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''54 papers'' 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:

How those papers were tagged:
''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:

 * "[[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

The new papers covered:
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||<)> - || [[http://www.citeulike.org/group/16008/tag/cloud|Cloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/project|Project]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/tools|Tools]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usepublic|UsePublic]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/howto|HowTo]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/refpublic|RefPublic]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usecloud|UseCloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/visualization|Visualization]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/isgalaxy|IsGalaxy]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/reproducibility|Reproducibility]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/uselocal|UseLocal]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/workbench|Workbench]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/methods|Methods]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/shared|Shared]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usemain|UseMain]] ||

= GigaScience Galaxy Series =

<<div(left)>><<BR>>[[http://www.gigasciencejournal.com/|{{attachment:Images/Logos/GigaScienceLogo250.png|GigaScience Journal|width="160"}}]]<<div>>

The ''[[http://www.gigasciencejournal.com/|GigaScience]]'' "Galaxy: Data Intensive and Reproducible Research" series [[http://blogs.biomedcentral.com/gigablog/2013/04/05/call-for-papers-for-a-special-gcc2013-galaxy-series/|announced]] for the [[Events/GCC2013|2013 Galaxy Community Conference]] has just published its [[http://www.gigasciencejournal.com/series/Galaxy|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 [[http://dx.doi.org/10.1186/2047-217X-2-17|genome diversity tool collection]] presented from the Miller lab at Pennsylvania State, and a [[http://dx.doi.org/10.1186/2047-217X-3-1|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 [[http://galaxy.cbiit.cuhk.edu.hk/|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 [[http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/|blog posting]].

= Who's Hiring =

<<div(right)>>[[GalaxyIsHiring|{{attachment:GalaxyIsHiring/GalaxyIsHiringWordCloud2.png|Please Help! Yes you!|width="200"}}]]<<div>>

The Galaxy is expanding! Please help it grow.

 * [[http://france.list.galaxyproject.org/Galaxy-france-Fwd-bioinfo-Stage-M2-Recherche-Provenance-dans-un-systeme-de-workflows-pour-la-bioinfoe-td93.html|Stage M2 Recherche : Provenance dans un système de workflows pour la bioinformatique]]
 * [[http://france.list.galaxyproject.org/Galaxy-france-Fwd-bioinfo-Stage-M1-M2-Institut-Curie-Paris-td92.html|Stage M1/M2, Development and integration of computational methods into the Galaxy analysis framework]], Institut Curie, Paris
 * [[News/StatisticalGenomicsPostDocPennState|Statistical Genomics Postdoc]] opening in the Makova lab at Penn State
 * '''The [[GalaxyIsHiring|Galaxy Project is hiring software engineers and post-docs]]''', ''including positions at George Washington University''.

 * [[http://bit.ly/1eq5TvM|Postdoctoral position in genomics/bio-informatics (NGS)]] at University of Rennes 1 (France)

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

<<BR>>
||<)> 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]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/isgalaxy|IsGalaxy]] ||<)> 2 || [[http://www.citeulike.org/group/16008/tag/reproducibility|Reproducibility]] ||<)> 3 || [[http://www.citeulike.org/group/16008/tag/uselocal|UseLocal]] ||<)> 19 || [[http://www.citeulike.org/group/16008/tag/workbench|Workbench]] ||
||<)> 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]] ||
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'''[[http://www.globusworld.org/|GlobusWorld]]''' is this year’s biggest gathering of all things [[https://www.globus.org/|Globus]]. !GlobusWorld features a ''Biosciences/Genomics Program'' devoted to research data in genomics and biosciences including [[Cloud#Globus Genomics|Globus Genomics]], a Globus and Galaxy based platform for genomic analysis. [[http://www.globusworld.org/|GlobusWorld]] is being held April 15-17, in Chicago.

Learn how to get more out of your data, and connect with other HPC administrators, research scientists, and developers who are building and using cutting-edge solutions to wrangle data.

