|
|
(110 intermediate revisions by 5 users not shown) |
Line 1: |
Line 1: |
− | {{TocRight}}
| + | <div class="componentBox" style="width: 20em"> |
− | News that is relevant to the GMOD user and developer communities. This includes a wide range of topics, from [[Meetings|GMOD meetings]] and releases to user success stories and GMOD related publications. News items more than 6 months old are listed in the [[GMOD News Archives]].
| + | <wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" /> |
− | | + | |
− | If you have a news item you want added here, please send it to the [[GMOD Help Desk]] or add it to this page directly. See [[#Adding a News Item|Adding a News Item]] for how to do this.
| + | |
− | | + | |
− | <span class="plainlinks"> | + | |
− | This ''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 for how to do just that.
| + | |
− | | + | |
− | <startFeed /> | + | |
− | <!-- Add new Items here. Keep the Title Short! ***35 characters or less*** -->
| + | |
− | == March 2010 Calendar ==
| + | |
− | | + | |
− | {{ImageLeft|calendar_icon.gif|GMOD Calendar||Calendar}}
| + | |
− | There is always a lot going on that is of interest to the GMOD community. Anything that GMOD staff knows about is added to the GMOD [[Calendar]]. I'm going to start posting the GMOD calendar here for the upcoming month.
| + | |
− | | + | |
− | <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=20100301%2F20100301</embedurl>
| + | |
| </div> | | </div> |
− | Please [mailto:help@gmod.org let me know] if this is useful, and I'll keep doing it. If not, I'll stop and the GMOD News will be a little less cluttered.
| + | News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the '''[[GMOD News Archives]]'''. See also the [[Calendar|GMOD Calendar and Events List]]. |
| | | |
− | Thanks,
| + | GMOD News is also available as an '''[{{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed RSS feed]'''. [[File:RSSIcon16x16.gif|link={{gmod.org.url}}?title=Special%3ANewsChannel&format=rss20&limit=20&cat1=&cat2=&excat1=&wpSubmitNewsChannelParams=Create+feed|RSS feed]] |
| | | |
− | [[User:Clements|Dave Clements]]<br />
| + | == Recent News == |
− | [[GMOD Help Desk]]
| + | |
| | | |
− | ''2010/02/22''
| + | <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 Logo Program, Spring 2010 == | + | == [[GMOD News Archives|News Archives]] == |
| | | |
− | <div style="float: right; text-align: center">
| + | The [[GMOD News Archives]] lists all news items since autumn 2007. |
− | {{#icon: Gmod_cog170.png|The GMOD Logo||GMOD Logo Program}}<br>
| + | |
− | {{#icon: Lbcclogo.jpg|GMOD Logo Program||GMOD Logo Program}}
| + | |
− | </div>
| + | |
− | I am pleased to announce the first call for participation in the [[GMOD Logo Program]]. This program is for GMOD users and developers that would like a custom designed logo for their web site, database or software. This spring we will be working with students in an advanced design class at [[GMOD Logo Program#Linn-Benton Community College|Linn-Benton Community College]]. Interested GMOD users and developers will be paired with students and meet several times (remotely) over a 3 week period this spring, with the end result being a new logo.
| + | |
| | | |
− | '''Participation is limited to non-profits, and costs US$75.''' If you are interested, please see the [[GMOD Logo Program|program page]] for additional details and requirements, and an application form. '''The program is accepting applications until March 1.'''
| + | == Adding a News Item == |
| | | |
− | Thanks,
| + | '''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]] | + | |
| | | |
− | ''2010/02/03''
| + | === Short Instructions === |
| | | |
− | == GMOD Summer School - Americas ==
| + | Please follow these guidelines when adding a news item. |
| | | |
− | We are now [[2010 GMOD Summer School - Americas|accepting applications]] for the [[2010 GMOD Summer School - Americas]]. This will be a hands-on multi-day course aimed at teaching new GMOD administrators how to get [[GMOD Components]] up and running. The course will introduce participants to the GMOD project and then focus on installation, configuration and integration of popular [[GMOD Components]].
| + | # 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> |
| | | |
− | The course will be held May 6-9, at [http://nescent.org NESCent] in Durham, NC. These [[GMOD Components]] will be covered:
| + | === Longer Instructions === |
− | {|
| + | |
− | | align="center" |
| + | |
− | {{#icon: 2010SummerSchoolAmericas170.png|GMOD Summer School||2010 GMOD Summer School - Americas}}<br>
| + | |
− | <div style="font-size:120%">'''[[2010 GMOD Summer School - Americas|Apply Now]]'''</div>
| + | |
− | |
| + | |
− | |
| + | |
− | * [[Apollo]] - genome annotation editor
| + | |
− | * [[Chado]] - a modular and extensible database schema
| + | |
− | * [[Galaxy]] - workflow system
| + | |
− | * [[GBrowse]] - the Generic Genome Browser
| + | |
− | * [[GBrowse_syn]] - A generic synteny browser
| + | |
− | * [[JBrowse]] - genome browser
| + | |
− | * [[MAKER]] - Genome annotation pipeline
| + | |
− | * [[Tripal]] - Web front end for [[Chado]]
| + | |
− | |}
| + | |
− | '''The deadline for applying is the end of Friday, February 22. Admission is competitive and is based on the strength of the application (especially the statement of interest).''' In 2009 there were over 50 applications for the 25 slots. Any applications received after the deadline will be automatically placed on the waiting list.
| + | |
| | | |
− | Thanks,
| + | Please follow these guidelines when adding a news item. |
| | | |
− | [[User:Clements|Dave Clements]]<br />
| + | # 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'''. |
− | | + | #* The page must start with '''News/''', otherwise it won't be picked by the RSS news feed. |
− | {|
| + | # Enter the text of your news item. |
− | | valign="top" | PS:
| + | |
− | | We are also investigating holding a GMOD course in the Asia/Pacific region, sometime this fall. Watch the [[GMOD Mailing Lists]] and the [[GMOD News]] for updates.
| + | |
− | |}
| + | |
− | ''2010/01/29''
| + | |
− | | + | |
− | == GMOD @ February NextGenBUG ==
| + | |
− | | + | |
− | {{ImageRight|SBForumLogo.png|NextGenBUG 9 Feb Dundee|140|http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209}}
| + | |
− | If you are anywhere close to Dundee, Scotland on 9 February, consider attending the [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 NextGen Sequencing Bioinformatics User Group (NextGenBUG) meeting] being held at the [http://www.lifesci.dundee.ac.uk/visit University of Dundee]. The program includes two talks with GMOD related content.
| + | |
− | | + | |
− | * '''[http://insectacentral.org InsectaCentral] - assembling and annotating insect transcriptomes''', Alexie Papanicolau, Exeter
| + | |
− | *: [http://insectacentral.org InsectaCentral] uses [[GMOD Components]] (including [[Chado]] and [[GBrowse]]) extensively in its infrastructure.
| + | |
− | | + | |
− | * '''[[Galaxy]]: a stairway to [[Next Generation Sequencing|NGS]] heaven''', Chris Cole, Dundee
| + | |
− | *: Chris will be discussing how Dundee uses [[Galaxy]] to process their [[next generation sequencing]] data.
| + | |
− | | + | |
− | There will also be talks by [[User:DanBolser|Dan Bolser]] of Dundee and Darrol Baker of CLCBio. If you are interested in attending, please [http://genepool.bio.ed.ac.uk:16080/nextgenbug/meeting/20100209 add your name to the participants list].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/29
| + | |
− | | + | |
− | == GBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|GBrowse2Thumb.png|||GBrowse 2.0 HOWTO}}
| + | |
− | With thanks to the many people who have worked long and hard on this project, as well as the people who found and reported bugs during the prerelease stage, I am happy I announce that [[GBrowse 2.0 HOWTO|GBrowse 2.00]] is now available for downloading from [http://search.cpan.org/dist/GBrowse/ CPAN], and [https://sourceforge.net/projects/gmod/files/ SourceForge].
