Locked History Actions

Diff for "GalaxyUpdates/2014_04"

Differences between revisions 7 and 8
Revision 7 as of 2014-03-30 06:32:53
Size: 15818
Editor: DaveClements
Comment:
Revision 8 as of 2014-03-30 06:55:47
Size: 17963
Editor: DaveClements
Comment:
Deletions are marked like this. Additions are marked like this.
Line 13: Line 13:
''62 papers'' (a new monthly record) were added to the [[http://www.citeulike.org/group/16008/|Galaxy CiteULike Group]] in March. Some papers that may be particularly interesting to the Galaxy community: ''63 papers'' (a new monthly record) were added to the [[http://www.citeulike.org/group/16008/|Galaxy CiteULike Group]] in March. Some papers that may be particularly interesting to the Galaxy community:
Line 17: Line 17:
 * "[[http://dx.doi.org/10.1093/bioinformatics/btu119|Wrangling Galaxy's Reference Data]]," by [[Dan|Daniel Blankenberg]], James E. Johnson, [[JamesTaylor|James Taylor]], [[anton|Anton Nekrutenko]]; ''Bioinformatics'' (28 February 2014), doi:10.1093/bioinformatics/btu119

 * "[[http://www.biotechniques.com/BiotechniquesJournal/2014/March/Controlling-for-contamination-in-re-sequencing-studies-with-a-reproducible-web-based-phylogenetic-approach/biotechniques-350711.html|Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach]]," Benjamin Dickins, Boris Rebolledo-Jaramillo, Marcia Shu-Wei S. Su, Ian M. Paul, [[Dan|Daniel Blankenberg]], Nicholas Stoler, Kateryna D. Makova, [[anton|Anton Nekrutenko]], ''[[http://www.biotechniques.com/|BioTechniques]]'', Vol. 56, No. 3. (2014)

 * "[[http://dx.doi.org/10.1093/bioinformatics/btu135|Orione, a web-based framework for NGS analysis in microbiology]]," Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia, ''Bioinformatics'' (Oxford, England) (10 March 2014), doi:10.1093/bioinformatics/btu135

 * "[[http://dx.doi.org/10.1007/978-1-62703-986-4_1|Galaxy as a Platform for Identifying Candidate Pathogen Effectors]]," Peter J. Cock, Leighton Pritchard, In ''Plant-Pathogen Interactions'', Vol. 1127 (2014), pp. 3-15, doi:10.1007/978-1-62703-986-4_1

 * "[[http://dx.doi.org/10.1093/database/bau018|GigaDB: promoting data dissemination and reproducibility]]," Tam P. Sneddon, Xiao S. Zhe, Scott C. Edmunds, Peter Li, Laurie Goodman, Christopher I. Hunter, ''Database'', Vol. 2014 (01 January 2014), bau018, doi:10.1093/database/bau018

 * "[[http://dx.doi.org/10.4172/jpb.1000302|Prediction of Gene Activity in Early B Cell Development Based on an Integrative Multi-Omics Analysis]]," Mohammad Heydarian, Teresa Romeo Luperchio, Jevon Cutler, Christopher J. Mitchell1, Min-Sik Kim, Akhilesh Pandey, Barbara Sollner-Webb, Karen Reddy, ''Journal of Proteomics & Bioinformatics'', Vol. 07, No. 02. (2014), doi:10.4172/jpb.1000302
Line 18: Line 30:
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/cloud|Cloud]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/project|Project]] ||<)> 4 || [[http://www.citeulike.org/group/16008/tag/tools|Tools]] ||<)> 3 || [[http://www.citeulike.org/group/16008/tag/usepublic|UsePublic]] ||
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/howto|HowTo]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/refpublic|RefPublic]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/usecloud|UseCloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/visualization|Visualization]] ||
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/cloud|Cloud]] ||<)> 2 || [[http://www.citeulike.org/group/16008/tag/project|Project]] ||<)> 4 || [[http://www.citeulike.org/group/16008/tag/tools|Tools]] ||<)> 3 || [[http://www.citeulike.org/group/16008/tag/usepublic|UsePublic]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/howto|HowTo]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/refpublic|RefPublic]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/usecloud|UseCloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/visualization|Visualization]] ||
Line 21: Line 33:
||<)> 32 || [[http://www.citeulike.org/group/16008/tag/methods|Methods]] ||<)> 5 || [[http://www.citeulike.org/group/16008/tag/shared|Shared]] ||<)> 10 || [[http://www.citeulike.org/group/16008/tag/usemain|UseMain]] || ||<)> 33 || [[http://www.citeulike.org/group/16008/tag/methods|Methods]] ||<)> 6 || [[http://www.citeulike.org/group/16008/tag/shared|Shared]] ||<)> 11 || [[http://www.citeulike.org/group/16008/tag/usemain|UseMain]] ||

Hey! This is under construction!

April 2014 Galaxy Update

Galaxy Updates

Welcome to the April 2014 Galaxy Update, a 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.  

