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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.
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<wikitwidget class="twitter-timeline" href="https://twitter.com/gmodproject" data-widget-id="268391087838728192" />
 
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If you have a news item you want added here, please send it to the [[GMOD Help Desk]] or add it to this page directly.  See [[#Adding a News Item|Adding a News Item]] for how to do this.
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<span class="plainlinks">
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This ''GMOD News'' is also available as an [http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss RSS feed]. {{#icon: RSSIcon16x16.gif|RSS feed||http://gmod.org/w/index.php?title=GMOD_News&action=feed&feed=rss}}
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</span>
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= News Items =
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Want to add your news item here?  See [[#Adding a News Item|Adding a News Item]] below for how to do just that.
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<startFeed />
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<!-- Add new Items here.  Keep the Title Short! -->
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== GBrowse NGS Tutorial & Poster==
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{{ImageRight|BA2009Logo.png|GBrowse NGS Tutorial|100|GBrowse NGS Tutorial}}
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A tutorial on using [[GBrowse NGS Tutorial|GBrowse to visualize next generation sequencing (NGS) data]] is now available.  The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 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.
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The tutorial includes examples showing read depth coverage, individual reads - including mismatches, using color to show alignment quality, and read-pairs.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/11/04''
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== Galaxy Project Hiring ==
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{{ImageRight|GalaxyLogoSmall.png‎|Galaxy Project Hiring||http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2}}
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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.
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See the [http://bitbucket.org/galaxy/galaxy-central/wiki/job_rc2 official posting] for full details and contact information.
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''2009/11/02''
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== Visualizing Biological Data Workshop ==
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{{ImageRight|EMBO_Logo.png|Visualizing Biological Data (VizBi)||http://www.vizbi.org}}
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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.
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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.
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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.
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''2009/10/21''
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== Openings at Syngenta ==
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{{ImageRight|SyngentaLogo.png|Openings at Syngenta||http://www.syngentacareers.com/listing/}}
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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.
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[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.
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[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.
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Both positions will work with Chado and [[GBrowse]], and will help evaluate the adoption of additional GMOD tools. See the links for more details.
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[[User:Eric.ganko|Eric Ganko]]
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''2009/10/21''
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== Opening at SGD ==
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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.
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{{ImageRight|SGD-t.gif|Bioinformatics Analyst at SGD||http://yeastgenome.org}}
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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.
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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.
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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.
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''2009/10/20''
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== Apollo 1.11.2 Released ==
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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:
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: http://apollo.berkeleybop.org/current/
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Cheers,
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[[User:Elee|Ed Lee]]
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''2009/10/07''
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== 2009 GMOD Survey Results ==
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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:
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* [[2009 GMOD Community Survey#Use Cases|Use Cases]] - what people would like visualization software to do.
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* [[2009 GMOD Community Survey#Features|Feature Ranking]] - what features are the most (and least) important to users.
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* 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]].
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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.
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{{ImageRight|GMODMug150x150.jpg|GMOD Mug|100|http://www.cafepress.com/GenericMOD/}}
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And, finally, we have our 3 winners of [http://www.cafepress.com/GenericMOD/ GMOD Gear]:
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* James Estill of the [http://www.genetics.uga.edu/ University of Georgia]
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* Philippe Lamesch of [http://www.arabidopsis.org/ TAIR]
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* Sandra L&ouml;venich of [http://www.imsb.ethz.ch/ ETH Z&uuml;rich]
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Thanks to everyone who took the time to participate in the survey.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/10/05''
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== GMOD Tutorials! GMOD Training! ==
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{{ImageRight|GMOD2009Europe170.png|Summer School - Europe|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
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{{ImageRight|2009SummerSchoolAmericas170.png|Summer School - Americas|120|http://gmod.org/wiki/Training_and_Outreach#Online_Tutorials}}
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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.
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The [[:Category:Tutorials|tutorials]] are:
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* '''[[Apollo Tutorial]]''' - by [[User:Elee|Ed Lee]]
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* '''[[Artemis-Chado Integration Tutorial]]''' - by [[User:RobinHouston|Robin Houston]], [[User:TimCarver|Tim Carver]] and [[User:Buggy|Giles Velarde]]
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* '''[[BioMart Tutorial]]''' - by [[User:Junjun|Junjun Zhang]] and Syed Haider
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* '''[[Chado Tutorial]]''' - by [[User:Scott|Scott Cain]], [[User:Jorvis|Joshua Orvis]], and [[User:Clements|Dave Clements]]
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* '''[[GBrowse Tutorial]]''' - by [[User:Scott|Scott Cain]] and [[User:Mckays|Sheldon McKay]]'''
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* '''[[GBrowse_syn Tutorial]]''' - by [[User:Mckays|Sheldon McKay]]
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* '''[[JBrowse Tutorial]]''' - by [[User:MitchSkinner|Mitch Skinner]] and Ian Holmes
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* '''[[MAKER Tutorial]]''' - by [[User:Carsonholt|Carson Holt]]
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* '''[[Tripal Tutorial]]''' - by [[User:Sficklin|Stephen Ficklin]]
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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:
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{| class="wikitable"
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! Date
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! Topic
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! Conference / Location
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|-
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! October 12-27
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| '''[http://meetings.cshl.edu/courses/c-info09.shtml Programming for Biology]'''<br />This includes a session on [[GBrowse]].
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| [http://www.cshl.edu Cold Spring Harbor Laboratory], Cold Spring Harobr, NY, USA
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|-
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! October 21-22
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| '''[http://www.ashg.org/2009meeting/pages/workshops.shtml#ucsc Interactive Workshops on the UCSC Genome Browser and Galaxy Framework]
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| [http://www.ashg.org/2009meeting/ The American Society of Human Genetics (AHSG)], Honolulu, Hawaii, USA
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|-
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! October 27-30
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| '''[[GBrowse]] and [[Next Generation Sequencing]] Data'''
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| [http://meetings.cshl.edu/meetings/info09.shtml Genome Informatics], Cold Spring Harbor, New York, USA
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|-
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! rowspan="2" | October 28-30
