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 GMOD meetings and releases to user success stories and GMOD related publications.
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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]].
  
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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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]]
  
<span class="plainlinks">
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== Recent News ==
This page is also available as an [http://gmod.org/wiki/index.php?title=GMOD_News&action=feed&feed=rss RSS feed].
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[http://gmod.org/wiki/index.php?title=GMOD_News&action=feed&feed=rss http://gmod.org/wiki/images/4/47/RSSIcon16x16.gif]
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</span>
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= News Items =
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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>
  
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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== [[GMOD News Archives|News Archives]] ==
  
<startFeed />
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The [[GMOD News Archives]] lists all news items since autumn 2007.
  
== GMOD Summer School Update ==
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== Adding a News Item ==
  
<span style="float: right" class="plainlinks">[http://gmod.org/GMOD_Summer_School http://gmod.org/wiki/images/f/fa/SummerSchoolSmall.png]</span>
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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.
<span style="font-size: 120%; font-weight: bold">July 11-13, 2008<br />National Evolutionary Synthesis Center (NESCent)<br />Durham, North Carolina, USA</span>
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'''[[GMOD Summer School]]''' is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There is also a concurrent 1 day session aimed at principal investigators that will give decision makers a feel for what GMOD can do and what level of resources are needed to get a GMOD installation up and running.  The summer school was [[#GMOD Summer School|announced]] on March 7, 2008.
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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]].
  
The [[GMOD Summer School#Program|Implementation Track]] is now full.  '''However, you are still encouraged to [[GMOD Summer School Statement of Interest|submit an application]].'''  The course has a waiting list and we will pull people from that list as openings occur.
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=== Short Instructions ===
  
'''There is still space in the [[GMOD Summer School#Program|Principal Investigator Track]], and the application deadline for that has been extended to allow additional participants to register.'''
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Please follow these guidelines when adding a news item.
  
If you have applied for the GMOD Summer School you should have received an e-mail from the [[GMOD Help Desk|Help Desk]] informing you of your admission status.
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# 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'''.
 +
# Enter the text of your news item.
 +
#* '''The first link in the news item should point to the page/URL you want the RSS feed to link to.
 +
# Preview / save your changes. Edit and save the page until the news item looks like you want.
 +
# Once you are happy with how the item looks, insert this line at the end of it:
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: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
  
''2008/04/24''
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=== Longer Instructions ===
  
== Apollo 1.8 Released ==
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Please follow these guidelines when adding a news item.
  
