Difference between revisions of "GMOD News"

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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]].
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<wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" />
 
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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">
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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 =
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Want to add your news item here?  See [[#Adding a News Item|Adding a News Item]] below for how to do just that.
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<startFeed />
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<!-- Add new Items here.  Keep the Title Short!  ***35 characters or less*** -->
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== May 2010 Calendar ==
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{{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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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.
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<div style="margin-right: 24em">
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<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100501%2F20100501</embedurl>
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</div>
 
</div>
If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
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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]].
  
Thanks,
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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]]
  
[[User:Clements|Dave Clements]]<br />
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== Recent News ==
[[GMOD Help Desk]]
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''2010/04/22''
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<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>
  
== MaizeGDB: Choosing GBrowse ==
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== [[GMOD News Archives|News Archives]] ==
  
{{ImageRight|MaizeGDB.gif|Database Paper||http://database.oxfordjournals.org/cgi/content/abstract/baq007}}
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The [[GMOD News Archives]] lists all news items since autumn 2007.
  
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.
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== Adding a News Item ==
  
{{ImageRight|DatabaseJournal.jpg|Database Journal|265|http://database.oxfordjournals.org/}}
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'''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.
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.
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[[User:Clements|Dave Clements]]<br />
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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]].
[[GMOD Help Desk]]
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''2010/04/19''
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=== Short Instructions ===
== YAPC::NA 2010 is Almost Here! ==
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<div style="float: right; background-color: #121315">{{#icon: Yapc2010Logo.png|YAPC::NA 2010|220|http://conferences.mongueurs.net/yn2010/}}</div>
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Please follow these guidelines when adding a news item.
  
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 plannedThe conference will be held in the brand new beautiful [http://conferences.mongueurs.net/yn2010/wiki?node=ConferenceSummary The Ohio State Union].
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# Create a new page named "'''News/'''''News Item Title''".
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#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
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# Enter the text of your news item.
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#* '''The first link in the news item should point to the page/URL you want the RSS feed to link to.
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# Preview / save your changesEdit and save the page until the news item looks like you want.
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# Once you are happy with how the item looks, insert this line at the end of it:
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: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
  
Larry Wall, Damian Conway, Randal Schwartz, and many others will be in attendance.
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=== Longer Instructions ===
  
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
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Please follow these guidelines when adding a news item.
today!
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I hope to see you all at [http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] in beautiful Columbus, Ohio.
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# Create a new page named "'''News/'''''News Item Title''".
 
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#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
Heath Bair<br />
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#*  The page must start with '''News/''', otherwise it won't be picked by the RSS news feed.
[http://conferences.mongueurs.net/yn2010/ YAPC::NA 2010] Conference Chairman
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# Enter the text of your news item.
 
