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Galaxy on Jetstream Cloud

written 20 months ago by Galaxy News

Want your own Galaxy server, for free? You can now easily create Galaxy servers on the new NSF Jetstream cloud. Each server comes preconfigured with hundreds of tools and commonly used reference datasets. It only takes a couple of minutes to start one. Once running, you can use it or change it up any way you like. How do I get access? You must be a US-based academic to access Jetstream cloud. Access is free but it is necessary to have an XSEDE account (go to https://www.xsede.org/ to sign up) and have an active resource allocation. Getting the resource allocation is matter of writing a summary of your research in less than 100 words and waiting ~24 hrs for the application to get approved. Go to http://jetstream-cloud.org/allocations.php → "Submit and manage allocation requests" to get started; choose Startup type of allocation. How do I launch my own Galaxy server? After you have your XSEDE account and an active allocation: Visit https://use.jetstream-cloud.org/ Browse the available images and choose "Galaxy 16.01 Standalone" Follow the prompts on the screen to launch an instance In less than 5 minutes, you should have your own, fully configured Galaxy server More documentation about the process can be found on Galaxy’s wiki: https://wiki.galaxyproject.org/Cloud/Jetstream Posted to the Galaxy News on 2016-04-07-- Delivered by Feed43 service

Galaxy on Jetstream Cloud

written 20 months ago by Galaxy News

Want your own Galaxy server, for free? You can now easily create Galaxy servers on the new NSF Jetstream cloud. Each server comes preconfigured with hundreds of tools and commonly used reference datasets. It only takes a couple of minutes to start one. Once running, you can use it or change it up any way you like. How do I get access? You must be a US-based academic to access Jetstream cloud. Access is free but it is necessary to have an XSEDE account (go to https://www.xsede.org/ to sign up) and have an active resource allocation. Getting the resource allocation is matter of writing a summary of your research in less than 100 words and waiting ~24 hrs for the application to get approved. Go to http://jetstream-cloud.org/allocations.php → "Submit and manage allocation requests" to get started. How do I launch my own Galaxy server? Visit https://use.jetstream-cloud.org/ Browse the available images and choose "Galaxy 16.01 Standalone" Follow the prompts on the screen to launch an instance In less than 5 minutes, you should have your own, fully configured Galaxy server More documentation about the process can be found on Galaxy’s wiki: https://wiki.galaxyproject.org/Cloud/Jetstream Posted to the Galaxy News on 2016-04-07-- Delivered by Feed43 service

Galactic News! April Edition

written 20 months ago by Galaxy News

The April Galaxy News brings more than the usual amount of News of the Galaxy. First, there are a plethora of events coming up around the world: GCC2016: Oral abstracts due April 8 Scholarship applications due May 1 Register now and save big Please welcome the the Indiana Health Industry Forum (IHIF) as a GCC2016 Sponsor Two events sponsored by ELIXIR (and others) are coming up, both prominently featuring Galaxy: Galaxy DevOps Workshop, 6-7 April, Heidelberg, Germany. And there is still space. Hackathon: Tools, Workflows and Workbenches, 18-20 May, Paris, France There is also a report from the RADSeq Tools and Workflows Hackathon held in March. Plus 12 additional events on three continents over the next three months. And a lot of new Papers (86 of them, 6 highlighted) Open positions (10 of them) Halogen Bonding Galaxy server Galaxy Community Hub entries (4 of them) Releases (Planemo and CloudMan) ToolShed Contributions And some other news too. Happy April, Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-03-31-- Delivered by Feed43 service

16.03 Galaxy CloudMan release

written 20 months ago by Galaxy News

We just released an update to Galaxy CloudMan on AWS. 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 or imposed quotas. Once running, you have complete control over Galaxy, including the ability to install new tools. Most notable changes include: Galaxy 16.01 release A fine-grained control over auto-scaling options Several fixes to cluster sharing and cloning See the CHANGELOG for a more complete set of changes. Posted to the Galaxy News on 2016-03-24-- Delivered by Feed43 service

Galaxy DevOps Workshop - Heidelberg

written 21 months ago by Galaxy News

We would like to invite you to our Galaxy DevOps Workshop in Heidelberg from 6-7 of April, organised by de.NBI and ELIXIR. The workshop is intended for Bioinformaticians who want to learn the internals of the multi-omics Galaxy workbench learn how to set up and run a Galaxy server learn about Galaxy tool development get questions answered from experienced Galaxy admins and community members are interested in reproducible and accessible research For more information please see the workshop page. Björn Grüning Posted to the Galaxy News on 2016-03-17-- Delivered by Feed43 service