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| '''[[BA2009|Database Tools for Biologists: A Half-Day GMOD Workshop]]'''
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| rowspan="2" | [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia 2009 (BA2009)], Melbourne, Australia
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|-
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| '''Visualizing [[Next Generation Sequencing|Next Generation Sequence]] Data with [[GBrowse]] and [http://samtools.sourceforge.net SAMtools]''' (poster)
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|-
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| style="background-color: #cccccc" colspan="3" |
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|-
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! rowspan="2" | November 16-17
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| '''[http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine Data Warehouse Workshop]
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| Cambridge, UK
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|-
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| '''Comparative Genomics with GMOD'''
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| [http://colloque.inra.fr/isyip Information Systems for Insect Pests], Rennes, France
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|-
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| style="background-color: #cccccc" colspan="3" |
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|-
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! rowspan="3" | January 9-13
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| '''[[GBrowse PAG 2010 Workshop|The Generic Genome Browser: A Hands on Workshop for Installing, Configuring and Using Your Own GBrowse]]'''
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| 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.
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|-
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| '''[[GBrowse_syn PAG 2010 Workshop|Comparative Genomics with GBrowse_syn: A hands on workshop for visualizing your comparative genomics data with GBrowse_syn]]'''
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|-
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| '''[[MAKER PAG 2010 Workshop|MAKER: An easy to use genome annotation pipeline]]'''
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|-
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|}
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/10/02''
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== modENCODE & Gramene Openings ==
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The [http://www.modencode.org modENCODE] and [http://www.gramene.org Gramene] projects are both hiring.
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<span style="font-size:120%">'''modENCODE'''</span>
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{{ImageRight|ModENCODE logo.png|modENCODE Project Openings||http://blog.modencode.org/}}
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[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.
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Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data
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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.
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Please see the [http://blog.modencode.org/?p=350 complete job description] for details.
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[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.)
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<span style="font-size: 120%">'''Gramene'''</span>
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{{ImageRight|Gramene_logo180.jpg|Grameene Project Opening||http://news.gramene.org/}}
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[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.
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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.
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See [http://news.gramene.org/?p=392 the position announcement] for full details.
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''2009/10/02''
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== GMOD @ Bioinformatics Australia ==
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{{ImageRight|BA2009Logo.png|GMOD workshop at Bioinformatics Australia||BA2009}}
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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.
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Thanks to sponsorship from [http://www.bioplatforms.com/ Bioplatforms Australia] admission to the workshop is included in the conference registration fee.
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Please see the [[BA2009|workshop page]] or [mailto:help@gmod.org contact the GMOD Help Desk] for more information.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/10/01''
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== InterMine Data Warehouse Workshop ==
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{{ImageRight|InterMine.png|InterMine Workshop|180|http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html}}
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We are running another [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine workshop] in Cambridge, UK on November 16th-17th.
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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.
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The course is free to attend, more details and sign up information
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are available on the [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html workshop page].
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Please get in touch if you have any questions.
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Regards,
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[mailto:richard@flymine.org Richard Smith]
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''2009/09/29''
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== Tripal: A Web Front End for Chado ==
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{{ImageRight|TripalLogo.jpg|Tripal|200|Tripal}}
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[[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].
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Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.
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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.
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If you use or are considering using [[Chado]], please take a look at [[Tripal]].
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/09/28''
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== Reactome User Survey ==
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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.
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You can access the survey  at [http://www.surveymonkey.com/s.aspx?sm=Ph5q56zmGkqVabn9QNfemw_3d_3d SurveyMonkey]
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Thank you for taking part.
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+
Robin Haw
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Manager of Reactome Outreach
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Outreach [at] reactome.org
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http://www.reactome.org
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Posted by [[User:Scott|Scott Cain]]
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''2009/9/28''
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== DIYA: Do It Yourself Annotator ==
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{{ImageRight|DIYALogo.png|DIYA|100|DIYA}}
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[[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.
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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.
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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.
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/09/23''
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== Chado in RDF: OpenFlyData ==
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{{ImageRight|RDF_icon_96.gif‎|RDF||http://gmod.org/wiki/August_2009_GMOD_Meeting#Linked_Data_for_GMOD_Databases}}
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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].
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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.
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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].
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[[User:JunZhao|Jun Zhou]] and [[User:Clements|Dave Clements]]
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''2009/09/23''
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== Bioinformatics Position at SpBase ==
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{{ImageRight|SpBaseLogo.png|Position at SpBase||http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az}}
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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]:
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<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>
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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.
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SpBase uses several [[GMOD Components]], including [[GBrowse]], [[Apollo]], [[BioMart]], and [[Chado]].
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[[User:Clements|Dave C.]]<br />
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[[GMOD Help Desk]]
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+
''2009/09/22''
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== 2009 GMOD Community Survey ==
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<div style="float:right">
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{|
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| {{#icon: GMODMug150x150.jpg|GMOD Mug|100|}}
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| {{#icon: TShirtThumb.jpg|GMOD T Shirt||}}
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|}
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</div>
 
</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.
+
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]].
  