| + | |
− | | + | |
− | The following are highlights of the many new features that have been added since the 1.70 release:
| + | |
− | | + | |
− | * A completely rewritten internal rearchitecture loads tracks asynchronously, providing a more responsive user experience.
| + | |
− | * Different [[GBrowse 2.0 HOWTO#Database Definitions|database backends]] can be associated with each track, making backend management much simpler.
| + | |
− | * A revamped user interface for a less cluttered and more functional end-user experience.
| + | |
− | * A [[GBrowse 2.0 HOWTO#Themes|UI theming system]] with three predefined themes, including a cool "transparent" theme.
| + | |
− | * A custom [[GBrowse 2.0 HOWTO#Configuring the Uploaded Track Database|track upload and management system]] gives users much greater control over custom tracks.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#The Admin Interface|admin interface]] allows an authorized user to upload and manage public tracks without editing config files.
| + | |
− | * An optional [[GBrowse 2.0 HOWTO#Configuring the User Account Database|user registration and login system]] allows users to register stable GBrowse accounts and to keep their settings and custom tracks when they move from one computer to another.
| + | |
− | * Support for named subtracks (tracks within tracks) and filtering of those subtracks.
| + | |
− | * Support for [[GBrowse NGS Tutorial|next generation sequencing]] data.
| + | |
− | | + | |
− | There are also a number of features that ''didn't'' make it into the 2.00 release, most notably:
| + | |
− | | + | |
− | * The internal [[DAS]] server does not work, although the DAS client (ability to import DAS tracks) does. This will be added in a 2.01 release.
| + | |
− | * Internationalization has lagged way behind, and so most of the new features will be presented in English rather than in the user's preferred language (volunteers are needed to help with translations).
| + | |
− | | + | |
− | Please send help queries to the [https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse GBrowse mailing list], and file [https://sourceforge.net/tracker/?group_id=27707&atid=391291 bug reports at SourceForge].
| + | |
− | | + | |
− | On behalf of the GMOD team,
| + | |
− | | + | |
− | [[User:Lstein|Lincoln Stein]]
| + | |
− | | + | |
− | ''2010/01/28''
| + | |
− | | + | |
− | == WebGBrowse 2.0 ==
| + | |
− | | + | |
− | {{ImageRight|cgb_logo.png|WebGBrowse at the Center for Genomics and Bioinformatics||http://webgbrowse.cgb.indiana.edu/}}
| + | |
− | | + | |
− | [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] is now available at http://webgbrowse.cgb.indiana.edu. Here is some of ''what's new'' in WebGBrowse 2.0:
| + | |
− | * [http://webgbrowse.cgb.indiana.edu/ WebGBrowse 2.0] continues to help the inexperienced users of [[GBrowse]] with hosting their [[GFF3]] data without worrying about installation or configuration semantics.
| + | |
− | * Users now have a choice of [[GBrowse]] display between versions 1.7 and 2.0.
| + | |
− | * The display from one version can be migrated to the other by simple button clicks. This helps the users to compare their data display between the two versions without much hassle. It also helps the WebGBrowse users in upgrading/migrating their existing GBrowse displays to version 2.0 seamlessly.
| + | |
− | * A few bug fixes from the earlier version.
| + | |
− | * For those interested in installing WebGBrowse locally, the current installation package is lot more easier to install and less clumsy than the previous version.
| + | |
− | | + | |
− | Thanks,
| + | |
− | | + | |
− | Ram Podicheti<br />
| + | |
− | [http://cgb.indiana.edu/ Center for Genomics and Bioinformatics<br />Indiana University]
| + | |
− | | + | |
− | ''2010/01/25''
| + | |
− | | + | |
− | == Tripal v0.2 Released ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Triapl|120|Tripal}}
| + | |
− | I’d like to announce the release of the second version of [[Tripal]], v0.2. This version provides new support for [[Chado CV Module|controlled vocabularies]], [[Chado General Module|databases]] and several [[Chado Companalysis Module|analysis]] types. This includes better support and visualizations for [http://geneontology.org GO], new [http://www.genome.jp/kegg/pathway.html KEGG pathways] and [http://www.genome.jp/kegg/brite.html BRITE hierarchies], [http://www.ebi.ac.uk/Tools/InterProScan/ InterProScan] results and improved BLAST results.
| + | |
− | | + | |
− | [[Tripal]] has been freely and publicly available since May of 2009 and provides a PHP-based [http://drupal.org Drupal] front-end for the [[Chado]] database schema. It his highly customizable and is extendable by anyone with Drupal and PHP experience. We encourage end-users to develop new or improved modules that can be shared back with the community. We can offer assistance when needed in the development of new modules.
| + | |
− | | + | |
− | An updated [[Media:TripalUsersGuideJan2010.pdf|user’s manual]] is available, but not quite complete. An update to the manual will be added soon. If you have any questions please feel free to email the [https://lists.sourceforge.net/lists/listinfo/gmod-tripal Tripal mailing list] for assistance.
| + | |
− | | + | |
− | Tripal can be [http://www.genome.clemson.edu/software/tripal downloaded from the CUGI website] as a compressed package, or developers can retrieve the most up-to-date code from the GMOD [[SVN]].
| + | |
− | | + | |
− | Best Regards,
| + | |
− | | + | |
− | [[User:Sficklin|Stephen Ficklin]]<br />
| + | |
− | [http://www.genome.clemson.edu/ Clemson University Genomics Institute]
| + | |
− | | + | |
− | ''2010/01/23''
| + | |
− | | + | |
− | == CMap3D ==
| + | |
− | | + | |
− | {{ImageRight|CMap3DScreenshot.png|CMap3D|220|CMap3D}}
| + | |
− | [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D] is a 3D visualisation tool for comparative genetic maps that runs on top of a [[CMap]] database. [[CMap]], a [[GMOD Components|GMOD component]], is a common tool for the storage, comparison and visualisation of genetic maps. However, current map visualisation in CMap is limited to the comparison of adjacent aligned maps. CMap3D overcomes this limitation. Multiple genetic maps can now be compared in three-dimensional space. The CMap3D visualisation tool is based on a client server model ensuring operability with current [[CMap]] data repositories.
| + | |
− | | + | |
− | [[CMap3D]] can be applied to any species where genetic map information is available and enables rapid, direct comparison between multiple aligned maps. For more on [[CMap3D]] see the [http://acpfg.imb.uq.edu.au/cmap3d.php CMap3D page] at the [http://acpfg.imb.uq.edu.au/ Australian Centre for Plant Functional Genomics (ACPFG)], the [[:Image:PAG2010CMap3D.pdf|PAG 2010 presentation on CMap3D]] (and other tools), and the [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/2/273 CMap3D paper] in [http://bioinformatics.oxfordjournals.org/ Bioinformatics].
| + | |
− | | + | |
− | Chris Duran
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | == DAS Workshop 7-9 April 2010 ==
| + | |
− | | + | |
− | {{ImageRight|Das_logo_64x64.jpg|DAS Workshop||http://www.ebi.ac.uk/training/handson/DAS_070410.html}}
| + | |
− | There will be a [http://www.ebi.ac.uk/training/handson/DAS_070410.html Distributed Annotation System (DAS) Workshop] at [http://www.ebi.ac.uk/ EBI], 7-9 April 2010. In GMOD, DAS is supported by [[GBrowse]], and [[Chado]] (and DAS support in [[Apollo]] is in the works).
| + | |
− | | + | |
− | If you don't know about [[DAS]] and wish to know how to distribute your latest biological annotation to the world then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] may be for you.
