Difference between revisions of "GMOD News"

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News that is relevant to the GMOD user and developer communities.  News items more than 6 months old are listed in the '''[[GMOD News Archives]]'''.  If you have a news item you want added here, please see [[#Adding a News Item|Adding a News Item]] below.  Also see the [[Calendar|GMOD Calendar and Events List]].
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<wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" />
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This ''GMOD News'' is also available as an '''[http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss RSS feed]'''. {{#icon: RSSIcon16x16.gif|RSS feed||http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss}}
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</span>
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= News Items =
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{{TocRight}}
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Want to add your news item here?  See [[#Adding a News Item|Adding a News Item]] below.
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<startFeed />
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<!-- **** Add new Items here.  Keep the Title Short!  ***35 characters or less*** -->
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== WebGBrowse Joins GMOD ==
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{{ImageRight|WebGBrowseLogo.png|WebGBrowse now a part of GMOD|280|WebGBrowse}}
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[[WebGBrowse]], a web interface for setting up [[GBrowse]] instances, is now a part of GMOD. [[WebGBrowse]] enables biologists and bioinformaticians to
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# upload genome annotation information in [[GFF3]] format,
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# configure display of each genomic feature through simple mouse clicks on a web browser,
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# visualize the configured genome with the integrated GBrowse software.
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''There is no manual editing of GBrowse configuration files with WebGBrowse.''  WebGBrowse relieves both the burden of installing GBrowse and the need to learn the configuration semantics.  It is also a good way to learn the many [http://webgbrowse.cgb.indiana.edu/glyphdoc.html GBrowse glyphs] and how to configure them.
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WebGBrowse is a good match for any organization that has users who want to create their own GBrowse instances, but lack enough computing resources and expertise to do so. WebGBrowse was developed at [http://www.iub.edu/ Indiana University's] [http://cgb.indiana.edu/ Center for Genomics and Bioinformatics].
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WebGBrowse can be [http://webgbrowse.cgb.indiana.edu/software.html downloaded] and installed locally, or you can use the [http://webgbrowse.cgb.indiana.edu/ WebGBrowse at CGB].  The source is {{SF SVN|WebGBrowse/|available at SourceForge}}.  WebGBrowse comes with [http://webgbrowse.cgb.indiana.edu/tutorial.html a tutorial], [http://webgbrowse.cgb.indiana.edu/faq.html FAQ], and a [[WebGBrowse#Mailing Lists|user and support mailing list]].
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[[User:Mnrusimh|Ram Podicheti]]<br />
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[http://cgb.indiana.edu/ Center for Genomics and Bioinformatics]
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''2010/12/10''
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== New Topic-Based Mailing Lists ==
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Two new [[GMOD Mailing Lists#Topic Based Lists|GMOD mailing lists]] have been created as a result of the [[GMOD Evo Hackathon]] and subsequent {{NabbleThreadLink|New-Mailing-Lists-GMOD-PhenDiver-GMOD-CoGePhy-td2052650.html|feedback from the community}}.  The two lists are both based on [[GMOD Mailing Lists#Topic Based Lists|research topics]], rather than on specific components:
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{| class="wikitable"
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! Name
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! List Link
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! Topics
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! Archive(s)
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{{MailingListsCoGePhy}}
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{{MailingListsPhenDiver}}
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|}
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If you are interested in these topics, please subscribe to the lists and post any comments or questions that you just didn't know where to post before!
+
 
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Thanks,
+
 
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/12/08''
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PS: Also, while not (yet!) a part of GMOD, if you are interested in tree visualization, you are also encouraged to join the [http://groups.google.com/group/phylobox PhyloBox Google Group].  The PhyloBox group was well represented at the [[GMOD Evo Hackathon|hackathon]].
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== Sr. DB Programmer @ FlyBase ==
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{{ImageRight|Fly_logo.png|Senior Database Programmer at FlyBase|170|}}
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The FlyBase genome database project group at Harvard University is [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=22617BR looking for a new software developer] to work on [[Chado]] related activities.  See the [https://sjobs.brassring.com/1033/asp/tg/cim_jobdetail.asp?partnerID=25240&siteID=5341&AReq=22617BR job posting] for details.
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''2010/12/07''
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== Software Requirements V2.0? ==
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{{ImageRight|Gmod-gears.png|Software Requirements, Ver 2 Proposal||http://gmod.org/wiki/GMOD_Membership#Software}}
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GMOD's [[GMOD Membership#Software|procedures and requirements for software to become a part of GMOD]] were codified in February 2010, following the [[January 2010 GMOD Meeting]].  These requirements were in use before February, but were not documented or consistently applied.
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These ''Version 1'' requirements are:
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* Meets a common need
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* Useful over time
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* Configurable and Extensible
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* Open source license for all users
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* Interoperable with existing GMOD Components
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* Commitment of support
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We'd now like to add two new requirements that probably should have been there in the first version:
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# Component has a support [[GMOD Mailing Lists|mailing list]] that is publicly archived
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# Publicly accessible code repository
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We discussed these changes at the [[September 2010 GMOD Meeting#GMOD Membership Requirements|September 2010 GMOD Meeting]] , and attendees recommended they be implemented.  We are now contacting the community at large (you!) to solicit feedback on the proposal.
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If you have any comments, please post them to the [mailto:gmod-devel@lists.sourceforge.net membership requirements thread on the gmod-devel list] in the next two weeks.  If we reach consensus and approval, we'll update the requirements.
+
 
+
[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/12/07''
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== GMOD Spring Training: Apply Now ==
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[[2011 GMOD Spring Training#Applications|Applications are now being accepted]] for the [[2011 GMOD Spring Training]] course, a five-day hands-on school aimed at teaching new GMOD administrators how to install, configure and integrate popular [[GMOD Components]].  The course will be held March 8-12 at the [http://www.nescent.org US National Evolutionary Synthesis Center (NESCent)] in Durham, North Carolina, as part of [[GMOD Americas 2011]].
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These components will be covered at the school:
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{|
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| align="center" | {{#icon: GMODAmericas2011Logo.jpg|2011 GMOD Spring Training|170|2011 GMOD Spring Training}}<br />'''[[2011 GMOD Spring Training#Applications|Apply Now]]'''
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|
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* [[Apollo]] - genome annotation editor
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* [[Chado]] - biological database schema
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* [[Galaxy]] - workflow system
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* [[GBrowse]] - genome viewer
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* [[GBrowse_syn]] - synteny viewer
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* [[GFF3]] - genome annotation file format and tools
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* [[InterMine]] - biological data mining system
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* [[JBrowse]] - next generation genome browser
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* [[MAKER]] - genome annotation pipeline
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* [[Tripal]] - web front end to Chado databases
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|}
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'''The deadline for applying is the end of Friday, January 7, 2011.  Admission is competitive and is based on the strength of the application, especially the statement of interest.'''  The [[2010 GMOD Summer School - Americas|2010 school]] had over 60 applicants for the 25 slots.  Any application received after deadline will be automatically placed on the waiting list.
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The course [[2011 GMOD Spring Training#Prerequisites|requires some knowledge of Linux]] as a prerequisite.  The registration fee will be $265 (only $53 per day).  There will be a limited number of scholarships available.
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''This may be the only [[GMOD Schools|GMOD School]] offered in 2011.''  If you are interested, you are strongly encouraged to apply by January 7.
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Thanks,
+
 
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2010/12/03''
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== Phenotype RCN Launched ==
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<div style="float: right; padding-left: 1em; padding-bottom: 1em">http://www.nescent.org/images/rotate/begonia2h.jpg</div>
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We are pleased to inform you that NSF has recently funded the [http://phenotypercn.org/ Phenotype Research Coordination Network (RCN)] for researchers who are interested in searching and comparing phenotypes across species and in developing the tools and methods needed in making this possible.  The representation of morphology, behavior and other phenotypic features using computational methods such as ontologies and controlled vocabularies is in its infancy.  Integrating phenotypes with data across all levels of the biological hierarchy, however, is possible if standards are co-developed and coordinated.
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This RCN envisions building a broad base of community knowledge and resources so as to maximize the research potential of web-based data.  Funding for participation in meetings, presentations and laboratory exchanges for students, postdocs and faculty from ontology and taxonomic domains (initially plants, arthropods, and vertebrates) is [http://phenotypercn.org/opportunities/ available through the RCN].
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We are eager to have you join us!  Please [http://phenotypercn.org/participants/add/ sign up for our participant and mailing lists] for further information and feel free to contact one of the PIs: [mailto:pmabee@usd.edu Paula Mabee], [mailto:andy_deans@ncsu.edu Andy Deans], [mailto:huala@acoma.stanford.edu Eva Huala], and [mailto:selewis@lbl.gov Suzanna Lewis].
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Hope to hear from you soon,
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Paula, Andy, Eva, and Suzanna
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''2011/12/03''
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== Help Desk Transition ==
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{{ImageRight|GMODHelpDeskLogo.jpg|Help Desk Transition|170|GMOD Help Desk#Transition}}
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After three years at the [[GMOD Help Desk]] I have decided to take a similar position with the [[Galaxy]] project, starting on January 1.  I'll still be a part of the GMOD community (and I will still be involved in planning [[GMOD Americas 2011]]), but I will no longer be GMOD project staff.  I have enormously enjoyed my time on this project and I have learned a lot from working on the project and with the community.
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This transition make this an ideal time to reconsider and reconfigure what the GMOD Help Desk does.  The Help Desk's current core tasks will continue, including:
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* [[GMOD Help Desk#User Help|User help]]
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* [[GMOD Help Desk#GMOD Web Site and Documentation|Web site and documentation]]
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* [[GMOD Help Desk#Training and Outreach|Training, outreach, and community building]]
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* [[GMOD Help Desk#Developer support|Developer support]]
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What should the balance be between these tasks?  What additional tasks should be added to the mix?  If you have any suggestions on how the position should evolve, please send them to the [mailto:help@gmod.org Help Desk].  We'll compile your ideas and use them to guide the next incarnation of the help desk.
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We are also looking for someone to fill the updated position.  If you know of anyone, or are interested yourself, then please contact us as well.  It's a great job and there is no better community to work with.
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Thanks for everything.  It's been a great three years.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]] (for one more month)
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''2010/12/02''
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== Virtual Issue in Journal ''Database'' ==
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{{ImageRight|DatabaseJournal.jpg|Database: The Journal of Biological Databases and Curation|300|http://database.oxfordjournals.org/}}
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I recently had a chat with one of the editors of the journal [http://database.oxfordjournals.org/ ''Database''], an open access journal whose aim for publications lines up very nicely with the goals of GMOD.  During this discussion, the idea of a GMOD ''virtual issue'' came up, and it is one that I am very excited about.  Therefore, I'm reaching out to you (the GMOD community) for ideas as well as commitments to write peer reviewed articles for this publication.  Articles can be about theory, tutorial or community.  I expect we'll have papers covering many components and for some components we will have multiple papers with different emphases (for example, [[Chado]] theory, Chado tutorial, and Chado community papers).  Please [mailto:scott@scottcain.net contact me] if you'd like to discuss this further.
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The virtual issue approach that ''[http://database.oxfordjournals.org/ Database]'' takes is very appealing, in that the submitted papers do not need to be in by a certain cutoff date, as this is not going to put into a "dead tree" form :-)  So, the virtual issue can be created at any point, either when there is just one paper, or when there is a critical mass (which we would have control over), and more papers can be added to it at any time.  An example of a ''Database'' virtual issue is the [http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html one they created for the Biocurator meeting last year].
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I look forward to your ideas and commitments!
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[[User:Scott|Scott Cain]]<br />
+
GMOD Project Coordinator
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''2010/12/01'
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== December 2010 Calendar ==
+
 
