Difference between revisions of "GMOD News"

From GMOD
Jump to: navigation, search
m (News Items)
m (Moved news item list to top of page)
 
(224 intermediate revisions by 12 users not shown)
Line 1: Line 1:
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.
+
<div class="componentBox" style="width: 20em">
 
+
<wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" />
If you have a news item you want added here, please send it to the [[GMOD Help Desk]] or add it to this page directly.  See [[#Adding a News Item|Adding a News Item]] for how to do this.
+
 
+
<span class="plainlinks">
+
This page 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}}
+
</span>
+
 
+
= News Items =
+
 
+
Want to add your news item here?  See [[#Adding a News Item|Adding a News Item]] below for how to do just that.
+
 
+
<startFeed />
+
 
+
== NextGen Sequence in GBrowse ==
+
+
{{ImageRight|Aga_logo.png|Next Generation Genome Analysis in Non-Model Organisms--An American Genetic Association Special Event||http://www.regonline.com/Nextgeneration}}
+
 
+
There will be a [http://www.regonline.com/Nextgeneration talk] on visualizing next generation sequence data in [[GBrowse]] at [http://www.regonline.com/Nextgeneration Next Generation Genome Analysis in Non-Model Organisms], an [http://www.theaga.org American Genetic Association] Special Event held June 11-13, 2009 at the University of Connecticut.  The talk will demonstrate how GBrowse can visualize both individual reads and summary and derived data.
+
 
+
June will be a busy month for GMOD outreach.  If you can't make it to this meeting, there will also be [[#GMOD Workshops at SMBE, AGS|GMOD workshops]] at [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE] and the [http://www.k-state.edu/agc/symp2009/seminar.html Arthropod Genomics Symposium].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/05/19''
+
 
+
== WebGBrowse Has Arrived ==
+
{| width="100%"
+
! <div class="quotebox" style="font-size: 130%">[http://webgbrowse.cgb.indiana.edu/ WebGBrowse] - A Web Server for [[GBrowse]] Configuration Made Easy</div>
+
! {{#icon: cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://webgbrowse.cgb.indiana.edu/}}
+
|}
+
[http://webgbrowse.cgb.indiana.edu/ WebGBrowse] is a web site that guides users through the process of creating a [[GBrowse]] configuration file and then shows them how their data renders with that configuration.  Users can [[GBrowse Configuration HOWTO|configure]] GBrowse, either from scratch, or by uploading a preexisting GBrowse configuration file.  Tracks are defined using a graphical user interface where users first select the glyph to use ([http://webgbrowse.cgb.indiana.edu/webgbrowse/glyphdoc.html over 40 glyphs are currently supported]), and are then prompted for that glyph's settings.  Data is provided by uploading a [[GFF3]] file.
+
 
+
WebGBrowse has an extensive [http://webgbrowse.cgb.indiana.edu/webgbrowse/tutorial.html tutorial] and [http://webgbrowse.cgb.indiana.edu/webgbrowse/faq.html FAQ], and was just [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp239v1?papetoc published in Bioinformatics].  WebGBrowse is open source and can also be [http://webgbrowse.cgb.indiana.edu/webgbrowse/software.html installed locally].
+
 
+
WebGBrowse was created by Ram Podicheti, Rajesh Gollapudi, and Qunfeng Dong, all of the [http://cgb.indiana.edu/ The Center for Genomics and Bioinformatics (CGB)] at [http://www.indaina.edu Indiana University - Bloomington].  WebGBrowse was first presented by Ram Podicheti at the [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|January 2009 GMOD Meeting]].
+
 
+
WebGBrowse is an excellent way to get started with GBrowse, and to learn what glyphs are available, and what options each glyph supports.  Please [mailto:biohelp@cgb.indiana.edu contact the CGB] if you have any questions.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/04/22''
+
 