I'm excited to let everyone know that we're releasing a new version of
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# Create a new page named "'''News/'''''News Item Title''".
[[Apollo]] (1.8.0) today.  There are many additions/bug fixes with this
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#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
release.  Most notably, due to popular demand, an 'undo' system.  You
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#*  The page must start with '''News/''', otherwise it won't be picked by the RSS news feed.
can now access the 'undo' function through 'Edit&rarr;Undo' (or ctrl-u).
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# Enter the text of your news item.
For more information on the changes, check out the [http://gmod.cvs.sourceforge.net/gmod/apollo/doc/release-notes/release-1.8.0-notes?view=markup release doc].
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On another note, the official Apollo URL has changed.  It's no longer:
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http://www.fruitfly.org/annot/apollo
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but rather:
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http://apollo.berkeleybop.org
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Please update your bookmarks accordingly.
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Ed Lee
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''2008/04/10''
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== Sea Urchin Genome Database ==
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<span style="float: right" class="plainlinks">[http://spbase.org http://gmod.org/wiki/images/4/4c/SpBaseLogo.png]</span>
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Today, Tuesday April 4th, the [http://spbase.org Sea Urchin Genome Database] went public.  Based on the GMOD tools and applications the site organizes and displays the genome sequence and annotations produced by the [http://www.hgsc.bcm.tmc.edu/ Baylor College of Medicine Human Genome Sequencing Center] and the sea urchin research community.  This site housed at the Center for Computational Regulatory Genomics, the [http://www.its.caltech.edu/~bi/ Beckman Institute] at [http://www.caltech.edu/ California Institute of Technology] plans to enrich and extend the sea urchin sequence and annotations.
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Visit us at [http://spbase.org SpBase].
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[[User:Acameron|Andy Cameron]]<br />
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''2008/04/08''
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== Chado Doc Reorganization ==
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Chado is the database schema of GMOD and it has quite a bit of documentation in this web site.  However, this documentation could be better organized and integrated.  We are launching the [[Chado Documentation Reorganization]] effort to do just that.
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During this effort the existing [[:Category:Chado|Chado documentation]] may be unstable.  We will do our best to make this reorganization be as painless as possible.
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The [[Chado Documentation Reorganization]] page summarizes our existing documentation and then [[Chado Documentation Reorganization#Plan|proposes a plan]] for restructuring it.  If you have any suggestions or comments on this then please send us your [[Chado Documentation Reorganization#Feedback|feedback]].
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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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''2008/04/04''
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== iPlant Collaborative Job Openings ==
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Cold Spring Harbor Laboratory is seeking experienced software developers/bioinformaticians to join the [http://www.iplantcollaborative.org/ iPlant Collaborative], a new NSF-funded initiative which seeks to develop a comprehensive national cyberinfrastructure which will unite researchers in every plant biology discipline.
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See the [http://www.iplantcollaborative.org/resources/job-postings/45-professional iPlant job board] for job descriptions.
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''2008/04/01''
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== GMOD 1.0 Released ==
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I am very pleased to announce the release of GMOD 1.0.  The file can be
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downloaded from SourceForge at:
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http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511
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This release comes at a time when both the [[Chado]] schema and its
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associated tools have matured and are now quite stable.  The plan going
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forward is to have more frequent releases with schema changes between
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versions clearly delineated.
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In addition to the Chado schema, this release includes:
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* Tools for creating a new database.
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* Tools for populating it with [[:Category:Ontologies|ontology]] data (using go-perl).
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* A fairly new tool for updating ontologies contributed by the developers of [[:Category:SGN|SGN]], the SOL Genomics Network.
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* Tools for loading sequence feature (i.e. GFF3) data.
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* GMODTools for creating bulk download files like GFF and Fasta (See [[GMODTools]] for more information).
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Other data can be loaded using [[XORT]].
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This release of Chado works well with the upcoming release of [[GBrowse]],
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as well as with the current versions of [[Apollo]] and [[CMap]].  It should also
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work well with [[GMODWeb]]/[[Turnkey]].
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With this release, there are so many people in the GMOD community that I
