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− | News that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from [[Meetings|GMOD meetings]] and releases to user success stories and GMOD related publications. News items more than 6 months old are listed in the [[GMOD News Archives]].
| + | <wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" /> |
− | | + | |
− | If you have a news item you want added here, please send it to the [[GMOD Help Desk]] or add it to this page directly. See [[#Adding a News Item|Adding a News Item]] for how to do this.
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− | | + | |
− | <span class="plainlinks"> | + | |
− | This ''GMOD News'' is also available as an [http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss RSS feed]. {{#icon: RSSIcon16x16.gif|RSS feed||http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss}}
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− | </span>
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− | | + | |
− | = News Items =
| + | |
− | | + | |
− | Want to add your news item here? See [[#Adding a News Item|Adding a News Item]] below.
| + | |
− | | + | |
− | <startFeed /> | + | |
− | <!-- Add new Items here. Keep the Title Short! ***35 characters or less*** -->
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− | | + | |
− | == ISMB 2010 Talks & Posters == | + | |
− | | + | |
− | {{ImageRight|ISMB2010_logo.jpg|GMOD @ ISMB 2010|150|ISMB 2010}}
| + | |
− | | + | |
− | You can now view most of the [[ISMB 2010|GMOD-related presentations and posters from ISMB 2010]]. This includes
| + | |
− | * [[:Image:DeployingGalaxyCloudBOSC2010.pdf|Deploying Galaxy on the Cloud]], Enis Afgan
| + | |
− | * [[:Image:NGSTranscriptomeISGAErgatis.pdf|Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis]], [[User:Chemmeri|Chris Hemmerich]]
| + | |
− | * [http://prezi.com/nx4jy4etq-ug/gbrowse-20-and-jbrowse-for-ismb/ GMOD Presents GBrowse 2.0 and JBrowse], [[User:Scott|Scott Cain]]
| + | |
− | * [[:Image:PathwayToolsPosterISMB2010.pdf|An Advanced Web Query Interface for Biological Databases]] ([[Pathway Tools]]), Peter Karp
| + | |
− | * [[:Image:GalaxyNGSISMB2010.pdf|Galaxy NGS functionality from sample tracking to SNP calling]], Ramkrishna Chakrabarty
| + | |
− | | + | |
− | Plus additional talks and posters on [[GBrowse]], [[DIYA]], [[Pathway Tools]], and [[Galaxy]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/07/19''
| + | |
− | | + | |
− | == Hiring @ Dolan DNALC ==
| + | |
− | | + | |
− | {{ImageRight|DolanDNALCLogo.jpg|Opening @ Dolan DNA Learning Center, job ID 934||http://www.cshl.edu/hr/jobs.html}}
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− | | + | |
− | There's an [http://www.cshl.edu/hr/jobs.html opening (Job ID 934)] at the [http://www.dnalc.org Dolan DNA Learning Center (DNALC)] of [http://www.cshl.edu Cold Spring Harbor Laboratory] for a programmer to develop cyberinfrastructure to support plant biology research. The programmer will work with a multi-disciplinary team to design, develop, and maintain applications for interfacing public APIs, SQL databases, and large data sets.
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− | | + | |
− | The successful candidate should come from a bioinformatics background that includes work with [[BioPerl]], genome databases (such as [[Chado]]), browsers, and annotation tools. Expertise in Java, SQL and database schema, and Unix/Linux are essential. Experience developing web user interfaces – templating, Javascript/AJAX, DOM, and CSS – is also desirable.
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− | | + | |
− | For more information, go to the [http://www.cshl.edu/hr/jobs.html CSHL jobs site] and search for Job ID 934.
| + | |
− | | + | |
− | ''2010/07/14''
| + | |
− | == GBrowse 2.13 Release ==
| + | |
− | {{ImageRight|GBrowseLogo.png|GBrowse 2.13 Released|200|GBrowse}}
| + | |
− | | + | |
− | [[GBrowse]] version 2.13 has been released. 2.13 is a maintenance update to 2.12. GBrowse 2.13 and 2.12 include these changes:
| + | |
− | | + | |
− | ;New features & enhancements:
| + | |
− | * The [[DAS]] server and client are now functional. You will need {{CPAN|Bio::Das}} version 1.17 and {{CPAN|Bio::Graphics}} version 2.11 for best results.
| + | |
− | * The "import track" function now allows you to specify the URL of either a {{GlossaryLink|BAM|BAM}} or a BigWig file. The track will be displayed without physically copying the file onto the GBrowse server. You will need {{CPAN|Bio::DB::Sam}} and {{CPAN|Bio::DB::BigWig}} for these features to work.
| + | |
− | * Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to be installed.
| + | |
− | * There is now a '''Get chromosome sizes''' entry in the File menu.
| + | |
− | * Calling GBrowse with the CGI argument <tt>action=scan</tt> will generate a quick summary of track contents.
| + | |
− | * Improved performance when working with truly huge (>1000 track definition) configuration files.
| + | |
− | * Fasta, [[GFF3]], {{GlossaryLink|SAM|SAM}} and wiggle dumps now include the genome build ID if that information is provided in the data source "metadata" configuration variable.
| + | |
− | | + | |
− | ;Bug fixes
| + | |
− | * When [[MySQL]] is used as the back end for user uploads, it will no longer fail on long filenames.
| + | |
− | * Fixed the "eurl" CGI parameter for importing data sets by their URLs.
| + | |
− | * Fasta and GFF3 dumps are now working when invoked from the File menu.
| + | |
− | * Fixed SAM file processing so as not to die when presented with a SAM @SQ header. This requires {{CPAN|Bio::DB::Sam}} 1.20 to work properly.
| + | |
− | * Fixed upload listing table so as not to duplicate track labels.
| + | |
− | * Fixed track importation via the eurl parameter so that it works when the user's uploadid is empty (due to clearing cache of cookies).
| + | |
− | * Fixed DAS server handling of the link option.
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− | | + | |
− | Please use the [https://sourceforge.net/tracker/?group_id=27707 GMOD bug tracking system] to report [https://sourceforge.net/tracker/?atid=391291&group_id=27707&func=browse bugs] or [https://sourceforge.net/tracker/?atid=391294&group_id=27707&func=browse feature requests].
| + | |
− | | + | |
− | [[User:Lstein|Lincoln Stein]]
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− | | + | |
− | ''2010/07/13''
| + | |
− | | + | |
− | == Pathway Tools Workshop 2010 ==
| + | |
− | {{ImageRight|SRILogo.png|Pathway Tools Workshop 2010||http://bioinformatics.ai.sri.com/ptools10/}}
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− | | + | |
− | Registration is now open for the [http://bioinformatics.ai.sri.com/ptools10/ Pathway Tools Workshop 2010], held October 25th - 29th, 2010 in Menlo Park, CA. Early registration ends September 1.
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− | | + | |
− | This workshop is oriented around SRI's [[Pathway Tools]] software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.
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− | | + | |
− | The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:
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− | | + | |
− | * Advances in pathway bioinformatics, model organism databases, genome annotation, and systems biology
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− | * Scientific results achieved with Pathway Tools and BioCyc
| + | |
− | * Share expertise on how to develop new organism-specific databases with Pathway Tools
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− | * Share experiences on how to make the most of Pathway Tools
| + | |
− | * Presentations by users on extensions they have developed to Pathway Tools
| + | |
− | * Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
| + | |
− | | + | |
− | Please visit our [http://bioinformatics.ai.sri.com/ptools10/ registration website] for details on speakers, fees, travel, and hotels.
| + | |
− | | + | |
− | Looking forward to seeing you at an upcoming Pathway Tools event.
