>Sold out<<div>> ||
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||<class="th"> November 28 - December 4 || ''[[http://fasta.bioch.virginia.edu/cshl/|Computaional & Comparative Genomics Course]]''<<div(indent)>>This was rescheduled due to hurricane Sandy<<div>> || [[http://www.cshl.edu/|Cold Spring Harbor Laboratory]], New York, United States || [[http://www.cs.virginia.edu/brochure/profs/pearson.html|William Pearson]], [[JamesTaylor|James Taylor]] ||
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||<class="th"> January 12-16 ||'''[[http://www.intlpag.org/|Plant and Animal Genome (PAG 2013)]]''' || San Diego, California, United States || [[DaveClements|Dave Clements]] ||
||<class="th"> January 28 - February 1 || '''''[[http://bit.ly/PmKgUI|Phylotastic Hackathon]]'''''<<div(indent red)>>[[http://tinyurl.com/PhyloTastic2|Apply by November 16]]<<div>> || [[http://bio5.arizona.edu/about-bio5|Tucson, Arizona, United States]] || Arlin Stoltzfus ||
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 * {{{xxx}}}:  * {{{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 [[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/~mdehoon/software/cluster/software.htm|Cluster3.0 program]], which implements "the most commonly used clustering methods for gene expression data analysis."
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There were [[DevNewsBriefs|new Galaxy distributions]] in October: The '''[[DevNewsBriefs/2012_10_23|October 23, 2012 distribution]]''' includes an '''[[DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix|important security fix]]'''; integration with a [[DevNewsBriefs/2012_10_23#New_Trello_Issue_Board|new Trello Issue Board]]; [[Tool Shed|Tool Shed]] direct updates; [[DevNewsBriefs/2012_10_23#API|API]] fixes, tuneups, and brand-new methods to control libraries; multiple [[DevNewsBriefs/2012_10_23#Source|Admin]] changes enable better access to user data to solve problems; and updates to the [[DevNewsBriefs/2012_10_23#Visualization_framework|Visualization]] tool set cover Trackster, Circster, and the new Scatter Plot tool.

The '''[[DevNewsBriefs/2012_10_05|October 5, 2012 distribution]]''' included [[DevNewsBriefs/2012_10_05#BWA_Migration_to_Tool_Shed|migrating BWA]] to the [[http://toolshed.g2.bx.psu.edu/|Galaxy Main Tool Shed]], accessible tool versions in the UI, and new exit code features enable [[DevNewsBriefs/2012_10_05#Tools|clearer experimental tracking and ease reproducibility]]. This release also includes [[DevNewsBriefs/2012_10_05#Visualization_framework|Visualization]] updates, a new admin tool for [[DevNewsBriefs/2012_10_05#Dataset_Cleanup|PostgreSQL dataset cleanup]], and improvements in [[DevNewsBriefs/2012_10_05#AP|API]], [[DevNewsBriefs/2012_10_05#Workflows|Workflow]], and [[DevNewsBriefs/2012_10_05#Security_Fixes|Security]] components.
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 *  * Phylogenies! Hacking! Tucson in January! And, hopefully Galaxy too. If you are interested in coding, phylogenies, and tool integration please take a look at the [[devthread:phylotastic-hackathon-Jan-28-Feb-1-Tucson-AZ-of-possible-interest-to-galaxy-developers-td4656850.html|Phylotastic Hackathon Announcement]]. Apply by November 16.
 * Slides for all [[http://bit.ly/gxyswiss|11 talks at 1st Swiss Galaxy Day]] are now available online.
 * Slides for [[Events#A2012|5 other Galaxy related events]] in October are also now available.
 * [[http://rubygems.org/gems/workflow-to-galaxy|workflow-to-galaxy (0.3.4) @ RubyGems.org]]: Acquires information for a taverna 2 workflow from myExperiment (or from a file) and generates a Galaxy tool ({{{.xml}}} and {{{.rb}}} files).
 * American Internet Services (AIS) unveils [[http://bloom.bg/TQEcGz|Life Sciences SaaS]], featuring Galaxy
 * The '''[[Tool Shed|Tool Shed Wiki]]''' wiki has been re-written with a new, cleaner presentation. And check out all the [[DevNewsBriefs/2012_10_05#Tool_Shed|new features]]!

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 44 papers added to the Galaxy CiteULike group since the last Galaxy Update.

And, there are now 500 papers in the Galaxy CiteULike Group.


New Trello Issue Board

The Galaxy project has a new issue tracking system, implemented with Trello. To report an issue, fill out the form at http://galaxyproject.org/trello and submit (use markdown for formatting, if desired). You can also comment on and vote for issues directly on the Trello issue board itself.

The same guidelines for creating issues used previously apply here as well - report software issues and change requests, but get support and ask questions on the mailing list: galaxy-dev@bx.psu.edu.

All open galaxy-central bitbucket issues were imported and, though they still need to be sorted out, comments/voting on them are more than welcome. Our hope is that this issue tracker will be a more effective community interface than the Bitbucket issues were, with the voting features and simpler visibility.

2012_10_23_trello-inbox

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

  • ICG & Bio-IT APAC 2012 abstract and poster deadlines (Oct 31 and Nov 15)

  • Next Generation Sequencing Workshop application deadline (U Adelaide, Nov 2)
  • Rocky 2012 early registration deadline (Nov 8)
  • ISCB-Asai/SCCG 2012 early registration deadline (Nov 12)

November conferences include ASHG 2012 (with 2 Galaxy workshops), Personal Genomes @ CSHL, NETTAB 2012, and ICG & Bio-IT APAC 2012. Course and workshops include The Genome Access Course at CSHL (includes Galaxy), NGS workshops at Queensland and Adelaide, and Generation and Analysis of NGS data workshop @ Ghent.

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

Events

Date

Topic/Event

Venue/Location

Contact

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

November 28 - December 4

Computaional & Comparative Genomics Course

This was rescheduled due to hurricane Sandy

Cold Spring Harbor Laboratory, New York, United States

William Pearson, James Taylor

January 12-16

Plant and Animal Genome (PAG 2013)

San Diego, California, United States

Dave Clements

January 28 - February 1

Phylotastic Hackathon

Tucson, Arizona, United States

Arlin Stoltzfus

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 Distributions

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.

The October 5, 2012 distribution included migrating BWA to the Galaxy Main Tool Shed, accessible tool versions in the UI, and new exit code features enable clearer experimental tracking and ease reproducibility. This release also includes Visualization updates, a new admin tool for PostgreSQL dataset cleanup, and improvements in API, Workflow, and Security components.

Other News