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would like to thank that I couldn't possibly list them all, but at a
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bare minimum, I would like to thank the developers at [[:Category:FlyBase|FlyBase]] and the
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Berkeley Drosophila Genome Project, especially Chris Mungall and Dave
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Emmert, as well as others who have contributed code to the GMOD project
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over the past several years.
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Please direct any questions about using this release to the GMOD schema mailing list, [mailto:gmod-schema@lists.sourceforge.net gmod-schema@lists.sourceforge.net].
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[[User:Scott|Scott Cain]]
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''2008/03/31''
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== CMap 1.0 Released ==
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Version 1.0 of CMap has been released.
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You can get the new version from SourceForge, http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129
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Highlights of this release are:
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* Ribbon option for correspondences
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* New Feature Glyphs
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* A dot-plot view
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* An image_only URL parameter allowing a CMap image to be embedded in another page
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* Easier install with directory guessing
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* API better documented for writing custom scripts to load data
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If you have any questions, please email the [mailto:gmod-cmap@lists.sourceforge.net CMap mailing list].
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Ben
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''2008/03/28''
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== GMOD Meeting July 16-17, Toronto ==
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<span style="float: right" class="plainlinks">[http://gmod.org/July_2008_GMOD_Meeting http://gmod.org/wiki/images/4/4a/July2008LogoSmall.png]</span>
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The next [[July 2008 GMOD Meeting|GMOD community meeting]] has been scheduled for July 16-17, 2008 at the University of Toronto, immediately before [http://www.iscb.org/ismb2008/ ISMB 2008] (also in Toronto), and just a few days after the 2008 [[GMOD Summer School]].
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Watch the [[July 2008 GMOD Meeting]] page for more information as the meeting gets nearer. If you have any questions or requests about the July 2008 meeting, please contact the [[GMOD Help Desk]] at [mailto:help@gmod.org help@gmod.org].  See the [[:Category:Meetings|notes from previous meetings]] for an idea of what is discussed at GMOD meetings.
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Thanks, <br />
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2008/03/25''
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== SynBrowse Developers Needed ==
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<span style="float: right" class="plainlinks">[http://gmod.org/SynBrowse http://gmod.org/wiki/images/c/cb/SynBrowse_logoNoText.png]</span>
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The [[SynBrowse]] [[synteny]] viewer, a GMOD component, is moving towards its second major release.  Xiaokang Pan, the project's lead developer, is looking for volunteer developers to help get this release out sooner.
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SynBrowse2 is written in Perl, and is built on several open source components, including parts of [[GBrowse]].  SynBrowse2 need particular improvements in run-time performance and its alignment parsing tools.  Ideally, programmers will develop SynBrowse2 using a set of animal or microbial genomes (Xiaokang is already working with several plant genomes).  Programmers can improve the alignment parsing tools, fix potential bugs and hopefully improve other parts of SynBrowse as well.
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If you have any interest in and/or experience with multiple alignment or synteny visualization tools please considering contributing to the SynBrowse project.  Xiaokang can be reached at [mailto:xiaokangpan@gmail.com xiaokangpan@gmail.com].
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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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''2008/03/21''
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== GMOD at ParameciumDB ==
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<span style="float: right" class="plainlinks">[http://gmod.org/ParameciumDB http://gmod.org/wiki/images/2/24/ParameciumDBIcon133x42.png]</span>
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Curious to know what is involved in becoming a GMOD user and creating a GMOD based web site?  You can now read the GMOD User Story, an article about [[ParameciumDB]]'s experience with implementing GMOD.  The article describes what GMOD components ParameciumDB uses and how they connect them together.  [[ParameciumDB]] uses several GMOD components, including [[Chado]], [[GMODWeb]], [[Apollo]], and [[GBrowse]].  Please contact [[User:Sperling|Linda Sperling]] <[mailto:linda.sperling@cgm.cnrs-gif.fr linda.sperling@cgm.cnrs-gif.fr]> if you have questions about GMOD at ParameciumDB.
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This is the first of a series of articles on how different organizations use GMOD components to achieve their goals. User stories will give readers a feel for what implementation choices are involved and which ones each organization made.  If you are interested in describing your experience with GMOD, please consider creating a user story page for your project.  You can just start writing (this is a wiki!) or contact the [[GMOD Help Desk]] for assistance.  If we aren't swamped with volunteers, then I will be asking (cajoling?) several not-so-randomly picked projects to write user stories describing their experiences.  I'm hoping to have a new story every other month or so.
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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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''2008/03/18''
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== Beta Test CMap: Win a T-Shirt! ==