Galaxy will have a presence at this meeting, and [[Events/GCC2014|GCC2014]] is a Silver Sponsor of [[http://www.globusworld.org/|GlobusWorld]].
'''[[http://www.globusworld.org/|GlobusWorld]]''' is this year’s biggest gathering of all things [[https://www.globus.org/|Globus]]. !GlobusWorld 2014 features a features a ''Using Globus Genomics to Accelerate Analysis Tutorial'', and a full half day on [[Cloud#Globus Genomics|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

[[Cloud#Globus Genomics|Globus Genomics]] is a Globus and Galaxy based platform for genomic analysis. [[http://www.globusworld.org/|GlobusWorld]] is being held April 15-17, in Chicago. And, [[Events/GCC2014|GCC2014]] is a Silver Sponsor of [[http://www.globusworld.org/|GlobusWorld]].
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=== Oral Presentation Abstract Submission Closes April 4 ===

[[Events/GCC2014/Abstracts|Abstract submission for oral presentations closes April 4]], '''which is this Friday.''' 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.

<<div(left)>>[[http://www.gigasciencejournal.com/|{{attachment:Images/Logos/GigaScienceLogo250.png|GigaScience Journal|width="150"}}]]<<div>>

Accepted talks and selected posters from GCC2014 are also eligible for consideration to appear in the ''[[http://www.gigasciencejournal.com/|GigaScience]]'' [[http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibility-first-papers-in-our-galaxy-series-utilizing-our-gigagalaxy-platform/|"Galaxy: Data Intensive and Reproducible Research"]] series.
<<BR>><<BR>>
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=== Abstract Submission is Open ===

[[Events/GCC2014/Abstracts|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 ''[[http://www.gigasciencejournal.com/|GigaScience]]'' [[#GigaScience Galaxy Series|"Galaxy: Data Intensive and Reproducible Research"]] series described above.

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== UC Davis 2014 Bioinformatics Workshop ==

<<div(right)>>[[http://training.bioinformatics.ucdavis.edu/2014/02/13/using-galaxy-for-analysis-of-high-throughput-sequence-data-june-16-20-2014/|{{attachment:Images/Logos/UCDavisGenomeCenterLogo.jpg|Using Galaxy for Analysis of High Throughput Sequence Data Workshop|}}]]<<BR>>
&nbsp;{{attachment:Images/Logos/galaxyLogoSymbol.png|Galaxy|width="75"}}<<div>>

'''Registration is now open for the [[http://training.bioinformatics.ucdavis.edu/2014/02/13/using-galaxy-for-analysis-of-high-throughput-sequence-data-june-16-20-2014/|Using Galaxy for Analysis of High Throughput Sequence Data Workshop]]''' being held at UC Davis, June 16-20, 2014 from 9-5 each day. The workshop will cover modern high throughput sequencing technologies, applications, and ancillary topics, including:

 * Illumina !HiSeq / !MiSeq, and !PacBio RS technologies
 * Read Quality Assessment & Improvement
 * Genome assembly
 * SNP and indel discovery
 * RNA-Seq differential expression analysis
 * Experimental design
 * Hardware and software considerations
 * Cloud Computing

<<div(right)>>[[https://training.bioinformatics.ucdavis.edu/|{{attachment:Images/Logos/UCDavisLogoSmall.gif|UC Davis|}}]]<<div>>

The workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and !PacBio data for hands-on exercises. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data. Workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the [[http://aws.amazon.com/|Amazon Cloud]] which allows for powerful web-based data analyses. There are no prerequisites other than basic familiarity with genomic concepts.