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''2010/04/13''
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== Don Gilbert Nominated for BFA ==
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{{ImageRight|BioinformaticsOrganization.png|Don Gilbert Nominated for Benjamin Franklin Award|140|http://www.bioinformatics.org/franklin/}}
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The Bioinformatics Organization has announced its nominees for the the [http://www.bioinformatics.org/forums/forum.php?forum_id=7956 2010 Benjamin Franklin Award].
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<div class="indent">
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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.
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</div>
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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].
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''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.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/04/01''
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== April 2010 Calendar ==
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{{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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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.
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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&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100401%2F20100401</embedurl></div>
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If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/03/25''
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== Google Summer of Code & OBF ==
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{{ImageRight|OBF logo.png|OBF in GSoC||http://open-bio.org/wiki/Google_Summer_of_Code}}
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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!
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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].
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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.
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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.
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Thanks to all who helped make OBF's application to GSoC a success, and let's have a great, productive summer of code!
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[[User:RobertBuels|Rob Buels]]
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[http://open-bio.org/wiki/Google_Summer_of_Code OBF GSoC 2010 Administrator]
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''2010/03/21''
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== InterMine is Hiring ==
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{{ImageRight|InterMine.png|InterMine is hiring|180|http://intermine.org/wiki/NowHiring}}
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We have [http://intermine.org/wiki/NowHiring four vacancies] on [[InterMine]] related projects at The University
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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.
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The closing date for applications is 2nd April 2010.
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The [[InterMine]] Team.
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''2010/03/19''
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== Internships @ Dow AgroSciences ==
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{{ImageRight|das_header_logo.gif|Dow AgroSciences|200}}
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[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]
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Navin Elango
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''2010/03/16''
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== Sr. DB Programmer @ FlyBase ==
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{{ImageRight|Fly_logo.png|FlyBase Opening|200}}
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[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].
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Dave Emmert
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''2010/03/09''
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== NGS Analyses in Galaxy ==
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{{ImageRight|GalaxyLogoSmall.png|NGS Analyses in Galaxy||http://main.g2.bx.psu.edu/u/aun1/p/ngs-analysis-service}}
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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:
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# '''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.
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# '''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.
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# '''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.
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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.
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Anton Nekrutenko
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''2010/03/08''
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== Openings @ SGD ==
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{{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}}
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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.
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[[:Category:SGD|SGD]] is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user.
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''2010/03/05''
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== Logo Program Deadline Extended ==
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{{ImageRight|Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
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'''The first call to participate in the [[GMOD Logo Program]] has been extended to March 19.'''
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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.
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/03/03''
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== March 2010 Calendar ==
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{{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
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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.
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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&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100301%2F20100301</embedurl>
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</div>
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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.
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/02/22''
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== GMOD Logo Program, Spring 2010 ==
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<div style="float: right; text-align: center">
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{{#icon: Gmod_cog170.png|The GMOD Logo||GMOD Logo Program}}<br>
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{{#icon: Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
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</div>
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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.
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'''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.'''
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/02/03''
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== GMOD Summer School - Americas ==
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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]].
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The course will be held May 6-9, at [http://nescent.org NESCent] in Durham, NC.  These [[GMOD Components]] will be covered:
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{|
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| align="center" |
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{{#icon: 2010SummerSchoolAmericas170.png|GMOD Summer School||2010 GMOD Summer School - Americas}}<br>
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<div style="font-size:120%">'''[[2010 GMOD Summer School - Americas|Apply Now]]'''</div>
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| &nbsp;&nbsp;
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|
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* [[Apollo]] - genome annotation editor
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* [[Chado]] - a modular and extensible database schema
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* [[Galaxy]] - workflow system
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* [[GBrowse]] - the Generic Genome Browser
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* [[GBrowse_syn]] - A generic synteny browser
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* [[JBrowse]] - genome browser
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* [[MAKER]] - Genome annotation pipeline
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* [[Tripal]] - Web front end for [[Chado]]
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|}
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'''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.
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Thanks,
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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{|
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| valign="top" | PS:
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| 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.
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|}
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''2010/01/29''
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== GMOD @ February NextGenBUG ==
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{{ImageRight|SBForumLogo.png|NextGenBUG 9 Feb Dundee|140|http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209}}
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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.
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* '''[http://insectacentral.org InsectaCentral] - assembling and annotating insect transcriptomes''', Alexie Papanicolau, Exeter
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*: [http://insectacentral.org InsectaCentral] uses [[GMOD Components]] (including [[Chado]] and [[GBrowse]]) extensively in its infrastructure.
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* '''[[Galaxy]]: a stairway to [[Next Generation Sequencing|NGS]] heaven''', Chris Cole, Dundee
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*: Chris will be discussing how Dundee uses [[Galaxy]] to process their [[next generation sequencing]] data.
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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].
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/01/29
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== GBrowse 2.0 ==
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{{ImageRight|GBrowse2Thumb.png|||GBrowse 2.0 HOWTO}}
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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].
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The following are highlights of the many new features that have been added since the 1.70 release:
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* A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
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* Different [[GBrowse 2.0 HOWTO#Database Definitions|database backends]] can be associated with each track, making backend management much simpler.
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* A revamped user interface for a less cluttered and more functional end-user experience.
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* A [[GBrowse 2.0 HOWTO#Themes|UI theming system]] with three predefined themes, including a cool "transparent" theme.
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* A custom [[GBrowse 2.0 HOWTO#Configuring the Uploaded Track Database|track upload and management system]] gives users much greater control over custom tracks.
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* 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.
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* 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.
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* Support for named subtracks (tracks within tracks) and filtering of those subtracks.
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* Support for [[GBrowse NGS Tutorial|next generation sequencing]] data.
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There are also a number of features that ''didn't'' make it into the 2.00 release, most notably:
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* 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).
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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].
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On behalf of the GMOD team,
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[[User:Lstein|Lincoln Stein]]
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''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''
+
 
+
== Galaxy Developer Conference ==
+
 
+
{{ImageLeft|GalaxyLogoSmall.png|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
+
{{ImageRight|CSHL Logo75x75.gif|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
+
 
+
The [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp First Galaxy Developer Conference] will be held at [http://www.cshl.edu/ Cold Spring Harbor Laboratory]
+
May 15-17, 2010, immediately after the [http://meetings.cshl.edu/meetings/genome10.shtml Biology of Genomes] conference.  [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp Registration] is now open.
+
 
+
This meeting is aimed at developers of analysis tools, bioinformatics staff, and IT managers of sequencing facilities.  The meeting will focus on these features of the [[Galaxy]] framework:
+
 
+
* tool integration and distributed job management
+
* deployment of private Galaxy instances on local resources and on the cloud
+
* management of large datasets with the Galaxy Library System
+
* using the Galaxy LIMS functionality for managing sample submission at [[Next Generation Sequencing|NGS]] sequencing facilities.
+
 
+
Please [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp register now] if you are interested in using and extending [[Galaxy]].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/12/28''
+
 
+
== Arthropod Genomics Consortium ==
+
 
+
{{ImageRight|AGSBug170.png|Arthropod Genomics Consortium|100|http://arthropodgenomes.org}}
+
The [http://arthropodgenomes.org Arthropod Genomics Consortium] encourages collaboration and information exchange amongst arthropod researchers. The consortium, launched at the [http://www.k-state.edu/agc/symp2009/ 2009 Arthropod Genomics Symposium], has now started [http://arthropodgenomes.org a wiki] to enable this community to self-organize:
+
 
+
: ''Our goal is to provide a central location for information about arthropod genomics projects, bioinformatics tools, and people interested in arthropod genomics.  We think this is a great way to "identify the community"; information from the wiki can be used to support white papers and grant proposals. It will also serve as a central location for links to arthropod genomics resources, news releases and meeting announcements.''
+
:: [http://www.ksu.edu/biology/faculty_pages/brown.html Sue Brown], Director, [http://www.k-state.edu/agc/ K-State Arthropod Genomics Center]
+
 
+
If you are an arthropod researcher, please consider [http://arthropodgenomes.org/wiki/Main_Page#tab=Adding_data_to_this_wiki joining this growing consortium].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/12/18''
+
 
+
== BioPerl Podcast ==
+
 
+
{{ImageRight|BioPerl_logo.jpg|BioPerl Podcast|70|http://twit.tv/floss96}}
+
 
+
A [http://twit.tv/floss96 podcast on the BioPerl project] is available at [http://twit.tv/FLOSS FLOSS Weekly].  It's about an hour long and it's a good introduction to [[BioPerl]], a set of libraries that many popular [[GMOD Components]] are built upon.  The podcast is an interview with BioPerl heavy hitters [[User:Cjfields|Chris Fields]] and [[User:Stajich|Jason Stajich]].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
''2009/11/23''
+
 
