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News/Archive/2012

2012 News Item Archive

This page shows news items that have were posted to the Galaxy News page/feed in 2012.

See also 

 

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Complete News Brief

Highlights:

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 36ad8aa7b922

Best wishes for a safe and happy holiday,

The Galaxy Team

Posted to the Galaxy News on 2012-12-21

2013 Galaxy Community Conference (GCC2013) Training Day
2013 Galaxy Community Conference (GCC2013)

Nominations are now open for Training Day topics for the 2013 Galaxy Community Conference (GCC2013).

GCC2013 will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions.

Any topic of interest to the Galaxy Community can be nominated (see what was offered at GCC2012). Topics can be repeats from last year or brand new, and you are encouraged to nominate as many topics as you like. The 2013 Galaxy Community Conference (GCC2013) will start on 30 June with a Training Day featuring 4 parallel tracks, each with three, two hour workshops, for a total of twelve sessions. Nominations will be compiled into a uniform list, and then topics will be voted on by the Galaxy Community starting in late January.

Topic nomination closes 11 January.

GCC2013 Organizing Committee

Posted to the Galaxy News on 2012-12-03

Complete News Brief

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Highlights:
  • NGS: Mapping tools Bowtie and Lastz have moved from the Galaxy distribution to the Galaxy Main Tool Shed.

  • Improvements in the display of http://wiki.galaxyproject.org/Tool Shed repository dependencies and contents.

  • More Tool Shed updates including details of the Functional test framework, a new hgweb.config file and HgWebConfigManager tool, plus other management features.

  • Updated UI display and functionality for datasets and histories: new paused state and "resume/paused" toggle, new History menu options (seen at right →), and improved Scatterplot visualizations.

  • The SGE job runner has now been fully deprecated and replaced with DRMAA.

  • Several enhancements to aid with reproducibility: "Re-run" and "Extract workflow" validates datasets and tools, respectively, and a new data tables registry within the Administration menu, along with associated tools, corrects or warns about tool migration issues.

  • Highlights from the new Galaxy CloudMan release and December 2012 Galaxy Update.

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r f364d992270c

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2012-12-03

Complete News Brief

dist-readthedocs
Read the DocsSphinx Python Documentation Generator
Highlights:

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

http://galaxy-dist.readthedocs.org

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 5dcbbdfe1087

Thanks for using Galaxy!

The Galaxy Team

Posted to the Galaxy News on 2012-11-14

Nature Biotechnology

"NGS analysis by visualization with Trackster" is a new article in the November 2012 issue of Nature Biotechnology. Trackster is Galaxy's "visual analysis environment for next-generation sequencing data that tightly couples interactive visualization with data analysis." Trackster includes support for "parameter-space visualization and exploration, systematic sweeps of parameter values and dynamic filtering." To learn more read the article and give Trackster a spin on a Galaxy instance near you.

The Galaxy Team

Posted to the Galaxy News on 2012-11-09

November 2012 GalaxyAdmins Meetup

The next meeting of the GalaxyAdmins Group will be held on November 14, 2012, at 10 AM Central US time. Curtis Hendrickson of the University of Alabama Birmingham's Center for Clinical and Translational Science (UAB CCTS) will speak on Deploying Galaxy on a shared-node cluster at UAB. The meeting will also include time for open discussion. As always, please come prepared for an active discussion.

Date

November 14, 2012

Time

10 am Central US Time (-6 GMT)

Presentation

Deploying Galaxy on a shared-node cluster at UAB

Presenter

Curtis Hendrickson, UAB CCTS

Link

Connect to Webinar [Password: 110516]
Meeting Invite


GalaxyAdmins is a discussion group for Galaxy community members who are responsible for large Galaxy installations.

Srinivas Maddhi

Posted to the Galaxy News on 2012-11-05

November 2012 Galaxy Update

The November 2012 Galaxy Update is now available.

Highlights:

If you have anything you would like to see in the December Galaxy Update, please let us know.

Dave Clements and the Galaxy Team

Posted to the Galaxy News on 2012-10-31

Complete News Brief

scatterplot-partialscreen
Highlights:
  • Important Security Fix - upgrade NOW.

  • New Trello Issue Board replaces BitBucket} Issue Tracker. Learn how to submit, vote, and comment on tickets.

  • Tool Shed direct updates and changes in Galaxy improve metadata updating, repository management, and more control over tool config.

  • Updates to the Visualization tool set cover Trackster, Circster, and new Scatter Plot tool. That's an example plot on the right ->

  • New API fixes, tuneups, and brand-new methods to control libraries.