'''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.
+
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]]
  
Please contact the [mailto:help@gmod.org GMOD Help Desk] if you have any questions.
+
== Recent News ==
  
Thank you,
+
<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>
  
[[User:Clements|Dave Clements]]<br>
+
== [[GMOD News Archives|News Archives]] ==
[[GMOD Help Desk]]
+
  
''2009/09/16''
+
The [[GMOD News Archives]] lists all news items since autumn 2007.
  
== CVS to SVN Conversion: Done ==
+
== Adding a News Item ==
<div style="float: right">
+
{|
+
| {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
+
| <span style="font-size: 200%; font-weight: bold">&rArr;</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]].
+
'''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.
  
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]].
+
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]].
  
Finally, ''many'' thanks to [[User:RobertBuels|Rob Buels]] of Cornell / [[:Category:SGN|SGN]] for doing the work.
+
=== Short Instructions ===
  
[[User:Clements|Dave Clements]]
+
Please follow these guidelines when adding a news item.
  
''2009/09/15''
+
# 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>
  
== FlyBase Bioinformatics Engineer position ==
+
=== Longer Instructions ===
  
{{ImageRight|Fly_logo.png|FlyBase Opening|200}}
+
Please follow these guidelines when adding a news item.
  
Please see the [http://flybase.org/static_pages/news/positions.html official advert] for full details and application procedure.
+
# Create a new page named "'''News/'''''News Item Title''".
 
+
#* Please make ''News Item Title'' be as short as possible, '''and no more 35 characters at most'''.
The [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.
+
#*  The page must start with '''News/''', otherwise it won't be picked by the RSS news feed.
 
+
# Enter the text of your news item.
[[User:Jogoodma|Josh Goodman]]
+
 
+
''2009/09/14''
+
 
+
== Server Maintenance: Sept 9 ==
+
 
+
<span style="float: left">{{#icon: WorkInProgressTools.gif|||}}&nbsp;</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''
+
 
+
== August 2009 GMOD Meeting Report ==
+
 
+
{{ImageRight|Aug2009MeetingPhoto.JPG|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
+
The [[August 2009 GMOD Meeting]] was held 6-7 August, 2009 in Oxford, UK, immediately following the [[2009 GMOD Summer School - Europe]].  It was the first [[Meetings|GMOD meeting]] outside North America and it was an excellent way to finish [[GMOD Europe 2009]].  The meeting was attended by ~45 people representing almost 30 different organizations.  The meeting report and links to presentations are now available on the [[August 2009 GMOD Meeting]] page.  There were [[August 2009 GMOD Meeting#Presentations|17 presentations]] by GMOD users, developers, and project staff.
+
 
+
Some highlights:
+
* [[August 2009 GMOD Meeting#Quest for Standard: Sequence alignment/map format (SAM) and SAMtools|SAM and SAMtools]]: file formats and programs for compact representation of [[Next Generation Sequencing]] data, and a talk on [[August 2009 GMOD Meeting#Visualising NGS Data in GBrowse 2|using SAM/SAMtools in GBrowse]].
+
* An [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|RDF implementation]] of data from a Chado database.
+
* Reports from 2 power GBrowse users, [[August 2009 GMOD Meeting#GMOD in the Trenches|the CBRG at Oxford]], and [[August 2009 GMOD Meeting#GBrowse: Lessons Learned and Statement of Interest|Bayer CropScience]]
+
* New [[August 2009 GMOD Meeting#A DBIx::Class layer for Chado|Perl]] and [[August 2009 GMOD Meeting#GMOD Biological Object Layer|Java]] [[:Category:Middleware|middleware]] packages for [[Chado]].
+
Plus many other excellent presentations on topics ranging from [[August 2009 GMOD Meeting#DAS update|DAS]] to [[August 2009 GMOD Meeting#GBrowse.org|GBrowse.org]].
+
 
+
Please take a look at the [[August 2009 GMOD Meeting|meeting report]] for an update on what's going on in the GMOD community.
+
 
+
Finally, I'd like to thank the [http://www.molbiol.ox.ac.uk/ Computational Biology Research Group (CBRG) at the University of Oxford] for hosting and financially supporting [[GMOD Europe 2009]].  We could not have done this without you.
+
 
+
[[User:Clements|Dave Clements]]
+
<br />[[GMOD Help Desk]]
+
 
+
''2009/08/29''
+
 
+
== Bio::Chado::Schema 0.03 Released ==
+
The first official release of [[Bio::Chado::Schema]] is now on the [http://search.cpan.org/~rbuels/Bio-Chado-Schema/ CPAN].  This project establishes a standard set of base modules for building Chado middleware in Perl.  The project is looking for development help, and discussion is on the [https://lists.sourceforge.net/lists/listinfo/gmod-schema GMOD Schema mailing list].
+
 
+
--[[User:RobertBuels|RobertBuels]] 22:10, 29 August 2009 (UTC)
+
 
+
''2009/08/29''
+
 
+
== InterMine 0.91 Released ==
+
{{ImageRight|InterMine.png|InterMine|200|InterMine}}
+
We've released [[InterMine]] 0.91 and there is a new subversion branch and tar.gz for download. The main changes are fixes to some [http://www.intermine.org/wiki/GettingStartedAdvanced QueryBuilder] features, occasional export issues and improved password security.  There is a new [http://www.treefam.org/ TreeFam] parser and an improvement to ontology querying.
+
 