+
== InterMine 0.92 Released ==
+
 
+
{{ImageRight|InterMine.png|InterMine Release Notes|180|http://www.intermine.org/wiki/ReleaseNotes}}
+
 
+
We have released version 0.92 of [[InterMine]].
+
 
+
The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.
+
 
+
Version 0.92 has [http://www.intermine.org/wiki/ReleaseNotes Release Notes] and [http://www.intermine.org/wiki/UpgradeInterMine upgrade information].
+
 
+
Upgrade should be quite straightforward from either 0.9 or 0.91.  The
+
only issue is compatibility of the GO enrichment widget with old
+
databases built before 0.91.
+
 
+
[mailto:dev@mail.intermine.org Let us know] if you have problems or suggestions for the next releases.
+
 
+
The InterMine team.
+
 
+
''2009/11/23''
+
 
+
== CMap Paper in Bioinformatics ==
+
 
+
{{ImageRight|BionformaticsCover.gif|Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040}}
+
 
+
A [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 paper] describing the [[CMap]] comparative map viewer is in the [http://bioinformatics.oxfordjournals.org/content/vol25/issue22/index.dtl current issue] of ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'':
+
 
+
: [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 CMap 1.01: a comparative mapping application for the Internet], by Ken Youens-Clark, [[User:Faga|Ben Faga]], Immanuel V. Yap, [[User:Lstein|Lincoln Stein]] and Doreen Ware.
+
 
+
[[CMap]] is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.
+
 
+
See the [[CMap|CMap page]] to learn more.  CMap will also be covered in the [http://www.intl-pag.org/18/18-gramene.html Gramene workshop] and in a poster at [[PAG 2010]].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/11/14''
+
 
+
== January 2010 GMOD Meeting ==
+
 
+
{{ImageRight|Jan2010MtgLogo170.png|January 2010 GMOD Meeting||January 2010 GMOD Meeting}}
+
 
+
 
+
<div style="font-size: 140%; text-align: center">[[January 2010 GMOD Meeting|Register for the January 2010 GMOD Meeting]]</div>
+
 
+
 
+
I am pleased to announce that the [[January 2010 GMOD Meeting|January GMOD meeting]] will be taking place on January 14 and 15, 2010 in San Diego at the [[January 2010 GMOD Meeting#Lodging|Best Western Seven Seas]]
+
(the same location as last year).  Please see the [[January 2010 GMOD Meeting|meeting page]] for registration information.
+
 
+
Please also take a moment to [[January 2010 GMOD Meeting#Agenda Proposals|add suggestions for the agenda]].  There is no registration fee for this meeting.  However, there is limited space, so please register early.
+
 
+
The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the [[January 2010 GMOD Meeting|GMOD meeting]] and the [[PAG 2010|Plant and Animal Genome meeting]] before it may stay at the Best Western the entire time.
+
 
+
Please direct follow up questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-devel gmod-devel mailing list] ([mailto:gmod-devel@lists.sourceforge.net gmod-devel@lists.sourceforge.net]).
+
 
+
Thanks and I look forward to seeing you in San Diego!
+
 
+
[[User:Scott|Scott]]
+
 
+
''2009/11/13''
+
 
+
== Long Term Database Funding ==
+
 
+
You may have heard about [http://www.arabidopsis.org/doc/about/tair_funding/410 TAIR's funding situation].  Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources.  This news was sent to the TAIR community (and posted on the [http://mailman.tairgroup.org/mailman/listinfo/biocurator Biocurator list]) on October 22.  A day later the paper "[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Models for financial sustainability of biological databases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''.
+
 
+
All GMOD users need to give at least some thought to long term funding issues.  A [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International Society for Biocuration]'s (ISB) [http://biocurator.proboards.com/ forum site].
+
 
+
{{ImageRight|TAIR_logo.gif|TAIR Funding Update and Discussion Forum||http://www.arabidopsis.org/doc/about/tair_funding/410}}
+
[http://www.arabidopsis.org/ TAIR] asked people to do a couple things:
+
# Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
+
# Contribute to a [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion on the TAIR web site] about
+
## the bioinformatics needs of the ''Arabidopsis'' and wider plant biology communities and
+
## how resources like TAIR should be funded.
+
 
+
The [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion at TAIR] is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising.  It also contains many statements that none of those options will work.  The ''[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Database]'' paper discusses similar proposals, plus some others.
+
 
+
If you are interested in long-term funding issues, I encourage you to participate in the [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion at ISB].  If you use TAIR and want to see it funded, please [http://www.arabidopsis.org/doc/about/tair_funding/410 post a comment at the TAIR web site].  And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.
+
 
+
[[User:Clements|Dave Clements]]
+
 
+
''2009/11/06''
+
 
+
== Two Openings at Bayer CropScience ==
+
{{ImageRight|Logo_BayerCropScience.gif|Open positions at Bayer CropScience||http://www.mybayerjob.com/en}}
+
'''1. BioAnalyst Scientist:'''
+
 
+
You will provide support in various activities: [[Next Generation Sequencing]] (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.
+
 
+
More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUE2NjQ4RkNFNjUwMDlBRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Scientist]
+
 
+
'''2. BioAnalyst Researcher:'''
+
 
+
You will support and foster the data management and analysis of [[Next Generation Sequencing]] (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. [[Glossary#Perl|perl]] and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.
+
 
+
More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUI3NUU2MzIzRDcwMTEyRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Researcher]
+
 
