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GCC2012 Early Registration ends in 1 week
by Dave Clements 04 Jun '12

04 Jun '12

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 01 Jun '12

01 Jun '12

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GCC2012 Update
by Dave Clements 14 May '12

14 May '12

Hello all, The 2012 Galaxy Community Conference (GCC2012), being held in Chicago, Illinois, July 25-27, is *now just 10 weeks away*. We have updates on: 1. Help set the topics covered on Training Day (by this Friday) 2. Early registration closes June 11 3. Confirmed Speaker List As always, please let me know if you have any questions, and I hope to see you in Chicago! Thanks, Dave Clements on behalf of the GCC2012 Organizing Committee *1. Training Day Topics: Vote by this Friday * A day of tutorials has been added to the agenda this year. The GCC2012 Training Day has 3 parallel tracks, each featuring four, 90 minute workshops and covering between and 7 and 12 different topics. *Please take a few minutes to vote on topics that you would like to see presented: * http://bit.ly/GCC2012TDSurvey The survey ends this Friday, May 18, so please provide your feedback now. *2. Early Registration: Ends June 11 * The GCC2012 early registration is now just 4 weeks away. Registering early saves* 36 to 42%* on registration costs, and allows you to book discounted conference lodging before it fills up. *Register now at* http://galaxy.psu.edu/gcc2011/Register.html *3. Confirmed Speakers and Abstracts Posted * A list of confirmed speakers and abstracts are now available on the conference web site at http://wiki.g2.bx.psu.edu/Events/GCC2012/Program#Confirmed_Speakers This list is not yet finished, but will give you a pretty accurate idea of the range of topics that will be discussed during the main meeting. -- 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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May 11, 2012 Galaxy Development News Brief
by Jennifer Jackson 12 May '12

12 May '12

Dear Galaxy Community, The May 11, 2012 Galaxy Distribution has been released at: http://bitbucket.org/galaxy/galaxy-dist/ Complete News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_05_11> *Highlights:* * *EMBOSS* tools and datatypes have now moved from the _/Galaxy distribution/_ <http://bitbucket.org/galaxy/galaxy-dist/> to the /Galaxy Main Tool Shed/ <http://toolshed.g2.bx.psu.edu>. * Tool Integration Tests <http://wiki.g2.bx.psu.edu/Tool%20Shed#Using_Galaxy.27s_functional_test_fram…>, Custom Tool Panel Configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Configurable Tool Output Locations <http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files>. * Improved Multiprocess Job Handling <http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal…> and Enhanced OpenID <http://openid.net> Support. * GATK <http://www.broadinstitute.org/gsa/wiki> version 1.4, FreeBayes <http://github.com/ekg/freebayes>, Updated *Megablast* using NCBI BLAST+ <http://blast.ncbi.nlm.nih.gov/Blast.cgi>, Trinity <http://trinityrnaseq.sourceforge.net>, WormBase 2 <http://www.wormbase.org>, and IGB <http://bioviz.org/igb/index.html> external display. * Trackster <http://wiki.g2.bx.psu.edu/Learn/Visualization> upgrades include /strand coloring/, /interval datatype support/, and /tabix indexing/ (fast!!). * Updated *User Interface*, *Workflow-API* upgrades, and *Custom UCSC Display*. *http://getgalaxy.org* *new*: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist *upgrade*: % hg pull -u -r 17d57db9a7c0 /Thanks for using Galaxy!/ Jennifer Jackson Galaxy Team <http://wiki.g2.bx.psu.edu/Galaxy%20Team> http://galaxyproject.org

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May 2012 Galaxy Update
by Dave Clements 01 May '12

01 May '12

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GCC2012 Abstract Submission Deadline is April 16, one week from today.
by Dave Clements 16 Apr '12