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UPDATE: We have our winners.  Even still, please feel free to give the release candidate a try and let us know how it goes.
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We need beta testers for the [[CMap]] 1.0 release candidate.
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<div style="float: right; border: 1px solid blue; margin: 0.5em" class="plainlinks">[http://www.cafepress.com/genericmod.238973590 http://gmod.org/wiki/images/b/bd/TShirtThumb.jpg]<br /><center>Win this shirt!</center></div>
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If I get four (or more) people who let me know that they will try out the release candidate, I will draw two of their names (or email addresses) and buy them each a GMOD T-shirt (based on random drawing, void where prohibited, etc).  Testers from around the world are welcome (and eligible for the shirts as long as Cafe Press ships there and it isn't prohibited by law).
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You can get the release candidate from [http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=55129&release_id=583120 SourceForge].
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To view the T-shirt or get one for yourself visit
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[http://www.cafepress.com/genericmod.238973590 Cafe Press].  Note: There is no price markup for GMOD.  The only one making money on the shirts is Cafe Press.
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If the threshold is broken, I will hold the drawing on Friday the 15th at 1pm CST (2pm Eastern) and email the winners for their addresses and shirt sizes.  If you don't want to be entered in the drawing just let me know.  There is already one beta tester, so only three to go.
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Remember: ''If no one beta tests, everyone beta tests.''
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Thanks,
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[[User:Faga|Ben Faga]],<br />[mailto:faga.cshl@gmail.com faga.cshl@gmail.com]
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''2008/03/11''
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== GMOD Summer School ==
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<span style="float: right" class="plainlinks">[http://gmod.org/GMOD_Summer_School http://gmod.org/wiki/images/f/fa/SummerSchoolSmall.png]</span>
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<span style="font-size: 120%; font-weight: bold">July 11-13, 2008<br />National Evolutionary Synthesis Center (NESCent)<br />Durham, North Carolina, USA</span>
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The first annual [[GMOD Summer School]] will be held July 11-13, 2008 at the [http://nescent.org National Evolutionary Synthesis Center (NESCent)], in Durham, North Carolina, USA.  This is a 2 1/2 day hands-on workshop aimed at teaching new GMOD users how to get up and running with popular GMOD components. There will also be a concurrent 1 day session aimed at principal investigators that will give decision makers an overview of what GMOD can do, how the project operates, and what level of resources are needed to get a GMOD installation up and running.  If you are interested in attending please submit a [[GMOD Summer School Statement of Interest|Statement of Interest]] before April 15, 2008.  The course is free but class size is limited.  See the [[GMOD Summer School]] page for more information and a tentative program.
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''2008/03/07''
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== Ten Recent Web Site Changes ==
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This entry summarizes several recent changes in the [[Main Page|GMOD web site]].  These changes are designed to make the site more useful, and hopefully will make your GMOD web site experience more pleasant.
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'''Ten Recent Web Site Changes to Make Your GMOD Life Easier:'''
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# '''[[Categories]]''' - Most of the pages in the GMOD web site have now been tagged, and those tags can be used as an alternative way to navigate the site.  We have also added tools that make it easier to assign tags when creating content. (Note: The category hierarchy is still work in progress.  Suggestions are welcome.)
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# '''GMOD News''' (this page) - News items of interest to the GMOD community. This is also available as an RSS feed.
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# '''[[Main Page]]''' - Items from the GMOD News page and recently edited pages (non-minor edits) now show up in the right sidebar.
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# '''[[Calendar]]''' - Calendar of events of interest to the GMOD project.
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# '''[[Glossary]]''' - Short definitions of non-biological terms used in GMOD.
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# '''[[GMOD Mailing Lists]]''' - Shows more lists, and sorts them into Overview, Component, and Inactive lists. If your list isn't here, please add it.
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# '''[[Site Guidelines]]''' - Guidelines for creating and editing content on the GMOD web site.
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# '''[[GMOD Help Desk]]''' - Explains services offered by the help desk.
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# '''[[Computing Requirements]]''' - Description of expertise and computing systems you'll need to set up a GMOD installation.
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# '''[[Databases and GMOD]]''' - An overview of database concepts and how databases are used in GMOD.
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Note that several of these pages need continuing contributions from the community.  '''That means you!'''  We particularly encourage you to get in the habit of submitting new [[Calendar]], [[Glossary]], and News items.
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Our next big goal for the web site is to reorganize the [[:Category:Chado|Chado documentation]].  Watch the web site for details on this.
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As always, please let us know if you have any questions or comments.
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Thanks,
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Dave Clements, [[GMOD Help Desk]]<br />
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[mailto:help@gmod.org help@gmod.org]
+
 
