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December 2014 Galaxy Newsletter
by Dave Clements 01 Dec '14

01 Dec '14

Hello all, As always there's a lot going on in the Galaxy this month. "Like what?" you say. Well, read the dang December Galaxy Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12> we say! Highlights include: - Galaxy Day! In Paris! This Wednesday! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Galaxy_Day:_3_December…> - Near Richmond, Virginia? There's a Galaxy Workshop at Virginia State U on December 12 <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Intro_to_Galaxy_Worksh…> . - GCC2015 needs sponsors <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#GCC2015:_6-8_July.2C_N…> ! - Other upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_Events> on two continents - *96 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Papers>*, including 6 highlighted papers, referencing, using, extending, and implementing Galaxy. - Job openings at 7+ organizations <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Who.27s_Hiring> - A new mailing list: Galaxy-Training <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#New_Galaxy-Training_Ma…> - 15 new ToolShed repositories from 10 contributors <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#ToolShed_Contributions> - And, 10 other juicy <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News> (well maybe not *juicy*, but certainly not *crunchy*) bits of news <https://wiki.galaxyproject.org/GalaxyUpdates/2014_12#Other_News> Happy December! Dave Clements and the *crisp* Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Galaxy Mailing Lists are moving
by Nate Coraor 11 Nov '14

11 Nov '14

Hello Galaxy Community, *Galaxy Mailing Lists are moving!* During the week of November 17-21, 2014, Galaxy mailing lists (including this one) will be migrated from lists.bx.psu.edu to lists.galaxyproject.org . This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu to galaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. As always, you can manage your subscription for any Galaxy mailing list by following the link instructions at the bottom of this announcement. If you should notice any problems after the migration, please do not hesitate to let us know, via email to both "<list>-owner(a)lists.galaxyproject.org" (after the move) and to myself. Thanks, --nate, and the Galaxy Team

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(no subject)
by Dave Clements 03 Nov '14

03 Nov '14

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Galaxy Training Network
by Dave Clements 16 Oct '14

16 Oct '14

Hello all, We are pleased to announce the *Galaxy Training Network (GTN) <https://wiki.galaxyproject.org/Teach/GTN>*, a network of trainers who teach bioinformatics using Galaxy, or teach about Galaxy itself. The GTN aims to make it easy to find Galaxy trainers <https://wiki.galaxyproject.org/Teach/Trainers>, and to share and discover the wealth of training resources available for Galaxy. This includes training materials <https://wiki.galaxyproject.org/Teach/Resources>, a trainer directory <https://wiki.galaxyproject.org/Teach/Trainers>,best practices <https://wiki.galaxyproject.org/Teach/BestPractices>, and guidance on computing platforms <https://wiki.galaxyproject.org/Teach/ComputingPlatforms> for teaching with Galaxy. The Galaxy Training Network is accessible to the entire community. If you teach with Galaxy, then please consider adding your organization <https://wiki.galaxyproject.org/Teach/Trainers#Add_a_Trainer>, materials <https://wiki.galaxyproject.org/Teach/Resources#Add_a_Training_Resource>, and best practices <https://wiki.galaxyproject.org/Teach/BestPractices>. The Trainer Directory <https://wiki.galaxyproject.org/Teach/Trainers> already includes 16 organizations and there may be one (or 6!) near you <http://bit.ly/gxytrnmap>. Thanks, The Galaxy Training Network (GTN) <https://wiki.galaxyproject.org/Teach/Trainers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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October 2014 Galaxy Newsletter
by Dave Clements 01 Oct '14

01 Oct '14

Hello all, A lot is happening in in the Galaxy in October, and a lot of good stuff happened in September too. Take a look at the October 2014 Galaxy Newsletter <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10> for the complete story, but here are some highlights: - *Galaxy needs your input! <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Galaxy_Needs_Your_Inpu…>* You may even get rewarded for your input ... - IRC channel to be logged <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#IRC_Channel_Policy_Cha…>, starting this month - Slides from ECCB'14 and upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Events> - 71 new papers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Papers>, including 6 featured papers - Who's Hiring? <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Who.27s_Hiring> Lots of places, that's who - Two new public Galaxy Servers <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#New_Public_Servers> - New Deployment Catalog and Log Board entries <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Community_Galaxy_Hubs> - 36 new ToolShed repos <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#ToolShed_Contribution> - And a smattering of other news <https://wiki.galaxyproject.org/GalaxyUpdates/2014_10#Other_News> too Happy October! Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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2014 Galaxy Questionnaire
by Dave Clements 30 Sep '14

