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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.
| + | <wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" /> |
− | | + | |
− | <span class="plainlinks"> | + | |
− | This ''GMOD News'' is also available as an '''[http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss RSS feed]'''. {{#icon: RSSIcon16x16.gif|RSS feed||http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss}}
| + | |
− | </span> | + | |
− | | + | |
− | = News Items = | + | |
− | | + | |
− | Want to add your news item here? See [[#Adding a News Item|Adding a News Item]] below.
| + | |
− | | + | |
− | <startFeed />
| + | |
− | <!-- Add new Items here. Keep the Title Short! ***35 characters or less*** -->
| + | |
− | | + | |
− | == 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&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20101101%2F20101101</embedurl>
| + | |
| </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.
| + | 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]] |
| | | |
− | Thanks,
| + | == Recent News == |
| | | |
− | [[User:Clements|Dave Clements]]<br />
| + | <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]]
| + | |
| | | |
− | ''2010/10/22''
| + | == [[GMOD News Archives|News Archives]] == |
| | | |
− | == Pathway Tools 2010 Deadline! ==
| + | The [[GMOD News Archives]] lists all news items since autumn 2007. |
− | {{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.
| + | == Adding a News Item == |
| | | |
− | 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.
| + | '''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. |
| | | |
− | [[User:Clements|Dave Clements]]<br /> | + | GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the [[GMOD News]] and [[GMOD News Archives]] pages, and in the news tracker on the [[Main Page|home page]]. |
− | [[GMOD Help Desk]] | + | |
| | | |
− | ''2010/10/19/''
| + | === Short Instructions === |
| | | |
− | == InterMine 0.94.1 Release ==
| + | Please follow these guidelines when adding a news item. |
| | | |
− | {{ImageRight|InterMineLogo.png|InterMine 0.94.1 release|170|InterMine}}
| + | # Create a new page named "'''News/'''''News Item Title''". |
| + | #* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''. |
| + | # Enter the text of your news item. |
| + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
| + | # Preview / save your changes. Edit and save the page until the news item looks like you want. |
| + | # Once you are happy with how the item looks, insert this line at the end of it: |
| + | : <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre> |
| | | |
− | [[InterMine]] 0.94.1 is now released, and available as a subversion branch and zip file.
| + | === Longer Instructions === |
| | | |
− | 0.94.1 contains fixes for bugs discovered by users when upgrading to 0.94 and a number of minor enhancements.
| + | Please follow these guidelines when adding a news item. |
| | | |
− | InterMine 0.94 is a major release with many new features, including:
| + | # Create a new page named "'''News/'''''News Item Title''". |
− | * a new full text search over the entire database
| + | #* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''. |
− | * template queries with optional constraints
| + | #* The page must start with '''News/''', otherwise it won't be picked by the RSS news feed. |
− | * selection of multiple values in template query constraints
| + | # Enter the text of your news item. |
− | * 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
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− | * Next Generation Sequencing Workshop
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− | * RECOMB Comparative Genomics Satellite
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− | * 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&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]]
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− | | + | |
− | ''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>
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− | The Ontario Institute for Cancer Research (OICR) has [http://www.recruitingsite.com/csbsites/oicr/careers.asp four BioMart or BioMart-related openings]:
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− | * [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]
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− | | + | |
− | 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]]
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− | | + | |
− | ''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.
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− | | + | |
− | [[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}}
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− | {{#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 £50 to £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&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 £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&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 → How to upload, download, and install tools'''.
| + | |
− | | + | |
− | We hope that you will find this site useful for hosting tools that you would like to contribute and share.
| + | |
− | | + | |
− | We'll keep you informed as the site's features evolve.
| + | |
− | | + | |
− | Greg Von Kuster
| + | |
− | | + | |
− | ''2010/07/08''
| + | |
− | | + | |
− | == Logo Program Logos! ==
| + | |
− | | + | |
− | <div style="float: right; border: 0.5em solid gray; margin: 0.5em;">
| + | |
− | {|
| + | |
− | | align="center" | {{#icon: ApolloLogo.png|Apollo logo by Audra Radke|150|Spring 2010 Logo Program}}
| + | |
− | |-
| + | |
− | | align="center" | {{#icon: RedFlyLogo.png|REDFly logo by Alex Read|65|Spring 2010 Logo Program}} {{#icon: CMapLogo.png|CMap logo by Kathy Bracken|40|Spring 2010 Logo Program}}
| + | |
− | |-
| + | |
− | |
| + | |
− | |-
| + | |
− | | align="center" | [[Spring 2010 Logo Program|Some of the new logos]]
| + | |
− | |}
| + | |
− | </div>
| + | |
− | | + | |
− | 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 />
| + | |
− | [[User:Carsonholt|Carson Holt]]
| + | |
− | | + | |
− | ''2010/06/01'' | + | |
− | | + | |
− | == Load Chado into BioMart ==
| + | |
− | <div style="float: right; text-align: center">
| + | |
− | {{#icon: Biomart250.png|Load Chado into BioMart|125|http://gmod.org/wiki/BioMart#How_to_Load_a_Chado_Database_into_BioMart}}<br /><br />
| + | |
− | {{#icon: Urgi.png|INRA URGI|105|http://urgi.versailles.inra.fr/}}
| + | |
− | </div>
| + | |
− | A group at INRA URGI have documented "[[BioMart#How to Load a Chado Database into BioMart|How to load a Chado database into BioMart]]". This step by step document details what how to configure BioMart for Chado, and includes some specific use cases useful with [[Chado]]. This guide is based on experience at [http://urgi.versailles.inra.fr/ INRA URGI], and was written by Aminah Keliet, Joëlle Amselem, Sandra Derozie, and Delphine Steinbach.