+
Operating language in the company is English.
+
 
+
'''Interested in any of these positions?''' You can apply [http://www.mybayerjob.com/en here] or send your CV to [mailto:Laurent.viau@bayercropscience.com Laurent Viau]
+
 
+
[[User:ErickAntezana|Erick Antezana]]
+
 
+
''2009/11/06''
+
 
+
== GBrowse NGS Tutorial & Poster==
+
 
+
{{ImageRight|BA2009Logo.png|GBrowse NGS Tutorial|100|GBrowse NGS Tutorial}}
+
A tutorial on using [[GBrowse NGS Tutorial|GBrowse 2 to visualize next generation sequencing (NGS) data]] is now available.  The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 2 genome browser to display [[next generation sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the [[BA2009|Bioinformatics Australia 2009 (BA2009) GMOD Workshop]].  The tutorial includes a [[VMware]] image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.
+
 
+
The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.
+
 
+
A [[:Image:GBrowse_nextgen_poster.pdf|poster]] (by [[User:Scott|Scott Cain]]) demonstrating how to use the adaptor with ''GBrowse 1 and GBrowse 2'' is also available.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/11/04''
+
 
+
== Galaxy Project Hiring ==
+
 
+
{{ImageRight|GalaxyLogoSmall.png‎|Galaxy Project Hiring||http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2}}
+
There are several open [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 software engineer and postdoc positions] with the [[Galaxy]] project.  Galaxy is looking for engineers with with experience in distributed computing, visualization, and usability.  The positions will initially focus on making [[next generation sequencing]] (NGS) data analysis more widely accessible, transparent, and reproducible, as well as development of bioinformatic tools in areas enabled by NGS: re-sequencing, ''de novo'' assembly, metagenomics, transcriptome analysis and epigenetics. Postdoc positions will address biological questions (''e.g.'', mutagenesis and sex chromosome evolution from NGS data) using [[Galaxy]] tools.
+
 
+
See the [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 official posting] for full details and contact information.
+
 
+
''2009/11/02''
+
 
+
== Visualizing Biological Data Workshop ==
+
 
+
{{ImageRight|EMBO_Logo.png|Visualizing Biological Data (VizBi)||http://www.vizbi.org}}
+
 
+
The first [http://www.vizbi.org/ EMBO Workshop on Visualizing Biological Data (VizBi)] will be held 3-5 March 2010, at the [http://www.embl.de/training/eicat/atc/index.html EMBL Advanced Training Centre] in Heidelberg, Germany.
+
 
+
The goal of the workshop is to bring together researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging).  The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.
+
 
+
The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a ''fastforward'' presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please [http://vizbi.org submit an abstract and image] related to your work. Submissions close on 16 November 2009.
+
 
+
''2009/10/21''
+
 
+
== Openings at Syngenta ==
+
{{ImageRight|SyngentaLogo.png|Openings at Syngenta||http://www.syngentacareers.com/listing/}}
+
There are two openings at [http://www.syngentacareers.com/listing/ Syngenta], recently named one of the top biotechnology employers by [http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_10_02/science.opms.r0900079 Science], in Research Triangle Park, NC.
+
 
+
[http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={2258BBC6-9CD1-4991-9F4A-3099220C760D}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genomic Database Specialist (#1435)]: We are currently using the [[Chado]] schema, and this individual will be responsible for maintaining and optimizing database systems for genome annotation and related information.  Experience overseeing database systems is required and experience with Oracle and [[PostgreSQL]] is desirable. The ideal candidate will have a solid understanding of genomics and a background in a life sciences setting. Strong competency with Unix and Perl is required.
+
 
+
[http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={D9207D76-4EFC-49B7-B4A5-E0F2988E9DF5}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genome Annotation Specialist (#1434)]: This individual will be responsible for implementing automated annotation pipelines for genome, transcript, and proteins sequences. Advanced knowledge of sequence analysis tools is required. Experience with modern high throughput sequencing analytics is desirable. A strong competency with Unix and scripting in a language such as Perl is required.
+
 
+
Both positions will work with Chado and [[GBrowse]], and will help evaluate the adoption of additional GMOD tools. See the links for more details.
+
 
+
[[User:Eric.ganko|Eric Ganko]]
+
 
+
''2009/10/21''
+
 
+
== Opening at SGD ==
+
 
+
There is an [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 opening for a Bioinformatics Analyst] at the [http://yeastgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast.
+
 
+
{{ImageRight|SGD-t.gif|Bioinformatics Analyst at SGD||http://yeastgenome.org}}
+
The position includes interacting with international research laboratories, working with genomic data, evaluating new technologies, analysis via computational methods created by others but integrated at SGD, knowledge of new experimental methodology, large genomic datasets and their computational analysis, and bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with [[Comparative Genomics|comparative genomics]] is also desirable.
+
 
+
SGD is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user, and this position will work with the [[GBrowse]] genome viewer as well as other GMOD tools.
+
 
+
See the [http://jobs.stanford.edu Stanford jobs site] (search for posting [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 36125]) for more.
+
 
+
''2009/10/20''
+
 
+
== Apollo 1.11.2 Released ==
+
 
+
I've just cut a new [[Apollo]] release that fixes some [[GFF3]] and [[Chado]] writeback issues.  As usual, you can get the most current version of Apollo at:
+
 
