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News/Archive/2011

2011 News Item Archive

News items that have were posted to the Galaxy News page/feed in 2011.

See also





Galaxy Web Search Galaxy Mailing List Search Using Galaxy Web Search Galaxy administration, tool, and deployment search

Galaxy now has several Google Custom Search engines that make it much easier to find answers to your questions about Galaxy. They are:

Name & URL

Description

Galaxy Web Search
http://galaxyproject.org/search/web

Searches Galaxy Main, the mailing list archives, the Galaxy wiki, Galaxy's source code at Bitbucket (now at GitHub), and the Tool Shed. The results are returned in a unified list, and are also grouped into several categories.

Galaxy Mailing List Search
http://galaxyproject.org/search/mailinglists

Searches all the Galaxy mailing list archives.

UseGalaxy Search
http://galaxyproject.org/search/usegalaxy

Search for information about using Galaxy. Searches Galaxy Main (UseGalaxy.org), this wiki (excluding the Admin pages), and the Galaxy-User and Galaxy-Announce mailing list archives.

GetGalaxy Search
http://galaxyproject.org/search/getgalaxy

Search for information about installing, customizing, and developing Galaxy. Searches the Galaxy Bitbucket (source) site (now at GitHub), the Tool Shed, this wiki (excluding the Learn pages), and the Galaxy-Dev and Galaxy-Announce mailing list archives.

We strongly encourage you to give these try. Please feedback and suggestions to Galaxy Outreach <outreach AT galaxyproject DOT org>.

Thanks,

Dave Clements

Posted to the Galaxy News on 2011-12-20, updated 2016-08-11

Galaxy at CiteULike Social Bookmarking Service

A new Galaxy Group has been created at the CiteULike social bookmarking service to organize papers that are about, use, or reference Galaxy. The Galaxy Group is open to any CiteULike user (and anyone can become a CiteULike user). Group members can add papers to the group, assign tags, and rate papers.

CiteULike makes extensive use of tags to organize and categorize papers. The Galaxy group uses this set of tags to categorize papers. There are tags for the Galaxy project itself, galaxy installations, shared Galaxy objects, tutorials, papers on scientific workflow software, persistence and reproducibility, papers that use Galaxy in their methods (the largest group), and "other." Every paper has at least one tag (even if it is just "other").

If you want to help other Galaxy users and sites find papers that are relevant to them, or help the Galaxy Project keep track of what papers (and communities) are using Galaxy, then please help by adding relevant papers to the Galaxy Group Library and/or rating the papers that are there. We particularly need help with papers that were published before this year.

Update: Thanks to the efforts of Stephen Turner at the University of Virginia, the Galaxy CiteULike group is now mirrored on Mendeley.

Dave Clements

Posted to the Galaxy News on 2011-12-14, updated 2011-12-15

Galaxy Developer Workshop  Plant and Animal Genome (PAG 2012)   Reproducible workflows for next generation sequencing analysis   DDBJ

The January Events list is going out a little early this month, mainly because of a December 15 application deadline for the Galaxy Developer Workshop in the Czech Republic. If you have a Galaxy related event please send it to <outreach AT  galaxyproject DOT org> and we will help you get the word out.

There are Galaxy-related events on (at least) 3 continents next month:

Date

Topic/Event

Venue/Location

Contact

January 8-21

2012 Workshop on Genomics
Features Galaxy and much more.

Český Krumlov, Czech Republic

James Taylor

January 14-18

Galaxy Session @ GMOD Workshop, and
The Galaxy Platform: Running Analyses in the Cloud @ Cloud Computing Session

PAG 2012, San Diego, California, United States

Dave Clements
Dannon Baker

January 17

Reproducible workflows for next generation sequencing analysis

Nowgen, University of Manchester, United Kingdom

Tom Hancocks

January 23

Galaxy Developer Workshop
Application deadline is December 15.

Český Krumlov, Czech Republic, immediately following the Workshop on Genomics, (which also features Galaxy content)

James Taylor

January 26

今回の講習会では,「Next-Generation Sequencer(NGS) 微生物解析と Galaxy ツール」を中心に講義と実習を行ないます。講義内容をよりよく理解して 頂くために,PC を使用した実習を行ないます。
(Next-Generation Sequencing (NGS) and microbiological analysis with Galaxy)

DNA Data Bank of Japan (DDBJ), National Institute of Genetics

DDBJ


And I apologize in advance if I messed up the translation of the event at DDBJ!