+
{{ImageRight|calendar_icon.gif|GMOD Calendar||Calendar}}
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There are almost no submission deadlines in December.  (However, to buck the trend, the deadline for applying to the [[2011 GMOD Spring Training]] School will probably be in December.)  There are a number of interesting events though:
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* BioInfoSummer 2010 and the NETTAB Workshop on Bio-wikis (these both start in November and end in December)
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* Automated Imaging and High-Throughput Phenotyping
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* International Digital Curation Conference
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* Australasian Ontology Workshop
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* EMBO Course o Bioinformatics and Comparative Genome Analysis
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* International Conference on Genome Informatics
+
 
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<div style="margin-right: 26em">
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<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20101201%2F20101201</embedurl>
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</div>
 
</div>
 +
News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the '''[[GMOD News Archives]]'''. See also the [[Calendar|GMOD Calendar and Events List]].
  
If you know of any upcoming events that are not on the calendar, please send them to me.
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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]]
  
Happy holidays,
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== Recent News ==
  
[[User:Clements|Dave Clements]]<br />
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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>
[[GMOD Help Desk]]
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''2010/11/23''
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== [[GMOD News Archives|News Archives]] ==
  
== GMOD Americas: March 2011 ==
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The [[GMOD News Archives]] lists all news items since autumn 2007.
  
{{ImageRight|GMODAmericas2011Logo.jpg|GMOD Americas 2011|150|GMOD Americas 2011}}
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== Adding a News Item ==
  
'''[[GMOD Americas 2011]]''' has been scheduled for March 5-12 at the [http://www.nescent.org/ National Evolutionary Synthesis Center (NESCent)], in Durham, North Carolina.  [[GMOD Americas 2011]] will include:
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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.
* '''[[March 2011 GMOD Meeting]]'''
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: The next [[Meetings|GMOD Community Meeting]] will be held March 5-6.  For the first time, it will be preceded by an ''[[March 2011 GMOD Meeting#Friday: Introduction to GMOD|Introduction to GMOD]]'' session on the evening of March 4.  This session will be targeted at GMOD newcomers.
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* '''[[Satellite Meetings - GMOD Americas 2011|Satellite Meetings]]'''
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: GMOD community members gather to discuss and work on common topics of interest.
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* '''[[2011 GMOD Spring Training]]'''
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: A 5 day [[GMOD Summer School|GMOD Course]] covering installation, configuration and integration of [[GMOD Components]].
+
  
The details for each of these will be filled in shortly. In particular, we expect to start taking applications for the [[2011 GMOD Spring Training|course]] in December.  Registration for the meetings will likely open in January.
+
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]].
  
In the meantime, if you have any topics you want to discuss at the [[March 2011 GMOD Meeting|Community Meeting]] or the [[Satellite Meetings - GMOD Americas 2011|Satellite Meetings]], please add your idea to the meeting page, or contact the [mailto:htlp@gmod.org GMOD Help Desk].
+
=== Short Instructions ===
  
''Mark your calendars!''
+
Please follow these guidelines when adding a news item.
  
[[User:Clements|Dave Clements]]<br />
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# Create a new page named "'''News/'''''News Item Title''".
[[GMOD Help Desk]]
+
#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
 +
# Enter the text of your news item.
 +
#* '''The first link in the news item should point to the page/URL you want the RSS feed to link to.
 +
# Preview / save your changes.  Edit and save the page until the news item looks like you want.
 +
# Once you are happy with how the item looks, insert this line at the end of it:
 +
: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
  
''2010/11/23''
+
=== Longer Instructions ===
  
== Positions @ JCVI ==
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Please follow these guidelines when adding a news item.
  
From the Galaxy mailing list:
+
# Create a new page named "'''News/'''''News Item Title''".
<div class="indent">
+
#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
We have a few open [https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d Bioinformatics/Software Engineers positions] at the [http://www.jcvi.org/ J.Craig  Venter Institute], {{ImageRight|JCVILogo.jpg|Galaxy/Python and Bioinformatics Engineers positions at the J.Craig Venter Institute||https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d}} one of which involves largely developing further the [[Galaxy]] platform for use in-house (writing additional Galaxy wrappers for internal pipelines / tools, integrating Galaxy with existing cluster systems, SGE etc.)
+
#*  The page must start with '''News/''', otherwise it won't be picked by the RSS news feed.
 
+
# Enter the text of your news item.
Besides working with Galaxy, these positions involve quite a broad range of software development opportunities (languages ranging from Perl to Java), while at the same time they offer great learning opportunities for working with next-generation sequencing datasets, and learning fundamental techniques related to bioinformatic analysis of these types of data.
+
 
+
Please pass the word, feel free to [mailto:kkrampis@jcvi.org email me] for additional information, or
+
even go to the [https://careers.jcvi.org/careers/Careers.aspx?adata=Q%2fhMgU9ioOU2Q2IBMeDlPzojZaM309CBtHV%2b%2bLtKWW0PRb6H39%2fWK4hiwgS3QLR6dvwqIVTrFzs%3d careers page] to apply.
+
 
+
many thanks !
+
 
+
Konstantinos (Ntino) Krampis, Ph.D.<br />
+
Bioinformatics Engineer<br />
+
[http://www/jcvi.org J.Craig Venter Institute]
+
</div>
+
''2010/11/18''
+
 
+
== Comparative Genomics Workshop ==
+
 
+
{{ImageRight|CeskyKrumlov.jpg|Workshop on Comparative Genomics||http://www.molecularevolution.org/workshops/WCG}}
+
 
+
The [http://www.molecularevolution.org/workshops/WCG Workshop on Comparative Genomics] is being held in Český Krumlov, Czech Republic, 9-21 January 2011.  The workshop consists of a [http://www.molecularevolution.org/workshop_schedule?workshop=2 series of lectures, demonstrations and computer laboratories] that cover various aspects of comparative genomics.  Faculty include Anton Nekrutenko leading a session on [[Galaxy]] and [[User:Mckays|Sheldon McKay]] leading a session on [[GBrowse_syn]].
+
 
+
The course is designed for established investigators, postdoctoral scholars, and advanced graduate students. Scientists with strong interests in the uses of short-read sequence data, analytical methods, comparative structure of genomes, SNP detection and analysis, CNV, genome visualization tools and related areas are encouraged to apply for admission. Lectures and computer laboratories total ~90 hours of scheduled instruction.  No programming experience is required.
+
 
+
The official application deadline has passed, but there are still a few openings for qualified candidates.  There are also some openings in the [http://www.molecularevolution.org/workshops/WME Workshop on Molecular Evolution], being held immediately after.
+
 
+
''2010/11/03''
+
 
+
== Modware Status Update ==
+
 
+
{{ImageRight|ModwareLogo.png|Modwware Middleware|200|Modware}}
+
 
+
Good news and update on the current status of [[Modware]] development. Modware is getting back on track and is currently being actively developed at [http://dictybase.org dictyBase] since last few months. It is being written using {{CPAN|Moose}} and {{CPAN|DBIx::Class}} (more precisely [[Bio::Chado::Schema]] or BCS) ORM. This part of development is done in sync with dictyBase's major data migration project which includes literature and gene ontology annotations. So, the first release of this new version  is expected to deal with publication and ontology datasets in [[Chado]]. Handling of feature module will be added after the first release gets settled down. Like any other standard Perl module Modware's public release will be available from CPAN and the bleeding edge can be grabbed from [http://github.com/cybersiddhu/Modware github].
+
 
+
Relevant documentations and guidelines will also be added to the [[Modware|GMOD wiki]].  The first CPAN release is expected to be early next year.
+
 
+
Thanks,
+
 
+
Siddhartha Basu<br />
+
[[Modware]] developer,  [http://dictybase.org dictyBase]
+
 
+
''2010/10/28''
+
 
+
== Opening @ Cancer Research UK ==
+
{{ImageRight|CancerResearchUKLogo.jpg|Bioinformatician and Pancreatic Expression Database|180|http://webapps.qmul.ac.uk/hr/vacancies/jobs.php?id=2042}}
+
 
+
There is an [http://webapps.qmul.ac.uk/hr/vacancies/jobs.php?id=2042 opening for a bioinformatician] at the [http://www.cancer.qmul.ac.uk/research/molecular_oncology_imaging/index.html Centre Barts Cancer Research UK for Molecular Oncology and Imaging] working on the [http://www.pancreasexpression.org/ Pancreas Expression Database]:
+
 
+
: ... contribute to the development of the pancreatic cancer bioinformatics platform and tools. Working mainly with [[BioMart]], the successful candidate will be expected to address bioinformatics needs related to the update, maintenance and expansion of the pancreatic expression database ([http://www.pancreasexpression.org www.pancreasexpression.org]) to set up the Bioinformatics Infrastructure. The successful candidate will additionally be responsible for pancreatic cancer literature data curation, release cycles as well as the wider development and extension of the analytical side of this platform.
+
 
+
See the [http://webapps.qmul.ac.uk/hr/vacancies/jobs.php?id=2042 full announcement] for details.  A [http://webapps.qmul.ac.uk/hr/vacancies/jobs.php?id=2039 related position] in the same group is also open.  Applications close 12 November.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/10/25''
+
 
+
== Pathway Tools 2010: ''Virtual, Now'' ==
+
 
+
{{ImageRight|PathwayToolsGraph.png|Attend the Pathway Tools Workshop Remotely|180|http://bioinformatics.ai.sri.com/ptools10/teleconferencing.html}}
+
 
+
We are offering individuals the ability to [http://bioinformatics.ai.sri.com/ptools10/teleconferencing.html attend presentations at the Pathway Tools Workshop remotely]. We will be broadcasting the presentation slides via WebEx, and you can hear the voice of the presenter by calling in to a conference call.  Please see the [http://bioinformatics.ai.sri.com/ptools10/teleconferencing.html workshop teleconference page] for information on how to connect via WebEx and how to call into the conference call.  See the [http://bioinformatics.ai.sri.com/ptools10/agenda.html Workshop agenda], for complete talk titles and times.
+
 