+
: http://apollo.berkeleybop.org/current/
+
 
+
Cheers,
+
 
+
[[User:Elee|Ed Lee]]
+
 
+
''2009/10/07''
+
 
+
== 2009 GMOD Survey Results ==
+
 
+
The [[2009 GMOD Community Survey|results of the 2009 GMOD Community Survey]] are now available online.  This year's survey focused on genomic and comparative genomics visualization was taken by 45 respondents.  The survey includes:
+
* [[2009 GMOD Community Survey#Use Cases|Use Cases]] - what people would like visualization software to do.
+
* [[2009 GMOD Community Survey#Features|Feature Ranking]] - what features are the most (and least) important to users.
+
* Plus general feedback on [[2009 GMOD Community Survey#Other Feedback on Visualization Tools|visualization tools]], [[2009 GMOD Community Survey#Documentation|documentation]], and the [[2009 GMOD Community Survey#Other Feedback|project]].
+
 
+
The survey results will be used to improve GMOD and guide its future direction.  This year's survey complements the [[2008 GMOD Community Survey]], which covered all of GMOD.
+
 
+
{{ImageRight|GMODMug150x150.jpg|GMOD Mug|100|http://www.cafepress.com/GenericMOD/}}
+
And, finally, we have our 3 winners of [http://www.cafepress.com/GenericMOD/ GMOD Gear]:
+
 
+
* James Estill of the [http://www.genetics.uga.edu/ University of Georgia]
+
* Philippe Lamesch of [http://www.arabidopsis.org/ TAIR]
+
* Sandra L&ouml;venich of [http://www.imsb.ethz.ch/ ETH Z&uuml;rich]
+
 
+
Thanks to everyone who took the time to participate in the survey.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/10/05''
+
 
+
== GMOD Tutorials! GMOD Training! ==
+
 
+
{{ImageRight|GMOD2009Europe170.png|Summer School - Europe|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
+
{{ImageRight|2009SummerSchoolAmericas170.png|Summer School - Americas|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
+
 
+
Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[GMOD Summer School|2009 GMOD Summer Schools]].  Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image.
+
 
+
The [[:Category:Tutorials|tutorials]] are:
+
* '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
+
* '''[[Artemis-Chado Integration Tutorial]]''' - by [[User:RobinHouston|Robin Houston]], [[User:TimCarver|Tim Carver]] and [[User:Buggy|Giles Velarde]]
+
* '''[[BioMart Tutorial]]''' - by [[User:Junjun|Junjun Zhang]] and Syed Haider
+
* '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
+
* '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]'''
+
* '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
+
* '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]] and Ian Holmes
+
* '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
+
* '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
+
 
+
 
+
There is also a plethora of GMOD related [[Training and Outreach|training and outreach]] going on in the next few months.  Here's what I know about:
+
{| class="wikitable"
+
! Date
+
! Topic
+
! Conference / Location
+
|-
+
! October 12-27
+
| '''[http://meetings.cshl.edu/courses/c-info09.shtml Programming for Biology]'''<br />This includes a session on [[GBrowse]].
+
| [http://www.cshl.edu Cold Spring Harbor Laboratory], Cold Spring Harobr, NY, USA
+
|-
+
! October 21-22
+
| '''[http://www.ashg.org/2009meeting/pages/workshops.shtml#ucsc Interactive Workshops on the UCSC Genome Browser and Galaxy Framework]
+
| [http://www.ashg.org/2009meeting/ The American Society of Human Genetics (AHSG)], Honolulu, Hawaii, USA
+
|-
+
! October 27-30
+
| '''[[GBrowse]] and [[Next Generation Sequencing]] Data'''
+
| [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics], Cold Spring Harbor, New York, USA
+
|-
+
! rowspan="2" | October 28-30
+
| '''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'''
+
| rowspan="2" | [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia
+
|-
+
| '''Visualizing [[Next Generation Sequencing|Next Generation Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
+
|-
+
| style="background-color: #cccccc" colspan="3" |
+
|-
+
! rowspan="2" | November 16-17
+
| '''[http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine Data Warehouse Workshop]
+
| Cambridge, UK
+
|-
+
| '''Comparative Genomics with GMOD'''
+
| [http://colloque.inra.fr/isyip Information Systems for Insect Pests], Rennes, France
+
|-
+
| style="background-color: #cccccc" colspan="3" |
+
|-
+
! rowspan="3" | January 9-13
+
| '''[[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]]'''
+
| rowspan="3" | [[PAG 2010|Plant and Animal Genome XVII Conference (PAG 2010)]], San Diego, CA, USA<br />See '''[[PAG 2010]]''' for links to many talks and presentations.
+
|-
+
| '''[[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn]]'''
+
|-
+
| '''[[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]]'''
+
|-
+
|}
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/10/02''
+
 
+
 
+
== modENCODE & Gramene Openings ==
+
 
+
The [http://www.modencode.org modENCODE] and [http://www.gramene.org Gramene] projects are both hiring.
+
 
+
<span style="font-size:120%">'''modENCODE'''</span>
+
 
+
{{ImageRight|ModENCODE logo.png|modENCODE Project Openings||http://blog.modencode.org/}}
+
[http://www.modencode.org modENCODE] is [http://blog.modencode.org/?p=350 looking for a few consultants].  The project's aim is to discover and explore the genomes of ''C. elegans'' and ''D. melanogaster'', using new scientific strategies and new technologies for discovery.
+
 
+
Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data
+
of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.
+
 
+
Please see the [http://blog.modencode.org/?p=350 complete job description] for details.
+
 
+
[http://www.modencode.org modENCODE] is a power GMOD user.  The project uses [[GBrowse]], [[Chado]], [[InterMine]], [[JBrowse]], and [[GBrowse_syn]].  (See [[January 2009 GMOD Meeting#modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display|Nicole Washington's talk]] at the [[January 2009 GMOD Meeting]] for some details on how they are used.)
+
 