30 Sep '14

Hello all, The Galaxy Project is preparing for our next grant cycle and we are seeking your feedback and comments on on all things Galaxy. We have created two questionnaires, each focused on a different way to interact with Galaxy: 1. *Galaxy User Questionnaire <https://docs.google.com/forms/d/1NT3ma2g7rR-mWA_vgOg2Ia_6VTFiZ86um2JhX2SecC…>* 2. *Galaxy Admin, Tool Developer, and Galaxy Developer Questionnaire <https://docs.google.com/forms/d/1lszXJ2lDJ2dYCWKXBk1qT1jO7XdDDfxXmGRCUMZFX2…>* Please take a few minutes and fill out the surveys that apply to you. The questionnaires are structured so you can skip topics (whole pages!) that don't apply to you, and every question is optional. *And, to thank you for your time and effort, the Galaxy Project will increase your storage quota on usegalaxy.org <https://usegalaxy.org/> by 50GB. *That's a 20% increase. Let your voice be heard (and, get some storage)! The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Proposal: Create a public archive of the GalaxyProject IRC Channel
by Dave Clements 02 Sep '14

02 Sep '14

Hello all, We would like to change the logging policy for the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel>: - *Starting later this fall, the #galaxyproject IRC channel <https://wiki.galaxyproject.org/GetInvolved#IRC_Channel> will be logged online in a format that can be searched.* Currently, this channel is not logged anywhere. This change will only be made if the community agrees that a searchable online log would be an improvement. *If you have thoughts or comments on this proposal, then please post them to this Biostar thread <http://bit.ly/gxybs8804>*. In two weeks' time (around September 17, 2014), we'll summarize the discussion and publish a decision. *Proposal Details:* Starting sometime after community discussion ends (and assuming that discussion is favorable): 1. At least two weeks before the change: 1. Warnings will be added to the IRC channel information and on the wiki, that the log will be publicly archived as of the given start date. 2. The policy change will be announced on Galaxy Biostar <https://wiki.galaxyproject.org/Support/Biostar> and the Galaxy-Dev and Galaxy-Announce mailing lists <https://wiki.galaxyproject.org/MailingLists>. 2. On the launch date 1. The IRC channel (and the wiki) will be updated to clearly state that the IRC channel is publicly logged. 2. Announcements of the change will be posted to Biostar and the mailing lists. 3. IRC postings from the announcement onward will start showing up in the public log. 4. The IRC channel log will be included in the Galaxy search engines <http://galaxyproject.org/search/>. *Why now?* The project's IRC channel came up at the GalaxyAdmins BoF meetup <https://wiki.galaxyproject.org/Events/GCC2014/BoFs/GalaxyAdmins> at GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014>, where it was lauded as both a great resource, *and cursed because it is not archived anywhere.* An action item from that meetup is to propose this change. The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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September 2014 Galaxy News
by Dave Clements 29 Aug '14

29 Aug '14

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Galaxy Events in Europe This Fall - Lots of them.
by Dave Clements 26 Aug '14