Dave Clements

Posted to the Galaxy News on 2011-12-08

http://lists.bx.psu.edu/listinfo/galaxy-announce

There is a new mailing list in the Galaxy: Galaxy-Announce.

Galaxy-Announce is a moderated, low-volume mailing list, and complements the existing Mailing Lists:

  • Galaxy-User: about the public server (a.k.a. Main) at UseGalaxy.org, and

  • Galaxy-Dev: about Galaxy deployment and development.

However, unlike those relatively high-volume mailing lists, Galaxy-Announce will only have a few messages each month. If you are looking for a Galaxy list that just covers the big stuff, this is your list.

To subscribe to the list please go to the Galaxy-Announce Mailman page and submit your email address to the list.

See Mailing Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists.

Dave Clements

Posted to the Galaxy News on 2011-12-02

A new version of CloudMan for running Galaxy on Amazon cloud has been released yesterday. Any new cluster will automatically use this version. Existing clusters will have a link displayed at the top of the CloudMan console offering to perform an automated update.

The new version brings the following updates/features:

  • Added ability to specify a path where Galaxy is installed as part of user data (using galaxy_home key). This allows custom Galaxy application to be installed and picked up by CloudMan instead of the default one. This works across cluster invocations as well as for shared clusters. For a complete list of user data options see Admin/Cloud/UserData

  • Use /etc/profile instead of /etc/bash.bashrc for system wide shell logins

  • Support for 3.0 Kernel on Ubuntu 11.10 for SGE. Contributed by Brad Chapman.
  • Fix for SGE install after cloud-init has run and changed /etc/hosts

  • post_start_service now runs if the script exists in the cluster bucket even if no URL was provided as part of current user data

  • Fix recognition of existing and attached file system volumes on instance reboot

EnisAfgan

Posted to the Galaxy News on 2011-11-29

Complete News Brief

Highlights:

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r b258de1e6cea 

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2011-11-19

GCC 2012

We are pleased to announce that the 2012 Galaxy Community Conference (GCC2012) has been scheduled for July 25-27 in Chicago, Illinois, United States.

GCC2012 will be held at the University of Illinois Chicago (UIC) campus in downtown Chicago. See the GCC2012 conference web page for more, including opportunities to sponsor this year's conference.

Some things will be the same as in previous years, but we are also using feedback from last year to guide the 2012 meeting. We will again be seeking talks (full and lightning) from the community. More information will be posted as it becomes available.

Please reserve July 25-27 on your calendars!

Dave Clements and Neil Bahroos

Posted to the Galaxy News on 2011-11-14

Galaxy Developer Workshop
A one day Galaxy Developer Workshop has been scheduled for 23 January in Český Krumlov, Czech Republic, immediately following the Workshop on Genomics, (which also features Galaxy content).

This workshop is aimed at:
  • IT and Bioinformatics staff:

    • Galaxy is an easy to use, web-based tool that enables your researchers to perform data integration and analysis, in house, without handholding from you. This workshop will teach you how to install your own instance of Galaxy, either on your local compute infrastructure, or on the cloud.

    Bioinformatics tool developers:

    • Galaxy provides mechanisms for integrating your own tools and the tools of others into Galaxy instances. This workshop will cover how to define your tools in Galaxy, and how to then make those definitions available for installation in any Galaxy instance, thus making your tools much more accessible to the research community.

This workshop also includes contributed talks from participants. If you have a topic of interest to the workshop’s audience, then please submit a short (500 words or less) abstract along with your registration. Topics do not have to be directly related to Galaxy, but they should be of interest to those working with the integration, analysis, and sharing of large biological datasets.

15 December is the preferred registration deadline. However, later registration will certainly be accepted dependent on availability. The registration fee is $200 USD (payment terms provided upon acceptance).

Dave Clements

Posted to the Galaxy News on 2011-11-11

CSHL Courses Plant and Animal Genome (PAG 2012)  Reproducible workflows for next generation sequencing analysis

There are several Galaxy related events going on at Cold Spring Harbor Laboratory in November, but if you aren't already registered for those it is now too late to get in. However, there are several deadlines in November and events in the coming months. See the Events page for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach@galaxyproject.org and we will help you get the word out.

Date

Topic/Event

Venue/Location

Contact

November 2-5

Best practices for variant discovery through Galaxy: Oscillating evolution within dual coding genes

Genome Informatics 2011, Cold Spring Harbor, New York, United States

Dan Blankenberg

November 8-21

Advanced Sequencing Technologies & Applications Course
Features Galaxy and much more.