March 2016 Galactic News

written 21 months ago by Galaxy News

The March 2016 Galactic News is hot off the presses: GCC2016 news: Oral presentation abstracts due March 20. If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase &amp; Software Demos are all opportunities to share your work. Register early and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students. Apply for a GCC2016 Scholarship. Applications from international applicants are due March 20. The 2016 GMOD Meeting will be held immediately following GCC2016, also at Indiana University. And, we have a returning sponsor: Please welcome BioTeam to GCC2016. March 7-8: Online IUC Contribution Fest - RADSeq Tools and Workflows Galaxy in Google Summer of Code Twelve other upcoming events 54 new publications, including 4 highlighted pubs New jobs New releases, including the new CloudBridge and two important security announcements Three new Galaxy servers New ToolShed Contributions Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-03-01-- Delivered by Feed43 service

Jan 2016 Galaxy Release (v 16.01)

written 21 months ago by Galaxy News

See the full release notes. The Galaxy Committers team is pleased to announce the January 2016 (v16.01) release of Galaxy. Galaxy administrators should also be aware of the security announcements linked to below. Highlights Interactive Tours The interactive tours framework allows developers and deployers to build interactive tutorials for users superimposed on the actual Galaxy web front end. Unlike video tutorials, these will not become stale and are truly interactive (allowing users to actually navigate and interact with Galaxy). Galaxy 16.01 ships with two example tours and new ones can easily be added by creating a small YAML file describing the tour. Try the Galaxy UI tour on Main. Wheels Galaxy’s Python dependencies have traditionally been distributed as eggs using custom dependency management code to enable Galaxy to distribute binary dependencies (enabling quick downloads and minimal system requirements). With this release all of that infrastructure has been replaced with a modern Python infrastructure based on pip and wheels. Work done as part of this to enable binary dependencies on Linux has been included with the recently released pip 8. Detailed documentation on these changes and their impact under a variety of Galaxy deployment scenarios can be found in the Galaxy Framework Dependencies section of the Admin documentation. Nested Workflows Workflows may now run other workflows as a single abstract step in the parent workflow. This allows for reusing or subworkflows in your analyses. Github New % git clone -b master https://github.com/galaxyproject/galaxy.git Update to latest stable release % git checkout master ...

GCC2016 Scholarships: Apply Now!

written 22 months ago by Galaxy News

We are pleased to offer scholarships for the 2016 Galaxy Community Conference, being held in Bloomington, Indiana, United States, June 25-29. Scholarships are available to students and post-docs in historically under-represented groups, and to those from or based in Low and Lower-Middle Income Economies, as defined by the World Bank. If this describes you or one of your students then we hope to receive an application. Scholarships cover registration and lodging during the GCC Meeting, and for any Training or Hackathon events the applicant chooses to attend. Scholarships do not cover travel or other expenses. Applicants are required to Either • Submit a poster and/or demo abstract. Or, • Submit a 200-250 word essay on how attending GCC2016 will benefit your research and career. Poster/demo abstracts are strongly preferred. The essay option should only be used by those who are starting their research careers. Have a faculty member / PI send a letter of recommendation to community-fund@lists.galaxyproject.org no later than May 10 or March 27 (depending on your deadline). Submit an application form. Have sufficient funds to cover your own travel and other expenses If you are submitting a poster or demo, please do so before submitting an application. You also need to identify and ask a faculty member to write a letter of recommendation prior to applying. The application deadline is May 1 for members of historically underrepresented groups and March 20 for those from Low and Lower-Middle Income Economies. Applicants will be notified of their scholarship status no ...