| + | |
− | | + | |
− | If you are interested in loading your [[Chado]] data into a [[BioMart]] instance then I recommend starting with this guide.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/27''
| + | |
− | | + | |
− | == June 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | The [[Calendar|next 5 weeks]] includes the a [[MAKER]] workshop at the [http://www.k-state.edu/agc/symp2010/ Arthropod Genomics Symposium], and deadlines for [http://www.iscb.org/ismb2010-deadlines ISMB] (Boston in July), [http://www.amatameeting.org/ AMATA] (Hobart in September), [http://gi-workshop.net/ GIW] (Hangzhou in December), [http://www.eccb10.org/ ECCB] (Ghent in September), [http://incob10.hgc.jp/ InCoB] (Tokyo in September), and [http://meetings.cshl.edu/meetings/infouk10.shtml Genome Informatics] (Hinxton in September).
| + | |
− | | + | |
− | <div style="margin-right: 26em">
| + | |
− | <embedurl>http://www.google.com/calendar/embed?src=0ajv0bm32ue3c2o2v1c8i889hk%40group.calendar.google.com&showTitle=0&showCalendars=0&height=350&mode=AGENDA&ctz=America/NewYork&dates=20100601%2F20100601</embedurl>
| + | |
− | </div>
| + | |
− | If you know of any other events or deadlines that the GMOD community would be interested in, please send them to me.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/24''
| + | |
− | | + | |
− | == gmod (Chado) 1.1 Released ==
| + | |
− | | + | |
− | I am pleased to announce that we released [https://sourceforge.net/projects/gmod/ gmod-1.1] today. This release has the GMOD database [[Glossary#Schema|schema]], [[Chado]], and a variety of tools for loading and working with the database. The release can be downloaded from the [https://sourceforge.net/projects/gmod/ GMOD SourceForge site].
| + | |
− | | + | |
− | There have been many people who have helped with getting this release done and I would like to thank all of them. I would like to especially thank [[User:RobertBuels|Rob Buels]] and [[User:NaamaMenda|Naama Menda]] and the rest of the people at the [http://solgenomics.net/ Sol Genomics Network (SGN)] for their code contributions, including a pub table loader that works with PubMed and an updated version of the script to calculate [[Chado CV Module#Transitive Closure|cvterm closures]].
| + | |
− | | + | |
− | There have been many changes and bug fixes since the [[GMOD News Archives#GMOD 1.0 Released|1.0 release just over two years ago]], but the schema itself has changed very little.
| + | |
− | For a [[Glossary#SQL|SQL]] summary of the changes, see [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes.sql?revision=23255&view=markup <tt>Changes.sql</tt>] in the release that contains SQL statements that should take a 1.0 release of the [[Chado]] schema to the 1.1 schema. See the [http://gmod.svn.sourceforge.net/viewvc/gmod/schema/tags/gmod-1.1/chado/Changes?revision=23255&view=markup <tt>Changes</tt>] file for a full list.
| + | |
− | | + | |
− | If you have been using Chado from a recent [[SVN|svn]] checkout, you don't need to modify your schema at all, since the last change to the schema was about a year ago.
| + | |
− | | + | |
− | Now that this release is out, the plan going forward is for frequent, smaller releases, with an eye on the [[Chado Natural Diversity Module Working Group|Natural Diversity]] schema modifications being worked on now.
| + | |
− | | + | |
− | Thanks for your continued support of the GMOD project,
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | | + | |
− | ''2010/05/24'' | + | |
− | | + | |
− | == GMOD in Boston in July? ==
| + | |
− | | + | |
− | From Scott on 2010/05/25:
| + | |
− | <div class="emphasisbox">
| + | |
− | Due to the short notice, I've decided not to have a GMOD meeting
| + | |
− | before BOSC/ISMB in July. I am hoping to plan an informal "GMOD
| + | |
− | lunch" sometime during BOSC or ISMB for people who are going to the
| + | |
− | meetings and would like to get together to chat.
| + | |
− | </div>
| + | |
− | | + | |
− | Scott Cain sent this question about the next [[Meetings|GMOD meeting]] out to several [[GMOD Mailing Lists|mailing lists]] on May 17:
| + | |
− | <div class="quotebox">
| + | |
− | Since the last GMOD meeting in January, I had been hoping to have a
| + | |
− | [[Meetings|GMOD meeting]] around the ISMB and BOSC meetings in Boston this July.
| + | |
− | Until this week, though, I had had a difficult time finding a place
| + | |
− | where a meeting could be held for a reasonable price. However, a kind
| + | |
− | soul at The Broad has offered a meeting space that would easily
| + | |
− | accommodate a GMOD meeting for two days before BOSC (either July 6-7
| + | |
− | or July 7-8). The only question I have is this: can people make it to
| + | |
− | a GMOD meeting with about 2 months notice? Please let me know your
| + | |
− | thoughts on this. While there would probably be a registration fee,
| + | |
− | it would be fairly low (I'm guessing in the ballpark of $50).