Cold Spring Harbor Laboratory, New York, United States

James Taylor

November 9-15

Compuational & Comparative Genomics Course
Features Galaxy and much more.

Cold Spring Harbor Laboratory, New York, United States

James Taylor

January 8-21 2012

2012 Workshop on Genomics
Features Galaxy and much more.
Application deadline is November 1.

Český Krumlov, Czech Republic

James Taylor

January 14-18 2012

Galaxy Session @ GMOD Workshop

PAG 2012, San Diego, California, United States

Dave Clements

January 17 2012

Reproducible workflows for next generation sequencing analysis

Nowgen, University of Manchester, United Kingdom

Tom Hancocks


Thanks,
Dave Clements

Posted to the Galaxy News on 2011-10-31

Complete News Brief

Highlights:

  • Main Public server at http://usegalaxy.org implements data & job quotas

  • User Interface updates and new features for managing data and more
  • Trackster (aka Galaxy Track Browser or GTB) at BioVis, too many new features to list out, try it!

  • It's official, Python 2.7 is the standard and 2.4 is deprecated
  • Smooth new Tool Shed functions make setting up a local Galaxy even easier (and it was pretty easy already)
  • Source updates, bug fixes, new scripts, wrapped tools, and custom tools

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 338ead4737ba

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2011-10-26

usegalaxy.org

Dear Galaxy User

Thank you very much for using our free and open public resource. Galaxy has become extremely popular and as a result many people rely on it daily for their analysis needs. Previously our service had no restrictions on usage, which is not sustainable in the long term. To continue providing our open service in a fair manner, we are now implementing quotas at the public Galaxy Main instance http://usegalaxy.org (http://main.g2.bx.psu.edu).

Thanks for using Galaxy!

The details, including administrative:

Quotas on Main

Maximum total user data on server:

250GB for registered users
5GB for unregistered users

Maximum concurrent jobs:

8 or less for registered/unregistered users


For those users with current account disk usage over the quota limit, we will be implementing a step-down program over the next several weeks. Details for that program will be emailed to those users directly.

Posted to the Galaxy News on 2011-10-25

Galaxy Events in October 2011 AMATA 2011  October 2011 GMOD Meeting  BioVis 2011

There are (at least) three Galaxy related events going on next month that you may want to consider attending. See the Events page for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach@galaxyproject.org and we will help you get the word out.

Date

Topic/Event

Venue/Location

Comments

Contact

October 9-12

Exploit your Data: Galaxy and the GMOD Tool Suite

AMATA 2011, Canberra, Australia

This workshop will cover both Galaxy and provide an overview of the GMOD tool suite. Many thanks to CSIRO and AMATA for sponsoring this workshop

Dave Clements

October 12-14

October 2011 GMOD Meeting and Galaxy Workshop

Ontario Institute for Cancer Research (OICR), Toronto, Canada

Dan will give a Galaxy update at the meeting, and then lead a satellite workshop on Galaxy the day following the meeting. (Or, if you already know all about Galaxy you could attend workshops on BioMart and InterMine, two data sources for Galaxy.) Register now as the meeting and associated workshop have limited space.

Dan Blankenberg

October 23-24

The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool

BioVis 2011, Providence, Rhode Island, United States

Learn about Trackster and other biological visualization. This is part of VisWeek 2011.

Jeremy Goecks


Thanks,
Dave Clements

Posted to the Galaxy News on 2011-09-28

Concurrency and Computation: Practice & Experience
A new paper, "A reference model for deploying applications in virtualized environments," by Enis Afgan, Dannon Baker et al. has been published in Concurrency and Computation: Practice and Experience. The paper describes a "reference model for deploying applications into virtualized environments" that "is rooted in the low-level components common to a range of virtualized environments" describing "how to compose those otherwise dispersed components into a coherent unit." The paper addresses the problem of "deploying applications so that they can take advantage of the elasticity of the environment and deliver it transparently to users" with the aim of enabling widespread adoption of virtualization.

Posted to the Galaxy News on 2011-09-01

Complete News Brief

Highlights:

  • An improved Galaxy Tool Shed for sharing tool definitions
  • New or updated tool definitions for Trinity, BWA, FASTQ Groomer, Cufflinks, Cuffdiff, amd Cuffcompare
  • Data visualization enhancements including bookmarking genomic regions, overview tracks, and increased user control
  • Better cloning of workflows, and uploading to myExperiment.
  • API improvements for managing histories and datasets, including creating histories from library items.