A similar workshop, [[http://training.bioinformatics.ucdavis.edu/2014/02/13/using-the-linux-command-line-for-analysis-of-high-throughput-sequence-data-september-15-19-2014/|using command line interfaces to perform the analysis]], is being offered September 15-19, 2014.
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[[Events/GCC2014|{{attachment:Images/Logos/GCC2014LogoWide200.png|GCC2014 early registration and abstract submission are now open|width="150"}}]]
<<div>>
[[http://www.tgac.ac.uk/SeqAhead_Scientific_Meeting_and_Management_Committee_Meeting/|{{attachment:Images/Logos/TGACLogo.png|NGS Data after the Gold Rush|height="50"}}]]&nbsp;
[[Events/GCC2014|{{attachment:Images/Logos/GCC2014LogoWide200.png|GCC2014 early registration and abstract submission are now open|width="150"}}]]&nbsp;<<div>>
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||<class="th"> April 8-9 || ''[[https://www.aanmelder.nl/nbic2014/wiki/parallel%20session%20m%3a%20infrastructrure%2c%20data%20%26%20technology#.Uytixq1dXfA|Building a scalable Galaxy cluster for biomedical research in The Netherlands]]'' || [[http://www.aanmelder.nl/nbic2014|Netherlands Bioinformatics Conference (NBIC2014)]], Lunteren, The Netherlands || [[http://nl.linkedin.com/in/djvanenckevort|David van Enckevort]], [[http://nl.linkedin.com/in/anthonypotappel|Anthony Potappel]] ||
||<class="th"> April 15-17 || ''Biosciences/Genomics Program'' || [[http://globusworld.org/|GlobusWorld]], Chicago, Illinois, United States || <<MailTo(outreach AT globus DOT org, Globus Outreach)>>, [[JohnChilton|John Chilton]] ||
||<|6 class="th"> April 29 -<<BR>>May 1 || ''[[http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=121423|W1: Integrated Research Data Management for Next Gen Sequencing Analysis Using Galaxy and Globus Online Software-as-a-Service]]'' ||<|6> [[http://www.bio-itworldexpo.com/|BioIT World]] || [[http://www.mcs.anl.gov/person/ravi-madduri|Ravi Madduri]], [[https://www.urmc.rochester.edu/people/21779848-alex-r-paciorkowski|Alex Paciorkowski]], [[http://www.ci.uchicago.edu/profile/328|Vas Vasiliadis]] ||
|| ''[[http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=135146|W4: Analyzing NGS Data in Galaxy]]'' || [[http://bioteam.net/company-leadership/|Anushka Brownley]], [[nate|Nate Coraor]], [[http://bioteam.net/company-leadership/|Adam Kraut]], Tristan Lubinski ||
|| ''[[http://www.bio-itworldexpo.com/Bio-It_Expo_Content.aspx?id=135152|W14: Running a Local Galaxy Instance]]'' || [[http://bioteam.net/company-leadership/|Adam Kraut]], [[nate|Nate Coraor]], [[http://bioteam.net/company-leadership/|Anushka Brownley]], Tristan Lubinski, James Reaney ||
|| ''[[http://www.bio-itworldexpo.com/Next-Gen-Sequencing-Informatics/|Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs]]'' || [[http://www.mcs.anl.gov/person/ravi-madduri|Ravi Madduri]] ||
|| ''[[http://www.bio-itworldexpo.com/Data-Visualization/|Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform]]'' || [[http://gehlenborg.com/|Nils Gehlenborg]] ||
|| ''[[http://www.bio-itworldexpo.com/Data-Visualization/|Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy]]'' || [[JeremyGoecks|Jeremy Goecks]] ||
||<class="th"> May 6-7 || ''Scaling Galaxy for Big Data'' || [[http://www.tgac.ac.uk/SeqAhead_Scientific_Meeting_and_Management_Committee_Meeting/|NGS Data after the Gold Rush]], [[http://www.tgac.ac.uk/|TGAC]], Norwich, United Kingdom || [[DaveClements|Dave Clements]] ||
||<class="th"> May 9 || ''Galaxy Workshop'' || [[http://www.tgac.ac.uk/|The Genome Analysis Centre (TGAC)]], Norwich, United Kingdom || [[DaveClements|Dave Clements]] ||
||<class="th"> May 27 || ''[[http://www.mipro.hr/LinkClick.aspx?fileticket=y1%2bUY%2b54jB4%3d&tabid=110&mid=461&language=en-US&forcedownload=true|Enabling Data Analysis with Galaxy CloudMan workshop]]'' || [[http://www.mipro.hr/CallForPapers/tabid/176/language/en-US/Default.aspx|MIPRO 2014]], Opatija, Croatia || [[EnisAfgan|Enis Afgan]] ||
||<class="th"> June 9-10 || ''[[http://bioinformatics.ca/workshops/2014/informatics-high-throughput-sequencing-data-2014|Informatics on High Throughput Sequencing Data Workshop]]'' || Toronto, Canada || [[http://bioinformatics.ca/person/cbw-experts/francis-ouellette|Francis Ouellette]] ||
||<class="th"> June 16-20 || ''[[http://training.bioinformatics.ucdavis.edu/2014/02/13/using-galaxy-for-analysis-of-high-throughput-sequence-data-june-16-20-2014/|Using Galaxy for Analysis of High Throughput Sequence Data]]'' || [[http://training.bioinformatics.ucdavis.edu/|UC Davis]], California, United States || <<MailTo(training DOT ucdbio AT gmail DOT com, UC Davis Bioinformatics Training)>> ||
||<class="th">June 28-30 || [[Events/GCC2014/Hackathon|Galaxy Hackathon]] ||<|2> [[http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewood_campus/|Homewood Campus]] of [[http://jhu.edu|Johns Hopkins University]], [[http://visitors.baltimorecity.gov/|Baltimore, Maryland]], United States || [[Events/GCC2014/Organizers|Organizers]] ||
||<class="th"> June&nbsp;30&nbsp;-<<BR>>July 2 || '''[[Events/GCC2014|2014 Galaxy Community Conference (GCC2014)]]''' || [[Events/GCC2014/Organizers|Organizers]] ||