  • Multiple Admin changes enable better access to user data to solve problems.

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r 12fcd068b12e

Thanks for using Galaxy!

Jennifer Jackson & the Galaxy Team

Posted to the Galaxy News on 2012-10-24

http://www.genetics.org/content/early/2012/10/11/genetics.112.144204.1.abstract

CloudMap is a Galaxy-based pipeline that greatly simplifies the analysis of mutant genome sequences from raw FASTQ reads all the way to mapping plots and short lists of candidate mutations. We demonstrate the utility of CloudMap for WGS analysis of C. elegans and Arabidopsis genomes and describe how other organisms (e.g. Zebrafish, Drosophila) can easily be accommodated. Automated workflows and extensive video user guides are available to detail the individual analysis steps performed.

For details, see

Greg Minevich and Dan Blankenberg

Posted to the Galaxy News on 2012-10-15

Complete News Brief

tool shed
Highlights:

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r b5bda7a5c345

Thanks for using Galaxy!

Jennifer Jackson & the Galaxy Team

Posted to the Galaxy News on 2012-10-06

October 2012 Galaxy Update

The October 2012 Galaxy Update is now available.

Highlights:

If you have anything you would like to see in the November Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-10-01

Complete News Brief

toolfactory
Highlights:

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r da9d740fce31

Thanks for using Galaxy!

Jennifer Jackson & the Galaxy Team

Posted to the Galaxy News on 2012-09-21

Complete News Brief

tool-shed-menu
Highlights:

http://getgalaxy.org

http://bitbucket.org/galaxy/galaxy-dist

new:     $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r e6444e7a1685

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2012-09-07

http://france.list.galaxyproject.org/

Cette liste a pour but de partager et communiquer sur nos différentes expériences avec Galaxy au sein de l'hexagone. La langue officielle de cette liste est le français.

  • Vous avez besoin d'aide dans l'utilisation de Galaxy,
  • Vous hébergez un serveur public Galaxy,
  • Vous maintenez une instance locale de Galaxy,
  • Vous venez de déposer un outil sur le toolshed,
  • Vous avez des trucs et astuces pouvant interresser la communauté,
  • Vous organisez des formations avec Galaxy,

Postez une annonce à <galaxy-france AT lists DOT bx DOT psu DOT edu>

Pour toutes les questions techniques (installation, développement d'outil) nous tenterons de vous aider dans la mesure du possible, mais nous vous conseillons de vous adresser en parallèle à la liste de développement, le temps que la communauté française se mette en place.

Pour vous aider dans votre utilisation de Galaxy, voici une liste de liens utiles (en plus de la présente liste):

A très bientôt sur la liste Galaxy France,

Les administrateurs: Alban Lermine, Olivier Inizan, Rémi Marenco, Dave Clements & Jennifer Jackson.

Alban Lermine

(Translate)

Posted to the Galaxy News on 2012-08-28

August 2012 Galaxy Update

The August 2012 Galaxy Update is now available.

Highlights:

If you have anything you would like to see in the September Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-07-31

Complete News Brief

genome-indexing
Highlights:
  • Freebayes has moved from the Galaxy distribution to the Galaxy's Main Tool Shed

  • EMBOSS version 5.0.0 tool dependencies in the emboss_5 repository of the Galaxy Main Tool Shed updated to include information for automatically installing.

  • Tool Shed now also supports specifying the third party tool dependencies to be automatically installed in new repositories

  • Admin Genome Indexing is now in BETA. Download, index, and track progress right from the admin UI! That's a screen shot on the right ->

  • Improved Error Handling that captures EXIT codes, STDOUT, and STDERR from tools in XML. Be sure to read full details.

  • TopHat2/Bowtie2 latest support includes option to 'report discordant pairs', updated tests, and more preset options.

  • Trackster new parameter space visualization. BRAND NEW!! More details coming soon, but give a test drive now.

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r ec29ce8e27a1

Thanks for using Galaxy! We hope to see everyone in Chicago @ GCC2012!!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2012-07-21

GalaxyCzars

The first conference call of the GalaxyCzars group was held on July 9. The slides and a screencast of the call are now available.

In addition to discussing group organization and logistics, Ann Black-Ziegelbein of the University of Iowa gave a talk about their experiences with setting up a large Galaxy instance and their thorough benchmarking experiments with different storage architectures. To summarize, they initially started with Lustre on HP MSA 2312sa P2000 G2 hardware, which failed badly. The Iowa team then benchmarked ZFS, Gluster, and a reconfigured Lustre using several network technologies. Currently gluster is the top performer and failover scenarios are being evaluated at Iowa.