+
 
+
<span style="font-size: 120%">'''Gramene'''</span>
+
 
+
{{ImageRight|Gramene_logo180.jpg|Grameene Project Opening||http://news.gramene.org/}}
+
 
+
[http://www.gramene.org Gramene] has [http://news.gramene.org/?p=392 several bioinformatics openings] in the [http://www.science.oregonstate.edu/bpp/faculty/jaiswal/ Jaiswal lab] at Oregon State University.
+
 
+
The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining ([[Textpresso]]) and biological ontology projects.  Gramene is a long-time GMOD user and is the home of the [[CMap]] comparative map viewer.
+
 
+
See [http://news.gramene.org/?p=392 the position announcement] for full details.
+
 
+
''2009/10/02''
+
 
+
== GMOD @ Bioinformatics Australia ==
+
 
+
{{ImageRight|BA2009Logo.png|GMOD workshop at Bioinformatics Australia||BA2009}}
+
There will be a half-day [[BA2009|pre-conference GMOD workshop]] on 28 October, 2009, at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia (BA2009)].  The workshop will introduce [[GMOD Components]] for [[visualization]], [[annotation]], and data management, and the GMOD project as a whole.  The workshop will also include a [[GBrowse]] demonstration with a worked example that includes [[next generation sequencing]] data.
+
 
+
Thanks to sponsorship from [http://www.bioplatforms.com/ Bioplatforms Australia] admission to the workshop is included in the conference registration fee.
+
 
+
Please see the [[BA2009|workshop page]] or [mailto:help@gmod.org contact the GMOD Help Desk] for more information.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/10/01''
+
 
+
<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 contentsIs 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 temperamentalIncorrect 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 dateThis 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]]

Latest revision as of 19:40, 13 December 2018

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 is also available as an RSS feed. RSS feed

Recent News

Prospecting for Proposals for GSoC 2024

The Open Genome Informatics group and GMOD has submitted an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of different sizes participate in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, don't hesitate to get in touch with us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email rhaw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2024/02/12

JBrowse2 v1.1.0 Released

We're pleased to announce a new release of JBrowse Web!

(Reposted by permission from https://jbrowse.org/jb2/blog/2021/03/29/v1.1.0-release

Changed callbacks language from JavaScript to Jexl

To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.

For details, see the callbacks section of our configuration guide.

Fetch intron and upstream/downstream sequences

We also have several other improvements including the ability to get intron and upstream/downstream sequence in the feature details

<img alt="Upstream downstream.png" src="http://gmod.org/mediawiki/images/thumb/7/76/Upstream_downstream.png/700px-Upstream_downstream.png" width="700" height="248" srcset="/mediawiki/images/thumb/7/76/Upstream_downstream.png/1050px-Upstream_downstream.png 1.5x, /mediawiki/images/thumb/7/76/Upstream_downstream.png/1400px-Upstream_downstream.png 2x" />

Interactive documentation using Storybook

Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. The docs contain live examples of how the LGV component can be used, along with source-code examples. The site can be found here.

Enhanced navigation to drawer widget stack

We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.

See below for demos of the new navigation UI.

<img alt="Minimize button demo.gif" src="http://gmod.org/mediawiki/images/0/0f/Minimize_button_demo.gif" width="480" height="414" />

Demo of using the minimize button in the drawer

Downloads

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.1.0 (2021-03-29)

🚀 Enhancement

core

  1. 1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
  2. 1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
  3. 1816 Remove some animation effects (@cmdcolin)
  4. 1778 Adds dropdown to show drawer widget stack (@teresam856)
  5. 1685 Change callbacks language from JavaScript to Jexl (@peterkxie)

Other

  1. 1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
  2. 1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
  3. 1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
  4. 1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

🐛 Bug Fix

core

  1. 1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
  2. 1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
  3. 1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
  4. 1723 A few bugfixes (@garrettjstevens)

Other

  1. 1815 Clear tracks when using "Return to import form" (@cmdcolin)
  2. 1819 Standardized sentence casing on drawer widget titles (@cmdcolin)
  3. 1796 Bump generic-filehandle for fixing CORS errors from Chrome cache pollution (@cmdcolin)

📝 Documentation

  1. 1824 Add storybook docs page for nextjs usage (@elliothershberg)
  2. 1770 1469 storybook deploy (@elliothershberg)
  3. 1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
  4. 1779 Collaborative release announcement editing (@rbuels)
  5. 1791 Add a couple more demos for our live version with MDX (@cmdcolin)

🏠 Internal

Other

  1. 1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
  2. 1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)

core

  1. 1834 Change jbrowse-components monorepo default branch from 'master' to 'main' (@rbuels)

Committers: 6

  • Colin Diesh (@cmdcolin)
  • Elliot Hershberg (@elliothershberg)
  • Garrett Stevens (@garrettjstevens)
  • Peter Xie (@peterkxie)
  • Robert Buels (@rbuels)
  • Teresa Martinez (@teresam856)


Posted to the GMOD News on 2021/03/30

Prospecting for Proposals for GSoC 2021

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2021/02/16

Codefest 2020


Handlery Hotel in the Balboa room
(down the street from the Town and Country Hotel)
San Diego, California
January 9-10, 2020 </strong>

Immediately before Plant and Animal Genome XXVIII (PAG 2020)

</center>

Participant list now available


There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to

We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.

Agenda

Thursday:

9:00-10:00 Introduction and working group organization
10:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-4:00 Working groups
4:00-5:00 Report on progress

Friday:

9:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-3:00 Working groups
3:00-3:45 Report on progress
  • Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.


Posted to the GMOD News on 2020/01/08

Tripal 3.5 Released

This Tripal release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update. Changes in this version:

  1. Performance improvements to the Cross References, Relationships, and References.
  2. A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
  3. A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
  4. Updates to the online documentation
  5. Bug fixes in web services
  6. Bug fixes in the OBO loader for ontologies that won't import.