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 949e4f5fa03a

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2011-08-31

The Galaxy project currently has open positions in both the Penn State and Emory groups.

Opening at Penn State
Penn State: System administrators/analysts

The Nekrutenko Lab at the Huck Institutes of Life Sciences at Penn State is currently recruiting system analysts/administrators with experience in building and maintaining complex performance compute environments. The areas of immediate need include:
  • Storage balancing and tiered storage
  • Virtualization
  • Schedulers
  • Deployment of Galaxy instances and dependence management
  • Relational databases and query optimization
  • User management

A minimum of 5 year experience with UNIX/Linux system administration is required. Applicants should submit a CV and list of references to <gxyhiring AT galaxyproject DOT org>.

Openings at Emory
Emory: Software Engineers and Post-Docs

The Taylor Lab in the Biology and Mathematics & Computer Science at Emory University is looking for software engineers and postdoctoral scholars to work on the Galaxy project.

We are seeking software engineers with expertise in distributed computing and systems programming, web-based visualization and visual analytics, informatics and data analysis and integration, and bioinformatics application areas such as re-sequencing, de novo assembly, metagenomics, transcriptome analysis and epigenetics. These are full time positions located in Atlanta, GA. See the official posting for full details.

Postdoctoral applicants should have expertise in Bioinformatics and Computational Biology and research interests that complement but extend the lab's current interests: The Galaxy project; distributed and high-performance computing for data intensive science; vertebrate functional genomics; and genomics and epigenomic mechanisms of gene regulation, the role of transcription factors and chromatin structure in global gene expression, development, and differentiation. See the announcement for full details.

Posted to the Galaxy News on 2011-08-29, updated 2015-10-09

GalaxyProject.org

After a long quiescence, the GalaxyProject.org site has been updated to more accurately reflect the state of the Galaxy project, which is vibrant, collaborative, and growing by leaps and bounds, in case you were wondering. GalaxyProject.org is a one stop shop for all things Galaxy, no matter if you want to use the free public server, install your own copy either locally or on the cloud, want to learn how to use Galaxy, or perhaps become an active participant in the Galaxy community.

The other well-known Galaxy URLs will continue to be used as well:

Please continue to use these wherever appropriate.

Thanks,

Dave Clements

Posted to the Galaxy News on 2011-08-24

Galaxy Events in September 2011 UAB Research Computing Day AWS Genomics Event

There are (at least) three Galaxy related events going on in September 2011 that you may want to consider attending. They are happening from one coast of the United States to the other:


See the Events page for a full listing of upcoming events. If you have a Galaxy related event please send it to outreach@galaxyproject.org and we will help you get the word out.

Thanks,
Dave Clements

Posted to the Galaxy News on 2011-08-24

User data and job quota limits are now implemented at the public Galaxy Test instance:

Quotas on Test

Maximum total user data on server:

10GB for registered users
1GB for unregistered users

Maximum concurrent jobs:

4 or less for registered/unregistered users


See the wiki Test page for full details.

While no quotas are currently implemented at the public Galaxy Main instance, http://usegalaxy.org, we do ask that users stay within certain usage limits.

Guidelines on Main

User data on server:

50G or less per dataset
200G or less per history

Maximum concurrent jobs:

4 or less per user (user managed)


If you find that you require additional resources, please consider alternative Galaxy options explained at Big Picture/Choices.

Posted to the Galaxy News on 2011-08-22

Outreach/Powered by Galaxy
Do you use Galaxy in your research? If so, please consider putting a Powered by Galaxy icon on your websites, presentations and posters. Increasing Galaxy's visibility has many benefits:
  1. People can't use Galaxy unless they know about it. It's a sinking feeling to get the results of your first run from the sequencing center and then not know how to exploit that data.
  2. Increased visibility leads to increased adoption of Galaxy and that leads to more people contributing back to the project.
  3. Increased adoption and development of Galaxy helps the project with funding.

This, along with Citing Galaxy, are two easy things that can be done to increase the visibility of Galaxy.

Thanks,

Dave Clements

Posted to the Galaxy News on 2011-08-19

Bioinformatics Jorunal

A new paper, "Making whole genome multiple alignments usable for biologists," by Daniel Blankenberg, et al. has been published (early access) in Bioinformatics. The paper describes "a set of tools implemented within the Galaxy platform designed to make analysis of multiple genome alignments truly accessible for biologists. These tools are available through both a web-based graphical user interface and a command-line interface."

The methods are described on a Galaxy Page as well.