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− | | + | |
− | Best regards,
| + | |
− | | + | |
− | [mailto:ptools-info@ai.sri.com Tomer Altman]
| + | |
− | | + | |
− | ''2010/07/09''
| + | |
− | | + | |
− | == Galaxy Community Tool Sharing ==
| + | |
− | | + | |
− | {{ImageRight|GalaxyLogoSmall.png|Galaxy Community Tool Sharing||http://usegalaxy.org/community}}
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− | | + | |
− | We have introduced a new [http://usegalaxy.org/community Galaxy tool sharing community site]. The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools. To learn how to use the community site, click on '''Help → How to upload, download, and install tools'''.
| + | |
− | | + | |
− | We hope that you will find this site useful for hosting tools that you would like to contribute and share.
| + | |
− | | + | |
− | We'll keep you informed as the site's features evolve.
| + | |
− | | + | |
− | Greg Von Kuster
| + | |
− | | + | |
− | ''2010/07/08''
| + | |
− | | + | |
− | == Logo Program Logos! ==
| + | |
− | | + | |
− | <div style="float: right; border: 0.5em solid gray; margin: 0.5em;">
| + | |
− | {|
| + | |
− | | align="center" | {{#icon: ApolloLogo.png|Apollo logo by Audra Radke|150|Spring 2010 Logo Program}}
| + | |
− | |-
| + | |
− | | align="center" | {{#icon: RedFlyLogo.png|REDFly logo by Alex Read|65|Spring 2010 Logo Program}} {{#icon: CMapLogo.png|CMap logo by Kathy Bracken|40|Spring 2010 Logo Program}}
| + | |
− | |-
| + | |
− | |
| + | |
− | |-
| + | |
− | | align="center" | [[Spring 2010 Logo Program|Some of the new logos]]
| + | |
− | |}
| + | |
| </div> | | </div> |
| + | News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the '''[[GMOD News Archives]]'''. See also the [[Calendar|GMOD Calendar and Events List]]. |
| | | |
− | The [[Spring 2010 Logo Program]] was a smashing success and 9 projects now have eye-catching logos that give each resource a strong graphic brand identify. See the [[Spring 2010 Logo Program|Spring 2010 page]] for a complete list of logos, as well as some of the alternatives that were not chosen.
| + | GMOD News is also available as an '''[{{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed RSS feed]'''. [[File:RSSIcon16x16.gif|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]] |
| | | |
− | I would like to thank
| + | == Recent News == |
− | * The '''[[Spring 2010 Logo Program#Linn-Benton Community College|design students]]''' who worked with the participants to understand their projects and produce an excellent [[Spring 2010 Logo Program#Other Logos|set of logos]] to pick from.
| + | |
− | * '''John Aikman''' of the [http://www.linnbenton.edu/go/graphic-arts Graphic Arts Department] at [http://www.linnbenton.edu/ Linn-Benton Community College (LBCC)] for being willing to take a chance on this program, and for being willing to work with to hammer out the details.
| + | |
− | * And the '''[[Spring 2010 Logo Program#Projects|participants]]''' for being willing to work the students to help them gain experience and to understand the projects they were creating logos for.
| + | |
| | | |
− | The [[GMOD Logo Program]] might return in the future. Please watch the [[GMOD News]] for details, probably later this year. In the mean time, if you would be interested in participating in the next one, please let me know. The more people I hear from, the more likely it is to happen.
| + | <rss text time="1800" number="20" desc="off" title="off">http://gmod.org/mediawiki/index.php?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed</rss> |
| | | |
− | Thanks,
| + | == [[GMOD News Archives|News Archives]] == |
| | | |
− | [[User:Clements|Dave Clements]]<br />
| + | The [[GMOD News Archives]] lists all news items since autumn 2007. |
− | [[GMOD Help Desk]] | + | |
| | | |
− | ''2010/07/07''
| + | == Adding a News Item == |
| | | |
− | == GMOD @ ISMB 2010 ==
| + | '''Note:''' If you don't want to do this yourself, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you. |
| | | |
− | {{ImageRight|ISMB2010_logo.jpg|GMOD @ ISMB 2010|150|ISMB 2010}}
| + | GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the [[GMOD News]] and [[GMOD News Archives]] pages, and in the news tracker on the [[Main Page|home page]]. |
| | | |
− | ISMB runs July 9-13 this year and [[ISMB 2010|GMOD has a strong presence on the program]]:
| + | === Short Instructions === |
− | * talks on [[Galaxy]], [[GBrowse]], [[JBrowse]], [[Pathway Tools]], [[WebGBrowse]], ...
| + | |
− | * a tutorial on [[Galaxy]],
| + | |
− | * many posters, and
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− | * several Special Interest Group (SIG) meetings relevant to GMOD members.
| + | |
| | | |
− | See the [[ISMB 2010|GMOD @ ISMB 2010]] page for a full listing of GMOD related content, including a [[ISMB 2010#Flier|session listing]] you can print in advance. See the [http://www.iscb.org/ismb2010 ISMB 2010 web site] for more on the conference.
| + | Please follow these guidelines when adding a news item. |
| | | |
− | [[User:Clements|Dave Clements]]<br />
| + | # Create a new page named "'''News/'''''News Item Title''". |
− | [[GMOD Help Desk]]
| + | #* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''. |
| + | # Enter the text of your news item. |
| + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
| + | # Preview / save your changes. Edit and save the page until the news item looks like you want. |
| + | # Once you are happy with how the item looks, insert this line at the end of it: |
| + | : <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre> |
| | | |
− | ''2010/07/02''
| + | === Longer Instructions === |
| | | |
− | == GMOD Meeting: Sept. 13-14 ==
| + | Please follow these guidelines when adding a news item. |
| | | |
− | {{ImageRight|Cambridge.jpg|September 2010 GMOD Meeting||September 2010 GMOD Meeting}}
| + | # Create a new page named "'''News/'''''News Item Title''". |
− | Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day [[September 2010 GMOD Meeting|GMOD community meeting]] starting on Monday September 13 in Cambridge, England. This meeting occurs immediately prior to the [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics meeting] in Hinxton (for which the abstract deadline is [[Calendar|June 25]]). Registration information for this meeting will be available in a few weeks. In the mean time, you can [[September 2010 GMOD Meeting|post topic suggestions]] to the [[September 2010 GMOD Meeting|meeting page]].
| + | #* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''. |
− | | + | #* The page must start with '''News/''', otherwise it won't be picked by the RSS news feed. |
− | Please feel free to tell your colleagues and to post to mailing lists that you think would be interested in this meeting.
| + | # Enter the text of your news item. |
− | | + | |
− | I look forward to seeing you in England this Fall.
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− | | + | |
− | [[User:Scott|Scott Cain]]
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− | | + | |
− | ''2010/06/17''
| + | |
− | == New GMOD Tutorials ==
| + | |
− | | + | |
− | {{ImageRight|2010SummerSchoolAmericas170.png|Summer School - Americas||http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
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− | | + | |
− | Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[2010 GMOD Summer School - Americas]]. Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image. This year we have a [[Galaxy Tutorial]] for the first time.