+
Feel free to forward this announcement to interested colleagues.
+
 
+
If you experience any difficulties with connecting, please contact [mailto:ptools-support@ai.sri.com PTools Support <ptools-support@ai.sri.com>]
+
 
+
Best regards,
+
 
+
Tomer Altman<br />
+
Pathway Tools Workshop Coordinator
+
 
+
''2010/10/24''
+
 
+
== November 2010 Calendar ==
+
 
+
{{ImageRight|calendar_icon.gif|GMOD Calendar||Calendar}}
+
 
+
November has a number of deadlines and meetings:
+
; Deadlines:
+
* '''[[PAG 2011]] abstract deadline for posters and demos - November 1'''
+
* SWAT4LS: Semantic Web Applications for Life Sciences posters and demos
+
* Rocky '10 early registration
+
 
+
; Conferences, Meetings, and Courses
+
* [http://www.ashg.org/2010meeting/ ASHG]: This include [http://www.ashg.org/2010meeting/pages/workshops_Genomic_tools.shtml#5a two workshops] on [[Galaxy]] and is preceded by an [http://blog.openhelix.eu/?p=5576 OpenHelix workshop] that covers [[BioMart]] and [[Galaxy]].
+
* Computational & Comparative Genomics Course at CSHL:  This will also include sessions on [[BioMart]] and [[Galaxy]].
+
* [[GMOD Evo Hackathon|GMOD Tools for Evolutionary Biology Hackathon]]
+
* [[#InterMine Workshop 15-16 Nov|InterMine Workshop]]
+
* Automated Functional Annotation and Data Mining Course
+
* BioInfoSummer 2010
+
* NETTAB Workshop on Bio-wikis
+
 
+
<div style="margin-right: 26em">
+
<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20101101%2F20101101</embedurl>
+
</div>
+
 
+
If you know of any upcoming events that are not on the calendar, please send them to me.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/10/22''
+
 
+
== Pathway Tools 2010 Deadline! ==
+
{{ImageRight|SRILogo.png|Pathway Tools Workshop 2010||http://bioinformatics.ai.sri.com/ptools10/}}
+
 
+
'''Registration for the [http://bioinformatics.ai.sri.com/ptools10/ Pathway Tools Workshop 2010] closes in two days, on Thursday, October 21'''.  The workshop is being held next week in Menlo Park, CA.  This workshop is oriented around SRI's [[Pathway Tools]] software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.
+
 
+
It will combine presentations by groups outside SRI, tutorials by SRI staff, and a hackathon.  See the [http://bioinformatics.ai.sri.com/ptools10/ workshop website] for more information and registration link.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/10/19/''
+
 
+
== InterMine 0.94.1 Release ==
+
 
+
{{ImageRight|InterMineLogo.png|InterMine 0.94.1 release|170|InterMine}}
+
 
+
[[InterMine]] 0.94.1 is now released, and available as a subversion branch and zip file.
+
 
+
0.94.1 contains fixes for bugs discovered by users when upgrading to 0.94 and a number of minor enhancements.
+
 
+
InterMine 0.94 is a major release with many new features, including:
+
* a new full text search over the entire database
+
* template queries with optional constraints
+
* selection of multiple values in template query constraints
+
* layout improvements to the template query form
+
* drag/drop selection of constraint order when creating templates
+
* better automatic data model generation from the Sequence Ontology
+
* sequences stored as CLOBs in the database
+
* major data loading and query/export performance improvements
+
* export of query results direct to [[Galaxy]]
+
 
+
See the [http://www.intermine.org/wiki/ReleaseNotes full release notes] for 0.94 and 0.94.1, and [http://www.intermine.org/wiki/UpgradeInterMine the upgrade instructions] if you are migrating from an earlier release.
+
 
+
As always, [[InterMine#Contact|let us know]] if you have any problems or questions.
+
 
+
Regards,
+
 
+
The [[InterMine]] developers
+
 
+
''2010/10/15''
+
 
+
== GMOD Europe 2010 Report ==
+
 
+
<div style="float: right">
+
{|
+
| align="center" valign="top" |
+
<div style="border: 2px solid #DDDDDD;">
+
{{#icon: Sept2010MtgLogo300.png|September 2010 GMOD Meeting|150|September 2010 GMOD Meeting}}<br /><br />
+
{{#icon: InterMineLogo.png|InterMine Workshop|150|http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010}}<br />
+
{{#icon:Biomart250.png|BioMart Workshop|170|http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010}}<br />
+
{{#icon: GMOD2010Europe300.png|GMOD Europe 2010|160|GMOD Europe 2010}}
+
</div>
+
|}
+
</div>
+
 
+
GMOD Europe 2010 was held 13-16 September, 2010 in Cambridge, UK.  More than 60 people attended one or more of the events during the week.  The [[September 2010 GMOD Meeting]] kicked off [[GMOD Europe 2010]].  [[September 2010 GMOD Meeting#Agenda|Summaries of all 19 talks]] are now available on the [[September 2010 GMOD Meeting]] page. Talks were given by GMOD users, developers and staff, including:
+
* [[September 2010 GMOD Meeting#The Open Microscopy Environment: Open Informatics for Biological Imaging|The Open Microscopy Environment: Open Informatics for Biological Imaging]]
+
* [[September 2010 GMOD Meeting#InterMine: new Mines and new features|InterMine: new Mines and new features]]
+
* [[September 2010 GMOD Meeting#BioPivot|BioPivot]]
+
* [[September 2010 GMOD Meeting#CpG Island and STR Annotator Plugins|CpG Island and STR Annotator Plugins]]
+
* Several web services and distributed resources talks:
+
** [[September 2010 GMOD Meeting#GMOD RPC API: The almost RESTful GMOD API|GMOD RPC API: The almost RESTful GMOD API]]
+
** [[September 2010 GMOD Meeting#CRAWL (Chado RESTful Access Web-service Layer)|CRAWL (Chado RESTful Access Web-service Layer)]]
+
** [[September 2010 GMOD Meeting#Overview of current resources and update on DAS Meeting Cambridge 2010|DAS Resource Overview and Update]]
+
 
+
Plus many other excellent presentations on topics ranging from [[September 2010 GMOD Meeting#Cosmic GBrowse: Visualising cancer mutations in genomic context|Cosmic GBrowse]] to [[September 2010 GMOD Meeting#GMOD Sustainability and Organization|GMOD Sustainability and Organization]].
+
 
+
Two '''{{SatelliteMeetingsSept2010Link}}''' followed the GMOD meeting.  These were lively discussions with ~10 participants on two topics of interest to the GMOD community:
+
* [[Post Reference Genome Tools]]
+
* [[Community Annotation - September 2010 Satellite|Community Annotation]]
+
 
+
There is also a [http://blog.openhelix.eu/?p=5551 writeup of the satellites] by Mary Mangan on the [http://blog.openhelix.eu/ OpenHelix blog].
+
 
+
The week finished with a {{BioMartWorkshopSept2010Link}}, which was full, and a {{InterMineWorkshopSept2010Link}} that was nearly sold out as well.
+
 
+
Finally, I'd like to thank the [http://www.ccbi.cam.ac.uk/ Cambridge Computational Biology Institute] and the [http://www.biomed.cam.ac.uk/gradschool/skills/bioinformatics.html School of Biological Sciences Bioinformatics Training Facility] for sponsoring and hosting the [[GMOD Europe 2010]] events.  I would also like to heap copious gratitude on Gos Micklem, Shelley Lawson, Dave Judge, Xose Fernandez, Syed Haider, and [[User:Rsmith|Richard Smith]] for their work on making this event happen.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/10/15''
+
 
+
== InterMine Workshop 15-16 Nov ==
+
 
+
{{ImageRight|InterMineLogo.png|InterMine Workshop|170|http://www.biomed.cam.ac.uk/gradschool/skills/intermine-developers.html}}
+
There will be an [http://www.biomed.cam.ac.uk/gradschool/skills/intermine-developers.html InterMine workshop] in Cambridge, UK on November 15th-16th.  You can register for both days or just attend either one.
+
 
+
; [http://www.biomed.cam.ac.uk/gradschool/skills/intermine-developers.html Day One - InterMine Developers]
+
: Building an InterMine data warehouse and deploying the web application.  This will use the new MineManager GUI to set up an example InterMine, load data and write a new parser to add custom data, deploy and configure the webapp including the new full text search.
+
 
+
; [http://www.biomed.cam.ac.uk/gradschool/skills/intermine-users.html Day Two (morning only) - InterMine Users]
+
: Advanced querying.  A brief tour of creating custom queries, creating your own templates and using the web service API to build and run queries from Perl or Java code.
+
 
+
[[InterMine]] is an open source system for building biological data warehouses with a powerful web interface and query API. See [http://www.flymine.org FlyMine] or [http://intermine.modencode.org modMine] for examples.  InterMine can integrate data from many common biological formats and is easy to extend to include your own data. Parsers are included to load data from [[Chado]], Ensembl, UniProt, KEGG, PubMed, TreeFam, [[GFF3]], FASTA, BioPax and many others.
+
 
+
The web application works out of the box for querying any data is easily customisable. It provides a custom query builder, template queries for creating simple 'canned queries', upload and operations on lists, graphical and statistical widgets for analysing lists of data and MyMine accounts for saving user data.
+
 
+
[[User:Rsmith|Richard Smith]]
+
 
+
''2010/10/13''
+
 
+
== Community Annotation Satellite ==
+
 
+
{{ImageRight|GMOD2010Europe300.png|Community Annotation Satellite Meeting Report|180|Community Annotation - September 2010 Satellite}}
+
 
+
The report from the [[Community Annotation - September_2010 Satellite|GMOD Europe 2010 Community Annotation Satellite Meeting]] is now [[Community Annotation - September_2010 Satellite|available]].  Nine participants from a range of research communities gathered for several hours to discuss their experiences with and thoughts on community annotation.  The report covers what has worked and what hasn't, as well as some analysis of why.  It also discusses possible models for doing successful community annotation in the future.  If you are interested in engaging your community to help you do annotation then I recommend reviewing this.
+
 
+
Many, many thanks to all who participated in this discussion and helped compile the report.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/09/29''
+
 
+
== October 2010 Calendar ==
+
 
+
{{ImageRight|calendar_icon.gif|GMOD Calendar||Calendar}}
+
 
+
October is calmer than September, but is still relatively full:
+
; Deadlines:
+
* SWAT4LS: Semantic Web Applications for Life Sciences abstracts
+
* Rocky '10 Bionformatics Conference abstracts
+
* [[PAG 2011|Plant and Animal Genome (PAG)]] early registration
+
* EMBO Global Exchange Lecture Course on Bioinformatics and Comparative Genome Analysis registration
+
 