| + | |
− | | + | |
− | If you know about [[DAS]] and are maybe a DAS client developer then the upcoming [http://www.ebi.ac.uk/training/handson/DAS_070410.html DAS workshop] is for you (as you will need to know about the upcoming DAS 1.6 Specification and how it may affect your software).
| + | |
− | | + | |
− | See the [http://www.ebi.ac.uk/training/handson/DAS_070410.html workshop page] for more information and registration details.
| + | |
− | | + | |
− | [[User:JWarren|Jonathan Warren]]
| + | |
− | | + | |
− | ''2010/01/21''
| + | |
− | | + | |
− | | + | |
− | == GBrowse.org ==
| + | |
− | | + | |
− | <div style="float:right; padding: 0em 0.5em; font-size: 110%; border: 3px #d0d0d0 solid; margin-left: 1em; margin-bottom: 1em; padding-bottom: 0.25em">
| + | |
− | {|
| + | |
− | |{{#icon: GBrowseOrgOrig.png|GBrowse.org|80|http://www.gbrowse.org/}}
| + | |
− | |-
| + | |
− | | align="center" | <span class="plainlinks">[http://www.gbrowse.org GBrowse.org]</span>
| + | |
− | |}
| + | |
− | </div>
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] is a resource for using and setting up [[GBrowse]] genome browsers. The site provides one location where biologists and bioinformaticians can find:
| + | |
− | | + | |
− | # Genome browser web sites for any organism that has them. If a species has a genome browser anywhere on the web, then we aim to link to it.
| + | |
− | # Links to sequence and annotation files that are available online.
| + | |
− | # Links to genome browser configuration files, when available
| + | |
− | # An FTP site containing genome annotation and configuration files for each annotated genome that does not have its own web site.
| + | |
− | | + | |
− | [http://www.gbrowse.org GBrowse.org] emphasizes the [[GBrowse]] genome browser in its organization, but also links to sites that use other browser packages such as UCSC, Ensembl, and [[JBrowse]].
| + | |
− | | + | |
− | <div class="emphasisbox" style="font-size: 120%; text-align: center">
| + | |
− | Also, we are currently conducting a [http://gbrowse.org/survey/index.php?sid=64264&lang=en survey] seeking input on future project direction. Please take a few minutes now to [http://gbrowse.org/survey/index.php?sid=64264&lang=en provide your feedback].
| + | |
− | </div>
| + | |
− | | + | |
− | GBrowse.org was first introduced at the [[August 2009 GMOD Meeting#GBrowse.org|August 2009 GMOD Meeting]].
| + | |
− | | + | |
− | Ciao,
| + | |
− | | + | |
− | [[User:Bilardi|Alessandra Bilardi]]<br />
| + | |
− | [http://genomics.cribi.unipd.it/Main_Page CRIBI Genomics, University of Padua]
| + | |
− | | + | |
− | ''2010/01/11'' | + | |
− | | + | |
− | == Bio::Chado::Schema 0.05 Released ==
| + | |
− | | + | |
− | I'd like to announce a new [[Bio::Chado::Schema]] release, version 0.05. Changes in this release:
| + | |
− | | + | |
− | * Got POD generation working, now all classes and methods have POD, '''including''' the embedded table and column comments! Thanks to the wonderful DBIx::Class::Schema::Loader folks.
| + | |
− | * Turned off DBIC's cascade_delete and cascade_copy on all relations (thanks to Siddhartha Basu for troubleshooting). Deletes break if these are on and you don't have every part of the schema installed.
| + | |
− | | + | |
− | I [http://search.cpan.org/dist/Bio-Chado-Schema/ uploaded] it to [http://cpan.org CPAN] a week ago, so it should have propagated by now to almost all of the CPAN mirrors.
| + | |
− | | + | |
− | See the [[Bio::Chado::Schema]] wiki page for more on what [[Bio::Chado::Schema]] is and what it's for.
| + | |
− | | + | |
− | [[User:RobertBuels|Rob Buels]]<br>
| + | |
− | [[:Category:SGN|SGN]]
| + | |
− | | + | |
− | ''2010/01/08'' | + | |
− | | + | |
− | == GMOD at PAG 2010 ==
| + | |
− | | + | |
− | GMOD will once again have a strong presence at the [[PAG 2010|Plant and Animal Genome Conference (PAG 2010)]], being held January 9-13 in San Diego. There will be [[PAG 2010|'''over 45 talks, workshops, demonstrations and posters''']] about [[GMOD Components]] and projects that use them. See the [[PAG 2010]] page for a full listing and a flier showing highlights. Highlights at [[PAG 2010]] include:
| + | |
− | {{ImageRight|Paglogo.gif|GMOD @ PAG||PAG 2010}}
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_913.html Animal Genomics with Galaxy], Saturday
| + | |
− | * [[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]], Saturday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/W26_PAGXVIII_192.html Database Resources at the EBI] (including [[BioMart]]), Sunday
| + | |
− | * [[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop]], Sunday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_858.html GBrowse And Next Generation Sequencing Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C02_PAGXVIII_938.html GMOD Project Update], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_919.html Using the JBrowse Genome Browser with Large Amounts of Data], Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_859.html Visualizing And Comparing Genomes] ([[CMap]]), Monday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/P08b_PAGXVIII_861.html Comparative Genomics Tools In GMOD], Monday
| + | |
− | * [http://www.intl-pag.org/18/18-gramene.html Using Gramene] (including [[CMap]]), Tuesday
| + | |
− | * [[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn]], Wednesday
| + | |
− | * [http://www.intl-pag.org/18/abstracts/C01_PAGXVIII_931.html Tripal: a Construction Toolkit for Online Genomic Databases], Wednesday
| + | |
− | | + | |
− | Many GMOD staff and developers ([[User:Scott|Scott Cain]], [[User:Clements|Dave Clements]], [[User:Sficklin|Stephen Ficklin]], [[User:Carsonholt|Carson Holt]], [[User:Mckays|Sheldon McKay]], Anton Nekrutenko, [[User:MitchSkinner|Mitch Skinner]], Ken Youens-Clark) and even more GMOD users will be at PAG. If you are attending please keep an eye open for us.
| + | |
− | | + | |
− | Finally, the [[January 2010 GMOD Meeting]] is being held immediately after PAG. The meeting is full (you are encouraged to add your name to the short waiting list), but there will be several [[January 2010 GMOD Meeting#Satellite Meetings|Satellite Meetings]], ''held during PAG'', that you can attend even if you don't go to the main GMOD Meeting.
| + | |
− | | + | |
− | See you in San Diego,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2010/01/05''
| + | |
− | | + | |
− | == Galaxy Developer Conference ==
| + | |
− | | + | |
− | {{ImageLeft|GalaxyLogoSmall.png|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
| + | |
− | {{ImageRight|CSHL Logo75x75.gif|Galaxy Developer Conference||http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp}}
| + | |
− | | + | |
− | The [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp First Galaxy Developer Conference] will be held at [http://www.cshl.edu/ Cold Spring Harbor Laboratory]
| + | |
− | May 15-17, 2010, immediately after the [http://meetings.cshl.edu/meetings/genome10.shtml Biology of Genomes] conference. [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp Registration] is now open.
| + | |
− | | + | |
− | This meeting is aimed at developers of analysis tools, bioinformatics staff, and IT managers of sequencing facilities. The meeting will focus on these features of the [[Galaxy]] framework:
| + | |
− | | + | |
− | * tool integration and distributed job management | + | |
− | * deployment of private Galaxy instances on local resources and on the cloud
| + | |
− | * management of large datasets with the Galaxy Library System
| + | |
− | * using the Galaxy LIMS functionality for managing sample submission at [[Next Generation Sequencing|NGS]] sequencing facilities.