+
This update shouldn't require any changes to Mines and sources you have created.  See [http://www.intermine.org/wiki/UpgradeInterMine details on upgrading] and the [http://www.intermine.org/wiki/ReleaseNotes release notes].
+
 
+
Please [mailto:dev@intermine.org let us know] if you have any bug reports or feature requests.
+
 
+
The [[InterMine]] team
+
 
+
''2009/08/27''
+
 
+
== CVS to SVN Conversion: Sept 15 ==
+
<div style="float: right">
+
{|
+
| {{#icon: Cvs_logo.gif|CVS|70|CVS to Subversion Conversion}}
+
| <span style="font-size: 200%; font-weight: bold">&rArr;</span>
+
| {{#icon: Subversion_logo.jpg|Subversion||CVS to Subversion Conversion}}
+
|}
+
</div>
+
GMOD's CVS source code repository will be [[CVS to Subversion Conversion|converted to Subversion (SVN)]] on September 15, 2009.  [[User:RobertBuels|Rob Buels]] of Cornell / [[:Category:SGN|SGN]] has generously offered to to do this.  Notes on the conversion are described on the [[CVS to Subversion Conversion]] page.  The discussion leading up to this decision on the [http://comments.gmane.org/gmane.science.biology.gmod.devel/364 GMOD Developers mailing list].
+
 
+
'''If you are not a GMOD developer then this will, at most, change how you get pre-release copies of GMOD components.'''  In the future you will do SVN checkouts instead of CVS checkouts.  The doc on this web site will be updated to describe how to do this.
+
 
+
<div class="emphasisbox">
+
'''If you are a GMOD developer and your project is in GMOD's [http://gmod.cvs.sourceforge.net/gmod/ CVS repository] then this move will significantly affect you.'''
+
</div>
+
 
+
See [http://gmod.cvs.sourceforge.net/gmod/ SourceForge] for a complete list of projects in GMOD CVS.  This list is reproduced on the [[CVS to Subversion Conversion]] page.  Between now and September 15, we will contact project developers to confirm what projects are still active.  All projects will be moved to SVN, but any projects that are no longer active will be placed in a separate archive directory.  This will significantly clean up the repository.  See the [[CVS to Subversion Conversion]] page for the current status of each project.
+
 
+
Rob has created a [http://bugs.sgn.cornell.edu/trac/gmod_test_svn/browser/ preview version of the repository].  Feel free to poke around.  This version does not have any projects archived.
+
 
+
Rob will move the projects on September 15.  '''Before then everyone with uncommitted code changes should commit them to CVS.'''  After September 15, all CVS checkouts you have should be removed and new checkouts made with SVN.  We'll provide doc on how to do this.  We will send out exact details on the move a few days before it happens.
+
 
+
 
+
Please let Rob and Dave know if you have any questions.  We'll send out a reminder and additional info a few days before the conversion.
+
 
+
Thanks,
+
 
+
[[User:Clements|Dave Clements]] and [[User:RobertBuels|Rob Buels]]
+
 
+
''2009/08/26''
+
 
+
== GBrowse 1.70 Released ==
+
 
+
Hello,
+
 
+
I am pleased to announce the official release of [[GBrowse]] 1.70.  This is a bug fix release for GBrowse 1.69.  It introduces no new functionality to the GBrowse portion of the application, however, [[GBrowse_syn]] is considerably improved along with [[GBrowse_syn|documentation]] and a [[GBrowse_syn Tutorial|tutorial]].
+
 
+
There will likely be one more release in the GBrowse 1 development path, which will introduce improved support for circular genomes.  After that, development on this path will end and further development will focus on [[:Category:GBrowse 2|GBrowse 2]].
+
 
+
GBrowse can be installed with the [[GBrowse Install HOWTO|GBrowse netinstaller]].
+
 
+
GBrowse 1.70 can be [http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download downloaded directly from SourceForge].
+
 
+
A big thanks to [[User:Lstein|Lincoln Stein]], the lead developer of GBrowse, [[User:Mckays|Sheldon McKay]], the developer of GBrowse_syn, and all of the GBrowse users who debug and provide help on the [[GMOD Mailing Lists|GBrowse mailing list]].
+
 
+
Changes from 1.69 to 1.70:
+
* Bug fixes for the Chado adapter, including improving wildcard searching and fixing a bug that caused ALL features on a reference sequence to be returned when the segment was at the beginning of the reference sequence.
+
* Fixed [[Galaxy]] support bug which caused prevented features from multiple tracks being selected.
+
* Fixed problem with feature highlighting which caused highlighting to get "stuck"on beige.
+
* Removed annoying debugging statements from log files
+
* Fixed character encoding issues for onClick popup balloons
+
* Killed annoying "missing path" warning on windows systems
+
* Fixed issue in which the selected region shown in the overview is offset from true region.
+
* Silenced log file warnings when inkscape isn't present.
+
* Added "merge searches" option to turn merging of similarly-named features on and off.
+
* Moved Bio::DB::Das::Chado and Bio::DB::BioSQL to their own packages and out of the GBrowse distribution so they can be updated independently via CPAN
+
* Fixed encoding of version number at the bottom of the page.
+
* Made the [[DAS]] script compatible with DAS Registry
+
 