+
''2008/02/13''
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== Pathway Tools at Pathway Analysis ==
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''2008/01/28''
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A [http://www.tri-conference.com/08_gdd_day2.asp session] at the Cambridge Healthtech [http://www.tri-conference.com/08_gdd.asp Pathway Analysis conference], March 26-28, 2008 in San Francisco, will describe [[Pathway Tools]], a GMOD component for modeling metabolic pathways and regulatory networks.  There will also be presentations by these GMOD [[MOD|member databases]] that use [[Pathway Tools]] in their databases:
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* [[:Category:MGI|Mouse]]
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* [[:Category:DictyBase|dictyBase]]
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* [[:Category:SGD|SGD]]
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* [[:Category:SGN|Solanaceae Genomics Network]]
+
 
+
Early registration is available until February 22, 2008
+
 
+
== GMOD at Arthropod Genomics ==
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''2008/01/21''
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There will be two [http://www.k-state.edu/agc/Workshop.shtml GMOD related workshops] at the [http://www.k-state.edu/agc/symposium.shtml Arthropod Genomics Symposium], April 10-13, 2008, in Kansas City.
+
* ''Community Contributions to Genome Annotation'' - Christine Elsik of [http://racerx00.tamu.edu/bee_resources.html BeeBase] will discuss how to install and use the [[Apollo]] genome annotation tool.
+
* ''Chado: A Database Schema for Integrating Biological Data'' - [[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]] will cover [[Chado]]'s logical concepts, the types of data it can represent, how to import and export data, and how Chado integrates with other GMOD components such as [[Apollo]] and [[GBrowse]].
+
 
+
GMOD has a particularly strong presence in the arthropod community (e.g., [http://bioinformatics.ksu.edu/BeetleBase/ BeetleBase], [http://racerx00.tamu.edu/bee_resources.html BeeBase], [http://flybase.org FlyBase],  [http://wfleabase.org/ wFleaBase], ...).  If you are an arthropod researcher interested in using [[GMOD Components]] then this meeting will be time well spent.
+
 
+
[http://www.k-state.edu/agc/Register.shtml Early registration] and [http://www.k-state.edu/agc/AbstractGuidelines.shtml poster abstract submissions] are both open until February 29.
+
 
+
 
+
== Apollo 1.7.0 Released ==
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''2008/01/11''
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Version 1.7.0 of [[Apollo]] has just been released.  You can access the updated Apollo page at http://www.fruitfly.org/annot/apollo
+
 
+
Changes in this version include
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* Added [[Glossary#GFF|GFF3]] support
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* Added program source filtering for reading off [[Chado]] databases
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* Lots of work on the ensj adapter to allow it to work better with recent ensembl schemas, handle ditags, give finer control of gene loading, increase speed of gene loading, bug fixes to history, cigar parsing in ensj layer, loading of contig features
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* Allow layout of display to be saved to / loaded from a file. Most useful for synteny where initial display set up can take time. The saved layout also includes the current base position and zoom factor, and on loading you can choose to use those.
+
* Ability to edit settings for a type (new popup menu item in feature popup). The settings which can be edited are the glyph used for drawing the feature and the columns in the table displayed in the evidence panel.
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* New drawing glyph which shades exons darker or lighter depending on their phase (DrawablePhaseHighlightGeneFeatureSet). Also a version of that which uses straight lines to join exons rather than 'hats' (DrawablePhaseHighlightNoHatGeneFeatureSet)
+
* Work on ensembl synteny adapter so it works with latest ensembl compara db schema, and basic support for allowing different alignment sets to be selected.
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* PureJDBCTransactionWriter added.  This entailed some changes to other classes, but in almost every case the changes are 1. reverse compatible and 2. invisible to the end user.
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* Uses of Log4J for generating log files.
+
 