| + | |
− | | + | |
− | Please [http://meetings.cshl.edu/meetings/meetingsregistration_galaxy10.asp register now] if you are interested in using and extending [[Galaxy]]. | + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/12/28''
| + | |
− | | + | |
− | == Arthropod Genomics Consortium ==
| + | |
− | | + | |
− | {{ImageRight|AGSBug170.png|Arthropod Genomics Consortium|100|http://arthropodgenomes.org}}
| + | |
− | The [http://arthropodgenomes.org Arthropod Genomics Consortium] encourages collaboration and information exchange amongst arthropod researchers. The consortium, launched at the [http://www.k-state.edu/agc/symp2009/ 2009 Arthropod Genomics Symposium], has now started [http://arthropodgenomes.org a wiki] to enable this community to self-organize:
| + | |
− | | + | |
− | : ''Our goal is to provide a central location for information about arthropod genomics projects, bioinformatics tools, and people interested in arthropod genomics. We think this is a great way to "identify the community"; information from the wiki can be used to support white papers and grant proposals. It will also serve as a central location for links to arthropod genomics resources, news releases and meeting announcements.''
| + | |
− | :: [http://www.ksu.edu/biology/faculty_pages/brown.html Sue Brown], Director, [http://www.k-state.edu/agc/ K-State Arthropod Genomics Center]
| + | |
− | | + | |
− | If you are an arthropod researcher, please consider [http://arthropodgenomes.org/wiki/Main_Page#tab=Adding_data_to_this_wiki joining this growing consortium].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/12/18''
| + | |
− | | + | |
− | == BioPerl Podcast ==
| + | |
− | | + | |
− | {{ImageRight|BioPerl_logo.jpg|BioPerl Podcast|70|http://twit.tv/floss96}}
| + | |
− | | + | |
− | A [http://twit.tv/floss96 podcast on the BioPerl project] is available at [http://twit.tv/FLOSS FLOSS Weekly]. It's about an hour long and it's a good introduction to [[BioPerl]], a set of libraries that many popular [[GMOD Components]] are built upon. The podcast is an interview with BioPerl heavy hitters [[User:Cjfields|Chris Fields]] and [[User:Stajich|Jason Stajich]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | ''2009/11/23''
| + | |
− | | + | |
− | == InterMine 0.92 Released ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine Release Notes|180|http://www.intermine.org/wiki/ReleaseNotes}}
| + | |
− | | + | |
− | We have released version 0.92 of [[InterMine]].
| + | |
− | | + | |
− | The main changes are some improvements to the way integration keys and priorities are configured and validated, a BioPax parser, performance enhancements and some webapp fixes.
| + | |
− | | + | |
− | Version 0.92 has [http://www.intermine.org/wiki/ReleaseNotes Release Notes] and [http://www.intermine.org/wiki/UpgradeInterMine upgrade information].
| + | |
− | | + | |
− | Upgrade should be quite straightforward from either 0.9 or 0.91. The
| + | |
− | only issue is compatibility of the GO enrichment widget with old
| + | |
− | databases built before 0.91.
| + | |
− | | + | |
− | [mailto:dev@mail.intermine.org Let us know] if you have problems or suggestions for the next releases.
| + | |
− | | + | |
− | The InterMine team.
| + | |
− | | + | |
− | ''2009/11/23''
| + | |
− | | + | |
− | == CMap Paper in Bioinformatics ==
| + | |
− | | + | |
− | {{ImageRight|BionformaticsCover.gif|Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040}}
| + | |
− | | + | |
− | A [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 paper] describing the [[CMap]] comparative map viewer is in the [http://bioinformatics.oxfordjournals.org/content/vol25/issue22/index.dtl current issue] of ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'':
| + | |
− | | + | |
− | : [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 CMap 1.01: a comparative mapping application for the Internet], by Ken Youens-Clark, [[User:Faga|Ben Faga]], Immanuel V. Yap, [[User:Lstein|Lincoln Stein]] and Doreen Ware.
| + | |
− | | + | |
− | [[CMap]] is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.
| + | |
− | | + | |
− | See the [[CMap|CMap page]] to learn more. CMap will also be covered in the [http://www.intl-pag.org/18/18-gramene.html Gramene workshop] and in a poster at [[PAG 2010]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/11/14''
| + | |
− | | + | |
− | == January 2010 GMOD Meeting ==
| + | |
− | | + | |
− | {{ImageRight|Jan2010MtgLogo170.png|January 2010 GMOD Meeting||January 2010 GMOD Meeting}}
| + | |
− | | + | |
− | | + | |
− | <div style="font-size: 140%; text-align: center">[[January 2010 GMOD Meeting|Register for the January 2010 GMOD Meeting]]</div>
| + | |
− | | + | |
− | | + | |
− | I am pleased to announce that the [[January 2010 GMOD Meeting|January GMOD meeting]] will be taking place on January 14 and 15, 2010 in San Diego at the [[January 2010 GMOD Meeting#Lodging|Best Western Seven Seas]]
| + | |
− | (the same location as last year). Please see the [[January 2010 GMOD Meeting|meeting page]] for registration information.
| + | |
− | | + | |
− | Please also take a moment to [[January 2010 GMOD Meeting#Agenda Proposals|add suggestions for the agenda]]. There is no registration fee for this meeting. However, there is limited space, so please register early.
| + | |
− | | + | |
− | The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the [[January 2010 GMOD Meeting|GMOD meeting]] and the [[PAG 2010|Plant and Animal Genome meeting]] before it may stay at the Best Western the entire time.
| + | |
− | | + | |
− | Please direct follow up questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-devel gmod-devel mailing list] ([mailto:gmod-devel@lists.sourceforge.net gmod-devel@lists.sourceforge.net]).
| + | |
− | | + | |
− | Thanks and I look forward to seeing you in San Diego!
| + | |
− | | + | |
− | [[User:Scott|Scott]]
| + | |
− | | + | |
− | ''2009/11/13''
| + | |
− | | + | |
− | == Long Term Database Funding ==
| + | |
− | | + | |
− | You may have heard about [http://www.arabidopsis.org/doc/about/tair_funding/410 TAIR's funding situation]. Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources. This news was sent to the TAIR community (and posted on the [http://mailman.tairgroup.org/mailman/listinfo/biocurator Biocurator list]) on October 22. A day later the paper "[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Models for financial sustainability of biological databases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''.
| + | |
− | | + | |
− | All GMOD users need to give at least some thought to long term funding issues. A [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International Society for Biocuration]'s (ISB) [http://biocurator.proboards.com/ forum site].
| + | |
− | | + | |
− | {{ImageRight|TAIR_logo.gif|TAIR Funding Update and Discussion Forum||http://www.arabidopsis.org/doc/about/tair_funding/410}}
| + | |
− | [http://www.arabidopsis.org/ TAIR] asked people to do a couple things:
| + | |
− | # Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
| + | |
− | # Contribute to a [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion on the TAIR web site] about
| + | |
− | ## the bioinformatics needs of the ''Arabidopsis'' and wider plant biology communities and
| + | |
− | ## how resources like TAIR should be funded.
| + | |
− | | + | |
− | The [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion at TAIR] is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising. It also contains many statements that none of those options will work. The ''[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Database]'' paper discusses similar proposals, plus some others.
| + | |
− | | + | |
− | If you are interested in long-term funding issues, I encourage you to participate in the [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion at ISB]. If you use TAIR and want to see it funded, please [http://www.arabidopsis.org/doc/about/tair_funding/410 post a comment at the TAIR web site]. And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/11/06'' | + | |
− | | + | |
− | == Two Openings at Bayer CropScience ==
| + | |
− | {{ImageRight|Logo_BayerCropScience.gif|Open positions at Bayer CropScience||http://www.mybayerjob.com/en}}
| + | |
− | '''1. BioAnalyst Scientist:'''
| + | |
− | | + | |
− | You will provide support in various activities: [[Next Generation Sequencing]] (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.