+
== GMOD Workshops at SMBE, AGS ==
+
 
+
There will be GMOD workshops at two major conferences in June 2009:
+
 
+
{|
+
| {{#icon: SMBE2009Corn.png|SMBE 2009|120|http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27}}
+
| <center>'''[http://ccg.biology.uiowa.edu/smbe/ Annual Meeting of the Society for Molecular Biology and Evolution (SMBE 2009)]'''<br />
+
June 3-7, 2009<br />Iowa City, Iowa</center>
+
| '''[http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 Database Tools for Evolutionary Genomics: An introduction to GMOD software for managing, annotating and visualizing genomic data]'''<br />
+
Saturday, June 6, 2:30-5:00pm<br />
+
This workshop will cover some of the most widely used GMOD software components, including the [[Chado]] database, the [[GBrowse]] genome browser, the [[CMap]] comparative map browser, and the [[Apollo]] genome curation tool. The workshop will also cover, in some depth, the [[GBrowse_syn]] comparative genomics viewer, and the [[MAKER]] genome annotation pipeline for eukaryotes.  Speakers ([[User:Faga|Ben Faga]], [[User:Mckays|Sheldon McKay]], Mark Yandell, and [[User:Clements|Dave Clements]]) will address both existing functionality and ongoing developments specifically targeted at better supporting evolutionary data and research. No knowledge of programming is necessary.
+
|-
+
! {{#icon: AGSBug170.png|Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2009/seminar.html}}
+
| <center>'''[http://www.k-state.edu/agc/symp2009/ 3rd Annual Arthropod Genomics Symposium]'''<br />
+
June 11 - 14, 2009<br />Kansas City, Missouri</center>
+
| '''[http://www.k-state.edu/agc/symp2009/seminar.html Chado Databases and Integration with GMOD Tools]'''<br />
+
Pre-Symposium Workshop - Thursday, June 11, 4:30-6:30 p.m.<br />
+
[[User:Scott|Scott Cain]], Ontario Institute for Cancer Research, will provide training on [[Chado]] database design, data loading and exporting, and integration with other GMOD tools such as [[Apollo]] and [[GBrowse]].  Particular emphasis will be given to comparative genomics tools.  There is no cost to attend this optional workshop, but registration is requested.
+
|}
+
 
+
Please let [[User:Clements|Dave]] (SMBE) or [[User:Scott|Scott]] (AGS) know if you have any questions about the workshops.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/04/09''
+
 
+
== Pathway Tools Workshop in August ==
+
<div class="emphasisbox">''[http://brg.ai.sri.com/ptools09/reg.html Registration] is now open for this workshop. 2009/04/24''</div>
+
{{ImageRight|SRILogo.png|Pathway Tools Workshop||http://brg.ai.sri.com/ptools09/}}
+
 
+
There will be a [http://brg.ai.sri.com/ptools09/ Pathway Tools Workshop], August 19-28, 2009 at [http://www.sri.com SRI International].  This two-part workshop covers [[Pathway Tools]] and the BioCyc Database Collection.
+
 
+
'''Part 1: Tutorial, August 19-21'''
+
 
+
This introductory tutorial will educate the new user on aspects of [[Pathway Tools]] including basic use of the Pathway/Genome Navigator, Editors, and PathoLogic. Students can bring a genome and leave with a draft Pathway/Genome Database.
+
 
+
Tutorial space is limited.
+
 
+
'''Part 2: Workshop August 24-28'''
+
 
+
The workshop will combine formal presentations by groups outside SRI International (invited speakers and speakers selected through an abstract-submission process), tutorials by SRI International staff, and a hackathon. Suggested topics include but are not limited to:
+
 
+
* Share expertise on how to develop new organism-specific databases with [[Pathway Tools]]
+
* Present new scientific results achieved with Pathway Tools and BioCyc
+
* Share experiences on how to make the most of Pathway Tools
+
* Presentations by users on extensions they have developed to Pathway Tools
+
* Presentations by SRI International on recent and planned  developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
+
* Discussions of requested future enhancements to Pathway Tools and    BioCyc
+
* Ideas for other software tools to integrate with Pathway Tools
+
* Group development of new Pathway Tools enhancements
+
 