See the meeting summary for more, and the slides and screencast for details and links to the benchmarking scripts used, and to reports for each combination tried.

The group decided to have calls every other month, with the next on in September. We will also have a GalaxyCzars breakout session at GCC2012. This first call had over 25 participants (dare I say czars?).

Many, many thanks to Ann Black-Ziegelbein for getting the group off to a great start.

Dave Clements

Posted to the Galaxy News on 2012-07-11

July 2012 Galaxy Update

The July 2012 Galaxy Update is now available.

Highlights:

If you have anything you would like to see in the August Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-06-28

SouthAfricaFlag.png

University of Pretoria

Stellenbosch University

outh African Genetics & Bioinformatics Society Joint Conference

There will be two 2-day Galaxy Workshops in South Africa in September 2012, presented by the University of Pretoria Genomics IRT

There are around 20 places available per workshop, at a cost of R 750 per person.

In addition, there will be a keynote talk on Galaxy at the South African Genetics & Bioinformatics Society Joint Conference, being held in Stellenbosch 10-12 September.

Deadlines for these events are in the next few days:

Dave Clements

Posted to the Galaxy News on 2012-06-28

RGalaxy Bioconductor Package

Normally, in order to expose an R function as a tool in a Galaxy instance, you need to manually create an XML fi le with information about the function, and modify an additional XML file. The new RGalaxy package in Bioconductor automates this process, pulling most of the necessary information from the R function itself and its manual page (you provide the remaining information as arguments to the Galaxy function).

RGalaxy itself comes with a man page, and a reference manual.

Please note that the package is now available only in the development branch of Bioconductor. So to install it, you need to have R-2.15, and do the following:

   1 source("http://bioconductor.org/biocLite.R")
   2 useDevel()
   3 biocLite("RGalaxy")

Dan Tenenbaum
Bioconductor Core Team
Fred Hutchinson Cancer Research Center

Posted to the Galaxy News on 2012-06-28

Current Protocols in Bioinformatics

Two new Galaxy-related papers are now available in Current Protocols in Bioinformatics:

Both papers feature hands-on, step by step protocols, accompanied by numerous and detailed figures at each step.

We would like to thank Wiley for making both of these publications be open access.

Galaxy Team

Posted to the Galaxy News on 2012-06-18

We just released an update to CloudMan. 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.

This update brings a large number of updates and new features, the most prominent ones being:

  • Support for OpenStack and OpenNebula cloud middleware, allowing easy deployment on private, OpenStack or OpenNebula based clouds (see CloudBioLinux and mi-deployment projects for an easy way to deploy CloudMan on any machine image)

  • Start your instance via biocloudcentral.org on any supported cloud by simply filling out a 4-field web form. See this screencast for an example of using it with the Australian National Research Cloud, NeCTAR

  • Support for Amazon Spot instances, giving you an opportunity to reduce cost of running your cluster on AWS

  • Ability to mount any S3 bucket as a local file system via the Admin page, giving you instant and easy file-based access to any of your buckets or public buckets, such as the 1000genomes one

Other notable enhancements and features:

  • Added the ability to disable running of jobs on the master instance (via the Admin page), allowing you to (1) run a smaller instance type longer for the same cost and (2) not see the responsiveness of the master instance degrade with jobs being submitted
  • Significantly enhanced the details pane for individual worker nodes on the main interface, adding support for terminating and restarting individual nodes
  • Added MPI and SMP parallel environments to SGE; do qconf -spl to see the list and qsub -pe <pe_name> <slots> to use it for your cluster jobs

  • Removal of data volumes now happens in parallel, shortening the cluster shutdown time
  • Added worker_post_start_script_url and share_string user data options. See the User Data wiki page for the complete list.

  • Added a messaging framework to allow system information to easily and prominently be shown on the main interface. For example, if an instance was restarted in the wrong zone for its data volume - an explicit message will be shown indicating there was an error and what should be done.
  • Support for Ubuntu 12.04
  • Enhancements to logging by progressively reducing the frequency of log output as no user interaction takes place and also introduced log rotation

This update comes as a result of 113 code changesets; for a complete list of changes, see the commit messages.

Any new cluster will automatically start using this version of CloudMan. Existing clusters will be given an option to do an automatic update once the main interface page is refreshed.