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− | | + | |
− | The [[:Category:Tutorials|tutorials]] are:
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− | * '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
| + | |
− | * '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], and [[User:Jorvis|Joshua Orvis]].
| + | |
− | * '''[[Galaxy Tutorial]]''' - by [[User:JamesTaylor|James Taylor]]
| + | |
− | * '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]]
| + | |
− | * '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
| + | |
− | * '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]]
| + | |
− | * '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
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− | * '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
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− | | + | |
− | The [[2010 GMOD Summer School - Americas]] got the best [[2010 GMOD Summer School - Americas|reviews]] of any [[GMOD Summer School|course]] GMOD has ever done. I'd like to thank this year's instructors and participants for making it such a success.
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− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
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− | | + | |
− | ''2010/06/14''
| + | |
− | | + | |
− | == ISGA Pipeline Service ==
| + | |
− | | + | |
− | {{ImageRight|ISGAHomePageThumb.png|ISGA at the Center for Genomics and Bioinformatics||http://isga.cgb.indiana.edu/}}
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− | | + | |
− | [http://isga.cgb.indiana.edu/ Integrated Services for Genomic Analysis (ISGA)] is an [[Ergatis]]-based bioinformatics pipeline service based at [http://cgb.indiana.edu/ Indiana University's Center for Genomics and Bioinformatics]. ISGA is also a [http://sourceforge.net/projects/isga/ free, open-source software package] that you can install locally to provide a biologist-friendly web interface to your computational resources. ISGA currently provides prokaryotic annotation and prokaryotic assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as [[GBrowse]] and Blast for visualizing and analyzing pipeline results. Since ISGA utilizes the [[Ergatis]] workflow system to execute pipelines, ISGA pipeline can be submitted back to the Ergatis community and other Ergatis pipelines can be adapted to use ISGA. (See [[#Ergatis Update|Ergatis Update]] below for what's new with Ergatis.)
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− | | + | |
− | For more on ISGA, see the manuscript [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 "An Ergatis-based prokaryotic genome annotation web server"] in ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'', the [http://isga.cgb.indiana.edu/Help/Tutorial ISGA pipeline and account tutorials], and the [http://isga.cgb.indiana.edu/Help/FAQ ISGA FAQ page]. For help using or installing ISGA, join the [https://lists.sourceforge.net/lists/listinfo/isga-users isga-users mailing list].
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− | | + | |
− | [[User:Chemmeri|Chris Hemmerich]]
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− | | + | |
− | ''2010/06/07''
| + | |
− | | + | |
− | == MAKER 2.0, AGS Workshop ==
| + | |
− | | + | |
− | <div style="Float: right;">
| + | |
− | {|
| + | |
− | |{{ImageRight|MAKERLogo.png|MAKER 2.0 Released|170|MAKER}}<br>
| + | |
− | |-
| + | |
− | | {{ImageRight|AGSBug170.png|Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2010/seminar.html}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | [[MAKER]], the easy to use genome annotation pipeline, is now version 2.0.
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− | | + | |
− | Some of the current features and other improvements
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− | | + | |
− | * Improved gene model preparation and evidence filtering...
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− | * mRNAseq data in your annotations (use output from programs like [http://tophat.cbcb.umd.edu/ TopHat], [http://cufflinks.cbcb.umd.edu/ CuffLinks], and others in [[MAKER]])...
| + | |
− | * Annotate eukaryotes and prokayotes...
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− | * Pass through any kind of evidence evidence from any source via [[GFF3]] pass-through...
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− | * Easy single-command-line dump of MAKER output to a [[Chado]] database and to [[JBrowse]]...
| + | |
− | * Same directory parallelization - just start MAKER on top of itself, and it will share the workload with the new process...
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− | * Auto recovery - start, stop, and restart MAKER at any time; MAKER will always just pick up where it left off...
| + | |
− | * optional web base GUI for a local MAKER installation
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− | | + | |
− | | + | |
− | There will also be a [http://www.k-state.edu/agc/symp2010/seminar.html workshop on MAKER] on June 12 at the [http://www.k-state.edu/agc/symposium.shtml 4th Annual Arthropod Genomics Symposium] in Kansas City. If you are attending AGS and are interested in genome annotation, please consider attending.
| + | |
− | | + | |
− | | + | |
− | Thanks,<br />
| + | |
− | [[User:Carsonholt|Carson Holt]]
| + | |
− | | + | |
− | ''2010/06/01'' | + | |
− | | + | |
− | == Load Chado into BioMart ==
| + | |
− | <div style="float: right; text-align: center">
| + | |
− | {{#icon: Biomart250.png|Load Chado into BioMart|125|http://gmod.org/wiki/BioMart#How_to_Load_a_Chado_Database_into_BioMart}}<br /><br />
| + | |
− | {{#icon: Urgi.png|INRA URGI|105|http://urgi.versailles.inra.fr/}}
| + | |
− | </div>
| + | |
− | A group at INRA URGI have documented "[[BioMart#How to Load a Chado Database into BioMart|How to load a Chado database into BioMart]]". This step by step document details what how to configure BioMart for Chado, and includes some specific use cases useful with [[Chado]]. This guide is based on experience at [http://urgi.versailles.inra.fr/ INRA URGI], and was written by Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach.
| + | |
− | | + | |
− | If you are interested in loading your [[Chado]] data into a [[BioMart]] instance then I recommend starting with this guide.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/27'' | + | |
− | | + | |
− | == June 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | The [[Calendar|next 5 weeks]] includes the a [[MAKER]] workshop at the [http://www.k-state.edu/agc/symp2010/ Arthropod Genomics Symposium], and deadlines for [http://www.iscb.org/ismb2010-deadlines ISMB] (Boston in July), [http://www.amatameeting.org/ AMATA] (Hobart in September), [http://gi-workshop.net/ GIW] (Hangzhou in December), [http://www.eccb10.org/ ECCB] (Ghent in September), [http://incob10.hgc.jp/ InCoB] (Tokyo in September), and [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics] (Hinxton in September).
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− | | + | |
− | <div style="margin-right: 26em">
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− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100601%2F20100601</embedurl>
| + | |
− | </div>
| + | |
− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/24'' | + | |
− | | + | |
− | == gmod (Chado) 1.1 Released ==
| + | |
− | | + | |
− | I am pleased to announce that we released [https://sourceforge.net/projects/gmod/ gmod-1.1] today. This release has the GMOD database [[Glossary#Schema|schema]], [[Chado]], and a variety of tools for loading and working with the database. The release can be downloaded from the [https://sourceforge.net/projects/gmod/ GMOD SourceForge site].
| + | |
− | | + | |
− | There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank [[User:RobertBuels|Rob Buels]] and [[User:NaamaMenda|Naama Menda]] and the rest of the people at the [http://solgenomics.net/ Sol Genomics Network (SGN)] for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate [[Chado CV Module#Transitive Closure|cvterm closures]].
| + | |
− | | + | |
− | There have been many changes and bug fixes since the [[GMOD News Archives#GMOD 1.0 Released|1.0 release just over two years ago]], but the schema itself has changed very little.