Galaxy Goes Mobile

written 22 months ago by Galaxy News

Galaxy is now accessible from your IOS and Android devices. The Galaxy Portal app is a quick and easy way to monitor the status of biomedical research on any Galaxy server. With this app you can set up a list of Galaxy connections and browse your analyses histories in a user-friendly format and take a peek at your data on the go. The app has been in development for over a year at the University of Oslo as part of Claus Børnich's masters thesis and is described in Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Čech, and Geir Kjetil Sandve. Galaxy Portal: Interacting with the Galaxy platform through mobile devices. Bioinformatics first published online January 27, 2016 doi:10.1093/bioinformatics/btw042 A user manual, additional information, and the full source are available on GitHub. Galaxy Portal is provided free of charge. Posted to the Galaxy News on 2016-02-02-- Delivered by Feed43 service

February 2016 Galactic News

written 22 months ago by Galaxy News

The February 2016 Galactic News is hot off the presses. Here are some highlights: GCC2016 early registration and abstract submission are now open. Register early and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students. Abstract submission is open as well. If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase &amp; Software Demos are all opportunities to share your work. And, we have two new sponsors: Please welcome Lenovo and Globus Genomics to GCC2016. And lots of new, new, new, new: New Tutorials ... and Interactive Tours! 156 new publications, including 8 highlighted pubs New jobs New releases New Galaxy servers New ToolShed Contributions And other cool bits too: Galaxy Goes Mobile Galaxy on Windows and OS X using Kitematic Ten upcoming events Happy February! Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-02-02-- Delivered by Feed43 service

Disease Transcriptome Postdoc, Oslo

written 22 months ago by Galaxy News

A postdoc position in bioinformatics is available in Oslo (Norway) on development of methods for transcriptome analysis of disease-specific cells. The postdoc will be part of a newly established research center and will work in the intersection between two environments: A research group at immunology will provide hypotheses and challenges at the forefront of research on autoimmunity, as well as a rich collection of unique data, including transcriptomic data on sharply selected populations of B cells in a disease-relevant setting. A research group at computer science has long experience with development of software systems, algorithms and statistical methodology for the analysis of genomic and epigenomic data, including an established codebase for genome analysis (the Galaxy-based Genomic HyperBrowser") that can be drawn on for future computational development. The salary is good and there are good future career opportunities. Further details on the positions and how to apply are available in the full announcement. Posted to the Galaxy News on 2016-02-01-- Delivered by Feed43 service

Oct 2015 Galaxy Release (v 15.10)

written 23 months ago by Galaxy News

October 2015 Galaxy Release Notes Release Notes v 15.10 Release Highlights Reports Application- The reports web application has been greatly enhanced - including improved styling, new landing page, more reports, pagination, and sparklines. Huge thanks to Daniel Bouchard (@Airistotal) for these enhancements. Upload - The Galaxy upload widget now features support for composite datatypes and improved styling. Data Libraries - Improved API and UI for data libraries - including support for library folder management and search. About Get Galaxy! Prior Releases Github Thanks for using Galaxy! The Galaxy Team Posted to the Galaxy News on 2016-01-13-- Delivered by Feed43 service

GCC2016 Training Topic Vote!

written 23 months ago by Galaxy News

Vote now! Voting is now open on what training topics are offered at GCC2016 Training. There are nominated topics spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. Topic voting closes November 6. The Training schedule, including instructors, will be published before early registration opens. About GCC2016 Training: The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. GCC2016 features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCC2016 to present your work and to learn from others. As always, please let us know if you have any questions. Thanks, The GCC2016 Exec Posted to the Galaxy News on 2015-10-26-- Delivered by Feed43 service

GCC2016 Training Day Topic Nominations

written 23 months ago by Galaxy News

Nominate a topic now! The 2016 Galaxy Community Conference (GCC2016) features two full days of training on June 26-27. Each day will have multiple tracks, with each track featuring several sessions throughout the day. GCC2016 will be held at Indiana University in Bloomington, Indiana, United States. GCC2016 Training topics are nominated by you, the Galaxy Community. Please give some thought to what topics you would like to see offered, or that you would like to offer, and then submit them as topic nominations. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see Topics nominated for GCC2015 Topics nominated for GCC2014 Topics nominated for GCC2013 The Galaxy Events page, which lists what training the community is offering outside of GCCs. Topics that have already been nominated for GCC2016 Nominated topics will be published as they come in. Topic nomination closes Friday, October, 16.. Topics will be compiled into a uniform list by the GCC2016 Organizing Committee, and topics will be voted on by the Galaxy Community from October 26 through November 6. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. GCC2016 Exec Committee Posted to the Galaxy News on 2015-09-28-- Delivered by Feed43 service

January 2016 Galactic News

written 23 months ago by Galaxy News

The January 2016 Galactic News is hot off the presses. 51 new publications, including 6 highlighted pubs Event News GCC2016 registration rates and training schedule GCC2016 is seeking sponsors Metagenomics Tools and Workflows Codefest Reports All upcoming events Who's Hiring Two new public Galaxy servers New Releases Galaxy 15.10 galaxy-lib 16.1.0 - 16.1.7 CloudMan 15.12 Pulsar 0.6.0 - 0.6.1 ToolShed Contributions from December and some other news too. Dave Clements and the Galaxy Team Posted to the Galaxy News on 2016-01-04-- Delivered by Feed43 service