= Who's Hiring =

<<div(right)>>[[GalaxyIsHiring|{{attachment:GalaxyIsHiring/GalaxyIsHiringWordCloud2.png|Please Help! Yes you!|width="200"}}]]<<div>>

The Galaxy is expanding! Please help it grow.

 * [[News/StatisticalGenomicsPostDocPennState|Statistical Genomics Postdoc]] opening in the Makova lab at Penn State
 * '''The [[GalaxyIsHiring|Galaxy Project is hiring software engineers and post-docs]]'''

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

<<BR>>
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xx new [[PublicGalaxyServers|public Galaxy servers]], [[PublicGalaxyServers#|]] Three [[PublicGalaxyServers|public Galaxy servers]] were added to the published list in March:

== Biomina ==

<<div(right solid)>>[[http://biominavm-galaxy.biomina.be/galaxy/|{{attachment:PublicGalaxyServers/Biomina300.png|Biomina Galaxy|}}]]<<div>>

 * ''Link:''
   [[http://biominavm-galaxy.biomina.be/galaxy/|Biomina Galaxy]]
 * ''Domain/Purpose:''
   A general purpose Galaxy instance that includes most "standard" tools for DNA/RNA sequencing, plus extra tools for panel resequencing, variant annotation and some tools for Illumina SNParray analysis.
 * ''Comments:''
   * Includes a number of workflows, including workflow from "[[http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.2899.html|A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP]]," by Helsmoortel, ''et al.'', ''[[http://www.nature.com/ng/|Nature Genetics]]'' (2014) doi:10.1038/ng.2899
 * ''User Support:''
   <<MailTo(geert DOT vandeweyer AT uantwerpen DOT be, Email support)>>
 * ''Quotas:''
   * Registered users : 50Gb. Can be increased up to 3Tb in collaborative projects.
   * There is NO backup of data inside this galaxy server.
   * Collaboration partner jobs have higher priority on the system.
 * ''Sponsor(s):''
   * [[http://www.ua.ac.be/main.aspx?c=.MEDGEN|Center of Medical Genetics]], [[http://www.ua.ac.be/|University of Antwerp]]
   * [[http://www.biomina.be/|Biomina research center]], [[http://www.ua.ac.be/|University]] and [[http://www.uza.be/|University Hospital]] of Antwerp.