| + | |
− | For a [[Glossary#SQL|SQL]] summary of the changes, see [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes.sql?revision=23255&view=markup <tt>Changes.sql</tt>] in the release that contains SQL statements that should take a 1.0 release of the [[Chado]] schema to the 1.1 schema. See the [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes?revision=23255&view=markup <tt>Changes</tt>] file for a full list.
| + | |
− | | + | |
− | If you have been using Chado from a recent [[SVN|svn]] checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.
| + | |
− | | + | |
− | Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the [[Chado Natural Diversity Module Working Group|Natural Diversity]] schema modifications being worked on now.
| + | |
− | | + | |
− | Thanks for your continued support of the GMOD project,
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | | + | |
− | ''2010/05/24'' | + | |
− | | + | |
− | == GMOD in Boston in July? ==
| + | |
− | | + | |
− | From Scott on 2010/05/25:
| + | |
− | <div class="emphasisbox">
| + | |
− | Due to the short notice, I've decided not to have a GMOD meeting
| + | |
− | before BOSC/ISMB in July. I am hoping to plan an informal "GMOD
| + | |
− | lunch" sometime during BOSC or ISMB for people who are going to the
| + | |
− | meetings and would like to get together to chat.
| + | |
− | </div>
| + | |
− | | + | |
− | Scott Cain sent this question about the next [[Meetings|GMOD meeting]] out to several [[GMOD Mailing Lists|mailing lists]] on May 17:
| + | |
− | <div class="quotebox">
| + | |
− | Since the last GMOD meeting in January, I had been hoping to have a
| + | |
− | [[Meetings|GMOD meeting]] around the ISMB and BOSC meetings in Boston this July.
| + | |
− | Until this week, though, I had had a difficult time finding a place
| + | |
− | where a meeting could be held for a reasonable price. However, a kind
| + | |
− | soul at The Broad has offered a meeting space that would easily
| + | |
− | accommodate a GMOD meeting for two days before BOSC (either July 6-7
| + | |
− | or July 7-8). The only question I have is this: can people make it to
| + | |
− | a GMOD meeting with about 2 months notice? Please let me know your
| + | |
− | thoughts on this. While there would probably be a registration fee,
| + | |
− | it would be fairly low (I'm guessing in the ballpark of $50).
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | </div>
| + | |
− | Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. '''If you have any thoughts on this, please [mailto:scott@scottcain.net send them to Scott] before 3pm Eastern US time on Monday, May 24.''' See the GMOD [[Calendar]] for a list of what else is going on in July.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/21, updated 2010/05/25''
| + | |
− | | + | |
− | == Ergatis Update ==
| + | |
− | | + | |
− | {{ImageRight|BionformaticsCover.gif|Ergatis Paper in Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1}}
| + | |
− | | + | |
− | The paper "[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1 Ergatis: A web interface and scalable software system for bioinformatics workflows]" is now available as an advance access manuscript in the journal ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]''. [[Ergatis]] "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."
| + | |
− | | + | |
− | Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.
| + | |
− | | + | |
− | New tools available that use Ergatis include [http://clovr.igs.umaryland.edu CloVR], which enables bioinformatic pipeline execution in compute clouds and the recently-awarded [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0959894 Data Intensive Academic Grid (DIAG)], which will provide a publicly-accessible Ergatis instance as one of its access methods. At the [[January 2010 GMOD Meeting]] Chris Hemmerich [[:Image:Jan2010ErgatisForBiologists.pdf|presented ISGA]], which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.
| + | |
− | | + | |
− | [[User:Jorvis|Joshua Orvis]]
| + | |
− | | + | |
− | ''2010/05/20''
| + | |
− | | + | |
− | | + | |
− | == May 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | The [[Calendar|next 5 weeks]] includes the [[2010 GMOD Summer School - Americas]] and the first [[Galaxy]] Developers Conference. Upcoming deadlines include the ISMB technology track (tomorrow), posters at Arthropod Genomics and ECCB10, and papers for GIW 2010.
| + | |
− | | + | |
− | <div style="margin-right: 24em">
| + | |
− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100501%2F20100501</embedurl>
| + | |
− | </div>
| + | |
− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/04/22''
| + | |
− | | + | |
− | == MaizeGDB: Choosing GBrowse ==
| + | |
− | | + | |
− | {{ImageRight|MaizeGDB.gif|Database Paper||http://database.oxfordjournals.org/cgi/content/abstract/baq007}}
| + | |
− | | + | |
− | A paper, "[http://database.oxfordjournals.org/cgi/content/abstract/baq007 Choosing a genome browser for a Model Organism Database: surveying the Maize community]," by the [http://maizegdb.org MaizeGDB] team has been published in ''[http://database.oxfordjournals.org/ Database].'' To prepare for the availability of a reference genome, MaizeGDB surveyed their community to assess genome visualization needs. This paper summarizes the survey and MaizeGDB's review of available browsers, and describes why they chose [[GBrowse]]. The paper finishes by describing how they implemented GBrowse, including the ''locus lookup tool'' ([http://bioinformatics.oxfordjournals.org/cgi/content/short/26/3/434 described here]), a MaizeGDB extension that uses maize's extensive physical and genetic mapping data to localize genomic regions in GBrowse. This is a great paper for anyone considering which genome browser to use.
| + | |
− | | + | |
− | {{ImageRight|DatabaseJournal.jpg|Database Journal|265|http://database.oxfordjournals.org/}}
| + | |
− | I'd also like to highlight the journal the paper appears in: ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation].'' "Biological Databases and Curation" are what GMOD is about and many of the papers cover issues and resources that are widely applicable in the GMOD community. The [http://database.oxfordjournals.org/content/vol2010/issue0/index.dtl current issue] also includes papers on [http://database.oxfordjournals.org/cgi/content/abstract/2010/0/baq009 community annotation using wikis], and [http://database.oxfordjournals.org/cgi/content/abstract/2010/0/baq001 a report on best practices in genome annotation] from the [http://biocurator.org/ ISB] [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html 3<sup>rd</sup> International Biocuration Conference]. ''Database'' is an open access publication, making it an even better match for GMOD.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/04/19''
| + | |
− | == YAPC::NA 2010 is Almost Here! ==
| + | |
− | | + | |
− | <div style="float: right; background-color: #121315">{{#icon: Yapc2010Logo.png|YAPC::NA 2010|220|http://conferences.mongueurs.net/yn2010/}}</div>
| + | |
− | | + | |
− | June 21st – 23rd 2010 is quickly approaching and Columbus.PM is getting very excited. Hotel reservation information is available, dorm reservation details are up and ready, the conference is quickly approaching. For everyone still looking for [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010 (Yet Another Perl Conference North America)] details, here is what we have planned. The conference will be held in the brand new beautiful [http://conferences.mongueurs.net/yn2010/wiki?node=ConferenceSummary The Ohio State Union].
| + | |
− | | + | |
− | Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.
| + | |
− | | + | |
− | The main dorm location is Morrison Tower and the Hotel conference block is in The Blackwell Inn (see [http://conferences.mongueurs.net/yn2010/wiki?node=Accommodations Accommodations]). Early registration is quickly coming to an end so make sure that you forward this to all of your friends and coworkers and get signed up
| + | |
− | today!
| + | |
− | | + | |
− | I hope to see you all at [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] in beautiful Columbus, Ohio.