+
; Conferences, Meetings, and Courses
+
* [[#Biocuration 2010|Biocuration 2010]]
+
* [[#Pathway Tools Workshop 2010|Pathway Tools Workshop]]
+
* Programming for Biology course
+
* Next Generation Sequencing Workshop
+
* RECOMB Comparative Genomics Satellite
+
* Automated Functional Annotation and Data Mining course
+
* VisWeek 2010
+
 
+
<div style="margin-right: 26em">
+
<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20101001%2F20101001</embedurl>
+
</div>
+
 
+
If you know of any upcoming events that are not on the calendar, please send them to me.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/09/23''
+
 
+
== InterMine Java / DB Developer ==
+
 
+
{{ImageRight|InterMineLogo.png|InterMine Java Developer|180|http://www.intermine.org/wiki/NowHiring}}
+
 
+
We are [http://www.intermine.org/wiki/NowHiring looking for a software developer] to work with Java and [[PostgreSQL]] as part of the Wellcome Trust funded [[InterMine]] project here in the Department of Genetics.  [[InterMine]] is an open source software system for building data warehouses of biological data. It can integrate data from many different formats into a central database and makes the data available to query via a flexible web application and web services. InterMine is used at several high profile genomics databases around the world including databases that we build and maintain in Cambridge. See [http://www.intermine.org InterMine.org] for more information.  Core InterMine development is carried out by a team of developers at Cambridge University. We need a developer to work on all aspects of the server side InterMine code, in particular taking responsibility for the database access and performance of the system.
+
 
+
See the [http://www.intermine.org/wiki/NowHiring position announcement] for full details.  The closing date for applications is 24 September 2010.
+
 
+
[[User:Rsmith|Richard Smith]]
+
 
+
''2010/09/16''
+
 
+
== BioMart Openings @ OICR ==
+
 
+
<div style="float: right">
+
{{ImageRight|OICRlogo.png|4 openings at OICR||http://www.recruitingsite.com/csbsites/oicr/careers.asp}}<br />
+
{{ImageRight|Biomart250.png|BioMart|130|BioMart}}
+
</div>
+
The Ontario Institute for Cancer Research (OICR) has [http://www.recruitingsite.com/csbsites/oicr/careers.asp four BioMart or BioMart-related openings]:
+
* [http://www.recruitingsite.com/csbsites/oicr/JobDescription.asp?JobNumber=633983 Bioinformatician/Data Manager]
+
* [http://www.recruitingsite.com/csbsites/oicr/JobDescription.asp?JobNumber=634437 Outreach and Training Coordinator ICGC DCC]
+
* [http://www.recruitingsite.com/csbsites/oicr/JobDescription.asp?JobNumber=633985 Database programmer/Technical Analyst]
+
* [http://www.recruitingsite.com/csbsites/oicr/JobDescription.asp?JobNumber=633980 Scientific Associate Computational Biology]
+
 
+
The [[BioMart]] biological data warehouse system is developed at [http://www.oicr.on.ca/ OICR].  Please see the job postings for additional details.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/09/12''
+
 
+
== JBrowse 1.1 Released ==
+
 
+
{{ImageRight|JBrowse-announce-screenshot.png|JBrowse 1.1 Released|200|http://jbrowse.org/?p=56}}
+
 
+
[http://jbrowse.org/?p=56 JBrowse version 1.1 is released!]  You can [http://jbrowse.org/releases/jbrowse-1.1.zip find the code here].
+
 
+
What's new:
+
 
+
* '''Scalability:''' [[JBrowse]] can now handle very large data tracks, including human EST/SNP tracks, or tracks of next-gen sequence reads. Large datasets are broken into smaller chunks, so there is no loading delay for big tracks.
+
* '''Extensibility:''' A Perl module (<tt>ImageTrackRenderer.pm</tt>) for creating user-drawn image tracks is now available, based on the CPAN {{CPAN|GD.pm}} module. An example program is provided, <tt>draw-basepair-track.pl</tt>, that uses this module to draw arcs over a sequence representing the base-pairing interactions of RNA secondary structure.
+
* '''Bug fixes:''' Numerous display glitches have been fixed, including issues with wide-screen monitors and long mostly-offscreen features.
+
 
+
Note: The {{GlossaryLink|JSON|JSON}} format used by 1.1 ''is not backward compatible with previous releases.  If you are upgrading from an older version of JBrowse, you will have to regenerate all the JSON files on your server.
+
 
+
See the [http://jbrowse.org/?p=56 release notes] for full details.
+
 
+
[[User:MitchSkinner|Mitch Skinner]]
+
 
+
''2010/09/12''
+
 
+
== The TopoView Glyph Needs You! ==
+
 
+
{{ImageRight|TopoViewThumb.png|TopoView from FlyBase||:Image:Flybase_topoview.pdf}}
+
 
+
[[:Image:Flybase_topoview.pdf|TopoView]] is a [[GBrowse]] glyph created by Victor Strelets at [[:Category:FlyBase|FlyBase]] to show large amounts of quantitative data in limited screen space.  TopoView does this with a 3D plot, showing each new set of data just below and offset from the previous data set.  It was developed to display RNA-Seq data.
+
 
+
[[User:Jogoodma|Josh Goodman]] [[Media:Flybase_topoview.pdf|presented]] TopoView at the [[January 2010 GMOD Meeting]], and also discussed it with many attendees at [[ISMB 2010]] (and I'm sure will be willing to discuss it at [[GMOD Europe 2010]] next week).  There is a lot of interest in TopoView becoming a standard GBrowse glyph.  However, as Victor {{NabbleThreadLink|Need-some-help-submitting-TopoView-RNA-seq-stuff-to-GMOD-tp990941p990941.html|explains in this posting}}, TopoView is not yet ready for general release  It needs some more work before it is ready for production.
+
 
+
If you are interested in helping get this glyph production ready and in the released glyph set, then please [mailto:strelets@aardwolf.bio.indiana.edu contact Victor].  He is looking for folks to help get this out there.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/09/07''
+
 
+
== InterMine/BioMart Job @ FlyBase ==
+
 
+
<div style="float: right; text-align: center; margin-left: 0.5em;">
+
{{#icon: Fly_logo.png|Open position at FlyBase|220|http://www.bioinformatics.org/forums/forum.php?forum_id=8313}}<br />
+
{{#icon: InterMineLogo.png|InterMine|100|InterMine}}
+
{{#icon:Biomart250.png|BioMart|100|BioMart}}
+
</div>
+
[http://www.bioinformatics.org/forums/forum.php?forum_id=8313 FlyBase is looking for a qualified software engineer] to undertake a project to deploy the [[InterMine]] and [[BioMart]] data management systems. The developer will be responsible for the web and database aspects of these technologies, which will be hosted at the Indiana University [http://flybase.org FlyBase site] in Bloomington, IN. This includes the initial setup and configuration of these two systems, setting up and automating update cycles in sync with the existing FlyBase release cycle, evaluating the capabilities of each, aiding in the integration of these services with existing FlyBase reports and tools, and coordinating these efforts with other model organism databases (MODs). Loading and preprocessing of data for these systems will be performed at the Harvard University FlyBase site so close coordination with developers there will also be required.  See the [http://www.bioinformatics.org/forums/forum.php?forum_id=8313 position announcement] for details.
+
 
+
''2010/09/03''
+
 
+
== GMOD Europe 2010 Update ==
+
 
+
{{ImageRight|GMOD2010Europe300.png|GMOD Europe 2010|200|GMOD Europe 2010}}
+
 
+
[[GMOD Europe 2010]] starts in less than two weeks.  If you are planning on attending and haven't yet [[GMOD Europe 2010#Registration|registered]], then please do so in the next few days.  The [[BioMart Workshop - GMOD Europe 2010|BioMart Workshop]] has only a few slots left, and the registration fee for the [[September 2010 GMOD Meeting|GMOD Meeting]] goes from &pound;50 to &pound;65 on 6 September.  We are encouraging people to submit topic suggestions for the [[September 2010 GMOD Meeting#Agenda Suggestions|GMOD Meeting]] and the [[Satellite Meetings - GMOD Europe 2010|GMOD Satellite Meetings]].
+
 
+
We are also pleased to announce that [[September 2010 GMOD Meeting#Guest Speaker|Jason Swedlow of the University of Dundee]] will be the guest speaker at the [[September 2010 GMOD Meeting|GMOD Meeting]].  Jason will speak on ''The [http://www.openmicroscopy.org/ Open Microscopy Environment]: Open Informatics for Biological Imaging'', a particularly timely topic as many researchers move into image intensive areas such as phenotypes and gene expression, and as high-throughput imaging platforms become available.
+
 
+
There is still space available at [[GMOD Europe 2010|all 4 events]], and registration for the [[Satellite Meetings - GMOD Europe 2010|GMOD Satellite Meetings]], [[InterMine Workshop - GMOD Europe 2010|InterMine Workshop]] and [[BioMart Workshop - GMOD Europe 2010|BioMart Workshop]] are '''free'''.
+
 
+
[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]
+
 
+
''2010/08/25''
+
 
+
== Biocuration 2010 ==
+
 
+
{{ImageRight|ISBLogo.png|Biocuration 2010||http://hinv.jp/biocuration2010/}}
+
 
+
I would like to encourage the GMOD community to consider attending [http://hinv.jp/biocuration2010/ Biocuration 2010], being held October 11-14 in Tokyo, Japan.  Biocuration is one of the most directly relevant conferences to research communtities working with biological databases.  It is sponsored by the [http://www.biocurator.org/ International Society for Biocuration] (an organization which I strongly encourage [[GMOD Membership|GMOD members]] to join).
+
 
+
Biocuration 2010 "aims to invite all biocurators and their colleagues, providing them with a platform where all the participants including speakers and chairpersons can have intimate discussion and exchange of information under superb environments."
+
 
+
The ISB would particularly like to encourage students and new curators (with less than 5 years of experience) to attend. The ISB is sponsoring the registration fees for 5 students and 5 curators.  To apply, please [mailto:intsocbio@gmail.com send a request to the ISB] ''before September 6'', including the abstract of your presentation. Note that you must be an [http://colleagues.biocurator.org/join ISB member] to apply for sponsorship. If you are not already a member, you can [http://colleagues.biocurator.org/join sign up here].  ''Early bird [http://hinv.jp/biocuration2010/registration.html registration] also closes September 6''.
+
 
+
<div class="emphasisbox" style="font-size: 120%; text-align: center">The abstract submission deadline has been extended to August 31.</div>
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/08/24, updated 2010/08/25''
+
 
+
== ISGA Joins GMOD ==
+
 
+
{{ImageRight|ISGAHomePageThumb.png|ISGA||ISGA}}
+
 
+
[[ISGA]], Integrative Services for Genomic Analysis, is now a part of GMOD. ISGA is a biologist-friendly web interface for running and customizing [[Ergatis]] bioinformaitics pipelines with integrated tools for visualizing and searching results. ISGA was originally built for prokaryotic genome annotation and we have added a prokaryotic assembly pipeline, and transcriptome annotation and functional genomics pipelines are under development.
+
 