Posted to the Galaxy News on 2012-06-13

June 2012 Galaxy Update

The June 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

If you have anything you would like to see in the July Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-06-01

Complete News Brief

Highlights:

gatk-workflow

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

Posted to the Galaxy News on 2012-05-12

The email post "Interested in speaking with other institutions deploying Galaxy locally?" by Ann Black-Ziegelbein generated a huge amount of interest. Ann proposed a bi-monthly conference call to discuss the broader issues of doing Galaxy deployments.

   Take the survey!   

The resulting community, now dubbed GalaxyCzars, welcomes anyone who cares about Galaxy deployments and wants to share their experience, or learn from others. If that describes you, please help us get started by taking this short survey. This will help steer the teleconferences as we get going (and also alleviate having to spend time on the call providing the same background info). The results of the survey will be made public on the GalaxyCzars and Capacity Planning pages.

Dave Clements (channeling Ann Black-Ziegelbein)

Posted to the Galaxy News on 2012-05-07

May 2012 Galaxy Update

The May 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

If you have anything you would like to see in the June Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-05-01

Galaxy Tour de France 2012

We are pleased to announce the Galaxy Tour de France 2012, a series of workshops being held across France the week of 28 May through June 1. The Tour will make stops in Perpignan, Lyon and Paris. Each day will feature a Galaxy for Biologists workshop in the morning, and a Galaxy for Developers workshop in the afternoon. All workshops will be taught by Galaxy Team members Nate Coroar, Anton Nekrutenko and James Taylor.

Workshop registration is free, but space at each venue is limited. You are encouraged to reserve your spot as soon as possible.

The Tour is generously sponsored and hosted by the Laboratoire de Biologie Intégrative des Organismes Marins, the Laboratoire Biométrie et Biologie Evolutive, and the Inserm - Mines ParisTech - Institut Curie - Bioinformatics and Computational Systems Biology of Cancer. Further support for the workshops is provided by an Amazon Web Services (AWS) Education Grant.

Dave Clements

Posted to the Galaxy News on 2012-04-25

April 2012 Galaxy Update

The April 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complements the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

If you have anything you would like to see in the May Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-04-02

GCC2012 Registration is Open!

GCC2012 Training Day: July 25

We are pleased to announce that early registration for the 2012 Galaxy Community Conference (GCC2012) is now open. GCC2012 will be held July 25-27, at the UIC Forum, in Chicago, Illinois. The conference will feature two full days of presentations, discussions, lightning talks, and breakouts. We have also added a new full day of training 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 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 can also be booked. Low-cost rooms have been reserved on the UIC campus. You can also stay at the official conference hotel, at a substantial discount arranged for conference attendees. There are a limited rooms available in both, and you are encouraged to register early, if you would like to stay in either.

Finally, abstract submission is also open, from now through April 16. Abstracts on any topic of interest to the Galaxy community are strongly encouraged. See the Abstracts page for details.

Looking forward to seeing you in Chicago!

Dave Clements on behalf of the GCC2012 Organizing Committee

Posted to the Galaxy News on 2012-03-20

Complete News Brief

Highlights:

trackster-encode

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 40f1816d6857

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2012-03-12

March 2012 Galaxy Update

The March 2012 Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates complements the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

If you have anything you would like to see in the April Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-02-29

Want to work on one of the fastest growing open source bioinformatics projects around? The Galaxy Project, a highly successful high throughput data analysis platform for Life Sciences with over 15,000 users worldwide, is hiring.


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.


Opening at Penn State
Post-Docs at Penn State

The Nekrutenko Lab at the Huck Institutes of Life Sciences at Penn State is seeking highly opinionated and biologically inclined Postdoctoral researchers within the Galaxy Project to develop best practices for analysis of next-generation sequencing data in all areas of Life Sciences where NGS is used. Successful candidates will join a vibrant research group at the Center for Comparative Genomics and Bioinformatics at Penn State University.

Please send your CV to <jobs AT galaxyproject DOT org>.

Posted to the Galaxy News on 2012-02-29

Opening at University of Virginia Bioinformatics Core

We have an opening for a Bioinformatics Analyst at the University of Virginia Bioinformatics Core. The analyst will work with other core staff on grant-funded and chargeback-based projects to manage and analyze large-scale datasets produced by next-generation sequencing. In addition to what's listed in the job announcement, the ideal candidate will have both Galaxy experience and next-gen sequencing expertise.