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Plus many other changes.  See the [http://gmod.cvs.sourceforge.net/gmod/apollo/doc/release-notes/release-1.7.0-notes?view=markup release notes] for more.
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We are hoping to cut releases on a more regular basis (after the year and a half long hiatus).  So please [[Apollo#Contact|let us know]] if you find any bugs and they will be addressed and put into a new release as soon as possible.
+
 
+
== GBrowse Tutorial at PAG XVI ==
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''2007/12/27''
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Scott Cain will present a [http://www.intl-pag.org/16/16-gbrowse.html GBrowse tutorial] at the [http://www.intl-pag.org/ Plant and Animal Genome XVI Conference (PAG-XVI)], January 12-16, 2008, in San Diego.  This will be a hands-on tutorial on how to install and use the [[GBrowse]] genome browser.  If you are attending PAG and you are interested in GBrowse then please consider attending.
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See the [http://www.intl-pag.org/16/16-gbrowse.html PAG tutorial page] for additional information.
+
 
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== Modware Feedback Wanted ==
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''2007/12/11''
+
 
+
[[Modware]] provides an object-oriented Perl API for [[Chado]] suitable for use by any application based on GMOD.  This Chado API supports creating, retrieving and updating objects in a Chado database. Modware makes heavy use of [[bp:Main Page|BioPerl]] to provide a familiar and intuitive interface for objects stored inside of a Chado database.
+
 
+
Recently, a VMware Virutal Machine was released to make download and
+
testing of a fully configured and installed version of Modware
+
available.  Modware developers continue to add new features, including
+
representation of BLAST hits (currently on CVS HEAD).
+
 
+
One critical piece of the project that is missing is feedback from the
+
community.  If you are interested in a Chado API, please download the
+
Modware Virtual Machine found on the [http://gmod-ware.sourceforge.net Modware home page] and give it a try.  Email all feature requests, questions, and comments to [mailto:gmod-ware-users@sourceforge.net gmod-ware-users@sourceforge.net].
+
 
+
== November 2007 GMOD Meeting ==
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''2007/11/08''
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+
The [[November 2007 GMOD Meeting]] was attended by nearly 40 people from across the GMOD community.  Community annotation and comparative genomics were two popular topics at this meeting.  See [[November 2007 GMOD Meeting]] for a list of presentations and a summary of the meeting.
+
 
+
== GMODTools 1.1 Released ==
+
 
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''2007/10/16''
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+
Version 1.1 of [[GMODTools]] has been released.  Version 1.1 adds these features and corrections:
+
 
+
* No chromosome/scaffold/golden_path files. This change is needed to handle partially assembled genomes with many (1000s to 100,000s) of scaffolds. Flag no_csomesplit=1 to use this (should become default).
+
* Gene Ontology association file, see go_association tags in configurations
+
* Validate main variables in chado database: ${golden_path}, ${seq_ontology}. This step, on now by default, checks that database contains configured values. If failed, db is inspected for real values.
+
* Miscellany bugs cured and configuration updates, e.g., tables/overview now again active.
+
 
+
[[GMODTools]] is a Perl package that generates Fasta, GFF, DNA and other bulk genome annotation files from Chado databases.
+
 
+
== GMOD Help Desk is Back ==
+
 
+
''2007/10/01''
+
 
+
After a several month hiatus, the [[GMOD Help Desk]] is back.  Dave Clements has taken the role created by Brian Osborne earlier this year.  Dave will work on the same sorts of things that Brian did:  Maintaining and improving the GMOD web site and documentation, and supporting the GMOD user community.  See [[GMOD Help Desk]] for more.
+
 