+
[[User:Scott|Scott]]
+
 
+
''2009/08/24''
+
== Lepidoptera Bioinformatics Workshop ==
+
 
+
{{ImageRight|Butterfly1.jpg|International Workshop on Molecular Biology and Genetics of Lepidoptera||http://bio.demokritos.gr/leps/leps.htm}}
+
A session on data analysis, mining, general bioinformatics support, and related topics will be held on Friday, August 28th 2009, at the [http://bio.demokritos.gr/leps/leps.htm International Workshop on Molecular Biology and Genetics of Lepidoptera] in Crete.  The aim is to find solutions to common problems of annotation, curation and comparative analysis of the growing body of transcript and genomic sequences for lepidopteran species.  Several databases, including [http://insectacentral.org InsectaCentral] and [http://www.inra.fr/lepidodb LepidoDB], both of which use [[GMOD Components]], will be discussed in the workshop.
+
 
+
The session is held during the last conference day and is one hour long; we encourage Crete participants to talk to us during the week and point out related problems you are facing in your own work. We will then produce a list to be discussed during the session and focus on soliciting ideas on how to organize collaborative and centralized efforts to everyone's benefit. We would especially like to identify potential funding sources, groups willing to help write consultation papers and grant proposals and individuals willing to contribute to realistic solutions.
+
 
+
We would like to encourage those of you who are not planning to attend the Crete workshop to contact us with your thoughts and ideas on these and related subjects.
+
 
+
[mailto:mki101@uri.edu Marian Goldsmith], [mailto:a.papanicolaou@ex.ac.uk Alexie Papanicolaou], and [mailto:flegeai@rennes.inra.fr Fabrice Legeai].
+
 
+
''2009/08/18''
+
 
+
== Ant Genomics Assembly & DB Sysadmin ==
+
{{ImageRight|sib_logo.gif|Fourmidable opening||http://www.isb-sib.ch/about-sib/jobs/details/91-sib-bioinformatician-at-sib--unil.html}}
+
''The deadline for this position has now passed.''
+
 
+
The [http://www.isb-sib.ch/ Swiss Institute of Bioinformatics] and the [http://www.unil.ch/dee/page6763.html Keller lab] in Lausanne have an opening for a full-time bioinformatician.
+
In brief, this position will focus on the assembly and annotation of genomic sequence from ants, as well as sharing the results with molecular myrmecologists via a GMOD database.
+
 
+
Closing date: 15 September 2009
+
 
+
See the [http://www.isb-sib.ch/about-sib/jobs/details/91-sib-bioinformatician-at-sib--unil.html official ad] for full details and application procedure
+
 
+
Informal enquiries to yannick.wurm \at\ unil.ch or laurent.falquet \at\ isb-sib.ch
+
 
+
''2009/08/15, updated 2009/09/27''
+
 
+
== FlyBase Sys Admin/Developer position ==
+
 
+
{{ImageRight|Fly_logo.png|FlyBase Opening|200|http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487}}
+
The [http://www.gen.cam.ac.uk/Research/flybase.htm Cambridge (UK) division] of [http://flybase.org FlyBase] currently seeks a [http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487 Systems Administrator/Software Developer], working either full or part-time to support its team of genetic literature curators.
+
 
+
The core tasks of this role include systems administration and the maintenance of Perl scripts and files required by the curators in their work. These tasks will occupy approximately 50% of a full-time position, and we are happy to consider applicants who only wish to work part-time (50%) to perform these essential tasks. However, we would like to enhance the current scripts/files and develop additional software to aid curators, and the remaining 50% of the full-time position would be spent on these areas.
+
 
+
Closing date: 24 August 2009.
+
 
+
See the [http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=5487 official advert] for full details and application procedure.
+
 
+
Informal enquiries to Steven Marygold ([mailto:sjm41@gen.cam.ac.uk sjm41@gen.cam.ac.uk]).
+
 
+
''2009/07/31''
+
 
+
== Insect Pest Workshop, 16-17 Nov ==
+
 
+
<div style="text-align: center">
+
{{#icon: InformationSystemsForInsectPests.gif|Information Systems for Insect Pests|400|http://colloque.inra.fr/isyip}}
+
<div style="font-size: 120%">[http://colloque.inra.fr/isyip 1st International Workshop]</div>
+
<div style="font-size: 110%">16-17th November 2009<br />INRIA Rennes-Bretagne-Atlantique</div>
+
</div>
+
 
+
Given the development of cheaper high throughput sequencing technologies, it is easy to predict that in the very near future, new genomes of insects relevant to agriculture will be available. This opens several other challenges such as the bioinformatics treatment of the raw data (handling of billions of sequences, assembly of short reads…) and the development of databases opened to biologists for an easy, friendly and efficient extraction of information. With access to several insect species genomes, one will not only work on their favourite insect, but will take advantage of the increasing knowledge from genomic comparison analyses. This compels the community to develop standards for different tasks towards the exploitation of genome sequences: annotation, cross-species comparisons, interoperability between databases, ... Several tools and databases already exist and are used for genome browsing and annotation.
+
 
+
In that context, the purpose of this workshop will be:
+
* To exchange within an international panel of attendants our views on the present and future of insect genome databases
+
* To settle an international community that will form a functional network for insect genome and database development
+
* To discuss strategies to meet the demand of increasing number of new insect genomes
+
* To prepare a new road map for integration of genomes databases for insects relevant to agriculture
+
 
+
The perimeter of that discussion encompasses insect species related to agriculture, either harmful (pests) or beneficial as controllers of pest populations or as producers of plant by-products (such as silk, honey, ...).
+
 
+
Registration for the meeting is free and has to be done online on [https://colloque.inra.fr/isyip/Registration/Symposium/Symposium-registration this website] and will be limited to 40 participants. A statement of interest is needed. A 10 minute presentation may be asked.
+
 