+
A public instance of ISGA is available at [http://isga.cgb.indiana.edu http://isga.cgb.indiana.edu]. ISGA is also available [http://cgb.indiana.edu/downloads/6 for download] and has a [http://sourceforge.net/mail/?group_id=295836 mailing list] and [http://wiki.cgb.indiana.edu/display/brp/Development+Blog development blog]. You can read the [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 ISGA manuscript] in ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]''
+
 
+
ISGA is currently under active development at the Center for Genomics and Bioinformatics at Indiana University, and developers or other community members interested in contributing should join the [http://sourceforge.net/mail/?group_id=295836 mailing list].
+
 
+
[[User:Chemmeri|Chris Hemmerich]]
+
 
+
''2010/08/23''
+
 
+
== September 2010 Calendar ==
+
 
+
{{ImageRight|calendar_icon.gif|GMOD Calendar||Calendar}}
+
There's a lot going on in the next 5 weeks that is of interest to the GMOD community.  September will be one of our busier months.  Upcoming events include:
+
; Deadlines:
+
* Apply to participate in the [[GMOD Evo Hackathon]] (August 25)
+
* [http://bioinformatics.ai.sri.com/ptools10/ Pathway Tools Workshop] early registration (September 1)
+
* Plus deadlines for [[PAG 2011]], RECOMB Comparative Genomics, Automatid Imaging and High-Throughput Phenotyping
+
; [[GMOD Europe 2010]]
+
* 4 days of events in Cambridge UK including the [[September 2010 GMOD Meeting]], [[Satellite Meetings - GMOD Europe 2010|GMOD Satellite Meetings]], an [[InterMine Workshop - GMOD Europe 2010|InterMine Workshop]], and a [[BioMart Workshop - GMOD Europe 2010|BioMart Workshop]] (which is almost full)
+
; Lots of relevant conferences
+
* IWGD, HIBB, Personal Genomes, BioCreative, AMATA, Genome Informatics, BioImage Informatics, Data Sharing International, PRIB, InCoB, ECCB, and Computational Biology
+
; Training
+
* Bioinformatics Short Course, Ensembl Developers Workshop
+
 
+
 
+
<div style="margin-right: 26em">
+
<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100901%2F20100901</embedurl>
+
</div>
+
 
+
 
+
If you aren't going to something in September, then you aren't trying!
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/08/23''
+
 
+
== Opening @ Phytozome (JGI) ==
+
 
+
{{ImageRight|PhytozomeLogo.jpg|Opening at Phytozome|180|http://careers.crijob.com/lbnlcareers/detailsRedirect.asp?jid=24813&p=1}}
+
 
+
[http://careers.crijob.com/lbnlcareers/detailsRedirect.asp?jid=24813&p=1 Phytozome has an opening for a web developer].  [http://www.phytozome.net Phytozome] is the public portal to [http://www.jgi.doe.gov/ JGI's] extensive plant genome data and analysis. The developer in this position will be responsible for creating web interfaces using PHP, CSS, and advanced Javascript. Both the absolute quantity and diversity of plant genomic data produced and integrated by the JGI will be increasing dramatically over the next few years. This is an opportunity to apply your web design and coding skills to an area of biological research undergoing explosive growth and change, working with the JGI's scientists, computational biologists, and developers in a state-of-the-art computational environment.
+
 
+
Phytozome currently incorporates [[GBrowse]] and [[Biomart]], as well as Jalview, Lucene, and MView, and will be integrating [[Galaxy]] and [[Chado]] over the next 12 months.
+
 
+
Please see the [http://careers.crijob.com/lbnlcareers/detailsRedirect.asp?jid=24813&p=1 job posting] for more information on this position.
+
 
+
''2010/08/19''
+
 
+
== Chado 1.11 Release ==
+
 
+
I am pleased to announce the [https://sourceforge.net/projects/gmod/files/gmod/chado-1.11/chado-1.11.tar.gz/download 1.11 release of Chado], the GMOD schema and related tools.  The file can be downloaded from [https://sourceforge.net/projects/gmod/files/gmod/chado-1.11/chado-1.11.tar.gz/download SourceForge]
+
 
+
In this release, the schema itself has not changed since the 1.1 release in May of this year, but there have been bug fixes (see [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/chado-1.11/chado/Changes?revision=23640&view=markup release notes]; thanks to [[User:NaamaMenda|Naama Menda]] for those fixes) and one added functionality to the materialized view tool. This functionality was required to support full text searching that will be included in the up coming release of the [[Chado]] [[GBrowse Adaptors|GBrowse adaptor]], {{CPAN|Bio::DB::Das::Chado}}.
+
 
+
Also note that the name of the release has changed: previously, releases of the [[Chado]] schema were called "gmod" (gmod-0.003, gmod-1.0, and gmod-1.1), but that led to a couple of different kinds of confusion, so with this release going forward, the releases will be called "chado-*".
+
 
+
Since the schema didn't change, if you already have a 1.1 schema and
+
want the bug fixes and added functionality, all you need to do for
+
installation is to go up to the install step and stop there, i.e.:
+
 
+
perl Makefile.PL
+
make
+
sudo make install
+
 
+
Happy ''GMODing'' and please direct questions about this release to the [https://lists.sourceforge.net/lists/listinfo/gmod-schema schema mailing list],
+
 
+
[[User:Scott|Scott Cain]]
+
 
+
''2010/08/06''
+
 
+
== GMOD Europe 2010 ==
+
<div style="border: 2px solid #DDDDDD; float: right; text-align: center; margin-left: 0.5em;">
+
{{#icon: GMOD2010Europe300.png|GMOD Europe 2010|160|GMOD Europe 2010}}<br /><br />
+
{{#icon: InterMineLogo.png|InterMine Workshop|150|http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010}}<br />
+
{{#icon:Biomart250.png|BioMart Workshop|170|http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010}}<br />
+
{{#icon: Sept2010MtgLogo300.png|September 2010 GMOD Meeting|150|September 2010 GMOD Meeting}}
+
</div>
+
We are pleased to announce ''[[GMOD Europe 2010]]'', four days of GMOD events being held 13-16 September 2010, at the University of Cambridge.  GMOD Europe 2010 includes:
+
{| class="wikitable"
+
! Event
+
! Date
+
! Description
+
|-
+
| '''[[September 2010 GMOD Meeting]]'''
+
| Mon-Tues<br />13-14 Sept
+
| valign="top" | A two day [[Meetings|community meeting]] featuring project updates, developer and user presentations and best practices, and project planning.  See the [[January 2010 GMOD Meeting]] for an idea of what goes on at GMOD meetings.
+
|-
+
| '''{{SatelliteMeetingsSept2010Link}}'''
+
| rowspan="2" | Wednesday<br />15 Sept
+
| valign="top" | [[Satellite Meetings - GMOD Europe 2010|Special interest groups]] where GMOD community members meet to discuss specific topics of interest.  If you have topics you want covered please add them.
+
|-
+
| '''{{InterMineWorkshopSept2010Link}}'''
+
| valign="top" | A [[InterMine Workshop - GMOD Europe 2010|one day workshop]] on installing, configuring and using the [[InterMine]] biological data warehouse system.
+
|-
+
| '''{{BioMartWorkshopSept2010Link}}'''
+
| Thursday<br />16 Sept
+
| valign="top" | A [[BioMart Workshop - GMOD Europe 2010|one day workshop]] on using the [[BioMart]] biological data warehouse system, including accessing data through {{GlossaryLink|API|APIs}}.
+
|}
+
 
+
[[GMOD Europe 2010#Registration|Registration is now open]] for these events.  There is a &pound;50 registration fee for the [[September 2010 GMOD Meeting|GMOD Meeting]] to cover catered lunches, coffee/tee breaks, and other expenses.  Registration for all other events is free.  Please register soon, as space is limited.
+
 
+
See you in Cambridge!
+
 
+
[[User:Scott|Scott Cain]] and [[User:Clements|Dave Clements]]
+
 
+
''PS: If you have topics you want to have covered (or you want to cover) at the [[September 2010 GMOD Meeting|GMOD Meeting]], or at the {{SatelliteMeetingsSept2010Link}}, please add them to the [[September 2010 GMOD Meeting#Agenda Proposals|meeting]] page, or to the {{SatelliteMeetingsSept2010Link}} list, or [mailto:help@gmod.org contact us].  We are also looking for [[September 2010 GMOD Meeting#Guest Speaker Nominations|guest speaker nominations]] for the meeting.''
+
 
+
''2010/08/04''
+
 
+
== GMOD Evo Hackathon Open Call ==
+
 
+
{{ImageRight|EvoHackathonLogo.png|GMOD Evo Hackathon Open Call for Participation|150|GMOD Evo Hackathon Open Call}}
+
 
+
We are [[GMOD Evo Hackathon Open Call|seeking participants]] for the [[GMOD Evo Hackathon|GMOD Tools for Evolutionary Biology Hackathon]], being held November 8-12, 2010 at the [http://nescent.org US National Evolutionary Synthesis Center (NESCent)] in Durham, NC.
+
 
+
This hackathon targets three critical gaps in the capabilities of the GMOD toolbox that currently limit its utility for evolutionary research:
+
# Visualization of comparative genomics data
+
# Visualization of phylogenetic data and trees
+
# Support for population diversity and phenotype data
+
 
+
If you are interested in these areas and have relevant expertise, you are strongly encouraged to apply.  Relevant areas of expertise include more than just software development: if you are a GMOD power user, visualization guru, domain expert (comparative, phylogenetics, population, ...), or documentation wizard, then your skills are needed!
+
 
+
See the [[GMOD Evo Hackathon Open Call]] for details, and for a link to the application form.  Applications are due August 25.
+
 
+
The GMOD Evo Hackathon Organizing Committee:
+
 
+
[[User:NLWashington|Nicole Washington]],  [[User:RobertBuels|Robert Buels]], [[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], [[User:Hlapp|Hilmar Lapp]], and [[User:Mckays|Sheldon McKay]]
+
 
+
''2010/08/01''
+
 
+
== GMOD Nomination: ISGA ==
+
 
+
{{ImageRight|ISGAHomePageThumb.png|ISGA||ISGA}}
+
 
+
I would like to nominate [[ISGA]] for [[GMOD Membership]].  ISGA is a bioinformatics pipeline service based on the [[Ergatis]] workflow system. ISGA comes with prokaryotic annotation and assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as [[GBrowse]] and BLAST for visualizing and analyzing pipeline results. Since ISGA utilizes Ergatis, ISGA pipelines can be submitted back to the Ergatis community and Ergatis pipelines can be adapted to use ISGA.
+
 