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | </div>
| + | |
− | Scott hasn't heard back, yea or nay, from very many people so far and we need to make a decision as soon as possible. '''If you have any thoughts on this, please [mailto:scott@scottcain.net send them to Scott] before 3pm Eastern US time on Monday, May 24.''' See the GMOD [[Calendar]] for a list of what else is going on in July.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/05/21, updated 2010/05/25''
| + | |
− | | + | |
− | == Ergatis Update ==
| + | |
− | | + | |
− | {{ImageRight|BionformaticsCover.gif|Ergatis Paper in Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1}}
| + | |
− | | + | |
− | The paper "[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq167v1 Ergatis: A web interface and scalable software system for bioinformatics workflows]" is now available as an advance access manuscript in the journal ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]''. [[Ergatis]] "enables users to build, execute, and monitor pipelines for computational analysis of genomics data."
| + | |
− | | + | |
− | Ergatis now includes pipeline templates for prokaryotic genome annotation and comparative genome analysis, as well as 174 modular 'components' that can be used to create custom pipelines, all of which can be executed either locally or on large compute clusters.
| + | |
− | | + | |
− | New tools available that use Ergatis include [http://clovr.igs.umaryland.edu CloVR], which enables bioinformatic pipeline execution in compute clouds and the recently-awarded [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0959894 Data Intensive Academic Grid (DIAG)], which will provide a publicly-accessible Ergatis instance as one of its access methods. At the [[January 2010 GMOD Meeting]] Chris Hemmerich [[:Image:Jan2010ErgatisForBiologists.pdf|presented ISGA]], which provides a customized, abstract interface to Ergatis designed for biologists with specific pipeline needs.
| + | |
− | | + | |
− | [[User:Jorvis|Joshua Orvis]]
| + | |
− | | + | |
− | ''2010/05/20''
| + | |
− | | + | |
− | <endFeed />
| + | |
− | | + | |
− | = [[GMOD News Archives|News Archives]] =
| + | |
− | | + | |
− | Items more than 6 months old are available in the [[GMOD News Archives]].
| + | |
− | | + | |
− | = Adding a News Item =
| + | |
− | | + | |
− | '''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
| + | |
− | | + | |
− | This page generates both an RSS feed and updates the GMOD News list on the [[Main Page|home page]]. Therefore, please follow these guidelines when adding a news item.
| + | |
− | # Edit the [[#News Items|News Items]] section of this page. This will allow you to see how big your news item title is, compared to existing news items. | + | |
− | # Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
| + | |
− | # Title
| + | |
− | #* '''Use a short title. Titles should be small enough to fit on a single line in the GMOD News list on the [[Main Page|home page]]'''.
| + | |
− | #* Place the title in a second level heading: <tt>== Your Title ==</tt>
| + | |
− | # News Text
| + | |
| #* Make the news item succinct. | | #* Make the news item succinct. |
− | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' | + | #* Do not start the item with a MediaWiki header ("== Header =="). |
− | #* End the news item with your name and the date in the format ''YYYY/MM/DD''. | + | #** It won't render very well. You should be able to avoid headers altogether. |
− | # Preview your changes | + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
− | #* Check the table of contents. Is the title no longer than any previous title? Is the title at the same depth as the other news item titles?
| + | #** For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' |
− | #* Check the news item. Does the text look good, does it look like the other news items, and does the first link point to where you want it to? | + | #* You can include images in your news item. See [[:Category:News Items|preexisting news items]] for what markup to use to do this. |
− | #* '''Make sure that your MediaWiki markup (links, italics, etc.) is correct.''' The MediaWiki extension that lists news items on the [[Main Page|home page]] is temperamental. Incorrect markup can lead to garbage on the home page. | + | # Preview / save your changes. Edit and save the page until the news item looks like you want. |
− | #* Revise until you like it and then save it.
| + | # Once you are happy with how the item looks, insert this line at the end of it: |
− | | + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre> |
− | Once you have saved the page, a link to the new item will show up on the home page in about an hour. (Why the delay? It uses an RSS feed of this page and it queries the feed infrequently.) | + | #: Where ''yyyy/mm/dd'' is the current date. This line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour. |
| + | # '''Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.''' |
| + | #* Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line: |
| + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}</nowiki></pre> |
| | | |
− | [[Category:GMOD Community]] | + | [[Category:GMOD_Community]] |
News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the GMOD News Archives. See also the GMOD Calendar and Events List.
GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the GMOD News and GMOD News Archives pages, and in the news tracker on the home page.
Please follow these guidelines when adding a news item.
Please follow these guidelines when adding a news item.