June 2012 - galaxy-announce - lists.galaxyproject.org

July 2012 Galaxy Update

by Dave Clements

Hello all, The July 2012 Galaxy Update is now available<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07>. *Highlights:* - GCC2012 is July 25-27!<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#GCC2012_is_July_25-27.21> - Register by July 18<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> - Other Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Upcoming_Events_and_Deadl...> ,* including these deadlines in the next several days* - Galaxy Workshops in South Africa<http://wiki.g2.bx.psu.edu/News/GalaxyWorkshopsInSouthAfrica>(deadline: *June 30*) and the South African Genetics & Bioinformatics Society Conference <http://genetics.cmc-uct.co.za/> (deadline *July 1*) - Systems Bioinformatics Workshop<http://gaggle.systemsbiology.net/workshop2012/>(deadline: *June 30*) - GMOD Summer School<http://gmod.org/wiki/2012%20GMOD%20Summer%20School>(deadline: *July 9*) - 31 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Papers>, including two new *Current Protocols* - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Who.27s_Hiring>at six different institutions - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Tool_Shed_Contributions> - A new CloudMan distribution was released last month<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#New_Distributions> - Plus <http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_07#Other_News> - Easily wrap your R functions as Galaxy tools - help schedule the first GalaxyCzars<http://wiki.g2.bx.psu.edu/Community/GalaxyCzars>conference call on July 9 or 10 - and lots of new screencasts, tutorials, and new genomes on main If you have anything you would like to see in the August *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave Clements -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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GCC2012 Early Registration ENDS THIS MONDAY JUNE 11

by Dave Clements

Hello all, Just a *final* reminder that early registration for the 2012 Galaxy Community Conference (GCC2012)<http://galaxyproject.org/wiki/Events/GCC2012> *closes on Monday June 11 (*which is probably* today* when you read this*)*. Registering early saves 36 to 42% on registration costs, and allows you to sign up for the GCC2012 Training Day<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>and book discounted conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging> *before they fill up*. *Register today <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>. * GCC2012 <http://galaxyproject.org/wiki/Events/GCC2012> will be held July 25-27, in Chicago, Illinois, United States. This year GCC2012 features a full day of tutorial sessions<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>with 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topic, including the newly added Variant and SNP Analsys, RNA-Seq Analysis, and Galaxy Code Architecture sessions<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>. The two-day main meeting<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Day_1:_July_26.2C_Thursday>includes over 25 talks by Galaxy community members and Galaxy developers addressing the challenges of integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. GCC2012 is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy <http://gmod.org/wiki/Galaxy>is an open web-based platform for data intensive biomedical research<http://galaxyproject.org>that is widely used and deployed at research organizations of all sizes around the world. See you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee<http://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee> Links: http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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Galaxy Main new native genomes & updated genomes

by Jennifer Jackson

Dear Galaxy Community, Recent genome additions and updates on the *Galaxy Main public instance* at http://usegalaxy.org include: * New native genome additions:* * *"mm10"*: Mouse (/Mus musculus/) Dec 2011, GRCm38, source UCSC * *"gorGor3"*: Gorilla (/Gorilla gorilla gorilla/) May 2011, WGS CABD02, source UCSC * *"bosTau6"*: Cow (/Bos taurus/) Nov 2009, UMD_3.1, source UCSC * Existing genomes with content updates:* * *"bosTau4, bosTauMd3, canFam2, mm9, panTro3, rn4"* * Details:* * /Native genomes/ are sometimes referred to as "/locally cached/" on tool forms. * New and updated indexes include: /NGS:+/ (all tools), /Lift-Over/ (Convert genome coordinates), and /Fetch Sequences/ (Extract DNA). * Currently, these additions and updates exclude the tools in the group /NGS: GATK Tools (beta)/, however new genomes will be added soon. For now, use the custom reference genome <http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> option with this tool group, if not using*"Homo sapiens b37 (hg_g1k_v37)"*. * Additional new genomes and updates are in progress and will be announced via Twitter @galaxyproject <http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter> and the galaxy-announce(a)bx.psu.edu <http://wiki.g2.bx.psu.edu/Mailing%20Lists#The_lists> mailing list. * Genome requests can be sent to the mailto:galaxy-user@bx.psu.edu <mailto:galaxy-user@bx.psu.edu>mailing list. Please include the full genome name, a link to the stable public source, and any build or species specific information you feel is relevant. This helps us to create a reference genome the entire Galaxy community can use. * Unfinished genomes or genomes not yet published to a stable source repository are still often best used as a custom reference genome <http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome> with tools, but please feel free to check in for feedback. /Thanks for using Galaxy!/ -- Jennifer Jackson http://galaxyproject.org

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GCC2012 Early Registration ends in 1 week

by Dave Clements

Hello all, Just a reminder that early registration for the 2012 Galaxy Community Conference (GCC2012) <http://galaxyproject.org/wiki/Events/GCC2012>, being held in Chicago, Illinois, July 25-27, *closes on June 11, one week from today*. Registering early saves 36 to 42% on registration costs, and allows you to book discounted conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging> *before it fills up*. Register now<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> . GCC2012 <http://galaxyproject.org/wiki/Events/GCC2012> is about integrating, analyzing, and sharing the diverse and very large datasets that are now typical in biomedical research. This is an opportunity to share best practices with, and learn from, a large community of researchers and support staff who are facing the challenges of data-intensive biology. Galaxy <http://gmod.org/wiki/Galaxy> is an open web-based platform for data intensive biomedical research <http://galaxyproject.org> that is widely used and deployed at research organizations of all sizes and around the world. The GCC2012 Training Day<http://galaxyproject.org/wiki/Events/GCC2012/TrainingDay>agenda has been finalized. It has 3 parallel tracks, each featuring four, 90 minute workshops and covering 10 different topics. The final schedule<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of speakers<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers>and abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are also now available. Hope to see you in Chicago! Dave Clements, on behalf of the GCC2012 Organizing Committee<http://galaxyproject.org/wiki/Events/GCC2012/Organizing%20Committee> -- http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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June 2012 Galaxy Update

by Dave Clements

Hello all, The June 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06>is now available. *Highlights:* - GCC2012 is Next Month!<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#GCC2012_is_Next_Month.21> - *Early registration ends June 11<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#GCC2012_is_Next_Month> * - New Public Server: GWIPS-Viz<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Public_Server:_GWIPS-Viz> - 32 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Who.27s_Hiring>at six different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Upcoming_Events_and_Deadl...> - *Early registration for ISMB/BOSC/BSI-SIG ends today<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Upcoming_Events_and_Deadl...> * - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Tool_Shed_Contributions> - A new distribution was released last month<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#New_Distribution> - GalaxyCzars survey results are in<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_06#Other_News> If you have anything you would like to see in the July *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave Clements -- *Galaxy Update <http://wiki.g2.bx.psu.edu/GalaxyUpdates>* is a (mostly) monthly summary of what is going on in the Galaxy community. *Galaxy Updates * complement the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. http://galaxyproject.org/GCC2012 <http://galaxyproject.org/wiki/GCC2012> http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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galaxy-announce June 2012