| + | |
− | | + | |
− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUE2NjQ4RkNFNjUwMDlBRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Scientist]
| + | |
− | | + | |
− | '''2. BioAnalyst Researcher:'''
| + | |
− | | + | |
− | You will support and foster the data management and analysis of [[Next Generation Sequencing]] (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. [[Glossary#Perl|perl]] and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.
| + | |
− | | + | |
− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUI3NUU2MzIzRDcwMTEyRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Researcher]
| + | |
− | | + | |
− | Operating language in the company is English.
| + | |
− | | + | |
− | '''Interested in any of these positions?''' You can apply [http://www.mybayerjob.com/en here] or send your CV to [mailto:Laurent.viau@bayercropscience.com Laurent Viau]
| + | |
− | | + | |
− | [[User:ErickAntezana|Erick Antezana]]
| + | |
− | | + | |
− | ''2009/11/06''
| + | |
− | | + | |
− | == GBrowse NGS Tutorial & Poster==
| + | |
− | | + | |
− | {{ImageRight|BA2009Logo.png|GBrowse NGS Tutorial|100|GBrowse NGS Tutorial}}
| + | |
− | A tutorial on using [[GBrowse NGS Tutorial|GBrowse 2 to visualize next generation sequencing (NGS) data]] is now available. The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 2 genome browser to display [[next generation sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the [[BA2009|Bioinformatics Australia 2009 (BA2009) GMOD Workshop]]. The tutorial includes a [[VMware]] image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.
| + | |
− | | + | |
− | The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.
| + | |
− | | + | |
− | A [[:Image:GBrowse_nextgen_poster.pdf|poster]] (by [[User:Scott|Scott Cain]]) demonstrating how to use the adaptor with ''GBrowse 1 and GBrowse 2'' is also available.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/11/04''
| + | |
− | | + | |
− | == Galaxy Project Hiring ==
| + | |
− | | + | |
− | {{ImageRight|GalaxyLogoSmall.png|Galaxy Project Hiring||http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2}}
| + | |
− | There are several open [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 software engineer and postdoc positions] with the [[Galaxy]] project. Galaxy is looking for engineers with with experience in distributed computing, visualization, and usability. The positions will initially focus on making [[next generation sequencing]] (NGS) data analysis more widely accessible, transparent, and reproducible, as well as development of bioinformatic tools in areas enabled by NGS: re-sequencing, ''de novo'' assembly, metagenomics, transcriptome analysis and epigenetics. Postdoc positions will address biological questions (''e.g.'', mutagenesis and sex chromosome evolution from NGS data) using [[Galaxy]] tools.
| + | |
− | | + | |
− | See the [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 official posting] for full details and contact information.
| + | |
− | | + | |
− | ''2009/11/02''
| + | |
− | | + | |
− | == Visualizing Biological Data Workshop ==
| + | |
− | | + | |
− | {{ImageRight|EMBO_Logo.png|Visualizing Biological Data (VizBi)||http://www.vizbi.org}}
| + | |
− | | + | |
− | The first [http://www.vizbi.org/ EMBO Workshop on Visualizing Biological Data (VizBi)] will be held 3-5 March 2010, at the [http://www.embl.de/training/eicat/atc/index.html EMBL Advanced Training Centre] in Heidelberg, Germany.
| + | |
− | | + | |
− | The goal of the workshop is to bring together researchers developing and using visualization systems across all areas of biology, including genomics, sequence analysis, macromolecular structures, systems biology, and imaging (including microscopy and magnetic resonance imaging). The primary focus will be on visualizing processed and annotated data in their biological context, rather than on processing of raw data.
| + | |
− | | + | |
− | The workshop is limited in the total number participants, and each participant is normally required to present a poster and to give a ''fastforward'' presentation about their work (limited to 30 seconds and 1 slide). To apply to join the workshop, please [http://vizbi.org submit an abstract and image] related to your work. Submissions close on 16 November 2009.
| + | |
− | | + | |
− | ''2009/10/21''
| + | |
− | | + | |
− | == Openings at Syngenta ==
| + | |
− | {{ImageRight|SyngentaLogo.png|Openings at Syngenta||http://www.syngentacareers.com/listing/}}
| + | |
− | There are two openings at [http://www.syngentacareers.com/listing/ Syngenta], recently named one of the top biotechnology employers by [http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2009_10_02/science.opms.r0900079 Science], in Research Triangle Park, NC.
| + | |
− | | + | |
− | [http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={2258BBC6-9CD1-4991-9F4A-3099220C760D}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genomic Database Specialist (#1435)]: We are currently using the [[Chado]] schema, and this individual will be responsible for maintaining and optimizing database systems for genome annotation and related information. Experience overseeing database systems is required and experience with Oracle and [[PostgreSQL]] is desirable. The ideal candidate will have a solid understanding of genomics and a background in a life sciences setting. Strong competency with Unix and Perl is required.
| + | |
− | | + | |
− | [http://careers2.hiredesk.net/viewjobs/JobDetail.asp?Comp=Yoh&sPERS_ID=&TP_ID=1&JB_ID=&PROJ_ID={D9207D76-4EFC-49B7-B4A5-E0F2988E9DF5}&LAN=en-US&BackUrl=ViewJobs/Default.asp Genome Annotation Specialist (#1434)]: This individual will be responsible for implementing automated annotation pipelines for genome, transcript, and proteins sequences. Advanced knowledge of sequence analysis tools is required. Experience with modern high throughput sequencing analytics is desirable. A strong competency with Unix and scripting in a language such as Perl is required.
| + | |
− | | + | |
− | Both positions will work with Chado and [[GBrowse]], and will help evaluate the adoption of additional GMOD tools. See the links for more details.
| + | |
− | | + | |
− | [[User:Eric.ganko|Eric Ganko]]
| + | |
− | | + | |
− | ''2009/10/21''
| + | |
− | | + | |
− | == Opening at SGD ==
| + | |
− | | + | |
− | There is an [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 opening for a Bioinformatics Analyst] at the [http://yeastgenome.org ''Saccharomyces'' Genome Database (SGD)], the model organism database for yeast.
| + | |
− | | + | |
− | {{ImageRight|SGD-t.gif|Bioinformatics Analyst at SGD||http://yeastgenome.org}}
| + | |
− | The position includes interacting with international research laboratories, working with genomic data, evaluating new technologies, analysis via computational methods created by others but integrated at SGD, knowledge of new experimental methodology, large genomic datasets and their computational analysis, and bioinformatic analysis of data types such as RNA transcription and second-generation sequencing. Experience with [[Comparative Genomics|comparative genomics]] is also desirable.
| + | |
− | | + | |
− | SGD is both a GMOD contributor (''e.g.'', [[BLAST Graphic Viewer]]) and GMOD user, and this position will work with the [[GBrowse]] genome viewer as well as other GMOD tools.
| + | |
− | | + | |
− | See the [http://jobs.stanford.edu Stanford jobs site] (search for posting [http://recruit.trovix.com/jobhostmaster/jobhost/ViewJobPostDetails.do?action=viewDetails&accountId=de85ad313f8598db1c42b567a3df24a00497ba22&jobId=36125 36125]) for more.