26 Aug '14

Hello all, There are several Galaxy related events in Europe this fall. These events are a great way to meet other Galaxy users and developers and learn and share best practices. Events start with ECCB and then wander the continent ending in Italy in November. If you are interested in learning more about Galaxy and/or the community, then please give these a look. Date Topic/Event Venue/Location Contact September 6-10 At least one tutorial, a panel of European Public Galaxy Instances, and 5 posters <https://wiki.galaxyproject.org/Events/ECCB2014> *European Conference on Computational Biology (ECCB'14) <https://wiki.galaxyproject.org/Events/ECCB2014>*, Strasbourg, France Presenters <https://wiki.galaxyproject.org/Events/ECCB2014> September 11 *Tools integration on Galaxy <http://go4bioinformatics.genouest.org/integration-doutils-dans-la-plateform…>* This event is now full. Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Cyril Monjeaud <https://www.e-biogenouest.org/members/1005>, Yvan Le Bras <https://www.e-biogenouest.org/members/1003> September 15 *Fourth GUGGO meeting <http://www.biogenouest.org/agenda/evenement/groupe-de-travail-des-utilisate…>* Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Cyril Monjeaud <https://www.e-biogenouest.org/members/1005>, Yvan Le Bras <https://www.e-biogenouest.org/members/1003> September 23-25 *Analisi dati Next Generation Sequencing con Galaxy <http://www.bioinformatica.crs4.it/next_generation_sequencing_course_with_ga…>* Cagliari, Italy CRS4 <ngs-courses(a)crs4.it> September 24 *Introduction to Galaxy - Data Manipulation and Visualisation <http://training.csx.cam.ac.uk/event/1222231>* University of Cambridge, United Kingdom Anne Pajon, Jing Su September 25 *RADseq analysis using STACKS on Galaxy <http://go4bioinformatics.genouest.org/analyse-de-donnees-de-type-rad-par-le…>* Galaxy User Group Grand Ouest <https://www.e-biogenouest.org/groups/guggo>, Rennes, France Yvan Le Bras <https://www.e-biogenouest.org/members/1003>, Cyril Monjeaud <https://www.e-biogenouest.org/members/1005> September 30 - October 2 *RNA-Seq & ChIP-Seq analysis course using Galaxy <http://www.fc3bio.fr/Analyse-des-donnees-RNA-seq-et-ChIP-seq-sequencage-hau…>* PRABI <http://www.prabi.fr/>, Lyon, France Navratil V <navratil(a)prabi.fr>., Oger C. <oger(a)prabi.fr>, Veber P. <veber(a)prabi.fr>, Deschamps C. <deschamps(a)prabi.fr>, Perriere G. <perriere(a)prabi.fr> September 30 - October 2 Galaxy Training and Demo Day <https://wiki.galaxyproject.org/Events/Switzerland2014/trainingday> Bern (Switzerland) Hans-Rudolf Hotz <https://wiki.galaxyproject.org/HansrudolfHotz> and Bjoern Gruening <https://wiki.galaxyproject.org/BjoernGruening> *(second Swiss) Galaxy Workshop <https://wiki.galaxyproject.org/Events/Switzerland2014>* SyBIT Tech Day, Bern (Switzerland) *German Galaxy Developers Day <https://wiki.galaxyproject.org/Events/Germany2014>* Freiburg (Germany) November 18-20 *Analisi dati Next Generation Sequencing con Galaxy <http://www.bioinformatica.crs4.it/training>* Cagliari, Italy CRS4 <ngs-courses(a)crs4.it> Europe does not have a monopoly on events in the coming months. There are also events in Australia and North America, See the Galaxy Events Page <https://wiki.galaxyproject.org/Events> for a complete list. Cheers / Au revoir / Ciao / Auf Wiedersehen, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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August 11, 2014 Galaxy Distribution
by Jennifer Jackson 15 Aug '14

15 Aug '14

August 11, 2014 Galaxy Distribution <http://wiki.galaxyproject.org/News/2014_08_11_Galaxy_Distribution> / <https://www.docker.com/>/ _Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2014_08_11>___ /Highlights:/// .Security alert <http://tinyurl.com/nhgmbc5>from July 31st, upgrade now .Citations <http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E…>: DOIs, bibtex, and much much more . Docker, docker,DOCKER <http://wiki.galaxyproject.org/Admin/Tools/Docker>. You voted, we've/got it/, with a little help from our friends (you!) . Significant Workflow, API, Job, Tool Shed, and Dataset management updates . Fixes, tunings, plus just a drop of ? Gossip *getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update latest_2014.06.02 /Thanks for using Galaxy!/ The Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>

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