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== GCC2016 Registration is Open ==

== Report on IUC Contribution Fest - Metagenomics Tools and Workflows ==

The [[https://github.com/galaxyproject/tools-iuc/issues/299|IUC Contribution Fest - Metagenomics Tools and Workflows]] was held on 30th of November and 1st of December for developers to work mainly on Galaxy metagenomic tools.

The remote nature of this gave people who don't have the opportunity to come to GCC hackathons (which have always been productive and a lot of fun) a chance to participate in a Galaxy hackathon. Having a well defined topic allowed us to accomplish a lot and let people who don't have particular tasks in mind find something to work on very quickly.

See [[https://github.com/galaxyproject/tools-iuc/issues/299|the event home page for more]].
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 * [[http://jobs.sciencecareers.org/job/383809/bioinformatics-of-mass-spectrometry-based-metabolomics/|Postdoc developing advanced MS-based metabolomics bioinformatics methods]], University of Minnesota. ''Closes November 30.''  * [[http://www.jobs.ac.uk/job/AMJ391/computational-biologist-bioinformatician/|Computational Biologist / Bioinformatician]], [[http://www.tsl.ac.uk/|The Sainsbury Laboratory]], Norwich, UK.
 * [[News/SoftwareEngineerOHSU|Software Engineer]], Oregon Health Sciences University, Portland, Oregon, United States
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   Closes 13 December 2015.
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[[PublicGalaxyServers|XX new publicly accessible Galaxy servers]] was added in November, bringing the total dangerously close to 80. [[PublicGalaxyServers|Two new publicly accessible Galaxy servers]] were added in November, bringing the total precipitously close to 80.

== Galaxy Integrated Omics (GIO) ==

<<div(right solid)>>[[http://gio.sbcs.qmul.ac.uk/|{{attachment:PublicGalaxyServers/GIOLogo.png|Galaxy Integrated Omics (GIO)|width="200"}}]]<<div>>

 * ''Link:''
   * [[http://gio.sbcs.qmul.ac.uk/|GIO Server]]
 * ''Domain/Purpose:''
   * "Proteomics Informed by Transcriptomics (PIT) methodology described in [[http://www.ncbi.nlm.nih.gov/pubmed/23142869|Evans et al. 2012]], and selection of surrogate peptides for targeted proteomics."
 * ''Comments:''
   * "Galaxy-based Integrated Omics (GIO) is a curated collection of new and pre-existing open source tools brought together for proteomics applications."
   * See [[http://www.mcponline.org/content/14/11/3087|Galaxy Integrated Omics: Web-based standards-compliant workflows for proteomics informed by transcriptomics]], Jun Fan, Shyamasree Saha, Gary Barker, Kate J. Heesom, Fawaz Ghali, Andrew R. Jones, David A. Matthews and Conrad Bessant, ''Molecular & Cellular Proteomics'', 14, 3087-3093.
 * ''User Support:''
   * [[http://gio.sbcs.qmul.ac.uk/static/Tutorial1.pdf|Tutorial 1:Getting started with GIO]]
   * [[http://gio.sbcs.qmul.ac.uk/static/Tutorial2.pdf|Tutorial 2:Getting started with GIO workflows]]
   * [[http://gio.sbcs.qmul.ac.uk/static/Tutorial3.pdf|Tutorial 3:Proteomics Informed by Transcriptomics (PIT)]]
   * [[http://gio.sbcs.qmul.ac.uk/static/Tutorial4.pdf|Tutorial 4:Targeted proteomics]]
   * For draft documentation please visit the [[https://code.google.com/p/gio-repository/|GIO repository]].
 * ''Quotas:''
 * ''Sponsor(s):''
   * "This project is led by [[http://www.bessantlab.org/|Conrad Bessant]] at Queen Mary and [[http://www.bristol.ac.uk/infection-immunity/people/person/37949|David Matthews]] at Bristol, with additional contributions from the groups of [[http://pcwww.liv.ac.uk/~jonesar/jonesar.html|Andy Jones]] at Liverpool and [[http://www.manchester.ac.uk/research/simon.hubbard/|Simon Hubbard]] at Manchester. GIO development was supported by BBSRC TRDF2 grants BB/L018438/1 (Proteomics Goes Viral), BB/K016075/1 (Galaxy Workflows for Proteomics Informed by Transcriptomics) and BB/K004123/1 (Integrating Genomes and Proteomes on the Cloud). Lead developer is [[http://www.sbcs.qmul.ac.uk/staff/drjunfan.html|Jun Fan]]."