| + | |
− | | + | |
− | ''2009/10/20''
| + | |
− | | + | |
− | == Apollo 1.11.2 Released ==
| + | |
− | | + | |
− | I've just cut a new [[Apollo]] release that fixes some [[GFF3]] and [[Chado]] writeback issues. As usual, you can get the most current version of Apollo at:
| + | |
− | | + | |
− | : http://apollo.berkeleybop.org/current/
| + | |
− | | + | |
− | Cheers,
| + | |
− | | + | |
− | [[User:Elee|Ed Lee]]
| + | |
− | | + | |
− | ''2009/10/07'' | + | |
− | | + | |
− | == 2009 GMOD Survey Results ==
| + | |
− | | + | |
− | The [[2009 GMOD Community Survey|results of the 2009 GMOD Community Survey]] are now available online. This year's survey focused on genomic and comparative genomics visualization was taken by 45 respondents. The survey includes:
| + | |
− | * [[2009 GMOD Community Survey#Use Cases|Use Cases]] - what people would like visualization software to do.
| + | |
− | * [[2009 GMOD Community Survey#Features|Feature Ranking]] - what features are the most (and least) important to users. | + | |
− | * Plus general feedback on [[2009 GMOD Community Survey#Other Feedback on Visualization Tools|visualization tools]], [[2009 GMOD Community Survey#Documentation|documentation]], and the [[2009 GMOD Community Survey#Other Feedback|project]].
| + | |
− | | + | |
− | The survey results will be used to improve GMOD and guide its future direction. This year's survey complements the [[2008 GMOD Community Survey]], which covered all of GMOD.
| + | |
− | | + | |
− | {{ImageRight|GMODMug150x150.jpg|GMOD Mug|100|http://www.cafepress.com/GenericMOD/}}
| + | |
− | And, finally, we have our 3 winners of [http://www.cafepress.com/GenericMOD/ GMOD Gear]:
| + | |
− | | + | |
− | * James Estill of the [http://www.genetics.uga.edu/ University of Georgia]
| + | |
− | * Philippe Lamesch of [http://www.arabidopsis.org/ TAIR]
| + | |
− | * Sandra Lövenich of [http://www.imsb.ethz.ch/ ETH Zürich]
| + | |
− | | + | |
− | Thanks to everyone who took the time to participate in the survey.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/05''
| + | |
− | | + | |
− | == GMOD Tutorials! GMOD Training! ==
| + | |
− | | + | |
− | {{ImageRight|GMOD2009Europe170.png|Summer School - Europe|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
| + | |
− | {{ImageRight|2009SummerSchoolAmericas170.png|Summer School - Americas|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
| + | |
− | | + | |
− | Detailed and hands-on [[Training and Outreach#Online Tutorials|online tutorials]] are now available for the [[GMOD Components]] that were covered at the [[GMOD Summer School|2009 GMOD Summer Schools]]. Each tutorial includes a [[VMware]] system image to work with, and detailed instructions on how to setup the component on that image.
| + | |
− | | + | |
− | The [[:Category:Tutorials|tutorials]] are: | + | |
− | * '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
| + | |
− | * '''[[Artemis-Chado Integration Tutorial]]''' - by [[User:RobinHouston|Robin Houston]], [[User:TimCarver|Tim Carver]] and [[User:Buggy|Giles Velarde]]
| + | |
− | * '''[[BioMart Tutorial]]''' - by [[User:Junjun|Junjun Zhang]] and Syed Haider
| + | |
− | * '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
| + | |
− | * '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]'''
| + | |
− | * '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
| + | |
− | * '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]] and Ian Holmes
| + | |
− | * '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
| + | |
− | * '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
| + | |
− | | + | |
− | | + | |
− | There is also a plethora of GMOD related [[Training and Outreach|training and outreach]] going on in the next few months. Here's what I know about:
| + | |
− | {| class="wikitable"
| + | |
− | ! Date
| + | |
− | ! Topic
| + | |
− | ! Conference / Location
| + | |
− | |-
| + | |
− | ! October 12-27
| + | |
− | | '''[http://meetings.cshl.edu/courses/c-info09.shtml Programming for Biology]'''<br />This includes a session on [[GBrowse]].
| + | |
− | | [http://www.cshl.edu Cold Spring Harbor Laboratory], Cold Spring Harobr, NY, USA
| + | |
− | |-
| + | |
− | ! October 21-22
| + | |
− | | '''[http://www.ashg.org/2009meeting/pages/workshops.shtml#ucsc Interactive Workshops on the UCSC Genome Browser and Galaxy Framework]
| + | |
− | | [http://www.ashg.org/2009meeting/ The American Society of Human Genetics (AHSG)], Honolulu, Hawaii, USA
| + | |
− | |-
| + | |
− | ! October 27-30
| + | |
− | | '''[[GBrowse]] and [[Next Generation Sequencing]] Data'''
| + | |
− | | [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics], Cold Spring Harbor, New York, USA
| + | |
− | |-
| + | |
− | ! rowspan="2" | October 28-30
| + | |
− | | '''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'''
| + | |
− | | rowspan="2" | [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia
| + | |
− | |-
| + | |
− | | '''Visualizing [[Next Generation Sequencing|Next Generation Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
| + | |
− | |-
| + | |
− | | style="background-color: #cccccc" colspan="3" |
| + | |
− | |-
| + | |
− | ! rowspan="2" | November 16-17
| + | |
− | | '''[http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine Data Warehouse Workshop]
| + | |
− | | Cambridge, UK
| + | |
− | |-
| + | |
− | | '''Comparative Genomics with GMOD'''
| + | |
− | | [http://colloque.inra.fr/isyip Information Systems for Insect Pests], Rennes, France
| + | |
− | |-
| + | |
− | | style="background-color: #cccccc" colspan="3" |
| + | |
− | |-
| + | |
− | ! rowspan="3" | January 9-13
| + | |
− | | '''[[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]]'''
| + | |
− | | rowspan="3" | [[PAG 2010|Plant and Animal Genome XVII Conference (PAG 2010)]], San Diego, CA, USA<br />See '''[[PAG 2010]]''' for links to many talks and presentations.
| + | |
− | |-
| + | |
− | | '''[[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn]]'''
| + | |
− | |-
| + | |
− | | '''[[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]]'''
| + | |
− | |-
| + | |
− | |}
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/02''
| + | |
− | | + | |
− | | + | |
− | == modENCODE & Gramene Openings ==
| + | |
− | | + | |
− | The [http://www.modencode.org modENCODE] and [http://www.gramene.org Gramene] projects are both hiring.
| + | |
− | | + | |
− | <span style="font-size:120%">'''modENCODE'''</span>
| + | |
− | | + | |
− | {{ImageRight|ModENCODE logo.png|modENCODE Project Openings||http://blog.modencode.org/}}
| + | |
− | [http://www.modencode.org modENCODE] is [http://blog.modencode.org/?p=350 looking for a few consultants]. The project's aim is to discover and explore the genomes of ''C. elegans'' and ''D. melanogaster'', using new scientific strategies and new technologies for discovery.
| + | |
− | | + | |
− | Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data
| + | |
− | of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.
| + | |
− | | + | |
− | Please see the [http://blog.modencode.org/?p=350 complete job description] for details.
| + | |
− | | + | |
− | [http://www.modencode.org modENCODE] is a power GMOD user. The project uses [[GBrowse]], [[Chado]], [[InterMine]], [[JBrowse]], and [[GBrowse_syn]]. (See [[January 2009 GMOD Meeting#modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display|Nicole Washington's talk]] at the [[January 2009 GMOD Meeting]] for some details on how they are used.)
| + | |
− | | + | |
− | | + | |
− | <span style="font-size: 120%">'''Gramene'''</span>
| + | |
− | | + | |
− | {{ImageRight|Gramene_logo180.jpg|Grameene Project Opening||http://news.gramene.org/}}
| + | |
− | | + | |
− | [http://www.gramene.org Gramene] has [http://news.gramene.org/?p=392 several bioinformatics openings] in the [http://www.science.oregonstate.edu/bpp/faculty/jaiswal/ Jaiswal lab] at Oregon State University.
| + | |
− | | + | |
− | The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining ([[Textpresso]]) and biological ontology projects. Gramene is a long-time GMOD user and is the home of the [[CMap]] comparative map viewer.