| + | |
− | | + | |
− | Heath Bair<br />
| + | |
− | [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] Conference Chairman
| + | |
− | | + | |
− | ''2010/04/13''
| + | |
− | | + | |
− | == Don Gilbert Nominated for BFA ==
| + | |
− | | + | |
− | {{ImageRight|BioinformaticsOrganization.png|Don Gilbert Nominated for Benjamin Franklin Award|140|http://www.bioinformatics.org/franklin/}}
| + | |
− | | + | |
− | The Bioinformatics Organization has announced its nominees for the the [http://www.bioinformatics.org/forums/forum.php?forum_id=7956 2010 Benjamin Franklin Award].
| + | |
− | | + | |
− | <div class="indent">
| + | |
− | The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.
| + | |
− | </div>
| + | |
− | This year's nominees include longtime GMOD contributor [[User:Dongilbert|Don Gilbert]], of Indiana University. Other 2010 nominees are Alex Bateman, David J. Lipman, G.P.S. Raghava, and John Quakenbush. Previous winners of the BFA include [http://www.bioinformatics.org/franklin/2003/ Jim Kent], Michael Ashburner, and another long-time GMOD contributor [http://www.bioinformatics.org/franklin/2004/ Lincoln Stein].
| + | |
− | | + | |
− | ''If you want a say on who should receive the 2010 award, please go to [http://www.bioinformatics.org/forums/forum.php?forum_id=7956 Bioinformatics.org] and cast your vote.'' If you are not already a member you will need to [http://www.bioinformatics.org/account/register.php join], but basic membership is free.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/04/01''
| + | |
− | | + | |
− | == April 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | There's a lot on the [[calendar]] in the next 5 weeks, including (among others) registration deadlines for Arthropod Genomics (early) and the Galaxy Developers Conference, and submission deadlines for ECCB, iEvoBio, BOSC, and ISMB.
| + | |
− | | + | |
− | <div style="margin-right: 26em">
| + | |
− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100401%2F20100401</embedurl></div>
| + | |
− | | + | |
− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/03/25''
| + | |
− | | + | |
− | == Google Summer of Code & OBF ==
| + | |
− | | + | |
− | {{ImageRight|OBF logo.png|OBF in GSoC||http://open-bio.org/wiki/Google_Summer_of_Code}}
| + | |
− | Great news: the [http://open-bio.org/wiki/Google_Summer_of_Code Open Bioinformatics Foundation (OBF)] has been accepted as a mentoring organization for this summer's Google Summer of Code!
| + | |
− | | + | |
− | GSoC is a Google-sponsored student internship program for open-source projects, open to students from around the world (not just US residents). Students are paid a $5000 USD stipend to work as a developer on an open-source project for the summer. For more on GSoC, see the [http://open-bio.org/wiki/Google_Summer_of_Code GSoC 2010 FAQ].
| + | |
− | | + | |
− | Student applications are due April 9, 2010 at 19:00 UTC. Students who are interested in participating should look at the [http://open-bio.org/wiki/Google_Summer_of_Code OBF's GSoC page], which lists project ideas, and who to contact about applying.
| + | |
− | | + | |
− | For current developers on OBF projects, please consider volunteering to be a mentor if you have not already, and contribute project ideas. Just list your name and project ideas on OBF wiki and on the relevant project's GSoC wiki page.
| + | |
− | | + | |
− | Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!
| + | |
− | | + | |
− | [[User:RobertBuels|Rob Buels]]
| + | |
− | | + | |
− | [http://open-bio.org/wiki/Google_Summer_of_Code OBF GSoC 2010 Administrator]
| + | |
− | | + | |
− | ''2010/03/21''
| + | |
− | | + | |
− | == InterMine is Hiring ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine is hiring|180|http://intermine.org/wiki/NowHiring}}
| + | |
− | | + | |
− | We have [http://intermine.org/wiki/NowHiring four vacancies] on [[InterMine]] related projects at The University
| + | |
− | of Cambridge, UK. We are looking for a Web Developer, Bioinformatics Software Developers and a Java Developer. See [http://intermine.org/wiki/NowHiring the position descriptions] for more information.
| + | |
− | | + | |
− | The closing date for applications is 2nd April 2010.
| + | |
− | | + | |
− | The [[InterMine]] Team.
| + | |
− | | + | |
− | ''2010/03/19''
| + | |
− | | + | |
− | == Internships @ Dow AgroSciences ==
| + | |
− | | + | |
− | {{ImageRight|das_header_logo.gif|Dow AgroSciences|200}}
| + | |
− | | + | |
− | [http://www.bioinformatics.org/forums/forum.php?forum_id=7919 Dow AgroSciences has 7 Bioinformatics summer internship positions open], 2 of which are related to GMOD. We are looking for candidates with experience in installing, configuring, and uploading data into GMOD. Experience with the [[GBrowse]] source code and modifying it to create new views (e.g creating new glyphs and modifying existing glyphs as per user needs) is highly preferred. We have started the interview process. Please email your resume ASAP to Navin Elango ([mailto:nelango@dow.com nelango@dow.com]). For more information about Dow AgroSciences, please visit our [http://www.dowagro.com/homepage/index.htm website]
| + | |
− | | + | |
− | Navin Elango
| + | |
− | | + | |
− | ''2010/03/16''
| + | |
− | | + | |
− | == Sr. DB Programmer @ FlyBase ==
| + | |
− | | + | |
− | {{ImageRight|Fly_logo.png|FlyBase Opening|200}}
| + | |
− | | + | |
− | [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=20510BR FlyBase has a single opening for a developer] to join the database team at Harvard University in Cambridge, Mass. The position consists of roles in two model organism database projects, [http://vectorbase.org VectorBase] and [http://flybase.org FlyBase], in the development and maintenance of production applications involving [[Chado]], [[Apollo]], Ensembl, and [[InterMine]]. For more information, see the [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=20510BR job posting].
| + | |
− | | + | |
− | Dave Emmert
| + | |
− | | + | |
− | ''2010/03/09'' | + | |
− | | + | |
− | == NGS Analyses in Galaxy ==
| + | |
− | | + | |
− | {{ImageRight|GalaxyLogoSmall.png|NGS Analyses in Galaxy||http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service}}
| + | |
− | The Galaxy team is [http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service announcing the launch of the first free public resource for NGS analysis]. This service is the beginning of our campaign to provide free web-based utilities for [[Next Generation Sequencing|NGS]] analysis and later in the year will take advantage of the Cloud resources. At present, there are three main groups of tools including:
| + | |
− | | + | |
− | # '''NGS QC and manipulation''' - contains a variety of tools for dealing with all flavors of fastq datasets as well as outputs of SOLiD and 454 instruments. | + | |
− | # '''NGS Mapping''' - currently includes [http://bowtie-bio.sourceforge.net/ Bowtie] (Illumina & SOLiD), [http://bio-bwa.sourceforge.net/ BWA] (Illumina), and [http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.01.50/README.lastz-1.01.50.html LASTZ] (454) mappers. [http://code.google.com/p/perm/ PerM] (SOLiD) is on the way and more will be added in the coming months. Transcriptome tools are also in the final stages of development.