== RNA-Seq Portal ==

<<div(right solid)>>[[http://weizhongli-lab.org/RNA-seq/|{{attachment:PublicGalaxyServers/RNA-SeqPortal.png|RNA-Seq Portal - Analyzing RNA-seq Data for Agricultural Animal Species|width="300"}}]]<<div>>

 * ''Links:''
  * [[http://weizhongli-lab.org/RNA-seq/|RNA-Seq Portal]]
  * [[http://weizhongli-lab.org:8088/|Galaxy server]]

 * ''Domain/Purpose:''
  * Analyzing RNA-seq Data for Agricultural Animal Species.
 * ''Comments:''
  * From the [[http://weizhongli-lab.org/RNA-seq/|portal landing page]]:
    The goal of this project is to develop a web portal with integrated tools for RNA-seq based gene expression analysis for agricultural animals.
     * improve genome annotation of agricultural animal species, including (but not limiting to) cattle, pig, chicken, turkey, horse, sheep, and goat as well as catfish;
     * develop and integrate needed bioinformatics tools and pipelines, visualization interfaces, and statistical methods;
     * build a web portal that enable RNA-seq based transcriptomics analysis in aforementioned animal species.
 * ''User Support:''
   * [[http://weizhongli-lab.org:8088/|Example usage]] (see center panel)
   * [[http://weizhongli-lab.org/RNA-seq/contact/|Web support]]
 * ''Quotas:''

 * ''Sponsor(s):''
  * The project is developed by [[http://weizhongli-lab.org/|Weizhong Li's lab]] at [[http://jcvi.org/|J. Craig Venter Institute]] with support from NIFA (award #2013-67015-21428).
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== Planemo 0.15.0 - 0.18.1 ==

[[https://pypi.python.org/pypi/planemo|Planemo]] saw a meteor storm (sorry!) of activity in November with 4+ releases.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. [[https://pypi.python.org/pypi/planemo/0.18.1#history|Planemo 0.18.1]] is the most recent release. See the [[http://planemo.readthedocs.org/en/latest/history.html#id2|release history]].

== BioBlend 0.7.0 ==

[[https://github.com/galaxyproject/bioblend/|BioBlend version 0.7.0]] was released few days ago. !BioBlend is a python library for interacting with CloudMan and the [[Learn/API|Galaxy API]]. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.) From the [[http://bit.ly/bbCHANGELOG|release CHANGELOG]].
== Planemo 0.19.0 - 0.20.0 ==

[[https://pypi.python.org/pypi/planemo|Planemo]] saw a regular Oort cloud of activity in November with 2 releases.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. [[https://pypi.python.org/pypi/planemo/0.20.0#history|Planemo 0.20.0]] is the most recent release. See the [[http://planemo.readthedocs.org/en/latest/history.html#id2|release history]].
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 '''!BioBlend 0.7.0'''

   [[https://github.com/galaxyproject/bioblend/|BioBlend version 0.7.0]] was released few days ago. !BioBlend is a python library for interacting with CloudMan and the [[Learn/API|Galaxy API]]. CloudMan offers an easy way to get a personal and completely functional instance of Galaxy in the cloud in just a few minutes, without any manual configuration.) From the [[http://bit.ly/bbCHANGELOG|release CHANGELOG]].
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 * From [[https://biostar.usegalaxy.org/u/4670/|Guy Reeves]]:
   'Hidden' Galaxy features which are really useful. For Scratchbook see [[http://vimeo.com/120839821|this video]].
 * Ever wondered who writes Galaxy?
   [[https://github.com/galaxyproject/galaxy/blob/dev/CONTRIBUTORS.md|These people do]].
 * See the [[https://galaxyproject.github.io|executive summary]] of free open source software the Galaxy community provides. (Big thanks to [[https://twitter.com/Eric_Rasche|Eric Rasche]].)
 * From [[https://github.com/natefoo|Nate Coraor]]
   An Ansible role for installing Galaxy Interactive Environments
 * [[https://www.msi.umn.edu/content/expanding-galaxy-platform|Expanding the Galaxy Platform]] at the [[https://www.msi.umn.edu/|Minnesota Supercomputing Institute]].
 * From [[https://twitter.com/bjoerngruening|Björn Grüning]]:
   The [[https://github.com/bgruening/docker-galaxy-stable/tree/dev|Galaxy Docker Image]] has gained TravisCI testing. Bioblend will test all functionality and tool installation.
 * Updated documentation:
   * [[Develop/SourceCode|The source code of Galaxy]]
   * [[Admin/Config/Jobs|Galaxy Job Configuration]]
   * [[Learn/Datatypes|Datatypes]]