+
Should you wish to make a presentation at the meeting, please submit a proposed title and abstract to [mailto:ptools-info@ai.sri.com ptools-info@ai.sri.com].
+
 
+
Please check the following [http://brg.ai.sri.com/ptools09/ website] for updates.
+
 
+
''2009/04/07, updated 2009/04/24''
+
 
+
== 2009 GMOD Summer Schools ==
+
 
+
{{Template:2009SummerSchoolApplicationBlurb}}
+
 
+
We are now accepting applications for the [[GMOD Summer School|2009 GMOD Summer Schools]].  GMOD Summer Schools are hands-on multi-day courses aimed at teaching new GMOD users how to get up and running with GMOD.  Summer schools introduce participants to the GMOD project and focus on installation, configuration and integration of popular [[GMOD Components]].  In 2009 we are proud to offer two schools, one on each side of the Atlantic:
+
{| style="vertical-align: middle; width=80%" cellpadding="10"
+
| align="center" | {{#icon: 2009SummerSchoolAmericas170.png|Americas||2009 GMOD Summer School - Americas}}
+
| <span style="font-size: 160%; line-height: 120%"><b>[[2009 GMOD Summer School - Americas|Americas]]</b></span><span style="font-size: 140%; line-height: 120%"><br />16-19 July<br />NESCent<br />Durham NC</span>
+
| rowspan="2" bgcolor="#eeeeee" width="2px" |
+
| rowspan="2" |
+
The courses include sessions on these popular GMOD components:
+
* [[GBrowse]] - the Generic Genome Browser
+
* [[Chado]] - a modular and extensible database schema
+
* [[Apollo]] - genome annotation editor
+
* [[BioMart]] - biological data warehouse system
+
* [[GBrowse_syn]] - a GBrowse based synteny viewer
+
* [[JBrowse]] - a brand new Web 2.0 genome browser
+
* Artemis-[[Chado]] Integration ([[2009 GMOD Summer School - Europe|Europe]] only)
+
* [[MAKER]] - Genome annotation pipeline ([[2009 GMOD Summer School - Americas|Americas]] only)
+
* [[User:Sficklin#Tripal|Tripal]] - Web front end for Chado ([[2009 GMOD Summer School - Americas|Americas]] only)
+
|-
+
| align="center" | {{#icon: GMOD2009Europe170.png|Europe||2009 GMOD Summer School - Europe}}
+
| <span style="font-size: 160%; line-height: 120%"><b>[[2009 GMOD Summer School - Europe|Europe]]</b></span><span style="font-size: 140%; line-height: 120%"><br />3-6 August<br />Oxford University<br />Oxford UK</span>
+
|}
+
The [[2009 GMOD Summer School - Europe|European summer school]] is part of [[GMOD Europe 2009]], a week long event which also includes the [[August 2009 GMOD Meeting]]. This is the first time a [[GMOD Summer School]] or [[Meetings|GMOD meeting]] will be held outside of North America.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/03/15, updated 2009/04/06, 2008/04/27''
+
 
+
== Apollo 1.10 Released ==
+
 
+
A new version of [[Apollo]] has been released.  Highlights for this release include:
+
 
+
* Support for remote NCBI BLAST (blastn, blastx, tblastx)
+
* Support for remote NCBI Primer BLAST (primer identification tool)
+
* Numerous bug fixes
+
 
+
The nice thing about the remote analysis support is that now users do not have to install those tools locally (which can be a pain) and don't need to download the very large NCBI databases.  These requests are handled in the background, so you can keep on working as usual and once the analysis is complete, the results will be automatically incorporated into the results track.
+
 
+
We're very interested in getting [mailto:apollo@fruitfly.org feedback from users] who may use the primer identification functionality.  If you could provide information on how you'd use such a tool and possibly what kind of filtering criteria you might need, it would be great so that we may incorporate these changes in future releases.
+
 