GCC2016 is Online!

written 24 months ago by Galaxy News

We are pleased to announce that the 2016 Galaxy Community Conference website is now online and includes registration information and the full training schedule. GCC2016 will be held June 25-29 at Indiana University in Bloomington, Indiana, United States. This will be the 7th annual gathering of the Galaxy community, and we are expecting over 200 participants again this year. Registration information includes the different registration packages, rates, and deadlines. Our inexpensive early registration rates start at less than $40 per day for students and post-docs. Registration will open within a month. The training schedule includes session descriptions, prerequisites, and instructors. Many thanks to everyone who nominated and voted on topics, and especially to the many instructors who are contributing their time and effort to make GCC2016 a success. Thanks also go to the Indiana University Pervasive Technology Institute (PTI), who are supporting GCC2016 as a Platinum Sponsor. PTI is home to the National Center for Genome Analysis Support (for which NSF funding was recently renewed), and the Galaxy Trinity instance, and is a long time supporter of the Galaxy Community. PTI pairs fundamental academic computational research with the widely known strengths of Indiana University through innovations and service delivery in networking and high performance computing. See the PTI website for more information. We continue to seek other sponsors as well and offer a wide range of sponsorship plans. If your organization is interested in having a presence at GCC2016, please contact the GCC2016 Exec &lt;gcc2016-exec@lists.galaxyproject.org&gt; for more information. The GCC2016 ...

December 2015 Galactic News

written 2.0 years ago by Galaxy News

The December Galactic News is hot off the presses. 81 new publications, including 4 highlighted pubs Event News Spanish Galaxy Community Meetup: 18 December, Barcelona Galaxy Day 2015 Presentations are online All upcoming events Who's Hiring Two new public Galaxy servers New Releases Planemo 0.19.0 - 0.21.1 ToolShed Contributions in October and November and lots of other news too. Dave Clements and the Galaxy Team Posted to the Galaxy News on 2015-12-01-- Delivered by Feed43 service

Galaxy Session @ III Bioinformatics and Computational Biology Symposium

written 2.1 years ago by Galaxy Events Calendar

When: Fri Dec 18, 2015 Where: Barcelona, Barcelona, Spain Event Status: confirmed Event Description: December 18 Galaxy Session III Bioinformatics and Computational Biology Symposium, Barcelona, Spain From the announcement: This year, we also plan to reserve some time for an informal session with users and developers of Galaxy to meet and to discuss all the possibilities that this platform offers to our field, as well as to plan the constitution of the Spanish Galaxy Community. Please, let us know your interest in attending through the registration form. See http://scb.iec.cat/wp-content/uploads/2015/11/jdB2015_anunci_.pdf http://www.iec.cat/jornades/bioinformatica2015.asp

Software Engineer, OHSU, Portland, OR

written 2.1 years ago by Galaxy News

Software Engineering Position at Oregon Health and Science University. People interested in Galaxy and large scale workflow deployment are encouraged to apply. The Computational Biology Program at Oregon Health and Science University (OHSU), Portland, Oregon is committed to leading the development of next-generation patient care through discoveries made by big data analytics, enabled by values of open access data, open source code, highly collaborative team science, and professional software engineering methodologies. Go to the OHSU jobs site and search for IRC50157 About OHSU OHSU is ranked as one of the nation’s top biomedical institutions in patient care, research, and education, with an annual operating budget of over $2.3 billion, over $340 million in annual grant funding, over 4,000 students and trainees, and nearly 1 million patient visits per year. Multiple departments rank among the top 5 in annual grant funding, including neuroscience, microbiology, ophthalmology, otolaryngology, and emergency medicine. OHSU is one of the nation’s fastest growing biomedical institutions, bolstered by long-term resource commitments, such as the $1 billion Phil and Penny Knight “challenge” to support research in OHSU’s Knight Cancer Institute, led by Dr. Brian Druker, who pioneered the concept of gene targeted therapy by demonstrating the efficacy of the revolutionary cancer drug Gleevec in chronic myelogenous leukemia. OHSU provides substantial resources to enable data intensive science, including a world-class exascale supercomputing cluster, close interactions and resource commitments by leading technology companies such as Intel, tight integration with clinical and basic research programs across campus, graduate training programs in quantitative ...