| + | |
− | | + | |
− | See [http://news.gramene.org/?p=392 the position announcement] for full details.
| + | |
− | | + | |
− | ''2009/10/02''
| + | |
− | | + | |
− | == GMOD @ Bioinformatics Australia ==
| + | |
− | | + | |
− | {{ImageRight|BA2009Logo.png|GMOD workshop at Bioinformatics Australia||BA2009}}
| + | |
− | There will be a half-day [[BA2009|pre-conference GMOD workshop]] on 28 October, 2009, at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia (BA2009)]. The workshop will introduce [[GMOD Components]] for [[visualization]], [[annotation]], and data management, and the GMOD project as a whole. The workshop will also include a [[GBrowse]] demonstration with a worked example that includes [[next generation sequencing]] data.
| + | |
− | | + | |
− | Thanks to sponsorship from [http://www.bioplatforms.com/ Bioplatforms Australia] admission to the workshop is included in the conference registration fee.
| + | |
− | | + | |
− | Please see the [[BA2009|workshop page]] or [mailto:help@gmod.org contact the GMOD Help Desk] for more information.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/01'' | + | |
− | | + | |
− | == InterMine Data Warehouse Workshop ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine Workshop|180|http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html}}
| + | |
− | | + | |
− | We are running another [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine workshop] in Cambridge, UK on November 16th-17th.
| + | |
− | | + | |
− | This is intended for software developers to learn the [[InterMine]] system. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.
| + | |
− | | + | |
− | The course is free to attend, more details and sign up information
| + | |
− | are available on the [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html workshop page].
| + | |
− | | + | |
− | Please get in touch if you have any questions.
| + | |
− | | + | |
− | Regards,
| + | |
− | | + | |
− | [mailto:richard@flymine.org Richard Smith]
| + | |
− | | + | |
− | ''2009/09/29'' | + | |
− | | + | |
− | == Tripal: A Web Front End for Chado ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Tripal|200|Tripal}}
| + | |
− | [[Tripal]] is a new web front end for [[Chado]] databases and is now a part of GMOD. Tripal is a collection of [http://www.drupal.org Drupal] modules initially developed by the [http://www.genome.clemson.edu/ Clemson University Genomics Institute (CUGI)]. Tripal is already powering several web sites, including the [http://www.marinegenomics.org Marine Genomics Project] and [http://www.fagaceae.org/ Fagaceae Genomics Web].
| + | |
− | | + | |
− | Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.
| + | |
− | | + | |
− | Tripal can be downloaded from the GMOD [[SVN]] repository. Tripal (already!) has an extensive [[Media:TripalUsersGuideJune2009.pdf|User's Guide]] and a [[Tripal Tutorial|tutorial]] to help users install, configure and extend Tripal.
| + | |
− | | + | |
− | If you use or are considering using [[Chado]], please take a look at [[Tripal]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/28''
| + | |
− | | + | |
− | == Reactome User Survey ==
| + | |
− | | + | |
− | Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.
| + | |
− | | + | |
− | You can access the survey at [http://www.surveymonkey.com/s.aspx?sm=Ph5q56zmGkqVabn9QNfemw_3d_3d SurveyMonkey]
| + | |
− | | + | |
− | Thank you for taking part.
| + | |
− | | + | |
− | Robin Haw
| + | |
− | Manager of Reactome Outreach
| + | |
− | Outreach [at] reactome.org
| + | |
− | http://www.reactome.org
| + | |
− | | + | |
− | Posted by [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | ''2009/9/28''
| + | |
− | | + | |
− | == DIYA: Do It Yourself Annotator ==
| + | |
− | | + | |
− | {{ImageRight|DIYALogo.png|DIYA|100|DIYA}}
| + | |
− | [[DIYA]], the ''Do It Yourself Annotator'' is now officially a part of GMOD. DIYA is a modular and configurable open source pipeline framework, written in Perl, used (initially) for the rapid [[annotation]] of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in [[GFF]] format. Current development seeks to integrate DIYA with the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] collection of assembly tools.
| + | |
− | | + | |
− | DIYA [http://sourceforge.net/projects/diyg/ resides in Sourceforge], where it has [http://sourceforge.net/mail/?group_id=205628 mailing lists] and a [http://sourceforge.net/apps/wordpress/diyg/ blog], and uses [http://sourceforge.net/apps/trac/diyg/ Trac] for development tracking. DIYA is stable and version 1.0 has been released.
| + | |
− | | + | |
− | DIYA is part of the ''[http://sourceforge.net/projects/diyg/ Do It Yourself Genomics (DIYG) Project]''. Developers of DIYA (and DIYG) include Andrew Stewart and [[User:Bosborne|Brian Osborne]] (formerly of the [[GMOD Help Desk]]). The DIYA community is looking for interested developers to contribute to DIYA. See the [[DIYA]] page for more.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Chado in RDF: OpenFlyData ==
| + | |
− | | + | |
− | {{ImageRight|RDF_icon_96.gif|RDF||http://gmod.org/wiki/August_2009_GMOD_Meeting#Linked_Data_for_GMOD_Databases}}
| + | |
− | | + | |
− | The [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|OpenFlyData project has ported the FlyBase Chado database]] and several other ''Drosophila'' gene expression databases to the [http://www.w3.org/RDF/ Resource Description Framework (RDF)]. Each source database has a separate [http://en.wikipedia.org/wiki/Triplestore RDF store], and [http://openflydata.org/ OpenFlyData] provides both a browser and a programmatic [http://www.w3.org/TR/rdf-sparql-query/ SPARQL-based] interface to each. Source databases include the [[Chado]] database from [[:Category:FlyBase|FlyBase]], [http://www.fruitfly.org/ BDGP], [http://www.flyatlas.org/ FlyAtlas] and [http://www.fly-ted.org/ FlyTED].
| + | |
− | | + | |
− | Transforming databases into RDF can be an effective way to merge these data, and does not require mapping everything to a central [[Glossary#RDBMS|relational]] [[Glossary#Schema|schema]]. The common graph-based data model facilitates the reuse of RDF data published by other projects, with fewer constraints on the kind of questions you can ask.
| + | |
− | | + | |
− | For more on [http://openflydata.org/OpenFlyData OpenFlyData], see the [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|''Linked Data for GMOD Databases'']] presentation from the [[August 2009 GMOD Meeting]], and the [http://openflydata.org OpenFlyData web site].
| + | |
− | | + | |
− | [[User:JunZhao|Jun Zhou]] and [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Bioinformatics Position at SpBase ==
| + | |
− | | + | |
− | {{ImageRight|SpBaseLogo.png|Position at SpBase||http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az}}
| + | |
− | | + | |
− | The [http://www.spbase.org Sea Urchin Model Organism database (SpBase)] has an opening for a Bioinformatician. From the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az position announcement]:
| + | |
− | <div class="indent">The computation group supporting the Sea Urchin Model Organism database, SpBase, is seeking a highly motivated individual to take responsibility for collecting, organizing and displaying gene expression information at all life stages of the purple sea urchin ''Strongylocentrotus purpuratus''. The individual will work with existing computer code as well as develop new software. A particular challenge of the project is to move data from various sourves and of various types to a common framework for presentation and manipulation by the user.</div>
| + | |
− | | + | |
− | See the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az job posting] for more on the position. Please contact [mailto:acameron@caltech.edu Andy Cameron] if you have questions about the position.
| + | |
− | | + | |
− | SpBase uses several [[GMOD Components]], including [[GBrowse]], [[Apollo]], [[BioMart]], and [[Chado]].