Posted to the GMOD News on 2021/02/08

JBrowse 2 release

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

  • New types of views, including circular, synteny, and dotplot views
  • Graphical configuration editing
  • Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here. To get started using JBrowse 2, visit our quickstart guide here.

We'd love to hear what you think! You can find information about how to contact us here.

The JBrowse Team

Posted to the GMOD News on 2020/11/09

Prospecting for Proposals for GSoC 2020

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2020/02/03

Call for PAG Abstracts

Call for PAG Abstracts

Time is short!

If you want to attend PAG and would like to present on a topic that would be of interest to the GMOD community, please send an abstract or at least a descriptive title to help@gmod.org. Types of talks typically include updates on GMOD software projects, usage stories for successful sites, proposals for new GMOD projects and descriptions of plugins for existing GMOD software projects like Tripal, JBrowse and Galaxy.

Please consider giving a talk and sharing your experience and ideas!


Posted to the GMOD News on 2016/11/04

New GMOD Server

GMOD.org has a new home

Due to a old server being retired, gmod.org has a new home. In the course of migrating the server, we also had to update the version of MediaWiki that is powering the site. If you notice any problems with gmod.org, please send an email to help at gmod dot org to let us know what's going on.


Posted to the GMOD News on 2016/09/29

GMOD-JBrowse 2016 Survey

Hello Genome Informaticians,

The following survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,

The JBrowse team


Posted to the GMOD News on 2016/09/23

GCC2016

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington. Galaxy is a GMOD Component which interacts with many other GMOD Components, including:

  • Tripal: A web front end for Chado databases. Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
  • JBrowse: A client-side genome browser and successor to the venerable GBrowse. JBrowse as a Galaxy Tool was presented by Eric Rasche at GCC2015. Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
  • MAKER: A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces. A MAKER-Galaxy by Agriculture and Agri-Food Canada was presented at ISMB 2014.
  • InterMine and BioMart: These are both popular data sources that are integrated with Galaxy.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.

Oral presentation abstract submission closes April 8; poster and demo abstract submission close May 20; and scholarship applications close May 1.


Posted to the GMOD News on 2016/04/04

2016 GMOD Meeting

The next GMOD Community Meeting will be held at Indiana University in Bloomington, Indiana, United States, June 30-July 1, directly after the 2016 Galaxy Community Conference (GCC2016). GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.


Please register online at Eventbrite by June 20th 2016. Early bird registration ends May 21.

For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.

If you have any suggestions or requests for the meeting, please contact the GMOD help desk.


Posted to the GMOD News on 2016/04/04

Please Support EcoCyc

EcoCyc, the E. coli information resource and one of the resources offered by the Pathway Tools group, is in need of letters of support from the community after receiving a poor grant review, which could result in a complete loss of funding on July 1st, 2014. If you are a user of EcoCyc, please consider writing a short letter in support of this vital resource. The deadline for letters is May 26th, 2014.

From the Pathway Tools website

ECOCYC FUNDING CRISIS -- DEADLINE MAY 26

EcoCyc received a very unfavorable grant review in February 2014. We are in discussions with the NIH to resolve this situation.

EcoCyc's usage has steadily increased. We made very strong progress on our challenging aims from the current grant period, and the project has produced many publications. EcoCyc received excellent reviews on previous grant applications. Furthermore, the needs of the prokaryotic research community for the content and software tools offered by EcoCyc have never been higher.

In the worst case, we will lose all funding on July 1, 2014 and be forced to re-apply. Even in the best case, we may receive a crippling funding cut that causes us to fall behind in its manual literature curation effort, and requires us to lay off experienced curation staff until funding can be obtained.

These events could seriously undermine EcoCyc, end the project altogether, or force us to begin charging usage fees.

To maintain EcoCyc as the free, up to date, and high-quality resource that you depend on, please tell the NIH what EcoCyc means to your research. Please click the button below to submit a PDF letter of support on institutional letterhead, or a short support statement, explaining the importance of EcoCyc.

We ask all regular users to submit; a short statement will take less than two minutes of your time. Students and post-docs, please ask your lab head to submit in addition to your submission.

More information on what to write and where to submit letters is available at the Pathway Tools website.


Posted to the GMOD News on 2014/05/21

June 2014 WebApollo Hackathon

Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us this summer for a WebApollo Hackathon at Lawrence Berkeley National Laboratory, California.

When: Monday, June 2 - 6, 2014

Where: Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104. 1 Cyclotron Rd, Berkeley, CA 94720

What: five days of intensive, collaborative WebApollo development!

For five days developers will work on new features of interest to their research communities, improve existing features, and collaborate on developing features of interest to other colleagues.

Participants should:

  • be able to set up their own WebApollo server before arriving in Berkeley, including Postgres, Tomcat, etc.
  • code comfortably in JavaScript (client) and Java (server).

What will we do while we are there? You tell us! Send your suggestions for feature development, your questions, and any additional comments to apollo [dash] dev [at] lists [dot] lbl [dot] gov

Registration is free of charge, but tickets are required. Register online!

Participants are responsible for arranging travel and accommodation on their own.

More details: WebApollo Hackathon information

via Monica Munoz-Torres


Posted to the GMOD News on 2014-04-22

Applications Open for GMOD Online Training

GMOD will be holding its first online training course for those interested in the set up and use of GMOD components.

The course will be held from Monday 19th May to Friday 23rd May 2014, and will cover core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database.

If you are interested in attending, please see GMOD Online Training 2014 for more information and to submit your application.