+
''2009/07/20''
+
 
+
== August 2009 GMOD Meeting ==
+
 
+
{{ImageRight|GMOD2009Europe170.png|August 2009 GMOD Meeting||August 2009 GMOD Meeting}}
+
 
+
 
+
<div style="font-size: 140%; text-align: center">[[August 2009 GMOD Meeting|Register for the August 2009 GMOD Meeting]]</div>
+
 
+
 
+
The [[August 2009 GMOD Meeting|next GMOD meeting]] will be held 6-7 August, at the University of Oxford, in Oxford, United Kingdom.  [[August 2009 GMOD Meeting#Cost and Registration|Registration is now open]].  Space is available on a first come, first served basis and there is room for 55 attendees. The meeting cost is &pound;50.
+
 
+
As with [[Meetings|previous GMOD meetings]], the meeting will have a mixture of project talks, [[GMOD Components|component]] talks, and user talks.  The agenda is driven by attendee suggestions, and you are encouraged to [[August 2009 GMOD Meeting#Agenda Suggestions|add your suggestions]] now.  For examples of what happens at a GMOD meeting, see the writeups of the [[January 2009 GMOD Meeting|January 2009]], [[July 2008 GMOD Meeting|July 2008]], or any [[Meetings|other previous meeting]].  GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project.
+
 
+
Details on transportation, suggested lodging, and other logistics are on the [[August 2009 GMOD Meeting]] page.
+
 
+
Please join us in Oxford this August,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/07/01''
+
 
+
'''Note:''' Unless you have applied to and been admitted to the [[2009 GMOD Summer School - Europe]], don't you dare register for it.  The registration web site will let you do this, but bureaucratic hellishness will ensue.
+
 
+
== Join the Int'l Society for Biocuration ==
+
 
+
{{ImageRight|ISB_logo.gif‎|International Society for Biocuration||http://colleagues.biocurator.org/join}}
+
 
+
The [http://biocurator.org/ International Society for Biocuration (ISB)] is now accepting [http://colleagues.biocurator.org/join member registrations].  I strongly encourage GMOD community members to think about joining ISB.  GMOD and ISB have [http://www.biocurator.org/mission.shtml many shared and complementary interests].
+
 
+
Membership rates start at less than US$20 for students to a little over US$100 for principal investigators from industry.
+
 
+
Please consider this investment,
+
 
+
[[User:Clements|Dave Clements]]<br />
+
[[GMOD Help Desk]]
+
 
+
''2009/06/25''
+
 
+
== Apollo 1.11.0 Released ==
+
 
+
A new version of [[Apollo]] has been released.  Highlights for this release include:
+
 
+
* The "Sequence Aligner" ("Exon Detail Editor" with alignment viewing) is now public
+
* Brought back the "Types panel" which works in conjunction with the the "Preferences editor"
+
* Various bug fixes
+
 
+
As always, you can download the current version at:
+
:http://apollo.berkeleybop.org/current/install.html
+
 
+
Ed Lee
+
 
+
''2009/06/05''
+
 
+
== NextGen Sequence in GBrowse ==
+
 
+
{{ImageRight|Aga_logo.png|Next Generation Genome Analysis in Non-Model Organisms--An American Genetic Association Special Event||http://www.regonline.com/Nextgeneration}}
+
 
+
There will be a [http://www.regonline.com/Nextgeneration talk] on visualizing next generation sequence data in [[GBrowse]] at [http://www.regonline.com/Nextgeneration Next Generation Genome Analysis in Non-Model Organisms], an [http://www.theaga.org American Genetic Association] Special Event held June 11-13, 2009 at the University of Connecticut.  The talk will demonstrate how GBrowse can visualize both individual reads and summary and derived data.  This talk will become a wiki page after the meeting.
+
 
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June will be a busy month for GMOD outreach.  If you can't make it to this meeting, there will also be [[#GMOD Workshops at SMBE, AGS|GMOD workshops]] at [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE] and the [http://www.k-state.edu/agc/symp2009/seminar.html Arthropod Genomics Symposium].
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[[User:Clements|Dave Clements]]<br />
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[[GMOD Help Desk]]
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''2009/05/19''
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<endFeed />
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= [[GMOD News Archives|News Archives]] =
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Items more than 6 months old are available in the [[GMOD News Archives]].
+
 
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= Adding a News Item =
+
 
+
'''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
+
 
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This page generates both an RSS feed and updates the GMOD News list on the [[Main Page|home page]].  Therefore, please follow these guidelines when adding a news item.
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# Edit the [[#News Items|News Items]] section of this page.  This will allow you to see how big your news item title is, compared to existing news items.
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# Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
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# Title
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#* '''Use a short title.  Titles should be small enough to fit on a single line in the GMOD News list on the [[Main Page|home page]]'''.
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#* Place the title in a second level heading: <tt>== Your Title ==</tt>
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# News Text
+
 
#* 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''.
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#** It won't render very well.  You should be able to avoid headers altogether.
# Preview your changes
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#* '''The first link in the news item should point to the page/URL you want the RSS feed to link to.
#* Check the table of contentsIs the title no longer than any previous title? Is the title at the same depth as the other news item titles?
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#** For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.'''
#* Check the news item.  Does the text look good, does it look like the other news items, and does the first link point to where you want it to?
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#* You can include images in your news item.  See [[:Category:News Items|preexisting news items]] for what markup to use to do this.
#* '''Make sure that your MediaWiki markup (links, italics, etc.) is correct.''' The MediaWiki extension that lists news items on the [[Main Page|home page]] is temperamentalIncorrect markup can lead to garbage on the home page.
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# 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.
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# Once you are happy with how the item looks, insert this line at the end of it:
 
+
#: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre>
Once you have saved the page, a link to the new item will show up on the home page in about an hour. (Why the delay?  It uses an RSS feed of this page and it queries the feed infrequently.)
+
#: Where ''yyyy/mm/dd'' is the current dateThis line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour.
 +
# '''Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.'''
 +
#* Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line:
 +
#: <pre><nowiki>{{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}</nowiki></pre>
  
[[Category:GMOD Community]]
+
[[Category:GMOD_Community]]

Latest revision as of 19:40, 13 December 2018

News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the GMOD News Archives. See also the GMOD Calendar and Events List.