+
== FlyBase Converts to Chado ==
+
 
+
''2007/09/01''
+
 
+
This summer, FlyBase [[June 2007 Progress Report#Chado/FlyBase|finished its reimplementation]] using [[Chado]], the modular GMOD database schema which [http://flybase.org/ FlyBase] originated and continues to develop
+
in collaboration with GMOD and several GMOD-affiliated database
+
projects.  The FlyBase implementation of Chado integrates over 100
+
years of ''Drosophila'' genetic and genomic research data.  In addition to
+
supporting the ongoing genome annotation and scientific literature
+
curation for ''D. melanogaster'', the main Drosophilid model organism,
+
FlyBase is currently working to incorporate  the new genome sequences,
+
annotations, and cross-species comparative data for eleven additional
+
Drosophila species into the single production instance of Chado.
+
 
+
PostgreSQL dumps of FlyBase-chado are available at ftp://ftp.flybase.net/releases/current/psql/
+
 
+
== Pathway Tools 11.5 Released ==
+
 
+
''2007/08/15''
+
 
+
Version 11.5 of Pathway Tools has been [http://bioinformatics.ai.sri.com/ptools/release-notes.html released].  Version 11.5 includes
+
* Support for cellular regulation.
+
* Electron transport information
+
* Zooming in genome view
+
* Stricter  pruning to eliminate pathway predictions that are likely to be false-positive predictions
+
 
+
See the [http://bioinformatics.ai.sri.com/ptools/release-notes.html Pathway Tools release notes] for details.
+
 
+
[[Pathway Tools]] is a comprehensive symbolic systems biology software package that supports several use cases in bioinformatics and systems biology.
+
 
+
== ISMB/Bioinformatics Chado Paper ==
+
 
+
''2007/07/13''
+
 
+
The paper '[http://bioinformatics.oxfordjournals.org/cgi/content/full/23/13/i337 A Chado case study: an ontology-based modular schema for representing genome-associated biological information]' by Chris Mungall, Dave Emmert, and The [http://flybase.org/static_pages/docs/consortium.html FlyBase Consortium], was presented at [http://www.iscb.org/ismbeccb2007/ ISMB/ECCB 2007], and is now available in the journal [http://bioinformatics.oxfordjournals.org/ Bioinformatics].
+
 
+
The paper describes the overall [[Chado]] philosophy and the 5 core Chado modules.
+
 
+
== BioMart 0.6 Released ==
+
 
+
''2007/06/15''
+
 
+
Version 0.6 of the BioMart has been [http://www.biomart.org/news.html released].  Version 0.6 includes support for a 1.5 [[DAS]] server, and improvements to MartView and MartBuilder.  See [http://www.biomart.org/news.html BioMart News] for more.
+
 
+
[[BioMart]] is a query oriented database management system for biological data.
+
 
+
== GBrowse 1.68 Released ==
+
 
+
''2007/04/17''
+
 
+
Version 1.68 of [[GBrowse]] is a stability release which improves the documentation and installation process. It includes a new script called <tt>gbrowse_netinstall.pl</tt>, which will semi-automatically install GBrowse across the Internet on [[GBrowse Windows HOWTO|Windows]], [[GBrowse MacOSX HOWTO|Mac OSX]] and [[GBrowse Linux HOWTO|Linux]] platforms.
+
 
+
== News Archive ==
+
 
+
Earlier news items are available at [http://sourceforge.net/news/?group_id=27707 SourceForge].
+
 
+
<endFeed />
+
 
+
= Adding a News Item =
+
 
+
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.
#* Revise until you like it and then save it.
+
# Preview / save your changes.  Edit and save the page until the news item looks like you want.
 
+
# Once you are happy with how the item looks, insert this line at the end of it:
Once you have saved the page, a link to the new item will show up on the home page in about an hour.
+
#: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
 
+
#: 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.
Note: If you don't want to do this on your own, please send the item to the [[GMOD Help Desk]] and we will post it.
+
# '''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.

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Longer Instructions

Please follow these guidelines when adding a news item.

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  2. Enter the text of your news item.
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  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.
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