New Papers

63 papers (a new monthly record) were added to the Galaxy CiteULike Group in March. Some papers that may be particularly interesting to the Galaxy community:

How those papers were tagged:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

1

Cloud 

2

Project 

4

Tools 

3

UsePublic

2

HowTo 

-

RefPublic 

1

UseCloud 

-

Visualization

2

IsGalaxy 

2

Reproducibility 

3

UseLocal 

19

Workbench

33

Methods 

6

Shared 

11

UseMain

GigaScience Galaxy Series


GigaScience Journal

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the 2013 Galaxy Community Conference has just published its first papers, and is continuing to take submissions. Whilst the series considers best practice papers, discussion, as well as novel uses of Galaxy, these first papers are examples of Galaxy toolkits, with a genome diversity tool collection presented from the Miller lab at Pennsylvania State, and a set of analytical and visualisation tools for Complete Genomics sequencing data from the Stubbs lab at Erasmus Medical College. The genome diversity toolkit is their first example that integrates with their GigaGalaxy server, with SVG graphs to help visualize how input datasets, workflows and histories are related to each example analysis in the paper. BGI is continuing to cover the article processing charges until the end of this year, so for more information see their blog posting.

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.


Events

Globus World 2014

Globus World 2014

GlobusWorld is this year’s biggest gathering of all things Globus. GlobusWorld 2014 features a features a Using Globus Genomics to Accelerate Analysis Tutorial, and a full half day on Globus Genomics in the main meeting, including a keynote by Nancy Cox and these accepted talks:

  • Globus Genomics: Enabling high-throughput cloud-based analysis and management of NGS data for Translational Genomics research at Georgetown, by Yuriy Gusev,

  • Improving next-generation sequencing variants identification in cancer genes using Globus Genomics, by Toshio Yoshimatsu

  • Globus Genomics: A Medical Center's Bioinformatics Core Perspective, by Anoop Mayampurath

  • Building a Low-budget Public Resource for Large-scale Proteomic Analyses, by Rama Raghavan

Globus Genomics is a Globus and Galaxy based platform for genomic analysis. GlobusWorld is being held April 15-17, in Chicago. And, GCC2014 is a Silver Sponsor of GlobusWorld.

GCC2014: June 30 - July 2, Baltimore

GCC2014: June 30 - July 2

The 2014 Galaxy Community Conference (GCC2014) will be held June 30 through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States.

Registration is Open

Early registration is now open. Early registration saves more than 70% on registration costs, and Training Day registration is an additional 55% off if you register for both at the same time. This is by far the most affordable option, with early registration fees starting at less than $50 per day. When you register you can also reserve lodging at Charles Commons, a very affordable housing option in the same building as the conference.

Training Day is an opportunity to learn about all things Galaxy including using Galaxy, deploying and managing Galaxy, extending Galaxy, and Galaxy internals. There are 5 parallel tracks, each with 3 sessions, with each of those sessions two and half hours long. That's 15 sessions and over 37 hours of workshop material.

Abstract Submission is Open

Abstract submission for both oral presentations and posters is also open. Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May 2. Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about it.

Accepted talks and selected posters from GCC2014 are also eligible for consideration to appear in the GigaScience "Galaxy: Data Intensive and Reproducible Research" series described above.

Sponsorships

There are still Silver and Bronze sponsorships available. Please contact the Organizers if your organization would like to help sponsor this event.

Exhibitors

In 2014 we are also adding non-sponsor exhibit spaces in addition to the sponsor exhibits. This will significantly increase the size of the exhibit floor. Please contact the Organizers if your organization would like to have an exhibit space at GCC2014.

Other Events

http://bit.ly/gxycal
There are several other events of interest in the next few months. Also see the Galaxy Events Google Calendar for details on other events of interest to the community.


[ATTACH]   Bio-IT World 2014   GCC2014 early registration and abstract submission are now open

Date

Topic/Event

Venue/Location

Contact

New Public Servers

Three public Galaxy servers were added to the published list in March:

Biomina

Biomina Galaxy

Image Analysis and Processing Toolkit

Image Analysis and Processing ToolKit
  • Links:

  • Domain/Purpose:

    • Image analysis and processing.
  • Comments:

    • This service provides a novel way of carrying out image analysis, reconstruction and processing tasks using cloud based service provided on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) infrastructure. The toolbox allows access to a wide range of useful blocks of functionalities (imaging functions) that can be connected together in workflows allowing creation of even more complex algorithms that can be re-run on different data sets, shared with others or additionally adjusted. The functions given are in the area of cellular imaging, advanced X-ray image analysis, computed tomography and 3D medical imaging and visualisation. The service is currently available on the website.

  • User Support:

  • Quotas:

    • A login is required to access the site. Logins are free and can be requested via email <admin@cloudimaging.net.au>

  • Sponsor(s):

Osiris

Osiris

Galaxy Distributions

The most recent release of Galaxy was February 10, 2014.

The most recent version of CloudMan was released in January 2014.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   
Describe your instance now



The Community Log Board and Deployment Catalog Galaxy community hubs were launched in December. If you have a deployment, or experience you want to share then please publish them.

ToolShed Contributions

Galaxy ToolShed

New Repositories in the Galaxy Project ToolShed

Other News