Posted to the Galaxy News on 2011-07-28

The new Galaxy wiki includes a Galaxy Events page that lists any upcoming events (such as ISMB/ECCB 2011 and the Workshop on Comparative Genomics) that have Galaxy related content.

The page also contains a link to the new Galaxy Events Google Calendar, that lists events and deadlines that may be of interest to the Galaxy community. For example, this week there are 5+ events going on and these 5 deadlines as well:

If you know of events that either have significant Galaxy content, or are of interest to the overall community, please send them to outreach@galaxyproject.org and they will be added to the Events page and the calendar.

Dave Clements

Posted to the Galaxy News on 2011-07-13

BOSC 2011   ISMB/ECCB 2011
Galaxy will have a strong presence at ISMB/ECCB 2011 and BOSC 2011.  There will be no less than
  • 3 BOSC talks
  • 2 ISMB workshops
  • 1 Proceedings Track talk
  • 5 Technology Track talks and 
  • 3 Posters

either about Galaxy or featuring Galaxy.  See the Events/ISMB-ECCB-BOSC 2011 page for a complete listing (and if it's not complete, please add your presentation).

One of the workshops, Genomics for Non-Model Organisms is organized by Galaxy and features 4 talks that use Galaxy (including a newly added talk by Marc Bras of INRA that uses Galaxy for SNP detection in grapevine).

Dave Clements

Posted to the Galaxy News on 2011-07-08

Galaxy Workshops at USC June 23-24
There will be two Galaxy workshops at the University of Southern California (USC) later this month. Both are presented by Jeremy Goecks of Emory University and the Galaxy team. Both workshops are open to the public:

Galaxy: A web‐based workbench for interactive and reproducible analysis of high‐throughput sequencing data, Thursday, June 23, 2011

  • At Aresty Auditorium, Harylene J Norris Cancer Research Tower, USC Health Science Campus, 1450 Biggy Street. Registration is free, but required.

    • 9:15am-Noon
      • Introduction to Galaxy including 30 min. Q&A Session

      2:00pm-5:00pm
      • High‐throughput sequencing data analysis including 45 min. Q&A Session

Progress and Challenges in Developing a Web-based Platform for Computational Biomedical Research, Friday, June 24, 2011

  • See the USC ISI AI Seminar Page for details on time and location.

    • The recent reliance on computation in biology has created an informatics crisis for biomedical researchers: computational resources are often difficult to use, communicating techniques and experiments is challenging, and reproducibility is very limited. Galaxy is one approach for addressing these problems. Galaxy is a popular Web-based platform for performing accessible, reproducible, and transparent genomics research. Galaxy provides a collaborative environment for performing complex analyses with automatic and unobtrusive provenance tracking; these features allow transparent sharing of both the precise computational details underlying an analysis and also intent, context, and narrative. Based on experiences with Galaxy, Jeremy will discuss some open problems that might be addressed using artificial intelligence methods and techniques.

Posted to the Galaxy News on 2011-06-17

GCC2011
NBIC, the host and co-sponsor of the 2011 Galaxy Community Conference (GCC2011) sponsored the videotaping of all talks at the meeting and has now made those recordings available for viewing online. See the GCC2011 page for links.

We had several requests for this, and I would like to thank NBIC for making this happen.

Dave Clements

Posted to the Galaxy News on 2011-06-11

Galaxy Community Conference registration is now open again. Early registration ends May 1. We had limited success in finding additional lodging for on May 24 and May 26:

May 24 Lodging: As expected, we were not able to secure additional hotel rooms at the conference centre for May 24, the evening before the meeting. We encourage people who need a room on May 24 to stay in Amsterdam that night, and then take the train to Lunteren the next morning. There is ample time to arrive before the 9:30am start of the meeting on the 25th. We regret the inconvenience that this will cause for people who will not be able to stay at the conference centre on May 24.

May 25 and 26 Lodging: We were able to reserve additional rooms for the night of May 26. We now have about 35 open hotel rooms reserved at the conference center on the nights of May 25 and May 26 (the night after the meeting).

However, we expect the rooms for May 25 to sell out, possibly in advance of the May 1 early registration deadline. If you are planning on staying at the conference centre, we strongly recommend that you register as soon as possible. Once those rooms are full, the whole centre will be full.

Thank you all for your patience while we worked on this. I apologize for and regret any inconvenience this has caused. As always, please let me know if you have any questions.

Thanks,

-- DaveClements

Posted to the Galaxy News on 2011-04-26