+
As always, you can download the current version at:
+
:http://apollo.berkeleybop.org/current/install.html
+
 
+
Ed Lee
+
 
+
''2009/03/02''
+
 
+
== Biocuration Conference, 16-19 April ==
+
 
+
{{ImageRight|2009BiocurationLogo.jpg|3rd International Biocuration Conference|400|http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html}}
+
 
+
The [http://projects.eml.org/sdbv/events/BiocurationMeeting/index.html 3rd International Biocuration Conference] will be held in Berlin, Germany, April 16-19, 2009.  This conference is a forum for curators and developers of biological databases to discuss their work, promote collaboration, and foster a sense of community in this active and growing area of research.  I don't think GMOD community members will find a higher concentration of people working on biological databases at any other conference.  Anyone interested in the methods and tools employed in biocuration is encouraged to attend.
+
 
+
Early [http://projects.eml.org/sdbv/events/BiocurationMeeting/registration.html registration] '''ends in two days''' (on 20 February, 2009).
+
 
+
[[User:Clements|Dave Clements]]
+
<br />[[GMOD Help Desk]]
+
 
+
''2009/02/18''
+
 
+
== Biomedical Ontology Conference, July ==
+
 
+
The [http://icbo.buffalo.edu/ International Conference on Biomedical Ontologies (ICBO)], will be held in Buffalo, New York from July 23-26, 2009.  Ontologies are widely used in GMOD for annotation, controlled vocabularies, reasoning, and data sharing.  [http://icbo.buffalo.edu/Call_for_Papers.pdf Paper submissions] are due March 1, and [http://icbo.buffalo.edu/Poster.pdf posters] are due April 10.  [http://icbo.buffalo.edu/ ICBO] will be held in conjunction with [http://www.bioontology.org/wiki/index.php/Tutorials_and_Classes four days of tutorials and classes] from July 20-23, 2009.
+
 
+
See the [http://icbo.buffalo.edu/ ICBO conference web site] for details.
+
 
+
[[User:Clements|Dave Clements]]
+
<br />[[GMOD Help Desk]]
+
 
+
''2009/02/17''
+
 
+
== January 2009 GMOD Meeting Report ==
+
 
+
{{ImageRight|Jan2009Meeting.JPG|January 2009 GMOD Meeting||January 2009 GMOD Meeting}}
+
The [[January 2009 GMOD Meeting]] was held January 15-16, 2009 in San Diego, immediately following the [[PAG 2009|Plant and Animal Genome (PAG)]] conference.  The meeting was attended by over 50 people representing about 35 different organizations.  The meeting report and links to presentations are now available on the [[January 2009 GMOD Meeting]] page.  There were [[January 2009 GMOD Meeting#Presentations|19 presentations]] by GMOD users and developers.
+
 
+
Some highlights:
+
* How best to [[January 2009 GMOD Meeting#Data Sharing|share data]]?
+
* [[January 2009 GMOD Meeting#BioMart|BioMart]] integration with other GMOD Components.
+
* [[January 2009 GMOD Meeting#JBrowse|JBroswe]] update
+
* [[January 2009 GMOD Meeting#WebGBrowse: GBrowse Configuration Management|WebGBrowse]] - [[GBrowse]] configuration on the web.
+
* A [[January 2009 GMOD Meeting#Drupal and MarineGenomics.org|Drupal interface to Chado]].
+
Plus 14 other excellent user and developer presentations.
+
 
+
Please take a look at the [[January 2009 GMOD Meeting|meeting report]] for an update on what's going on in the GMOD community.
+
 
+
We hope to see you at the upcoming [[August 2009 GMOD Meeting]], in Oxford UK (and our first meeting in Europe).
+
 
+
[[User:Clements|Dave Clements]]
+
<br />[[GMOD Help Desk]]
+
 
+
''2009/02/09''
+
 
+
== GBrowse User Tutorial ==
+
 
+
{{ImageRight|OpenHelixLogosmaller.jpg|OpenHelix||http://www.openhelix.com/gbrowse}}
+
 