GMOD News is also available as an RSS feed. RSS feed

Recent News

Prospecting for Proposals for GSoC 2024

The Open Genome Informatics group and GMOD has submitted an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of different sizes participate in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, don't hesitate to get in touch with us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email rhaw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2024/02/12

JBrowse2 v1.1.0 Released

We're pleased to announce a new release of JBrowse Web!

(Reposted by permission from https://jbrowse.org/jb2/blog/2021/03/29/v1.1.0-release

Changed callbacks language from JavaScript to Jexl

To allow users to safely and seamlessly share advanced configurations in sessions, we now use Jexl to express configuration callbacks. Note that this is a breaking change, function()-style callbacks will no longer work.

For details, see the callbacks section of our configuration guide.

Fetch intron and upstream/downstream sequences

We also have several other improvements including the ability to get intron and upstream/downstream sequence in the feature details

<img alt="Upstream downstream.png" src="http://gmod.org/mediawiki/images/thumb/7/76/Upstream_downstream.png/700px-Upstream_downstream.png" width="700" height="248" srcset="/mediawiki/images/thumb/7/76/Upstream_downstream.png/1050px-Upstream_downstream.png 1.5x, /mediawiki/images/thumb/7/76/Upstream_downstream.png/1400px-Upstream_downstream.png 2x" />

Interactive documentation using Storybook

Another new update is the first release of our interactive Storybook docs for the embeddable React Linear Genome View. The docs contain live examples of how the LGV component can be used, along with source-code examples. The site can be found here.

Enhanced navigation to drawer widget stack

We have added a dropdown to enhance navigation between stack of active widgets. The update also adds a minimize button to allow quick access to full screen JBrowse web.

See below for demos of the new navigation UI.

<img alt="Minimize button demo.gif" src="http://gmod.org/mediawiki/images/0/0f/Minimize_button_demo.gif" width="480" height="414" />

Demo of using the minimize button in the drawer

Downloads

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

1.1.0 (2021-03-29)

🚀 Enhancement

core

  1. 1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
  2. 1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
  3. 1816 Remove some animation effects (@cmdcolin)
  4. 1778 Adds dropdown to show drawer widget stack (@teresam856)
  5. 1685 Change callbacks language from JavaScript to Jexl (@peterkxie)

Other

  1. 1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
  2. 1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
  3. 1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
  4. 1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

🐛 Bug Fix

core

  1. 1811 Check for existence of window more robustly to allow in SSR or node applications (@elliothershberg)
  2. 1793 Fix dotplot rendering outside it's allowed bounds (@cmdcolin)
  3. 1783 Add hic aborting and fix remoteAbort signal propagation (@cmdcolin)
  4. 1723 A few bugfixes (@garrettjstevens)

Other

  1. 1815 Clear tracks when using "Return to import form" (@cmdcolin)
  2. 1819 Standardized sentence casing on drawer widget titles (@cmdcolin)
  3. 1796 Bump generic-filehandle for fixing CORS errors from Chrome cache pollution (@cmdcolin)

📝 Documentation

  1. 1824 Add storybook docs page for nextjs usage (@elliothershberg)
  2. 1770 1469 storybook deploy (@elliothershberg)
  3. 1807 Update developer guide to cover displays, and highlight working external plugins (@cmdcolin)
  4. 1779 Collaborative release announcement editing (@rbuels)
  5. 1791 Add a couple more demos for our live version with MDX (@cmdcolin)

🏠 Internal

Other

  1. 1820 Create v1.1.0.md, draft of release announcements (@garrettjstevens)
  2. 1823 Add note about previewing changelog to CONTRIBUTING.md (@garrettjstevens)

core

  1. 1834 Change jbrowse-components monorepo default branch from 'master' to 'main' (@rbuels)

Committers: 6

  • Colin Diesh (@cmdcolin)
  • Elliot Hershberg (@elliothershberg)
  • Garrett Stevens (@garrettjstevens)
  • Peter Xie (@peterkxie)
  • Robert Buels (@rbuels)
  • Teresa Martinez (@teresam856)


Posted to the GMOD News on 2021/03/30

Prospecting for Proposals for GSoC 2021

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2021/02/16

Codefest 2020


Handlery Hotel in the Balboa room
(down the street from the Town and Country Hotel)
San Diego, California
January 9-10, 2020 </strong>

Immediately before Plant and Animal Genome XXVIII (PAG 2020)

</center>

Participant list now available


There will be a GMOD codefest occurring before the Plant and Animal Genomes meeting in San Diego. The codefest will be at the Town and Country hotel on January 9 and 10. If you would like to suggest a problem or project to address, add it to this Google Doc. The codefest is open to anyone who'd like to work on any GMOD project (or, better yet, any combination of GMOD projects), including but not limited to

We already know that there will be Tripal, Chado, Apollo and JBrowse developers present.