Stephen Turner
Director

Posted to the Galaxy News on 2012-02-24

GigaScience Journal
BGI Honk Kong

GigaScience Journal and BGI Hong Kong are hiring a Bioinformatician/Senior Database Developer. This Hong Kong based position will be responsible for developing and managing BGI’s public and private databases, and will include working with a team at the Chinese University of Hong Kong integrating these resources with Galaxy software and the BGI cloud.

See the job posting for more responsibilities, qualifications, and contact information. We are in a bit of a hurry for this particular position (although some more software focused positions are likely to come up later in the year), so if you are interested or have any questions about the role please contact: editorial@gigasciencejournal.com.

Scott Edmunds
Editor, GigaScience

Posted to the Galaxy News on 2012-02-18

Events/GCC2012/Abstracts

Abstracts are now being accepted for oral presentations at the 2012 Galaxy Community Conference (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 for an idea of the breadth of topics that are 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 page for more details and how to submit.

GCC2012 will be held, July 25-27 in Chicago, Illinois, United States. GCC2012 will run for two full days, and be preceded by a full day of training workshops. 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 for you. Registration will open in March.

GCC2012 is hosted by the University of Illinois at Chicago, the University of Illinois at Urbana-Champaign, and the Computation Institute.

Dave Clements

Posted to the Galaxy News on 2012-02-13

Vilmorin & Co.

Duration: 4-6 months
Subject: Integration and optimization of tools for SNP data analysis

Vilmorin & Co. creates seeds with added value ​​for vegetable and field crops. We propose an internship project in bioinformatics in our laboratories in Chappes (France). The aim of this project is to integrate SNP marker data and optimize the interactions between databases and various bioinformatic tools.

Specific tasks:

  • Organize and integrate SNP information into a database (Perl, MySQL)
  • Process data for analysis and visualization (Galaxy, GBrowse)

  • Automate and optimize the process

Profile:

  • Currently in an undergraduate programme (Computer Sciences or Bioinformatics)
  • Proficiency in at least one programming language, preferably Perl
  • Good knowledge of a RDBMS (MySQL)
  • Knowledge of GNU / Linux
  • Familiarity with Web technologies and protocols
  • Some background in Biology and / or genetics would be a plus
  • Knowledge of French would be a social advantage

Thank you for sending your application to:

Hien LE (<hien.le AT vilmorin DOT info>)

Posted to the Galaxy News on 2012-02-01

Galaxy Updates

The inaugural edition of Galaxy Update is now available. Galaxy Update is a (mostly) monthly summary of what is going on in the Galaxy community. Galaxy Updates will complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

Highlights:

If you have anything you would like to see in the March Galaxy Update, please let me know.

Dave Clements

Posted to the Galaxy News on 2012-01-31

Complete News Brief

Highlights:

  • Important metadata and Python 2.5 support corrections
  • SAMtools upgraded for version 0.1.18. Mpileup added.

  • Dynamic filtering, easy color options, and quicker indexing enhance Trackster

  • Set up your Galaxy instance to run cluster jobs as the real user, not the Galaxy owner

  • Improvements to metadata handling and searching in the Tool Shed

  • Improved solutions for schema access, jobs management, & workflow imports and inputs.

  • New datatypes (Eland, XML), multiple tool enhancements, and bug fixes.

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 26920e20157f

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2012-01-28

Complete News Brief

Highlights:

  • New Object Store data integration layer introduced
  • RNA-seq updates: TopHat to 1.4.0 and Cufflinks, CuffDiff, & CuffCompare to 1.3.0.

  • Tool Shed installation features and many new community tool additions
  • Trackster performance upgrades and new drag & drop composite track creation

http://getgalaxy.org

new:     % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 63bc46cc73b7

Thanks for using Galaxy!

Jennifer Jackson

Galaxy Team

Posted to the Galaxy News on 2012-01-20

Galaxy @ Plant and Animal Genome (PAG 2012)

Plant and Animal Genome XX (PAG2012) starts in San Diego on January 14. If you are attending PAG then you will have (at least) a half-dozen opportunities to learn more about Galaxy and how it is being used to support research. There will be workshops introducing Galaxy, and on deploying Galaxy in the cloud, and talks and posters on using Galaxy and several local Galaxy deployments. See the Galaxy @ PAG2012 page and the conference website for more information.

Dannon Baker and Dave Clements from the Galaxy Team will also be there throughout the meeting. Please feel free to ask us questions, or just introduce yourself.

Hope to see you in San Diego,

Dave Clements and Dannon Baker
Galaxy Team

Posted to the Galaxy News on 2012-01-06