+
A comprehensive [http://www.openhelix.com/gbrowse GBrowse User Tutorial] was released by [http://www.openhelix.com OpenHelix] this week.  The narrated tutorial covers:
+
* the basic layout and search methods in [[GBrowse]]
+
* how to access detailed annotation data tied to genomic sequences
+
* how to select and customize annotations using tracks
+
* how to upload and incorporate your own data or other external data sources
+
* take a tour of different GBrowse installations at model organism databases
+
 
+
The tutorial also includes [http://www.openhelix.com/downloads/gbrowse/gbrowseslidesDL.shtml PowerPoint slides], [http://www.openhelix.com/downloads/gbrowse/gbrowsehandoutsDL.shtml handouts], and [http://www.openhelix.com/downloads/gbrowse/gbrowseexercisesDL.shtml exercises] that can be used for reference or for training others.  The narration is reproduced in the notes area on the slides.
+
 
+
The [http://www.openhelix.com/gbrowse GBrowse User Tutorial] is part of a [http://www.openhelix.com/model_organisms.shtml set of model organism resource tutorials] funded in a large part by [http://www.genome.gov/ NHGRI].  The set includes tutorials on how to navigate and use [http://www.openhelix.com/rgd RGD], [http://www.openhelix.com/mgi MGI], and [http://www.openhelix.com/wormbase WormBase], and in the future for [http://zfin.org ZFIN], [[:Category:FlyBase|FlyBase]], and [[:Category:SGD|SGD]] (''all'' of which are GMOD users and/or contributors).
+
 
+
This tutorial focuses on ''using'' GBrowse and  complements the [http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/docs/tutorial/tutorial.html?pathrev=stable GBrowse Administration Tutorial].  It is an excellent resource for any organization that wants to help its users use GBrowse better.
+
 
+
[[User:Clements|Dave Clements]]
+
 
+
[[GMOD Help Desk]]
+
 
+
''2009/02/05''
+
 
+
== Opening at Dow AgroSciences ==
+
 
+
{{ImageRight|Dow_AgroSciences_logo.gif|Dow AgroSciences||http://www.dowagro.com/}}
+
 
+
[http://www.dowagro.com/ Dow AgroSciences] has a short term contract position available for someone with GMOD experience. The candidate proposed here will be responsible for three main tasks and several secondary ones:
+
 
+
# Install the open source software components for the [[Chado]] database, data loaders, and genome browser.
+
# Deploy the [[GBrowse]] genome browser in a centralized location in our intranet, which can be used by Dow AgroSciences scientists across functions.
+
# Test the system by performing preprocess (e.g annotate, perform alignments) and upload whole-genome data from Arabidopsis.
+
# Link the genome browser to Dow AgroSciences major internal databases, such as Variety, markerDB, QTL locate, and microarray database.
+
# Provide integration tests to ensure the transparency of the data among the different systems.
+
# Present to other Dow AgroSciences scientists to raise awareness of capability.
+
# Complete written documentation of project development, implementation, and continued maintenance.
+
 
+
Interested candidates please send a resume to Mindi Dippold at [mailto:mdippold@dow.com mdippold@dow.com].
+
 
+
''2009/02/03''
+
 
+
== New Ergatis Release ==
+
 
+
A new version of [[Ergatis]], a web-based utility for creating, running and reusing computational analysis pipelines, is now [https://sourceforge.net/project/showfiles.php?group_id=148765 available for download].
+
 
+
This version includes
+
* Interface improvements
+
* New components, notably:
+
** RNAmmer - RNA identification on genomic sequence
+
** p_func - Derives gene function assertions based on tiers of provided evidence, such as BLAST, HMM, etc..
+
** 454_mplex_seq_bin_trim - A binning and trimming script for multiplex 454 sequence data
+
** phylip_dnadist - A wrapper for a parallelized version of PHYLIP's dnadist
+
* New pipeline templates
+
* Bug fixes
+
 