== Image Analysis and Processing Toolkit ==

<<div(right solid)>>[[http://cloudimaging.net.au/|{{attachment:PublicGalaxyServers/ImageAnalysisToolkit.png|Image Analysis and Processing ToolKit|}}]]<<div>>
 * ''Links:''
   * [[http://cloudimaging.net.au/|Image Analysis and Processing Toolkit Server]]
   * [[http://cloudimaging.blogspot.com.au/|Project blog]]
 * ''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 [[http://www.nectar.org.au|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 [[http://www.cloudimaging.net.au|on the website]].
 * ''User Support:''
   * <<MailTo(admin@cloudimaging.net.au, Email)>>
   * [[http://www.youtube.com/user/CloudImaging|Video tutorials]]
 * ''Quotas:''
   A login is required to access the site. Logins are free and can be <<MailTo(admin@cloudimaging.net.au, requested via email)>>
 * ''Sponsor(s):''
   [[http://www.nectar.org.au|NeCTAR]] and [[http://www.csiro.au/|CSIRO]]

== Osiris ==

<<div(right solid)>>[[http://galaxy-dev.cnsi.ucsb.edu/osiris/|{{attachment:PublicGalaxyServers/OsirisLogo.jpg|Osiris}}]]<<div>>

 * ''Links:''
   * [[http://galaxy-dev.cnsi.ucsb.edu/osiris/|Osiris Galaxy]]
   * [[http://osiris-phylogenetics.blogspot.com/|Osiris Blog]]
   * [[https://bitbucket.org/osiris_phylogenetics|Osiris code in Bitbucket]]
 * ''Domain/Purpose:''
   Pylogenetics
 * ''Comments:''
   "This server aims to demonstrate Osiris, a set of phylogenetics tools for the Galaxy Bioinformatics platform. Because it is only a demo, some computationally intensive tools are disabled. Other tools will be slow because this is a public, shared resource."
 * ''User Support:''
   * [[https://groups.google.com/forum/?hl=en&fromgroups#!forum/osiris-phylogenetics|Osiris-Phylogenetics Google Group]]
   * [[https://www.youtube.com/watch?v=mGMxwc20Yx4|Screencasts]]
 * ''Quotas:''
 * ''Sponsor(s):''
   [[https://labs.eemb.ucsb.edu/oakley/todd/|Oakley Lab]] at [[http://www.ucsb.edu/|UC Santa Barbara]]
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There was one new [[Community/Logs|Community Log Board]] entry in March:

 * [[Community/Log/2014/BasicGalaxyPuppetModule|Basic Galaxy Puppet Module]] (work by Olivier Inizan, Mikael Loaec of INRA-URGI)
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 * [[http://bit.ly/1jKpNsw|regex_find_replace]]: Use python regular expressions to find and replace text
 * [[http://bit.ly/1k9X5gK|samtools_phase]]: Call and phase heterozygous SNPs
 * [[http://bit.ly/1rSclEv|sample_seqs]]: Sub-sample sequences files (e.g. to reduce coverage)
 * [[http://bit.ly/1e05yiN|transpose]]: Transposes tabular-delimited data
 * [[http://bit.ly/1jmbFmM|proteomics_rnaseq_reduced_db_workflow]]: Filter Proteomics Search DB by RNA-seq transcript expression analysis
 * [[http://bit.ly/1k9UaEJ|proteomics_rnaseq_sap_db_workflow]]: Create Proteomics Search DB from RNA-seq Single amino acid Polymorphism detection
 * [[http://bit.ly/1f8hrqJ|proteomics_novel_peptide_filter_workflow]]: filter a Proteomics Search DB for novel peptides
 * [[http://bit.ly/P63sIa|proteomics_rnaseq_splice_db_workflow]]: create Proteomics Search DB from RNA-seq novel splice detection
 * [[http://bit.ly/1h7SvMa|rsem_datatypes]]: Custom galaxy datatypes definitions for use with RSEM
 * [[http://bit.ly/1jKlVrM|varscan_wrapper]]: Fork of fcaramia package correcting errors and additional options
 * [[http://bit.ly/1pryNlF|align_back_trans]]: Thread nucleotides onto a protein alignment (back-translation)
 * [[http://bit.ly/1mC67Yj|dna_visualizer]]: convert DNA sequence into a PNG image by representing each base with one colored pixel
 * [[http://bit.ly/1hnr0D1|bwa_mem]]: a software package for mapping low-divergent sequences against a large reference genome
 * [[http://bit.ly/1odsd53|samtool_filter2]]: Filter BAM/SAM on FLAG,MAPQ,RG,LB or by region & produce a BAM/SAM on demand
Line 125: Line 248:
 * [[http://bit.ly/1dIJIDG|phylorelatives]]: Relatedness of minor alelle sequences in NJ tree
 * [[http://bit.ly/1m6Gfkr|advanced_grep_from_file]]: Extended Grep Using Perl, fetch lines after match and get patterns from file
 * [[http://bit.ly/MwAlN3|getalleleseq]]: Generate FASTA sequence from alleles table
 * [[http://bit.ly/1jOLTtg|hetbox]]: minor variant boxplot
 * [[http://bit.ly/MwAPmq|find_in_reference]]: filter tab file where a field is a substring of a field in any line of a reference
 * [[http://bit.ly/1jDm1wY|filter_bed_on_splice_junctions]]: Filter out lines w/ junctions in reference bed file of known junctions
 * [[http://bit.ly/1eNHFKg|translate_bed_sequences]]: 3 frame translation of BED file augmented with a sequence column
 * [[http://bit.ly/1biTdtX|rsem]]: RNA SEQ by Expectation Maximization
 * [[http://bit.ly/1h2zMUr|snpeff_to_peptides]]: Creates a peptide fasta from a !SnpEff VCF output and an Ensembl all_peps.fa
 * [[http://bit.ly/1nLamwQ|synteny_mapper]]: find microrearrangements w/in syntenic regions, viz & compare UCSC features
 * [[http://bit.ly/1jOONxS|bamtools_wrappers]]: Wrappers for the bamtools package
 * [[http://bit.ly/1kSTVRV|fastq_qc_trimmer]]: Parallel FASTQ QC Trimmer
 * [[http://bit.ly/N74geH|fastq_all_to_sanger]]: Very Fast groomer of quality formats to Sanger
 * [[http://bit.ly/1miEAs8|prada]]: pipeline for RNAseq data analysis for Illumina paired end data
 * [[http://bit.ly/1myEYpV|shrnaseq]]: shRNAseq differential representation analysis using edgeR
 * [[http://bit.ly/1o4LyQx|segemehl]]: short read mapping with gaps
 * [[http://bit.ly/1euOkZK|blockbuster]]: Detection of blocks of overlapping reads
 * [[http://bit.ly/1mGzXf3|twistdna]]: prediction of superhelically destabilized regions
 * [[http://bit.ly/1myhRIE|rnaz]]: predicting structural noncoding RNAs
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 * GOBLET is collecting [[https://www.surveymonkey.com/s/GOBLETsurvey|Bioinformatics Training needs]] across the globe  * Galaxy reached a milestone of [[http://ohloh.net/p/galaxybx|100 contributors to our codebase]]! Thank you all!
 * Poster: "[[http://bit.ly/1kzoEkF|ChemicalToolBoX and its application on the study of the drug like and purchasable space]]," by Lucas. ''et al.'', ''Journal of Chemoinformatics''
 * [[https://urgi.versailles.inra.fr/About-us/News/new-tools-available-in-Galaxy|New tools available in Galaxy @ URGI]]: !SnpEff, Mapsembler2, BLAST+, Blast2GO, Peak predictor, ...