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/22''
| + | |
− | | + | |
− | == 2009 GMOD Community Survey ==
| + | |
− | <div style="float:right">
| + | |
− | {|
| + | |
− | | {{#icon: GMODMug150x150.jpg|GMOD Mug|100|}}
| + | |
− | | {{#icon: TShirtThumb.jpg|GMOD T Shirt||}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | Please take a few minutes to fill out the [http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009 2009 GMOD Community Survey] and your name will be entered to win a free GMOD T-shirt or mug! This year's survey focuses on genome and comparative genomics visualization (and is much shorter than the [[2008 GMOD Community Survey|2008 survey]]). We are asking all GMOD users and developers to provide your feedback.
| + | |
− | | + | |
− | '''Three randomly selected survey participants will receive the [http://www.cafepress.com/GenericMOD/ GMOD T-shirt or mug] of their choice. Names will be drawn from the first 100 responses, so get your response in early.''' The survey closes at the end of the day on September 25.
| + | |
− | | + | |
− | Please contact the [mailto:help@gmod.org GMOD Help Desk] if you have any questions.
| + | |
− | | + | |
− | Thank you,
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br>
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/16''
| + | |
− | | + | |
− | == CVS to SVN Conversion: Done ==
| + | |
− | <div style="float: right">
| + | |
− | {|
| + | |
− | | {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
| + | |
− | | <span style="font-size: 200%; font-weight: bold">⇒</span>
| + | |
− | | {{#icon: Subversion_logo.jpg|Subversion||CVS to Subversion Conversion}}
| + | |
− | |}
| + | |
− | </div>
| + | |
− | GMOD's CVS source code repository was [[CVS to Subversion Conversion|converted to Subversion (SVN)]] on September 15, 2009. Directions on how to use [[SVN]] are explained at [[Version Control System Access]]. Details of the conversion itself are at [[CVS to Subversion Conversion]].
| + | |
− | | + | |
− | Inactive projects were moved out of the main directory and placed in the <tt>{{SF_SVN|Inactive|Inactive}}</tt> directory. The CVS repository is still there and accessible, but it is now ''read-only''. The GMOD web site has been updated to reflect the move to [[Subversion]].
| + | |
− | | + | |
− | We have identified a few outstanding issues and these are [[CVS to Subversion Conversion#Outstanding Issues|listed on the conversion page]]. If you come across any additional issues, please either update [[CVS to Subversion Conversion#Outstanding Issues|that list]] or [mailto:help@gmod.org email] the [[GMOD Help Desk]].
| + | |
− | | + | |
− | Finally, ''many'' thanks to [[User:RobertBuels|Rob Buels]] of Cornell / [[:Category:SGN|SGN]] for doing the work.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/09/15''
| + | |
− | | + | |
− | == FlyBase Bioinformatics Engineer position ==
| + | |
− | | + | |
− | {{ImageRight|Fly_logo.png|FlyBase Opening|200}}
| + | |
− | | + | |
− | Please see the [http://flybase.org/static_pages/news/positions.html official advert] for full details and application procedure.
| + | |
− | | + | |
− | The [http://iub.edu Indiana University] division of [http://flybase.org FlyBase] in [http://en.wikipedia.org/wiki/Bloomington,_Indiana Bloomington, Indiana] is currently looking for a qualified software engineer to help with deploying the [http://intermine.org InterMine] and [http://biomart.org BioMart] data management systems. The developer will be responsible for the web accessible aspect of these technologies. 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.
| + | |
− | | + | |
− | [[User:Jogoodma|Josh Goodman]]
| + | |
− | | + | |
− | ''2009/09/14''
| + | |
− | | + | |
− | == Server Maintenance: Sept 9 ==
| + | |
− | | + | |
− | <span style="float: left">{{#icon: WorkInProgressTools.gif|||}} </span>
| + | |
− | The [[Main Page|GMOD website]] and server will be down for maintenance on Wednesday, September 9, 2009 for up to 90 minutes, sometime between 1pm and 5pm Eastern US time. The server is being moved to a new a data center. We apologize for any inconvenience this may cause you.
| + | |
− | | + | |
− | Please let us know if you have any questions.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/08''
| + | |
− | | + | |
− | == BioMart Ruby API ==
| + | |
− | {{ImageRight|Biomart250.png|BioMart Ruby API|200|http://github.com/dazoakley/biomart/}}
| + | |
− | | + | |
− | Daz Oakley of the Wellcome Trust Sanger Institute has released a [http://github.com/dazoakley/biomart/ Ruby library/API] for [[BioMart]]. Daz says "It's quite basic for the moment and only does single dataset queries, but it will be quite easy to build upon the base from here."
| + | |
− | | + | |
− | The source is [http://github.com/dazoakley/biomart available from GitHub], and the documentation is at [http://rdoc.info/projects/dazoakley/biomart rdoc.info].
| + | |
− | | + | |
− | The Ruby API is the latest addition to a growing list of third party software that supports [[BioMart]]. This list includes [[Galaxy]], [http://www.bioclipse.net/ Bioclipse], [http://bioconductor.org/packages/release/bioc/html/biomaRt.html biomaRt-BioConductor], [http://www.cytoscape.org/ Cytoscape], [http://www.mygrid.org.uk/ Taverna], and
| + | |
− | [http://weblab.cbi.pku.edu.cn/ WebLab]
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/08''
| + | |
− | | + | |
− | == JBrowse paper ==
| + | |
− | A [http://genome.cshlp.org/content/19/9/1630.full paper] on the [[JBrowse]] genome browser is in [http://genome.cshlp.org/content/19/9 this month's issue] of [http://genome.cshlp.org/ Genome Research]. If you haven't looked at [[JBrowse]] before, ''it feels both very familiar and radically different at the same time.''
| + | |
− | | + | |
− | JBrowse is a Web 2.0 genome browser that features:
| + | |
− | * Client side rendering, and very fast rendering at that.
| + | |
− | * As a consequence it has very low server disk space, server CPU, security and network bandwidth requirements.
| + | |
− | * An interface that is entirely [[Glossary#AJAX|AJAX]] based. ''Everything'' is done with AJAX.
| + | |
− | * [[GFF3]], [[Chado]] and/or [https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html Wiggle track] compatibility
| + | |
− | * [[Glossary#JSON|JSON]] based configuration files (very similar to GBrowse config files in their content)
| + | |
− | * Easy embedding in other web applications (an example of embedding a genome browser in a wiki is provided)
| + | |
− | | + | |
− | JBrowse features smooth panning, zooming, navigation, and track selection and sets a new standard for the genome browser interface.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]
| + | |
− | <br />[[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/01''
| + | |
− | | + | |
− | <endFeed />
| + | |
− | | + | |
− | = [[GMOD News Archives|News Archives]] =
| + | |
− | | + | |
− | Items more than 6 months old are available in the [[GMOD News Archives]].
| + | |
− | | + | |
− | = Adding a News Item =
| + | |
− | | + | |
− | '''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
| + | |
− | | + | |
− | This page generates both an RSS feed and updates the GMOD News list on the [[Main Page|home page]]. Therefore, please follow these guidelines when adding a news item.
| + | |
− | # Edit the [[#News Items|News Items]] section of this page. This will allow you to see how big your news item title is, compared to existing news items. | + | |
− | # Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
| + | |
− | # Title
| + | |
− | #* '''Use a short title. Titles should be small enough to fit on a single line in the GMOD News list on the [[Main Page|home page]]'''.
| + | |
− | #* Place the title in a second level heading: <tt>== Your Title ==</tt>
| + | |
− | # News Text
| + | |
| #* Make the news item succinct. | | #* Make the news item succinct. |
− | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' | + | #* Do not start the item with a MediaWiki header ("== Header =="). |
− | #* End the news item with your name and the date in the format ''YYYY/MM/DD''. | + | #** It won't render very well. You should be able to avoid headers altogether. |
− | # Preview your changes | + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
− | #* Check the table of 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.