16 Apr '12

Hello all, Just a reminder that the abstract submission deadline for the 2012 Galaxy Community Conference (GCC2012) is April 16, one week from today. See http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts for details. Thanks, and hope to see you in Chicago, Dave C On Mon, Feb 13, 2012 at 3:27 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> are now > being accepted for oral presentations at the 2012 Galaxy Community > Conference (GCC2012) <http://wiki.g2.bx.psu.edu/Events/GCC2012>. > Submissions on any topics of interest to the Galaxy community are > encouraged. Areas of interest include, but are not limited to: > > - Best practices for local Galaxy installation and management > - Integrating tools and/or data sources into the Galaxy framework > - Deploying galaxy on different infrastructures > - Compelling or novel uses of Galaxy for biomedical analysis > > See the GCC2011 program <http://wiki.g2.bx.psu.edu/Events/GCC2011> for an > idea of the breadth of topics that can be covered. Oral presentations will > be approximately 15-20 minutes long, including time for question and > answer. There will also be an opportunity for lightning talks, which will > be solicited at the meeting. The submission deadline is April 16. See the GCC2012 > Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for > more details and how to submit. > > GCC2012 <http://wiki.g2.bx.psu.edu/Events/GCC2012> will be held, July > 25-27 in Chicago, Illinois, United States. The main meeting will run for two > full days <http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>, and be > preceded by a full day of training workshops<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>. > If you are a bioinformatics tool developer, data provider, workflow > developer, power bioinformatics user, sequencing or bioinformatics core > staff, or a data and analysis archival specialist, then GCC2012 is relevant > to you. Registration will open in March. > GCC2012 is hosted by the University of Illinois at Chicago<http://uic.edu/>, > the University of Illinois at Urbana-Champaign <http://illinois.edu/>, > and the Computation Institute <http://www.ci.anl.gov/>. > > Links: > http://galaxyproject.org/GCC2012 > http://galaxyproject.org/wiki/Events/GCC2012/Abstracts > > Thanks, > > Dave Clements > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://galaxyproject.org/wiki/ > > -- 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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April 2012 Galaxy Update
by Dave Clements 02 Apr '12

02 Apr '12

Hello all, The April 2012 Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04>is now available. *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 * complements the *Galaxy Development News Briefs<http://wiki.g2.bx.psu.edu/DevNewsBriefs> * which accompany new Galaxy releases and focus on Galaxy code updates. *Highlights:* - 28 New Papers<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#New_Papers> - Open Positions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Who.27s_Hiring>at six different institutions - Upcoming Events and Deadlines<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Upcoming_Events_and_Deadlin…> - GCC2012 Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#GCC2012_Update>, including - Abstract submission deadline is April 16. - Early registration is now open. - Tool Shed Contributions<http://wiki.g2.bx.psu.edu/GalaxyUpdates/2012_04#Tool_Shed_Contributions>(at least 15 new repositories) If you have anything you would like to see in the May *Galaxy Update<http://wiki.g2.bx.psu.edu/GalaxyUpdates> *, please let me know. Thanks, Dave C. -- 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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2012 Galaxy Community Conference (GCC2012) Early Registration is Now Open
by Dave Clements 20 Mar '12

20 Mar '12

Hello all, We are pleased to announce that early registration<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>for the 2012 Galaxy Community Conference (GCC2012)<http://wiki.g2.bx.psu.edu/Events/GCC2012>is now open. GCC2012 will be held July 25-27, at the UIC Forum <http://www.uic.edu/depts/uicforum/>, in Chicago, Illinois. The conference will feature two full days<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>this year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: - Sequencing core facility staff - Bioinformatics core staff - Bioinformatics tool and workflow developers - Bioinformatics focused principal investigators and researchers - Data producers - Power bioinformatics users This event will help you with 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. Registration <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> is very affordable, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging>can also be booked. Low-cost rooms have been reserved on the UIC campus<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#James_Stuckel_Towers>. You can also stay at the official conference hotel<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Crowne_Plaza_Chicago_Met…>, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>, if you would like to take advantage of these. Abstract submission <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> is also open, from now through April 16. Abstract submissions<http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts>on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for details. Please let me know if you have any questions (or just talk to me at the April 2012 GMOD Meeting). Looking forward to seeing you in Chicago this July! Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements>, on behalf of the GCC2012 Organizing Committee<http://wiki.g2.bx.psu.edu/Events/GCC2012/Organizing%20Committee> PS: Please help get the word out! A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion. -- 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 is Now Open
by Dave Clements 20 Mar '12