| + | |
− | # '''NGS [http://samtools.sourceforge.net SAMTools]''' - includes a variety of utilities for SAM/BAM manipulation. Some are based on SAMtools library, some are written by [[Galaxy]] team.
| + | |
− | | + | |
− | See the [http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service announcement page] for more information and for links to several Galaxy ''Quickies'' (video tutorials) demonstrating the new service.
| + | |
− | | + | |
− | Anton Nekrutenko
| + | |
− | | + | |
− | ''2010/03/08''
| + | |
− | | + | |
− | == Openings @ SGD ==
| + | |
− | | + | |
− | {{ImageRight|SGD-t.gif|Scientific Application Programmers at SGD||http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer}}
| + | |
− | There are [http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer 3 openings for Scientific Application Programmers] at the [http://yeastgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast. These positions will be involved in enhancing databases and data pipelines for the sharing of genomic data. See the [http://recruit.trovix.com/jobhostmaster/jobhost/ListJobPosts.do?action=search&searchSectionActive=false&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&searchCategory=1424&searchStatus=226&searchKeywords=Scientific+Application+Programmer job postings] for more information.
| + | |
− | | + | |
− | [[:Category:SGD|SGD]] is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user.
| + | |
− | | + | |
− | ''2010/03/05''
| + | |
− | | + | |
− | == Logo Program Deadline Extended ==
| + | |
− | | + | |
− | {{ImageRight|Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
| + | |
− | '''The first call to participate in the [[GMOD Logo Program]] has been extended to March 19.'''
| + | |
− | | + | |
− | We still have some room for additional participants. If you are interested, please [[GMOD Logo Program|submit an application]]. '''Participation is limited to non-profits, and costs US$75.''' Please see the [[GMOD Logo Program|program page]] for additional details and requirements, and a link to an application form.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/03/03''
| + | |
− | | + | |
− | == March 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | There is always a lot going on that is of interest to the GMOD community. Anything that GMOD staff knows about is added to the GMOD [[Calendar]]. I'm going to start posting the GMOD calendar here for the upcoming month.
| + | |
− | | + | |
− | <div style="margin-right: 26em">
| + | |
− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100301%2F20100301</embedurl>
| + | |
− | </div>
| + | |
− | Please [mailto:help@gmod.org let me know] if this is useful, and I'll keep doing it. If not, I'll stop and the GMOD News will be a little less cluttered.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/02/22''
| + | |
− | | + | |
− | == GMOD Logo Program, Spring 2010 ==
| + | |
− | | + | |
− | <div style="float: right; text-align: center">
| + | |
− | {{#icon: Gmod_cog170.png|The GMOD Logo||GMOD Logo Program}}<br>
| + | |
− | {{#icon: Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
| + | |
− | </div>
| + | |
− | I am pleased to announce the first call for participation in the [[GMOD Logo Program]]. This program is for GMOD users and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced design class at [[GMOD Logo Program#Linn-Benton Community College|Linn-Benton Community College]]. Interested GMOD users and developers will be paired with students and meet several times (remotely) over a 3 week period this spring, with the end result being a new logo.
| + | |
− | | + | |
− | '''Participation is limited to non-profits, and costs US$75.''' If you are interested, please see the [[GMOD Logo Program|program page]] for additional details and requirements, and an application form. '''The program is accepting applications until March 1.''' | + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/02/03''
| + | |
− | | + | |
− | == GMOD Summer School - Americas ==
| + | |
− | | + | |
− | We are now [[2010 GMOD Summer School - Americas|accepting applications]] for the [[2010 GMOD Summer School - Americas]]. This will be a hands-on multi-day course aimed at teaching new GMOD administrators how to get [[GMOD Components]] up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular [[GMOD Components]].
| + | |
− | | + | |
− | The course will be held May 6-9, at [http://nescent.org NESCent] in Durham, NC. These [[GMOD Components]] will be covered:
| + | |
− | {|
| + | |
− | | align="center" |
| + | |
− | {{#icon: 2010SummerSchoolAmericas170.png|GMOD Summer School||2010 GMOD Summer School - Americas}}<br>
| + | |
− | <div style="font-size:120%">'''[[2010 GMOD Summer School - Americas|Apply Now]]'''</div>
| + | |
− | |
| + | |
− | |
| + | |
− | * [[Apollo]] - genome annotation editor
| + | |
− | * [[Chado]] - a modular and extensible database schema
| + | |
− | * [[Galaxy]] - workflow system
| + | |
− | * [[GBrowse]] - the Generic Genome Browser
| + | |
− | * [[GBrowse_syn]] - A generic synteny browser
| + | |
− | * [[JBrowse]] - genome browser
| + | |
− | * [[MAKER]] - Genome annotation pipeline
| + | |
− | * [[Tripal]] - Web front end for [[Chado]]
| + | |
− | |}
| + | |
− | '''The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest).''' In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be automatically placed on the waiting list.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | {|
| + | |
− | | valign="top" | PS:
| + | |
− | | We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the [[GMOD Mailing Lists]] and the [[GMOD News]] for updates.
| + | |
− | |}
| + | |
− | ''2010/01/29''
| + | |
− | | + | |
− | == GMOD @ February NextGenBUG ==
| + | |
− | | + | |
− | {{ImageRight|SBForumLogo.png|NextGenBUG 9 Feb Dundee|140|http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209}}
| + | |
− | If you are anywhere close to Dundee, Scotland on 9 February, consider attending the [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 NextGen Sequencing Bioinformatics User Group (NextGenBUG) meeting] being held at the [http://www.lifesci.dundee.ac.uk/visit University of Dundee]. The program includes two talks with GMOD related content.
| + | |
− | | + | |
− | * '''[http://insectacentral.org InsectaCentral] - assembling and annotating insect transcriptomes''', Alexie Papanicolau, Exeter
| + | |
− | *: [http://insectacentral.org InsectaCentral] uses [[GMOD Components]] (including [[Chado]] and [[GBrowse]]) extensively in its infrastructure.
| + | |
− | | + | |
− | * '''[[Galaxy]]: a stairway to [[Next Generation Sequencing|NGS]] heaven''', Chris Cole, Dundee
| + | |
− | *: Chris will be discussing how Dundee uses [[Galaxy]] to process their [[next generation sequencing]] data.
| + | |
− | | + | |
− | There will also be talks by [[User:DanBolser|Dan Bolser]] of Dundee and Darrol Baker of CLCBio. If you are interested in attending, please [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 add your name to the participants list].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/29
| + | |
− | | + | |
− | == GBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|GBrowse2Thumb.png|||GBrowse 2.0 HOWTO}}
| + | |
− | With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that [[GBrowse 2.0 HOWTO|GBrowse 2.00]] is now available for downloading from [http://search.cpan.org/dist/GBrowse/ CPAN], and [https://sourceforge.net/projects/gmod/files/ SourceForge].
| + | |
− | | + | |
− | The following are highlights of the many new features that have been added since the 1.70 release:
| + | |
− | | + | |
− | * A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
| + | |
− | * Different [[GBrowse 2.0 HOWTO#Database Definitions|database backends]] can be associated with each track, making backend management much simpler.
| + | |
− | * A revamped user interface for a less cluttered and more functional end-user experience.
| + | |
− | * A [[GBrowse 2.0 HOWTO#Themes|UI theming system]] with three predefined themes, including a cool "transparent" theme.