July 2015 Galaxy Release (v 15.07)

written 2.1 years ago by Galaxy News

The July 2015 Galaxy Release is out! Release Notes v 15.07 Release Highlights Interactive Environments - The interactive environments (IE) framework features several updates this release and Galaxy is now distributed with a new IE for RStudio implemented by Eric Rasche. Workflow Editor Enhancements - The workflow editor has been significantly revamped - it now uses newer tool form components and allow construction of workflows with tools explicitly producing output collections. Policies for Committers and Pull Requests - The process for adding committers to the project and fielding pull requests has been formalized and documented in the source code. Three new committers have been added to the project - Björn Grüning, Nicola Soranzo, and Eric Rasche. And much more Thanks for using Galaxy! The Galaxy Team September 2015 Galactic News The September Galactic News is hot off the presses. The IUC Tools &amp; Collections Hackathon will be September 17th and 18th online. Please join us. 97 new publications, including 7 highlighted ones in all 15 !CiteULike categories. And those 97 papers pushed the Galaxy CiteULike library past 2500 papers. August GalaxyAdmins Slides and Video Galaxy's Google Calendar is now two calendars Slides and video for the August GalaxyAdmins meetup are now available. 14 upcoming events in 5 countries on 3 continents in the next 2 months. Who's Hiring Two new public Galaxy servers: Workflow4Metabolomics and EpiToolKit Three security advisories, Recent Releases, and ToolShed Contributions Dave Clements and the Galaxy Team Posted to the Galaxy News on 2015-09-01-- Delivered by Feed43 ...

GCC2016 Hackathons

written 2.1 years ago by Galaxy Events Calendar

When: Sat Jun 25, 2016 to Sun Jun 26, 2016 Where: Indiana University, Bloomington, Indiana, United States Event Status: confirmed Event Description: Yes, they'll be back! Watch this space.

Analyse bioinformatique de séquences sous Galaxy

written 2.1 years ago by Galaxy Events Calendar

When: Mon Feb 15, 2016 to Fri Feb 19, 2016 Where: Montpellier SupAgro, 2 place Pierre Viala, 34060 Montpellier, France Event Status: confirmed Event Description: February 15-19 Analyse bioinformatique de séquences sous Galaxy Montpellier SupAgro, Montpellier, France Training offered by GTN Member See https://www.supagro.fr/web/pages/?idl=19&amp;page=1964&amp;id_page=2666

Advanced RNA-Seq DGE with Galaxy

written 2.1 years ago by Galaxy Events Calendar

When: Wed Nov 25, 2015 Where: VLSCI, Carlton, VIC, Australia Event Status: confirmed Event Description: Advanced RNA-Seq DGE with Galaxy VLSCI, Carlton, VIC, Australia Training offered by GTN Member VLSCI See https://www.eventbrite.com.au/e/advanced-rna-seq-dge-with-galaxy-registration-18774124913

Advanced Variant Calling with Galaxy

written 2.1 years ago by Galaxy Events Calendar

When: Thu Nov 5, 2015 Where: VLSCI, Carlton, VIC, Australa Event Status: confirmed Event Description: Advanced Variant Calling with Galaxy VLSCI, Carlton, VIC, Australia Training offered by GTN Member VLSCI See https://variant-calling-advanced-05-11-15.eventbrite.com.au/

RNA-Seq Differential Gene Expression Analysis using Galaxy

written 2.1 years ago by Galaxy Events Calendar

When: Thu Nov 5, 2015 Where: VLSCI, Carlton, VIC, Australa Event Status: confirmed Event Description: RNA-Seq Differential Gene Expression Analysis using Galaxy VLSCI, Carlton, VIC, Australia Training offered by GTN Member VLSCI See https://www.eventbrite.com.au/e/rna-seq-differential-gene-expression-analysis-using-galaxy-registration-18773633443
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Galaxy News
News items of interest to the Galaxy Community
141 posts, last updated 11 months ago
Galaxy Events Calendar
The Galaxy Events calendar lists any events that the Galaxy Project knows about that may be of interest to the Galaxy community. The event does not have to feature Galaxy in any way. For only events that feature Galaxy, see the Galaxy Events page at https://wiki.galaxyproject.org/Events.
445 posts, last updated 2.1 years ago

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