+
A new version of the automated Prokaryotic Annotation Pipeline is also included, as well as a pipeline creation tutorial.  For a full list of the changes, see the [http://ergatis.svn.sourceforge.net/viewvc/ergatis/tags/ergatis-v2r10b1/doc/CHANGELOG?revision=5828&view=markup&sortby=date CHANGELOG file].
+
 
+
As always, installation instructions can be found within each package and in [http://ergatis.sourceforge.net/documentation/install_guide.html web form].
+
 
+
''2009/01/27''
+
 
+
== Job Openings at Georgetown University ==
+
 
+
Two Positions Immediately Available at Georgetown University in Washington, DC
+
 
+
'''Bioinformatics Engineer'''
+
 
+
This position is part of the USDA-funded [http://genomes.arc.georgetown.edu/hymenoptera/ Hymenoptera Genome Database] project, which includes [http://www.beebase.org/ BeeBase] (honey bee genome) and [http://genomes.arc.georgetown.edu/nasonia/ NasoniaBase] (wasp genome). This person will implement GMOD software and develop new query interfaces; develop scripts for automated data retrieval and database loading; develop computational pipelines for updating homology, functional annotation data and [[GBrowse]] tracks. Requires MS degree in bioinformatics or related field, and demonstration of programming experience. Experience with Perl, HTML, CGI, Java, [[MySQL]] and [[PostgreSQL]] is preferred.
+
 
+
'''Bioinformatics Systems Analyst'''
+
 
+
Duties include system administration, bioinformatics database maintenance, system backup management, problem diagnosis, and creation of system documentation. Must have experience in Linux system administration Perl, Java, Apache PostgreSQL, and MySQL. Experience with GMOD and [[BioPerl]] is highly desired.
+
 
+
Contact Chris Elsik: [mailto:chris.elsik@gmail.com chris.elsik@gmail.com]
+
 
+
''2009/01/15''
+
 
+
== BioGraphics now housed at gmod.org ==
+
 
+
The Bio::Graphics modules which have long been a core part of [[BioPerl]] have been separated out and the code base is now housed in the [http://gmod.cvs.sourceforge.net/gmod/|GMOD cvs repository at SourceForge].  This action has been taken to give the authors more flexibility over releases, particularly so that frequent updates can occur as needed around new [[GBrowse]] releases.  Releases of Bio::Graphics are already on CPAN, so it can be installed in the cpan shell.  Additionally, the [[GBrowse_Install_HOWTO#The_NetInstaller|gbrowse_netinstall.pl]] script for installing GBrowse automatically has been updated to install Bio::Graphics before installing GBrowse.
+
 
+
''2009/1/6''
+
 
+
== GMOD at PAG 2009 ==
+
 
+
<div style="float: right; padding: 0.5em">{{#icon: Paglogo.gif|GMOD @ PAG||PAG 2009}}</div>
+
GMOD will once again have a strong presence at the [[PAG 2009|Plant and Animal Genome Conference (PAG 2009)]].  There will be [[PAG 2009|'''over 35''' talks, workshops, demonstrations and posters]] about [[GMOD Components]] and projects that use them.  See the [[PAG 2009]] page for a printable listing of GMOD related events.
+
 
+
The [[January 2009 GMOD Meeting]] is immediately after PAG, and many GMOD developers and users will likely attend both meetings.
+
 
+
If you haven't registered yet for either or the [[January 2009 GMOD Meeting Registration|GMOD meeting]], you are encouraged to do so.
+
 
+
''2009/01/03''
+
 
+
== GMOD Meeting Registration Open ==
+
 
+
<div style="float: right; padding: 0.5em">
+
{|
+
|{{#icon: Jan2009MtgLogoNoText.png|January in San Diego - think about that||January 2009 GMOD Meeting}}
+
|-
+
| '''[[January 2009 GMOD Meeting]]'''
+
|}
+
 
</div>
 
</div>
[[January 2009 GMOD Meeting Registration|Registration]] is now open for the [[January 2009 GMOD Meeting]]. The meeting will be held January 15-16, 2009 in sunny [http://www.sandiego.org/nav/Visitors San Diego], immediately following the [[PAG 2009|2009 Plant and Animal Genome Conference (PAG 2009)]].
+
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]].
  