20 Mar '12

Hello all, We are pleased to announce that early registration<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>for the 2012 Galaxy Community Conference (GCC2012)<http://wiki.g2.bx.psu.edu/Events/GCC2012>is now open. GCC2012 will be held July 25-27, at the UIC Forum <http://www.uic.edu/depts/uicforum/>, in Chicago, Illinois. The conference will feature two full days<http://wiki.g2.bx.psu.edu/Events/GCC2012/Program>of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training<http://wiki.g2.bx.psu.edu/Events/GCC2012/TrainingDay>this year, featuring 3 parallel tracks with four workshops each, covering seven different topics. The Galaxy Community Conference is for: - Sequencing core facility staff - Bioinformatics core staff - Bioinformatics tool and workflow developers - Bioinformatics focused principal investigators and researchers - Data producers - Power bioinformatics users This event will help you with 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. Registration <http://wiki.g2.bx.psu.edu/Events/GCC2012/Register> is very affordable this year, especially for post-docs and students. You can can save an additional 40% by registering on or before June 11. Conference lodging<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Lodging>can also be booked. Low-cost rooms have been reserved on the UIC campus<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#James_Stuckel_Towers>. You can also stay at the official conference hotel<http://wiki.g2.bx.psu.edu/Events/GCC2012/Logistics#Crowne_Plaza_Chicago_Met…>, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early<http://wiki.g2.bx.psu.edu/Events/GCC2012/Register>, if you would like to stay in either. Finally, abstract submission<http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts>is also open, from now through April 16. Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts <http://wiki.g2.bx.psu.edu/Events/GCC2012/Abstracts> page for details. Looking forward to seeing you in Chicago! Dave Clements <http://wiki.g2.bx.psu.edu/DaveClements>, on behalf of the GCC2012 Organizing Committee<http://wiki.g2.bx.psu.edu/Events/GCC2012/Organizing%20Committee> PS: Please help get the word out! A flyer and graphics are at http://wiki.g2.bx.psu.edu/Events/GCC2012/Promotion -- http://galaxyproject.org/GCC2012 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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March 12, 2012 Galaxy Development News Brief
by Jennifer Jackson 13 Mar '12

13 Mar '12

Dear Galaxy Community, The *latest Galaxy distribution* has been released: March 12, 2012 Galaxy Development News Brief <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_03_12> *Mercurial pull:* new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 40f1816d6857 *Important Upcoming Changes to Tool Organization: * The _*Emboss tools and Emboss datatypes will be eliminated from the Galaxy distribution in the NEXT release*_. Other tools currently in the Galaxy distribution will be eliminated in following releases. Those hosting local Galaxy instances should read this revised *"Migrating tools"* <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> section of the Galaxy tool shed wiki to understand how this process will work: *Migrating tools from the Galaxy distribution to the Galaxy Main tool shed <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…>* /(Summary)/ In 2012, the Galaxy development team will begin the process of /migrating the tools that are currently available in the Galaxy distribution to the Galaxy Main tool shed/. This will enable those that host local Galaxy instances much more flexibility in choosing to provide only those specific tools in which their users are interested. Read more... <http://wiki.g2.bx.psu.edu/Tool%20Shed#Migrating_tools_from_the_Galaxy_distr…> *Release Highlights: * * *Galaxy tools:* XML configuration <http://wiki.g2.bx.psu.edu/Tool%20Shed#XML_configuration_files_used_to_popul…>, managing tool panel layout <http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_to…>, and Galaxy tool versions <http://wiki.g2.bx.psu.edu/Tool%20Shed#Galaxy_Tool_Versions> * *RNA-Seq Tools:* Added *CuffMerge* <http://cufflinks.cbcb.umd.edu> version 1.0.0, Updated *TopHat* <http://tophat.cbcb.umd.edu> default parameters * *External Display Apps:* Added RViewer<http://rviewer.lbl.gov/rviewer>, Updated *IGV * <http://www.broadinstitute.org/igv/> * Visualize ENCODE<http://genome.ucsc.edu/ENCODE> "peak" datatype tracks in the Galaxy Track Browser (aka Trackster) * Multiple *Workflow* updates including enhancements to/input dataset options, display modes, and sharing * CloudMan<http://wiki.g2.bx.psu.edu/Admin/Cloud> now offers /preliminary support for OpenNebula cloud type <http://bitbucket.org/galaxy/cloudman/src/tip/cm/clouds/opennebula.py>/ and a larger default tools volume(10GB vs old 2GB) *Need help with a local instance? * * *Installation* and *Admin* Instructions: http://getgalaxy.org * *Search* with our custom google tools: * All Galaxy mailings lists <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>for prior Q & A * Information about deploying, developing, customizing, and administering <http://galaxyproject.org/search/getgalaxy> Galaxy * Information about using <http://galaxyproject.org/search/usegalaxy> Galaxy * *Consider* subscribing to the galaxy-dev <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing>mailing list Thanks for using Galaxy, The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org http://galaxyproject.org/wiki

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