+
ISGA (pronounced "I-S-G-A") was created at [http://cgb.indiana.edu/ Indiana University's Center for Genomics and Bioinformatics (CGB)] by [[User:Chemmeri|Chris Hemmerich]], Aaron Buechlein, Ram Podicheti, Kashi Revanna, and Qunfeng Dong. CGB also hosts a [http://isga.cgb.indiana.edu/ public installation of ISGA].
+
 
+
I believe that ISGA meets all of [[GMOD Membership#Requirements|GMOD's membership requirements]].  The CGB is willing to support ISGA for at least 2 years.  ISGA could be useful to anyone working with complex pipelines and is directly applicable to existing and potential [[Ergatis]] users.  Please see the [[ISGA]] page for more information.
+
 
+
If you have any feedback or comments on ISGA becoming a part of GMOD, please send [mailto:help@gmod.org send it to the help desk] by August 6.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/07/29''
+
 
+
== August 2010 Calendar ==
+
 
+
{{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
+
There's not a lot going on in [[Calendar|August]] but what is going on is significant. First there are submission deadlines for the International Digital Curation Conference (IDCC), and Data Integration in the Life Sciences (DILS 2010).  Several noteworthy conferences are also happening:
+
* ACM International Conference on Bioinformatics and Computational Biology
+
* YAPC::Europe 2010
+
* DILS 2010
+
* International Workshop on Genomics Databases (IWGD)
+
* High Performance Bioinformatics and Biomedicine (HiBB)
+
 
+
And, sometime in the next month GMOD will
+
* '''formally announce [[GMOD Europe 2010]] and'''
+
* '''start taking registrations for the [[September 2010 GMOD Meeting]]'''
+
 
+
<div style="margin-right: 26em">
+
<embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&amp;showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100801%2F20100801</embedurl>
+
</div>
+
If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/07/28''
+
 
+
== GMOD: Spread the Word! ==
+
 
+
{{ImageRight|PoweredByGMOD200.png|Help spread the word about GMOD||GMOD Promotion}}
+
 
+
Do you use GMOD tools in your research?  If so, then you can help others and GMOD by [[GMOD Promotion|getting the word out about GMOD and its tools]].
+
 
+
There are many ways to do this: [[GMOD Promotion#Citing GMOD|cite GMOD]] in publications, put a [[Powered by GMOD]] icon on your web pages, invite a [[GMOD Promotion#Speakers|GMOD speaker]] to your institution or event, include [[GMOD Promotion#Presentation Material|information on GMOD]] in your presentations.  See the [[GMOD Promotion]] page for these and other ideas.
+
 
+
Increasing GMOD's visibility has many benefits:
+
 
+
* It introduces biologists to tools that can help them learn from and exploit their data.
+
* Increased visibility will lead to increased adoption of GMOD tools.
+
* Increased adoption leads to more people contributing back to the project.
+
* Increased adoption and development helps GMOD and GMOD components get grant funding.
+
 
+
Finally, GMOD can also help raise the profile of your GMOD-related talk or event by [[GMOD Promotion#Presentation and Event Promotion|advertising it on GMOD resources]].
+
 
+
Please let me know if you have any questions or requests, and please help get the word out.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />[[GMOD Help Desk]]
+
 
+
''2010/07/26''
+
 
+
 
+
== ISMB 2010 Talks & Posters ==
+
 
+
{{ImageRight|ISMB2010_logo.jpg|GMOD @ ISMB 2010|150|ISMB 2010}}
+
 
+
You can now view most of the [[ISMB 2010|GMOD-related presentations and posters from ISMB 2010]].  This includes
+
* [[:Image:DeployingGalaxyCloudBOSC2010.pdf|Deploying Galaxy on the Cloud]], Enis Afgan
+
* [[:Image:NGSTranscriptomeISGAErgatis.pdf|Automated Annotation of NGS Transcriptome Data using ISGA and Ergatis]], [[User:Chemmeri|Chris Hemmerich]]
+
* [http://prezi.com/nx4jy4etq-ug/gbrowse-20-and-jbrowse-for-ismb/ GMOD Presents GBrowse 2.0 and JBrowse], [[User:Scott|Scott Cain]]
+
* [[:Image:PathwayToolsPosterISMB2010.pdf|An Advanced Web Query Interface for Biological Databases]] ([[Pathway Tools]]), Peter Karp
+
* [[:Image:GalaxyNGSISMB2010.pdf|Galaxy NGS functionality from sample tracking to SNP calling]], Ramkrishna Chakrabarty
+
 
+
Plus additional talks and posters on [[GBrowse]], [[DIYA]], [[Pathway Tools]], and [[Galaxy]].
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/07/19''
+
 
+
== Hiring @ Dolan DNALC ==
+
 
+
{{ImageRight|DolanDNALCLogo.jpg|Opening @ Dolan DNA Learning Center, job ID 934||http://www.cshl.edu/hr/jobs.html}}
+
 
+
There's an [http://www.cshl.edu/hr/jobs.html opening (Job ID 934)] at the [http://www.dnalc.org Dolan DNA Learning Center (DNALC)] of [http://www.cshl.edu Cold Spring Harbor Laboratory] for a programmer to develop cyberinfrastructure to support plant biology research. The programmer will work with a multi-disciplinary team to design, develop, and maintain applications for interfacing public APIs, SQL databases, and large data sets.
+
 
+
The successful candidate should come from a bioinformatics background that includes work with [[BioPerl]], genome databases (such as [[Chado]]), browsers, and annotation tools.  Expertise in Java, SQL and database schema, and Unix/Linux are essential.  Experience developing web user interfaces – templating, Javascript/AJAX, DOM, and CSS – is also desirable.
+
 
+
For more information, go to the [http://www.cshl.edu/hr/jobs.html CSHL jobs site] and search for Job ID 934.
+
 
+
''2010/07/14''
+
== GBrowse 2.13 Release ==
+
{{ImageRight|GBrowseLogo.png|GBrowse 2.13 Released|200|GBrowse}}
+
 
+
[[GBrowse]] version 2.13 has been released.  2.13 is a maintenance update to 2.12.  GBrowse 2.13 and 2.12 include these changes:
+
 
+
;New features & enhancements:
+
* The [[DAS]] server and client are now functional. You will need {{CPAN|Bio::Das}} version 1.17 and {{CPAN|Bio::Graphics}} version 2.11 for best results.
+
* The "import track" function now allows you to specify the URL of either a {{GlossaryLink|BAM|BAM}} or a BigWig file. The track will be displayed without physically copying the file onto the GBrowse server. You will need {{CPAN|Bio::DB::Sam}} and {{CPAN|Bio::DB::BigWig}} for these features to work.
+
* Uploading a Wig file now generates a BigWig database for improved performance and scalability. This requires Bio::DB::BigWig to be installed.
+
* There is now a '''Get chromosome sizes''' entry in the File menu.
+
* Calling GBrowse with the CGI argument <tt>action=scan</tt> will generate a quick summary of track contents.
+
* Improved performance when working with truly huge (>1000 track definition) configuration files.
+
* Fasta, [[GFF3]], {{GlossaryLink|SAM|SAM}} and wiggle dumps now include the genome build ID if that information is provided in the data source "metadata" configuration variable.
+
 
+
;Bug fixes
+
* When [[MySQL]] is used as the back end for user uploads, it will no longer fail on long filenames.
+
* Fixed the "eurl" CGI parameter for importing data sets by their URLs.
+
* Fasta and GFF3 dumps are now working when invoked from the File menu.
+
* Fixed SAM file processing so as not to die when presented with a SAM @SQ header. This requires {{CPAN|Bio::DB::Sam}} 1.20 to work properly.
+
* Fixed upload listing table so as not to duplicate track labels.
+
* Fixed track importation via the eurl parameter so that it works when the user's uploadid is empty (due to clearing cache of cookies).
+
* Fixed DAS server handling of the link option.
+
 
+
Please use the [https://sourceforge.net/tracker/?group_id=27707 GMOD bug tracking system] to report [https://sourceforge.net/tracker/?atid=391291&group_id=27707&func=browse bugs] or [https://sourceforge.net/tracker/?atid=391294&group_id=27707&func=browse feature requests].
+
 
+
[[User:Lstein|Lincoln Stein]]
+
 
+
''2010/07/13''
+
 
+
== Pathway Tools Workshop 2010 ==
+
{{ImageRight|SRILogo.png|Pathway Tools Workshop 2010||http://bioinformatics.ai.sri.com/ptools10/}}
+
 
+
Registration is now open for the [http://bioinformatics.ai.sri.com/ptools10/ Pathway Tools Workshop 2010], held October 25th - 29th, 2010 in Menlo Park, CA.  Early registration ends September 1.
+
 
+
This workshop is oriented around SRI's [[Pathway Tools]] software and BioCyc Database Collection and will explore pathway bioinformatics and Pathway/Genome Databases.
+
 
+
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:
+
 
+
* Advances in pathway bioinformatics, model organism databases, genome annotation, and systems biology
+
* Scientific results achieved with Pathway Tools and BioCyc
+
* Share expertise on how to develop new organism-specific databases with Pathway Tools
+
* Share experiences on how to make the most of Pathway Tools
+
* Presentations by users on extensions they have developed to Pathway Tools
+
* Presentations by SRI International on recent and planned developments to the software, and on software APIs and the database schema, to educate users on how to compute with PGDBs
+
 
+
Please visit our [http://bioinformatics.ai.sri.com/ptools10/ registration website] for details on speakers, fees, travel, and hotels.
+
 
+
Looking forward to seeing you at an upcoming Pathway Tools event.
+
 
+
Best regards,
+
 
+
[mailto:ptools-info@ai.sri.com Tomer Altman]
+
 
+
''2010/07/09''
+
 
+
== Galaxy Community Tool Sharing ==
+
 
+
{{ImageRight|GalaxyLogoSmall.png|Galaxy Community Tool Sharing||http://usegalaxy.org/community}}
+
 
+
We have introduced a new [http://usegalaxy.org/community Galaxy tool sharing community site].  The site currently allows you to upload an archive consisting of a single tool, but will soon allow you to upload an archive consisting of a suite of tools.  To learn how to use the community site, click on '''Help &rarr; How to upload, download, and install tools'''.
+
 
+
We hope that you will find this site useful for hosting tools that you would like to contribute and share.
+
 
+
We'll keep you informed as the site's features evolve.
+
 
+
Greg Von Kuster
+
 
+
''2010/07/08''
+
 
+
== Logo Program Logos! ==
+
 
+
<div style="float: right; border: 0.5em solid gray; margin: 0.5em;">
+
{|
+
| align="center" |  {{#icon: ApolloLogo.png|Apollo logo by Audra Radke|150|Spring 2010 Logo Program}}
+
|-
+
| align="center" |  {{#icon: RedFlyLogo.png|REDFly logo by Alex Read|65|Spring 2010 Logo Program}}&nbsp;&nbsp;&nbsp;{{#icon: CMapLogo.png|CMap logo by Kathy Bracken|40|Spring 2010 Logo Program}}
+
|-
+
|
+
|-
+
| align="center" | [[Spring 2010 Logo Program|Some of the new logos]]
+
|}
+
</div>
+
 