Hey! This is under construction!

Galactic December News!

Galaxy News

Welcome to the December 2015 Galactic News, a summary of what is going on in the Galaxy community.

If you have anything to include in the next News, please send it to Galaxy Outreach <outreach AT galaxyproject DOT org>.

New Papers

XX new papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in November. Highlights include:

The new papers were tagged with:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

-

Cloud

-

Project

-

Tools

-

UsePublic

-

HowTo

-

RefPublic

-

UseCloud

-

Visualization

-

IsGalaxy

-

Reproducibility

-

UseLocal

-

Workbench

-

Methods

-

Shared

-

UseMain


Events

Upcoming Events

There are upcoming events on XX continents in XX countries. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

Designates a training event offered by GTN Member

Designates a training event offered by GTN member(s)


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.



New Public Galaxy Servers

Two new publicly accessible Galaxy servers were added in November, bringing the total precipitously close to 80.

Galaxy Integrated Omics (GIO)

Galaxy Integrated Omics (GIO)

RNA-Seq Portal

RNA-Seq Portal - Analyzing RNA-seq Data for Agricultural Animal Species
  • Links:

  • Domain/Purpose:

    • Analyzing RNA-seq Data for Agricultural Animal Species.
  • Comments:

    • From the portal landing page:

      • The goal of this project is to develop a web portal with integrated tools for RNA-seq based gene expression analysis for agricultural animals.
        • improve genome annotation of agricultural animal species, including (but not limiting to) cattle, pig, chicken, turkey, horse, sheep, and goat as well as catfish;
        • develop and integrate needed bioinformatics tools and pipelines, visualization interfaces, and statistical methods;
        • build a web portal that enable RNA-seq based transcriptomics analysis in aforementioned animal species.
  • User Support:

  • Quotas:

  • Sponsor(s):


Releases


https://pypi.python.org/pypi/planemo/

Planemo 0.19.0 - 0.20.0

Planemo saw a regular Oort cloud of activity in November with 2 releases.

Planemo is a set of command-line utilities to assist in building tools for the Galaxy project. Planemo 0.20.0 is the most recent release. See the release history.

Other Releases

GalaxyProject

CloudMan

  • This is the most complete update of the Galaxy on the Cloud platform to date with all the cloud components being built from the ground up. See the CHANGELOG for a complete set of changes or just give it a try: see the all new Getting Started documentation.

  • Security Advisories

    • Three security vulnerabilities were announced and patched in August. The Galaxy Committers have released a number of fixes which have been rolled in to affected versions of Galaxy dating back to the 14.10 release.

  • Pulsar

    • Pulsar 0.5.0 was released in May. Pulsar is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the results are transferred back to the Galaxy server - eliminating the need for a shared file system.

    CloudMan

    blend4j v0.1.2

    • blend4j v0.1.2 was released in December 2014. blend4j is a JVM partial reimplemenation of the Python library bioblend for interacting with Galaxy, CloudMan, and BioCloudCentral.


Galaxy Community Hubs

Galaxy Training Network

Galaxy Community Log Board

Galaxy Deployment Catalog

Share your training resources and experience now

Share your experience now

Describe your instance now




Galaxy ToolShed

ToolShed Contributions

See list of tools contributed in November.


Other News