'''Registration is free.'''
+
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]]
  
If you haven't attended a [[:Category:Meetings|GMOD Meeting]] before then you are encouraged to find out why the [[2008 GMOD Community Survey#GMOD Meetings|overwhelming majority of past attendees]] have found meetings to be useful and well organized.  See the [[July 2008 GMOD Meeting]] report (or any of the other [[:Category:Meetings|previous report]]) for an idea of what goes on at GMOD Meetings.
+
== Recent News ==
  
Finally, if you have items that you would like on the agenda, please add them to the [[January 2009 GMOD Meeting|meeting page]].
+
<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>
  
As always, please let the [mailto:help@gmod.org GMOD Help Desk] know if you have any questions.
+
== [[GMOD News Archives|News Archives]] ==
  
Thanks,
+
The [[GMOD News Archives]] lists all news items since autumn 2007.
  
[[User:Clements|Dave Clements]]<br />
+
== Adding a News Item ==
[[GMOD Help Desk]]
+
  
''2008/11/20''
+
'''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.
  
== GMOD Community Survey Results ==
+
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 [[2008 GMOD Community Survey|results of the 2008 GMOD Community Survey]] are now available online.  The survey was taken by 89 respondents.  The survey includes questions on:
+
=== Short Instructions ===
* What GMOD Components they use
+
* Feedback on the specific components they use.
+
* The servers that GMOD runs on.
+
* GMOD Meetings
+
* GMOD Project overall (What is being done well, what needs improvement, what should be our focus for the next 12-18 months)
+
* GMOD Help Desk
+
* GMOD course in Europe and Asia/Pacific
+
* Organisms studied
+
* Biological areas of interest
+
  
Your responses will be used to improve GMOD and guide its future direction.
+
Please follow these guidelines when adding a news item.
  
And finally, we have our 3 winners of [[#Get GMOD Gear!|GMOD Gear]]:
+
# 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:
 +
: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
  
* Randall Svancara of [http://www.bioinfo.wsu.edu Washington State University]
+
=== Longer Instructions ===
* Victor Jun M. Ulat of the [http://www.irri.org International Rice Research Institute]
+
* Pinglei Zhou of [http://flybase.org FlyBase].
+
  
Please let the [mailto:help@gmod.org GMOD Help Desk] know if you have any questions about the survey.
+
Please follow these guidelines when adding a news item.
  
Thanks,
+
# 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'''.
[[User:Clements|Dave C]]<br />
+
#*  The page must start with '''News/''', otherwise it won't be picked by the RSS news feed.
[[GMOD Help Desk]]
+
# Enter the text of your news item.
 
+
''2008/11/20''
+
 
+
== January 2009 GMOD Meeting ==
+
 
+
<div style="float: right; padding: 0.5em">{{#icon: SanDiegoConvention.gif|January in San Diego - think about that||}}</div>
+
 
+
''Note: Registration is now open for the [[January 2009 GMOD Meeting]]. 2008/11/20''
+
 
+
The next GMOD community meeting will be held [[January 2009 GMOD Meeting|January 15-16, 2009]] in sunny [http://www.sandiego.org/nav/Visitors San Diego], immediately following the [[PAG 2009|2009 Plant and Animal Genome Conference (PAG 2009)]].  Early details on the GMOD meeting are now available on the [[January 2009 GMOD Meeting]] page.  We'll update that page as we have more.  If you want to know what happens at a GMOD meeting see the notes from the [[July 2008 GMOD Meeting]] or any of the other [[:Category:Meetings|previous meetings]].
+
 
+
It's also worth noting that GMOD will again have a [[PAG 2009|strong presence]] at the PAG 2009 meeting itself.  If you are interested in attending [http://www.intl-pag.org/ PAG 2009], early registration closes November 1.
+
 