+
The [[Spring 2010 Logo Program]] was a smashing success and 9 projects now have eye-catching logos that give each resource a strong graphic brand identify.  See the [[Spring 2010 Logo Program|Spring 2010 page]] for a complete list of logos, as well as some of the alternatives that were not chosen.
+
 
+
I would like to thank
+
* The '''[[Spring 2010 Logo Program#Linn-Benton Community College|design students]]''' who worked with the participants to understand their projects and produce an excellent [[Spring 2010 Logo Program#Other Logos|set of logos]] to pick from.
+
* '''John Aikman''' of the [http://www.linnbenton.edu/go/graphic-arts Graphic Arts Department] at [http://www.linnbenton.edu/ Linn-Benton Community College (LBCC)] for being willing to take a chance on this program, and for being willing to work with to hammer out the details.
+
* And the '''[[Spring 2010 Logo Program#Projects|participants]]''' for being willing to work the students to help them gain experience and to understand the projects they were creating logos for.
+
 
+
The [[GMOD Logo Program]] might return in the future.  Please watch the [[GMOD News]] for details, probably later this year.  In the mean time, if you would be interested in participating in the next one, please let me know.  The more people I hear from, the more likely it is to happen.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/07/07''
+
 
+
== GMOD @ ISMB 2010 ==
+
 
+
{{ImageRight|ISMB2010_logo.jpg|GMOD @ ISMB 2010|150|ISMB 2010}}
+
 
+
ISMB runs July 9-13 this year and [[ISMB 2010|GMOD has a strong presence on the program]]:
+
* talks on [[Galaxy]], [[GBrowse]], [[JBrowse]], [[Pathway Tools]], [[WebGBrowse]], ...
+
* a tutorial on [[Galaxy]],
+
* many posters, and
+
* several Special Interest Group (SIG) meetings relevant to GMOD members.
+
 
+
See the [[ISMB 2010|GMOD @ ISMB 2010]] page for a full listing of GMOD related content, including a [[ISMB 2010#Flier|session listing]] you can print in advance.  See the [http://www.iscb.org/ismb2010 ISMB 2010 web site] for more on the conference.
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/07/02''
+
 
+
== GMOD Meeting: Sept. 13-14 ==
+
 
+
{{ImageRight|Cambridge.jpg|September 2010 GMOD Meeting||September 2010 GMOD Meeting}}
+
Thanks to the prep work by Gos Micklem at Cambridge, I am pleased to announce that there will be a two day [[September 2010 GMOD Meeting|GMOD community meeting]] starting on  Monday September 13 in Cambridge, England.  This meeting occurs immediately prior to the [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics meeting] in Hinxton (for which the abstract deadline is [[Calendar|June 25]]).  Registration information for this meeting will be available in a few weeks.  In the mean time, you can [[September 2010 GMOD Meeting|post topic suggestions]] to the [[September 2010 GMOD Meeting|meeting page]].
+
 
+
Please feel free to tell your colleagues and to post to mailing lists that you think would be interested in this meeting.
+
 
+
I look forward to seeing you in England this Fall.
+
 
+
[[User:Scott|Scott Cain]]
+
 
+
''2010/06/17''
+
== New GMOD Tutorials ==
+
 
+
{{ImageRight|2010SummerSchoolAmericas170.png|Summer School - Americas||http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
+
 
+
Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[2010 GMOD Summer School - Americas]].  Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image.  This year we have a [[Galaxy Tutorial]] for the first time.
+
 
+
The [[:Category:Tutorials|tutorials]] are:
+
* '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
+
* '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], and [[User:Jorvis|Joshua Orvis]].
+
* '''[[Galaxy Tutorial]]''' - by [[User:JamesTaylor|James Taylor]]
+
* '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]]
+
* '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
+
* '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]]
+
* '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
+
* '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
+
 
+
The [[2010 GMOD Summer School - Americas]] got the best [[2010 GMOD Summer School - Americas|reviews]] of any [[GMOD Summer School|course]] GMOD has ever done.  I'd like to thank this year's instructors and participants for making it such a success.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2010/06/14''
+
 
+
== ISGA Pipeline Service ==
+
 
+
{{ImageRight|ISGAHomePageThumb.png|ISGA at the Center for Genomics and Bioinformatics||http://isga.cgb.indiana.edu/}}
+
 
+
[http://isga.cgb.indiana.edu/ Integrated Services for Genomic Analysis (ISGA)] is an [[Ergatis]]-based bioinformatics pipeline service based at [http://cgb.indiana.edu/  Indiana University's Center for Genomics and Bioinformatics].  ISGA is also a [http://sourceforge.net/projects/isga/  free, open-source software package] that you can install locally to provide a biologist-friendly web interface to your computational resources.  ISGA currently provides prokaryotic annotation and prokaryotic assembly pipelines and offers an intuitive interface for biologists to run and customize pipelines. ISGA also integrates tools such as [[GBrowse]] and Blast for visualizing and analyzing pipeline results. Since ISGA utilizes the [[Ergatis]] workflow system to execute pipelines, ISGA pipeline can be submitted back to the Ergatis community and other Ergatis pipelines can be adapted to use ISGA.  (See [[#Ergatis Update|Ergatis Update]] below for what's new with Ergatis.)
+
 
+
For more on ISGA, see the manuscript [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/8/1122 "An Ergatis-based prokaryotic genome annotation web server"] in ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'', the [http://isga.cgb.indiana.edu/Help/Tutorial ISGA pipeline and account tutorials], and the [http://isga.cgb.indiana.edu/Help/FAQ ISGA FAQ page].  For help using or installing ISGA, join the [https://lists.sourceforge.net/lists/listinfo/isga-users isga-users mailing list].
+
 
+
[[User:Chemmeri|Chris Hemmerich]]
+
 
+
''2010/06/07''
+
 
+
== MAKER 2.0, AGS Workshop ==
+
 
+
<div style="Float: right;">
+
{|
+
|{{ImageRight|MAKERLogo.png|MAKER 2.0 Released|170|MAKER}}<br>
+
|-
+
| {{ImageRight|AGSBug170.png|Arthropod Genomics Symposium|100|http://www.k-state.edu/agc/symp2010/seminar.html}}
+
|}
+
</div>
+
[[MAKER]], the easy to use genome annotation pipeline, is now version 2.0.
+
 
+
Some of the current features and other improvements
+
 
+
* Improved gene model preparation and evidence filtering...
+
* mRNAseq data in your annotations (use output from programs like [http://tophat.cbcb.umd.edu/ TopHat], [http://cufflinks.cbcb.umd.edu/ CuffLinks], and others in [[MAKER]])...
+
* Annotate eukaryotes and prokayotes...
+
* Pass through any kind of evidence evidence from any source via [[GFF3]] pass-through...
+
* Easy single-command-line dump of MAKER output to a [[Chado]] database and to [[JBrowse]]...
+
* Same directory parallelization -  just start MAKER on top of itself, and it will share the workload with the new process...
+
* Auto recovery - start, stop, and restart MAKER at any time; MAKER will always just pick up where it left off...
+
* optional web base GUI for a local MAKER installation
+
 
+
 
+
There will also be a [http://www.k-state.edu/agc/symp2010/seminar.html workshop on MAKER] on June 12 at the [http://www.k-state.edu/agc/symposium.shtml 4th Annual Arthropod Genomics Symposium] in Kansas City.  If you are attending AGS and are interested in genome annotation, please consider attending.
+
 
+
 
+
Thanks,<br />
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[[User:Carsonholt|Carson Holt]]
+
 
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''2010/06/01''
+
 
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<endFeed />
+
 
+
= [[GMOD News Archives|News Archives]] =
+
 
+
Items more than 6 months old are available in the [[GMOD News Archives]].
+
 
+
= Adding a News Item =
+
 
+
'''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
+
 
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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.
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# Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
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# Title
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#* '''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]]'''.
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#* Place the title in a second level heading: <tt>== Your Title ==</tt>
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# News Text
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#* 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 <nowiki>''YYYY/MM/DD''</nowiki>The two apostrophes will cause the date to be italicized: ''YYYY/MM/DD''
+
#** It won't render very well.  You should be able to avoid headers altogether.
# Preview your changes
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#* '''The first link in the news item should point to the page/URL you want the RSS feed to link to.
#* 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?
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#** 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.  '''Try not to revise and save repeatedly.'''  Each saved revision has the potential to send a new item to the RSS feed.  People will be watching you edit in real time. You don't want that.
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# Once you are happy with how the item looks, insert this line at the end of it:
 
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#: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
Once you have saved the page, a link to the new item will show up on the home page in about an hour(Why the delay?  It uses an RSS feed of this page and it queries the feed infrequently.)
+
#: Where ''yyyy/mm/dd'' is the current dateThis line will cause it to be added to the GMOD News RSS feed.  The item will show up in the feed within an hour.
 +
# '''Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.'''
 +
#* Every edit results in the news item being reposted to the RSS feedIf 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 2017

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 2017/01/30

Computational Biologist GrainGenes

GrainGenes is hiring a full-time Computational Biologist to be located in Albany, CA with a yearly salary range of $58,132 - $91,433 (GS-9/11). This is a USDA-ARS federal position for US citizens and nationals. The deadline is in two weeks on Dec 12, 2016.

To learn more about the position & apply, please go to:

https://www.usajobs.gov/GetJob/ViewDetails/457631400

Major Duties may include, but are not limited to:

  • Performs bioinformatics analyses on biological data
  • Ensures smooth, reliable, and secure operation of biological database computational infrastructure
  • Participates in designing, maintaining, documenting, and monitoring processes and workflow related to genomic data acquisition, data maintenance, and data integrity.
  • Serves as an informational resource on genomics database code and hardware, and provides guidance and assistance on the proper use and application of a biological database digital platform to users, team members, and researchers.
  • Guides researchers, technicians, and others on sequence data quality assurance, storage, and extraction.


Posted to the GMOD News on 2016/11/28

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

Now Hiring CTO Phoenix Bioinfo

Phoenix Bioinformatics Hiring a New CTO

Please see this job announcement for Phoenix Bioinformatics (home of TAIR). Phoenix is a non-profit data publishing company.