Posted to the GMOD News on 2014-03-31

Canto Workshop at Biocuration 2014

GMOD will be running a workshop at Biocuration 2014 to demonstrate the use of Canto, on Wednesday 9th April in the afternoon. Canto is a literature curation tool that allows users to create functional annotations for genes and gene products using OBO (ontology) terms. Canto will soon be added to GMOD in the Cloud, and this workshop will show participants how to get a GMOD in the Cloud instance up and running--it takes less than ten minutes!--and how to use Canto for literature curation.

We will have more information closer to the time.


Posted to the GMOD News on 2014/03/25

Tripal 2.0a released

The Tripal Development Team is pleased to announce an alpha release of Tripal 2.0 for Drupal 7. This release is expected to have bugs and there is some functionality still under development. However, this release is made to help early adopters of Tripal for Drupal 7. Reports of bugs or other issues are highly welcomed. Below are available resources for Tripal 2.0a

   Download Instructions
   New Functionality
   Installation and Tutorial
   Tripal 2.0 API site
   Tripal Mailing List
   Tripal Developer's Mailing List

The Installation tutorial is still under development but should have enough information for complete installation of Tripal v2.0a as well as loading of organisms and features.


Posted to the GMOD News on 2014/02/27

Precompiled Ontologies in Chado

Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.

Go to the download site.

The ontologies currently available are:

  • Chado Feature Properties
  • Gene Ontology
  • Plant Ontology
  • Relationship Ontology
  • Sequence Ontology

These are updated weekly; the workflow is as follows:

  • clone Chado from SVN
  • build
  • load ontologies
  • dump database as SQL
  • upload to a publicly accessible webserver

Please contact Eric if you are interested in having other ontologies added to the dumps, other builds with different (sub)sets of ontologies, or archived copies of schemas over time.

Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.


Posted to the GMOD News on 2014/02/20

GCC2014 Registration is Open

We are pleased to announce that Early Registration and Talk and Poster Abstract Submission are now open for the 2014 Galaxy Community Conference (GCC2014).

GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. GCC2014 starts with a Training Day featuring five parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!

Early registration is now open. Register early and avoid paying 70% more for regular registration costs.  Early registration is very affordable, with combined registration (Training Day + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options.

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 May2.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers, and is continuing to take submissions for this year's meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update.

Thanks, and hope to see you in Baltimore!

The http:GCC2014 Organizing Committee


Posted to the GMOD News on 2014/02/14

GMOD Paper Cuts, Feb 10th, 2014

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


Finding the missing honey bee genes: lessons learned from a genome upgrade [1]

The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.

Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Interesting findings from the new assembly of the honey bee genome, including many more genes than were found in the initial assembly. The Hymenoptera Genome Database uses numerous GMOD resources, including MAKER for automated genome annotation, JBrowse and GBrowse for sequence browsing, and WebApollo for community genome annotation.


Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila [2]

We and others recently demonstrated that the readily programmable CRISPR/Cas9 system can be used to edit the Drosophila genome. However, most applications to date have relied on aberrant DNA repair to stochastically generate frame-shifting indels and adoption has been limited by a lack of tools for efficient identification of targeted events. Here we report optimized tools and techniques for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences including screenable markers. Using these donors, we demonstrate the replacement of a gene with exogenous sequences and the generation of a conditional allele. To optimize efficiency and specificity, we generated transgenic flies that express Cas9 in the germline, and directly compared HDR and off-target cleavage rates of different approaches for delivering CRISPR components. We also investigated HDR efficiency in a mutant background previously demonstrated to bias DNA repair towards HDR. Finally, we developed a web-based tool that identifies CRISPR target sites and evaluates their potential for off-target cleavage using empirically rooted rules. Overall, we have found that injection of a dsDNA donor and guide RNA-encoding plasmids into vasa-Cas9 flies yields the highest efficiency HDR, and that target sites can be selected to avoid off-target mutations. Efficient and specific CRISPR/Cas9-mediated HDR opens the door to a broad array of complex genome modifications and greatly expands the utility of CRISPR technology for Drosophila research.

CRISPR is one of the most exciting recent technological advancements of the past couple of years. This paper reports new techniques and tools for using the CRISPR/Cas9 system for complex genome engineering. For more information, see the flyCRISPR website.


Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress [3]

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Check out the JBrowse-powered Brachypodium web genome browser and other resources on the new Brachypodium website!


Analyses of Hypomethylated Oil Palm Gene Space[4]

Demand for palm oil has been increasing by an average of ~8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

The newly-sequenced oil palm genome used the MAKER automated annotation pipeline. The oil palm is one of a number of genomics projects taking off in Malaysia at the moment. Perfect timing for a GMOD workshop!


Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian [5]

The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies.

[...]

The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”

Information and resources for the newly-sequenced cnidarian E. lineata; all genomic data is publicly available at EdwardsiellaBase, and can be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-86
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1534.2Fgenetics.113.160713
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0087499
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086728
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-71
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/02/10

News Archives

The GMOD News Archives lists all news items since autumn 2007.

Adding a News Item

Note: If you don't want to do this yourself, please send the item to the GMOD Help Desk and we will post it for you.

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.

Short Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • Please make News Item Title be as short as possible, and no more 35 characters at most.
  2. 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.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
{{NewsItem|yyyy/mm/dd}}

Longer Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • 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.
  2. Enter the text of your news item.
    • Make the news item succinct.
    • Do not start the item with a MediaWiki header ("== Header ==").
      • It won't render very well. You should be able to avoid headers altogether.
    • 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.
    • You can include images in your news item. See preexisting news items for what markup to use to do this.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
    {{NewsItem|yyyy/mm/dd}}
    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.
  5. 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:
    {{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}