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:

The new papers covered:

#

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

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.

Oral Presentation Abstract Submission Closes April 4

Abstract submission for oral presentations closes April 4, which is this Friday. 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.

GigaScience Journal

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

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.

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.

UC Davis 2014 Bioinformatics Workshop

Using Galaxy for Analysis of High Throughput Sequence Data Workshop
 Galaxy

Registration is now open for the Using Galaxy for Analysis of High Throughput Sequence Data Workshop being held at UC Davis, June 16-20, 2014 from 9-5 each day. The workshop will cover modern high throughput sequencing technologies, applications, and ancillary topics, including:

  • Illumina HiSeq / MiSeq, and PacBio RS technologies

  • Read Quality Assessment & Improvement

  • Genome assembly
  • SNP and indel discovery
  • RNA-Seq differential expression analysis
  • Experimental design
  • Hardware and software considerations
  • Cloud Computing

UC Davis

The workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools. We will cover the basics of several high throughput sequencing technologies, but will focus on Illumina and PacBio data for hands-on exercises. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data. Workshop exercises will be performed using the popular Galaxy platform (http://usegalaxy.org) on the Amazon Cloud which allows for powerful web-based data analyses. There are no prerequisites other than basic familiarity with genomic concepts.

A similar workshop, using command line interfaces to perform the analysis, is being offered September 15-19, 2014.

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   NGS Data after the Gold Rush  GCC2014 early registration and abstract submission are now open 

Date

Topic/Event

Venue/Location

Contact

April 8-9

Building a scalable Galaxy cluster for biomedical research in The Netherlands

Netherlands Bioinformatics Conference (NBIC2014), Lunteren, The Netherlands

David van Enckevort, Anthony Potappel

April 15-17

Biosciences/Genomics Program

GlobusWorld, Chicago, Illinois, United States

Globus Outreach <outreach AT globus DOT org>, John Chilton

April 29 -
May 1

W1: Integrated Research Data Management for Next Gen Sequencing Analysis Using Galaxy and Globus Online Software-as-a-Service

BioIT World

Ravi Madduri, Alex Paciorkowski, Vas Vasiliadis

W4: Analyzing NGS Data in Galaxy

Anushka Brownley, Nate Coraor, Adam Kraut, Tristan Lubinski

W14: Running a Local Galaxy Instance

Adam Kraut, Nate Coraor, Anushka Brownley, Tristan Lubinski, James Reaney

Globus Genomics: An End-to-End NGS Analysis Service on the Cloud for Researchers and Core Labs

Ravi Madduri

Integrated Analysis and Visualization of Large-Scale Biological Data with the Refinery Platform

Nils Gehlenborg

Web-Based Visualization and Visual Analysis for High-Throughput Genomics with Galaxy

Jeremy Goecks

May 6-7

Scaling Galaxy for Big Data

NGS Data after the Gold Rush, TGAC, Norwich, United Kingdom

Dave Clements

May 9

Galaxy Workshop

The Genome Analysis Centre (TGAC), Norwich, United Kingdom

Dave Clements

May 27

Enabling Data Analysis with Galaxy CloudMan workshop

MIPRO 2014, Opatija, Croatia

Enis Afgan

June 9-10

Informatics on High Throughput Sequencing Data Workshop

Toronto, Canada

Francis Ouellette

June 16-20

Using Galaxy for Analysis of High Throughput Sequence Data

UC Davis, California, United States

UC Davis Bioinformatics Training <training DOT ucdbio AT gmail DOT com>

June 28-30

Galaxy Hackathon

Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States

Organizers

June 30 -
July 2

2014 Galaxy Community Conference (GCC2014)

Organizers

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.


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.

There was one new Community Log Board entry in March:

ToolShed Contributions

Galaxy ToolShed

New Repositories in the Galaxy Project ToolShed

Other News