Posted to the GMOD News on 2016/11/01

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

Prospecting for Proposals for GSoC 2016

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 2016/01/30

Prospecting for Proposals for GSoC 2015

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 2015/02/10

Now Hiring JBrowse Lead Developer

Description

JBrowse is recruiting a new lead developer. If you are excited by the maturation of bioinformatics into a web-based, broad-utility discipline, this is the job for you. Since 2007 JBrowse has been bringing a modern dynamic HTML aesthetic to the “traditional” genome browser, being the first mainstream web-based genome browser with live panning, zooming, interactive track rearrangement and dynamic filtering of track lists. Since 2010, JBrowse has been the platform for Web Apollo, the first web-based tool for truly collaborative genome annotation, offering live visual feedback on gene model edits from non-local collaborators. In a sense, the JBrowse project represents both the “Google Maps” and the “Google Docs” of the genome browser space.

We have more exciting offshoots planned, from synthetic biology design aids to genome-based social networking tools. These will demand the visualization of more bioinformatic data types (e.g. gene ontology annotations, phylogenetic trees, sequence alignments, synteny relationships, gene pathways and networks) and integration of associated computational analysis tools. The job requirements go far beyond that of a “maintenance programmer” position, demanding a high level of knowledge of bioinformatics practise, involvement in all aspects of the software life cycle (initial R&D, prototyping, test development, devops deployment, maintenance) as well as clear and effective communication with users and stakeholders.

Your desk will be in the Holmes Lab on the UC Berkeley campus, co-located with the Web Apollo team in Stanley Hall, right at the nexus of genome engineering and applied bioinformatics in the SF Bay Area. This project has a high-visibility, high-impact position at the leading edge of web-based bioinformatics tool development. Previous incumbents of this position have “graduated” to high-responsibility equity-holding positions at key companies in the emerging computational genomics market, such as Foundation Medicine (cancer therapeutics) and Counsyl (prenatal genetic counseling).

Responsibilities

The primary role will be JBrowse development. JBrowse currently consists of a JavaScript frontend supported by server-side Perl scripts. A one-year goal is the release of JBrowse version 2, a refactoring-in-progress to facilitate integration with other web services and data backends. In the shorter term the role will also support of Web Apollo and various other collaborating projects. The job will also involve a small and limited amount of user support. Along the way there will be numerous opportunities to prototype and develop new web-based technologies for the collaborative analysis of genomic data.

Qualifications

Essential:

  • B.S. in Computer Engineering, Bioinformatics or a related field with a minimum of five years related experience, or an equivalent combination of education and experience. Advanced degree is preferred.
  • Experience in development with JavaScript in client contexts:
    • Experience in understanding and using a variety of libraries and resources in an application
    • Experience with class prototyping frameworks
    • Experience with graphics frameworks such as d3
    • Experience with client testing frameworks such as Selenium
    • Experience with user interface frameworks such as Dojo and jQuery UI
    • Experience with CSS and CSS3 (e.g. responsive layout, media queries)
  • Experience in development in UNIX server contexts:
    • JavaScript (NodeJS), Perl, and/or Ruby
    • Experience with server unit testing frameworks
  • Demonstrated experience in developing robust web-based user-facing software projects.
  • Familiarity with current issues in web development and design (e.g. HTML5, WebSockets, Web Workers, message queue frameworks).
  • Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
  • Excellent verbal and written communication skills.
  • Ability to perform research and make independent decisions about approaches and tools to reach specific goals.
  • Ability to apply analytical skills and creativity to solve complex software and data management problems.

Desirable:

  • Familiarity with genomic sequence data (next-gen sequencing, reads, assemblies)
  • Experience with ontologies for annotation of genomic data
  • Experience with collaborative coding and build tools and workflows (notably github)


Applications

Apply at jobs.berkeley.edu, job id# 18514.


Posted to the GMOD News on 2014/08/26

BBOP Job Openings

We're casting a wide net to find the right people for these two positions. To formally apply please go to the links below. If you have questions, please send them to Suzanna Lewis (selewis at lbl dot gov) and copy Chris Mungall (cjm at berkeleybop dot org). Please forward if you know of anyone who might be interested in looking at these for a fit.

https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=79548

https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=79554

Here are the two position descriptions:

Project Lead- Software Developer (Berkeley Bioinformatics Open-Source Projects-79548)

Description

This is not your typical programming job. This job requires imagination, technical savvy, drive, and a vision of bringing the latest developments in the software industry to bear on the challenges of medical diagnosis, systems biology, and biodiversity. There are large untapped opportunities in the ongoing explosion of molecular data. This position calls for an individual who can see potential connections between the latest developments in software technology and the challenges of biology, and use these insights to produce robust, flexible software that empowers researchers in the biological sciences. This experience will position them uniquely in the emerging computational genomics job market.

The Berkeley Bioinformatics Open-Source Projects is a small group of energetic individuals who are dedicated to developing tools and applying computational technologies to address fundamental biological research needs. Since 2003 BBOP has been supported by NIH research grants to innovate and build advanced data management and analysis technologies. Currently senior team members are Principal Investigators for the Gene Ontology Consortium (gene function and evolution), the Monarch Initiative (genotype to phenotype analysis), and the Apollo project (collaborative genome annotation). Everyone on the team is motivated to advance research by pioneering effective new strategies that can meet the many challenges of biological data management, representation, visualization and analysis. The group is highly collaborative and travel frequently to work with a global network of diverse investigators.

BBOP is seeking an experienced software engineer with strong technical project leadership ability. They will contribute to building an infrastructure that providing an ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in the context of genetic and genomic data, using semantics and statistics.

Responsibilities

The primary role will be developing and extending web-based genomics and functional collaborative annotation environments. These include: Apollo, a web based genomic annotation editor designed to support geographically dispersed researchers providing real-time synchronization across multiple clients, PAINT, a phylogenetically-based protein family functional annotation tool, and Noctua, an OWL-based graphical editor for richly describing the interplay of integrated gene networks and functional annotation data.

As a full stack engineer, this individual will be responsible for designing and implementing all aspects of the technology stack, working both server-side and client-side. They will also be responsible for supporting the open-source developer community, answering questions regarding the software, and occasionally traveling for workshops and conferences both nationally and internationally. In addition they will be responsible for cross-project integration, providing functionality for the Gene Ontology Project and the Monarch Initiative, and other international collaborative software/data projects.

Qualifications

Essential

  • B.S. in Computer Engineering, Bioinformatics or a related field with a minimum of five years related experience, or an equivalent combination of education and experience. Advanced degree is preferred.
  • Experience in development with JavaScript in client contexts:
    • Experience in understanding and using a variety of libraries and resources in an application
    • Experience with client testing frameworks a plus
    • Experience with frameworks such as Bootstrap and jQuery (UI)
    • Experience with CSS and CSS 3 (e.g. responsive layout, media queries) a plus
  • Experience in development with JavaScript in server contexts:
    • NodeJS and npm experience
    • Experience with server unit testing frameworks
  • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat).
  • Demonstrated experience in developing robust web-based user-facing software projects.
  • Familiarity with current issues in web development and design (e.g. HTML5, WebSockets).
  • Experience with a range of database technologies (e.g. relational, NoSQL, triplestores).
  • Excellent verbal and written communication skills.
  • Ability to perform research and make independent decisions about approaches and tools to reach specific goals.
  • Ability to apply analytical skills and creativity to solve complex software and data management problems.

Desirable

  • Familiarity with genomics data and ontologies (in particular, the GO)
  • Experience with semantically annotated data
  • Familiarity with OWL and associated reasoners
  • Experience with collaborative coding and build tools (github, maven, …)

Notes

This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Laboratory. Job may require occasional travel, weekend, and after-hours work.

Software Developer (Berkeley Bioinformatics Open-Source Projects-79554)

Description

This position opens the door to tons of opportunities for growth for someone interested in computational genomics. The current explosion of molecular data means there is also a demand for people who can build the bridges between the latest technology developments that will meet the challenges of medical diagnosis, systems biology, and biodiversity. The successful applicant will be working in a positive environment that recognizes and values the contribution of every team member. People who are enthusiastic and energized by the idea of contributing to fundamental research insights into genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes.

The Berkeley Bioinformatics Open-Source Projects is dedicated to developing tools and applying computational technologies that address biological research questions. Since 2003 BBOP has been supported by NIH research grants to develop and apply advanced data management and analysis technologies. Currently senior team members are Principal Investigators for the Gene Ontology Consortium (gene function and evolution), the Monarch Initiative (genotype to phenotype analysis), and the Apollo project (collaborative genome annotation).

BBOP is seeking an eager bioinformaticist who will contribute to all aspects of software development cycles and infrastructure, including initial R&D, developing test suites, deployment to production systems, and maintenance once software is released to the biological research community. The position requires the ability to: deliver bug fixes, changes, and features quickly; test and evaluate alternative technologies (e.g. Rhino vs. V8); develop effective test suites; handle user issues; and provide system reliability with minimal downtime.

Responsibilities

Initially the primary role will be supporting the GOC, in particular the AmiGO web-based tools for searching and browsing the terms and gene product annotations described by the Gene Ontology. AmiGO’s component parts are currently broken into three modules: the GOlr backend (a Solr document store), some legacy Perl in the frontend, and a JavaScript UI and API that communicates directly with the GOlr backend.

Requirements

Essential

  • B.S. in Computer Science, Bioinformatics or a related field with a minimum of two years related experience, or an equivalent combination of education and experience. MS degree is preferred.
  • Experience with collaborative coding and build tools (Jira, Confluence, SVN, Git, maven).
  • Demonstrable strong experience with Debian-based GNU/Linux systems (Ubuntu a plus).
  • Experience with “Cloud” and virtual machine management using KVM (libvirt tools a plus).
  • Experience with development for and deployment to cloud/PaaS:
    • AWS, Heroku, OpenShift, etc.
  • Client and server unit test experience (Selenium, HTMLUnit, …).
  • Experience with system monitoring (e.g. Nagios, Munin).
  • Familiarity with Java, including Java web application development and servlet container experience (Jetty/Tomcat).
  • Demonstrable fluency in Perl (server-side).
  • Experience with installing and tuning of common software servers and services (e.g. LAMP, Jetty + Solr, Apache, Nginx, Tomcat, Jenkins, OpenSSH, MySQL, Postgres…).
  • Experience with Drupal deployment, development, and management:
  • PHP, Drupal plugin, and theme development a plus.
  • Transferable skill sets with similar CMSs a plus.

Desirable

  • Familiarity with JavaScript (client-side).
  • Experience with big data wrangling, particularly genomic data.
  • Experience with team approaches to software construction.
  • Experience with RAID and LVM.
  • Prefer experience with bulk administration and setup tools:
    • apt-dater, Puppet, etc.
    • Debian packaging a plus.
  • Familiarity with networking and file systems (NFS and Fibre Channel, others a plus).
  • Experience with system/data backup and system/data recovery methods a plus.

Notes

This is a 1 year term appointment with the possibility of renewal and with the possibility of conversion to career based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs. Work will be performed at the Lawrence Berkeley National Lab in Berkeley, CA.


Posted to the GMOD News on 2014/06/27

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

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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".
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{{NewsItem|yyyy/mm/dd}}

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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