| + | |
− | * A custom [[GBrowse 2.0 HOWTO#Configuring the Uploaded Track Database|track upload and management system]] gives users much greater control over custom tracks.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#The Admin Interface|admin interface]] allows an authorized user to upload and manage public tracks without editing config files.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#Configuring the User Account Database|user registration and login system]] allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
| + | |
− | * Support for named subtracks (tracks within tracks) and filtering of those subtracks.
| + | |
− | * Support for [[GBrowse NGS Tutorial|next generation sequencing]] data.
| + | |
− | | + | |
− | There are also a number of features that ''didn't'' make it into the 2.00 release, most notably:
| + | |
− | | + | |
− | * The internal [[DAS]] server does not work, although the DAS client (ability to import DAS tracks) does. This will be added in a 2.01 release.
| + | |
− | * Internationalization has lagged way behind, and so most of the new features will be presented in English rather than in the user's preferred language (volunteers are needed to help with translations).
| + | |
− | | + | |
− | Please send help queries to the [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse GBrowse mailing list], and file [https://sourceforge.net/tracker/?group_id=27707&atid=391291 bug reports at SourceForge].
| + | |
− | | + | |
− | On behalf of the GMOD team,
| + | |
− | | + | |
− | [[User:Lstein|Lincoln Stein]]
| + | |
− | | + | |
− | ''2010/01/28''
| + | |
− | | + | |
− | == WebGBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://webgbrowse.cgb.indiana.edu/}}
| + | |
− | | + | |
− | [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] is now available at http://webgbrowse.cgb.indiana.edu. Here is some of ''what's new'' in WebGBrowse 2.0:
| + | |
− | * [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] continues to help the inexperienced users of [[GBrowse]] with hosting their [[GFF3]] data without worrying about installation or configuration semantics.
| + | |
− | * Users now have a choice of [[GBrowse]] display between versions 1.7 and 2.0.
| + | |
− | * The display from one version can be migrated to the other by simple button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.
| + | |
− | * A few bug fixes from the earlier version.
| + | |
− | * For those interested in installing WebGBrowse locally, the current installation package is lot more easier to install and less clumsy than the previous version.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | Ram Podicheti<br />
| + | |
− | [http://cgb.indiana.edu/ Center for Genomics and Bioinformatics<br />Indiana University]
| + | |
− | | + | |
− | ''2010/01/25''
| + | |
− | | + | |
− | == Tripal v0.2 Released ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Triapl|120|Tripal}}
| + | |
− | I’d like to announce the release of the second version of [[Tripal]], v0.2. This version provides new support for [[Chado CV Module|controlled vocabularies]], [[Chado General Module|databases]] and several [[Chado Companalysis Module|analysis]] types. This includes better support and visualizations for [http://geneontology.org GO], new [http://www.genome.jp/kegg/pathway.html KEGG pathways] and [http://www.genome.jp/kegg/brite.html BRITE hierarchies], [http://www.ebi.ac.uk/Tools/InterProScan/ InterProScan] results and improved BLAST results.
| + | |
− | | + | |
− | [[Tripal]] has been freely and publicly available since May of 2009 and provides a PHP-based [http://drupal.org Drupal] front-end for the [[Chado]] database schema. It his highly customizable and is extendable by anyone with Drupal and PHP experience. We encourage end-users to develop new or improved modules that can be shared back with the community. We can offer assistance when needed in the development of new modules.
| + | |
− | | + | |
− | An updated [[Media:TripalUsersGuideJan2010.pdf|user’s manual]] is available, but not quite complete. An update to the manual will be added soon. If you have any questions please feel free to email the [https://lists.sourceforge.net/lists/listinfo/gmod-tripal Tripal mailing list] for assistance.
| + | |
− | | + | |
− | Tripal can be [http://www.genome.clemson.edu/software/tripal downloaded from the CUGI website] as a compressed package, or developers can retrieve the most up-to-date code from the GMOD [[SVN]].
| + | |
− | | + | |
− | Best Regards,
| + | |
− | | + | |
− | [[User:Sficklin|Stephen Ficklin]]<br />
| + | |
− | [http://www.genome.clemson.edu/ Clemson University Genomics Institute]
| + | |
− | | + | |
− | ''2010/01/23''
| + | |
− | | + | |
− | == CMap3D ==
| + | |
− | | + | |
− | {{ImageRight|CMap3DScreenshot.png|CMap3D|220|CMap3D}}
| + | |
− | [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D] is a 3D visualisation tool for comparative genetic maps that runs on top of a [[CMap]] database. [[CMap]], a [[GMOD Components|GMOD component]], is a common tool for the storage, comparison and visualisation of genetic maps. However, current map visualisation in CMap is limited to the comparison of adjacent aligned maps. CMap3D overcomes this limitation. Multiple genetic maps can now be compared in three-dimensional space. The CMap3D visualisation tool is based on a client server model ensuring operability with current [[CMap]] data repositories.
| + | |
− | | + | |
− | [[CMap3D]] can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. For more on [[CMap3D]] see the [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D page] at the [http://acpfg.imb.uq.edu.au/ Australian Centre for Plant Functional Genomics (ACPFG)], the [[:Image:PAG2010CMap3D.pdf|PAG 2010 presentation on CMap3D]] (and other tools), and the [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/2/273 CMap3D paper] in [http://bioinformatics.oxfordjournals.org/ Bioinformatics].
| + | |
− | | + | |
− | Chris Duran
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | == DAS Workshop 7-9 April 2010 ==
| + | |
− | | + | |
− | {{ImageRight|Das_logo_64x64.jpg|DAS Workshop||http://www.ebi.ac.uk/training/handson/DAS_070410.html}}
| + | |
− | There will be a [http://www.ebi.ac.uk/training/handson/DAS_070410.html Distributed Annotation System (DAS) Workshop] at [http://www.ebi.ac.uk/ EBI], 7-9 April 2010. In GMOD, DAS is supported by [[GBrowse]], and [[Chado]] (and DAS support in [[Apollo]] is in the works).
| + | |
− | | + | |
− | If you don't know about [[DAS]] and wish to know how to distribute your latest biological annotation to the world then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] may be for you.
| + | |
− | | + | |
− | If you know about [[DAS]] and are maybe a DAS client developer then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software).
| + | |
− | | + | |
− | See the [http://www.ebi.ac.uk/training/handson/DAS_070410.html workshop page] for more information and registration details.
| + | |
− | | + | |
− | [[User:JWarren|Jonathan Warren]]
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | | + | |
− | == GBrowse.org ==
| + | |
− | | + | |
− | <div style="float:right; padding: 0em 0.5em; font-size: 110%; border: 3px #d0d0d0 solid; margin-left: 1em; margin-bottom: 1em; padding-bottom: 0.25em">
| + | |
− | {|
| + | |
− | |{{#icon: GBrowseOrgOrig.png|GBrowse.org|80|http://www.gbrowse.org/}}
| + | |
− | |-
| + | |
− | | align="center" | <span class="plainlinks">[http://www.gbrowse.org GBrowse.org]</span>
| + | |
− | |}
| + | |
− | </div>
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] is a resource for using and setting up [[GBrowse]] genome browsers. The site provides one location where biologists and bioinformaticians can find:
| + | |
− | | + | |
− | # Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it.
| + | |
− | # Links to sequence and annotation files that are available online.
| + | |
− | # Links to genome browser configuration files, when available
| + | |
− | # An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site.