+
And, ''just in case it slipped your mind,'' it is still not too late to fill out the [[2008 GMOD Community Survey|GMOD Community Survey]] and be entered to win [[#Get GMOD Gear!|GMOD gear]]!
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2008/10/23, updated 2008/11/20''
+
 
+
== 2008 GMOD Community Survey ==
+
 
+
{| class="wikitable"
+
| ''Thanks to everyone who participated in the [[2008 GMOD Community Survey]].  Survey results are [[2008 GMOD Community Survey|now available]].  The winners are Randall Svancara of [http://www.bioinfo.wsu.edu Washington State University], Victor Jun M. Ulat of the [http://www.irri.org International Rice Research Institute] and Pinglei Zhou of [http://flybase.org FlyBase]. 2008/11/20''
+
|}
+
Please take a few minutes to fill out the [[2008 GMOD Community Survey]] and your name will be entered to win a free [[#Get GMOD Gear!|GMOD T-shirt or mug]]!
+
 
+
We are asking all GMOD users and developers to provide input on how GMOD is doing, and how it can be improved.  All questions are optional, but please provide as much information as you can.  The survey covers GMOD in general, and any GMOD components that you use (and it only asks about components that you indicate you use).
+
 
+
'''Three randomly selected survey participants will receive the [http://www.cafepress.com/GenericMOD/ GMOD T-shirt or mug] of their choice.  Names will be drawn from the first 100 responses we receive, so get your response in early.'''
+
 
+
Please contact the [[GMOD Help Desk]] at [mailto:help@gmod.org|<help@gmod.org>]  if you have any questions.
+
 
+
Thank you,
+
 
+
''The GMOD Team''
+
 
+
''2008/10/17'', updated ''2008/11/20''
+
 
+
== Get GMOD Gear! ==
+
 
+
<div style="float:left; padding:0.5em">{{#icon: GMODMug150x150.jpg|GMOD Mug||http://www.cafepress.com/GenericMOD/}}</div>
+
<div style="float:right; padding:0.5em">{{#icon: TShirtThumb.jpg|GMOD T Shirt||http://www.cafepress.com/GenericMOD/}}</div>
+
 
+
 
+
<div style="text-align: center">
+
<div style="font-size: 135%">
+
Tired of not having a cool T-shirt to wear at meetings?
+
</div><div style="font-size: 135%">
+
Tired of drinking your coffee from a ''styrofoam'' cup?
+
</div><div style="font-size: 135%">
+
Want to show off your affiliation with GMOD and promote it at the same time?
+
</div><div style="font-size: 150%;">[http://www.cafepress.com/GenericMOD/ '''Be the first person in your lab, community, organization, building, campus or country to be seen with some GMOD gear!''']
+
</div>
+
</div>
+
 
+
 
+
'''Note:''' Want to win a shirt of mug for free?  Then participate in the [[#2008 GMOD Community Survey|2008 GMOD Community Survey]].  Three participants will be randomly selected to receive the GMOD item of their choice.
+
 
+
GMOD has a [http://www.cafepress.com/GenericMOD/ store] at CafePress where you can buy GMOD gear.  Currently there are two T-shirt styles and a coffee mug.  (We also take requests if you want to see additional gear - for example, a long sleeved T shirt or even a ''GMOD Pet Bowl'').
+
 
+
Please note:
+
* GMOD gear is offered at cost. GMOD does not make any money from the sale of these items.
+
* The ''GMOD News'' will return to its usual, somewhat more sedate, style with the next posting.
+
 
+
 
+
[[User:Clements|Dave Clements]]<br>
+
[[GMOD Help Desk]]
+
 
+
''2008/10/09''
+
 
+
''Updated 2008/10/17''
+
 
+
 
+
<endFeed />
+
 
+
= News Archives =
+
 
+
Items more than 6 months old are available in the [[GMOD News Archives]].
+
 
+
= 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.
#* '''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.'''
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.
+
#* 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}}