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] emphasizes the [[GBrowse]] genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and [[JBrowse]].
| + | |
− | | + | |
− | <div class="emphasisbox" style="font-size: 120%; text-align: center">
| + | |
− | Also, we are currently conducting a [http://gbrowse.org/survey/index.php?sid=64264&lang=en survey] seeking input on future project direction. Please take a few minutes now to [http://gbrowse.org/survey/index.php?sid=64264&lang=en provide your feedback].
| + | |
− | </div>
| + | |
− | | + | |
− | GBrowse.org was first introduced at the [[August 2009 GMOD Meeting#GBrowse.org|August 2009 GMOD Meeting]].
| + | |
− | | + | |
− | Ciao,
| + | |
− | | + | |
− | [[User:Bilardi|Alessandra Bilardi]]<br />
| + | |
− | [http://genomics.cribi.unipd.it/Main_Page CRIBI Genomics, University of Padua]
| + | |
− | | + | |
− | ''2010/01/11''
| + | |
− | | + | |
− | == Bio::Chado::Schema 0.05 Released ==
| + | |
− | | + | |
− | I'd like to announce a new [[Bio::Chado::Schema]] release, version 0.05. Changes in this release:
| + | |
− | | + | |
− | * Got POD generation working, now all classes and methods have POD, '''including''' the embedded table and column comments! Thanks to the wonderful DBIx::Class::Schema::Loader folks.
| + | |
− | * Turned off DBIC's cascade_delete and cascade_copy on all relations (thanks to Siddhartha Basu for troubleshooting). Deletes break if these are on and you don't have every part of the schema installed.
| + | |
− | | + | |
− | I [http://search.cpan.org/dist/Bio-Chado-Schema/ uploaded] it to [http://cpan.org CPAN] a week ago, so it should have propagated by now to almost all of the CPAN mirrors.
| + | |
− | | + | |
− | See the [[Bio::Chado::Schema]] wiki page for more on what [[Bio::Chado::Schema]] is and what it's for.
| + | |
− | | + | |
− | [[User:RobertBuels|Rob Buels]]<br>
| + | |
− | [[:Category:SGN|SGN]]
| + | |
− | | + | |
− | ''2010/01/08''
| + | |
− | | + | |
− | == GMOD at PAG 2010 ==
| + | |
− | | + | |
− | GMOD will once again have a strong presence at the [[PAG 2010|Plant and Animal Genome Conference (PAG 2010)]], being held January 9-13 in San Diego. There will be [[PAG 2010|'''over 45 talks, workshops, demonstrations and posters''']] about [[GMOD Components]] and projects that use them. See the [[PAG 2010]] page for a full listing and a flier showing highlights. Highlights at [[PAG 2010]] include:
| + | |
− | {{ImageRight|Paglogo.gif|GMOD @ PAG||PAG 2010}}
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_913.html Animal Genomics with Galaxy], Saturday
| + | |
− | * [[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]], Saturday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI] (including [[BioMart]]), Sunday
| + | |
− | * [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop]], Sunday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_858.html GBrowse And Next Generation Sequencing Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C02_PAGXVIII_938.html GMOD Project Update], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_919.html Using the JBrowse Genome Browser with Large Amounts of Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_859.html Visualizing And Comparing Genomes] ([[CMap]]), Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_861.html Comparative Genomics Tools In GMOD], Monday
| + | |
− | * [http://www.intl-pag.org/18/18-gramene.html Using Gramene] (including [[CMap]]), Tuesday
| + | |
− | * [[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn]], Wednesday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_931.html Tripal: a Construction Toolkit for Online Genomic Databases], Wednesday
| + | |
− | | + | |
− | Many GMOD staff and developers ([[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], [[User:Sficklin|Stephen Ficklin]], [[User:Carsonholt|Carson Holt]], [[User:Mckays|Sheldon McKay]], Anton Nekrutenko, [[User:MitchSkinner|Mitch Skinner]], Ken Youens-Clark) and even more GMOD users will be at PAG. If you are attending please keep an eye open for us.
| + | |
− | | + | |
− | Finally, the [[January 2010 GMOD Meeting]] is being held immediately after PAG. The meeting is full (you are encouraged to add your name to the short waiting list), but there will be several [[January 2010 GMOD Meeting#Satellite Meetings|Satellite Meetings]], ''held during PAG'', that you can attend even if you don't go to the main GMOD Meeting.
| + | |
− | | + | |
− | See you in San Diego,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/05''
| + | |
− | | + | |
− | <endFeed />
| + | |
− | | + | |
− | = [[GMOD News Archives|News Archives]] =
| + | |
− | | + | |
− | Items more than 6 months old are available in the [[GMOD News Archives]].
| + | |
− | | + | |
− | = Adding a News Item =
| + | |
− | | + | |
− | '''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
| + | |
− | | + | |
− | This page generates both an RSS feed and updates the GMOD News list on the [[Main Page|home page]]. Therefore, please follow these guidelines when adding a news item.
| + | |
− | # Edit the [[#News Items|News Items]] section of this page. This will allow you to see how big your news item title is, compared to existing news items. | + | |
− | # Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
| + | |
− | # Title
| + | |
− | #* '''Use a short title. Titles should be small enough to fit on a single line in the GMOD News list on the [[Main Page|home page]]'''.
| + | |
− | #* Place the title in a second level heading: <tt>== Your Title ==</tt>
| + | |
− | # News Text
| + | |
| #* Make the news item succinct. | | #* Make the news item succinct. |
− | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' | + | #* Do not start the item with a MediaWiki header ("== Header =="). |
− | #* End the news item with your name and the date in the format ''YYYY/MM/DD''. | + | #** It won't render very well. You should be able to avoid headers altogether. |
− | # Preview your changes | + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
− | #* Check the table of contents. Is the title no longer than any previous title? Is the title at the same depth as the other news item titles?
| + | #** For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' |
− | #* Check the news item. Does the text look good, does it look like the other news items, and does the first link point to where you want it to? | + | #* You can include images in your news item. See [[:Category:News Items|preexisting news items]] for what markup to use to do this. |
− | #* '''Make sure that your MediaWiki markup (links, italics, etc.) is correct.''' The MediaWiki extension that lists news items on the [[Main Page|home page]] is temperamental. Incorrect markup can lead to garbage on the home page. | + | # Preview / save your changes. Edit and save the page until the news item looks like you want. |
− | #* Revise until you like it and then save it.
| + | # Once you are happy with how the item looks, insert this line at the end of it: |
− | | + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre> |
− | Once you have saved the page, a link to the new item will show up on the home page in about an hour. (Why the delay? It uses an RSS feed of this page and it queries the feed infrequently.) | + | #: Where ''yyyy/mm/dd'' is the current date. This line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour. |
| + | # '''Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.''' |
| + | #* Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line: |
| + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}</nowiki></pre> |
| | | |
− | [[Category:GMOD Community]] | + | [[Category:GMOD_Community]] |
News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the GMOD News Archives. See also the GMOD Calendar and Events List.
GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the GMOD News and GMOD News Archives pages, and in the news tracker on the home page.
Please follow these guidelines when adding a news item.
Please follow these guidelines when adding a news item.