Agenda

Thursday:

9:00-10:00 Introduction and working group organization
10:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-4:00 Working groups
4:00-5:00 Report on progress

Friday:

9:00-12:00 Working groups
12:00-1:30 Lunch (on your own)
1:30-3:00 Working groups
3:00-3:45 Report on progress
  • Note: the Tripal steering committee will meet on Friday from 12:00 - 3:00 pm at the Postcard Bistro in the Handlery.


Posted to the GMOD News on 2020/01/08

Tripal 3.5 Released

This Tripal release includes major performance improvements including an improved and blazing fast GFF3 loader. Follow standard Drupal updating procedures to update. Changes in this version:

  1. Performance improvements to the Cross References, Relationships, and References.
  2. A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
  3. A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
  4. Updates to the online documentation
  5. Bug fixes in web services
  6. Bug fixes in the OBO loader for ontologies that won't import.


Posted to the GMOD News on 2021/02/08

JBrowse 2 release

We are pleased to announce the first public release of JBrowse 2!

JBrowse 2 is the successor to JBrowse, but is a completely new application written with modern web standards and frameworks.

Some of the features new to JBrowse 2 include:

  • New types of views, including circular, synteny, and dotplot views
  • Graphical configuration editing
  • Connections to resources such as UCSC Track Hubs

You can see some demos of JBrowse 2 in action here. To get started using JBrowse 2, visit our quickstart guide here.

We'd love to hear what you think! You can find information about how to contact us here.

The JBrowse Team

Posted to the GMOD News on 2020/11/09

Prospecting for Proposals for GSoC 2020

The Genome Informatics group and GMOD will be submitting an application for Google Summer of Code (GSoC) this year, and we are soliciting project ideas from people and groups involved in the GMOD project.

GSoC is a global program run by Google to encourage students to get real-world experience of participating in a software project; students work on a project over the summer months and receive a stipend from Google for participating. Thousands of organizations of many different sizes take part in GSoC, with the common factor being that they must produce open-source code.

Please take a look at the GSoC wiki page and think about any projects that might work well for a GSoC student, and add them to the wiki. If you are interested in being a mentor, please contact us at robin.haw@oicr.on.ca help@gmod.org.

If you have any questions--e.g. what constitutes an appropriate project; whether your idea is sufficiently GMOD-related--please feel free to email robin.haw@oicr.on.ca and help@gmod.org for advice!


Posted to the GMOD News on 2020/02/03

Call for PAG Abstracts

Call for PAG Abstracts

Time is short!

If you want to attend PAG and would like to present on a topic that would be of interest to the GMOD community, please send an abstract or at least a descriptive title to help@gmod.org. Types of talks typically include updates on GMOD software projects, usage stories for successful sites, proposals for new GMOD projects and descriptions of plugins for existing GMOD software projects like Tripal, JBrowse and Galaxy.

Please consider giving a talk and sharing your experience and ideas!


Posted to the GMOD News on 2016/11/04

New GMOD Server

GMOD.org has a new home

Due to a old server being retired, gmod.org has a new home. In the course of migrating the server, we also had to update the version of MediaWiki that is powering the site. If you notice any problems with gmod.org, please send an email to help at gmod dot org to let us know what's going on.


Posted to the GMOD News on 2016/09/29

GMOD-JBrowse 2016 Survey

Hello Genome Informaticians,

The following survey is aimed at users (and potential users) of GMOD genome databases, especially the JBrowse genome browser. It will directly inform the priorities for renewal of the R01 that funds JBrowse software development and the GMOD helpdesk.

We know surveys are thankless and dull. Your time in filling out this one is GREATLY appreciated.

https://goo.gl/forms/1bKIuAMjGKrS0hUi1

Thanks & best wishes,

The JBrowse team


Posted to the GMOD News on 2016/09/23

GCC2016

The 2016 Galaxy Community Conference (GCC2016) will be held June 25-29, at Indiana University in Bloomington, Indiana, United states, immediately before the June 2016 GMOD Meeting, also in Bloomington. Galaxy is a GMOD Component which interacts with many other GMOD Components, including:

  • Tripal: A web front end for Chado databases. Galaxy is working with the Tripal project to make Galaxy be Tripal's analysis engine.
  • JBrowse: A client-side genome browser and successor to the venerable GBrowse. JBrowse as a Galaxy Tool was presented by Eric Rasche at GCC2015. Ian Holmes, the JBrowse PI, has put JBrowse-Galaxy integration at "top of the list" for JBrowse's infrastructure upcoming infrastructure work.
  • MAKER: A genome annotation pipeline that integrates several gene annotation engines, and combines them to produce annotation that is better than any individual tool produces. A MAKER-Galaxy by Agriculture and Agri-Food Canada was presented at ISMB 2014.
  • InterMine and BioMart: These are both popular data sources that are integrated with Galaxy.

Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, lightning talks and breakouts, all about high-throughput biology and the tools that support it.  The conference also includes two days of training offering in-depth topic coverage across several concurrent sessions, and two days of hackathons.

Oral presentation abstract submission closes April 8; poster and demo abstract submission close May 20; and scholarship applications close May 1.


Posted to the GMOD News on 2016/04/04

2016 GMOD Meeting

The next GMOD Community Meeting will be held at Indiana University in Bloomington, Indiana, United States, June 30-July 1, directly after the 2016 Galaxy Community Conference (GCC2016). GMOD Meetings are a mix of user and developer presentations, and are a great place to find out what is happening in the project, what's coming up, and what others are doing.


Please register online at Eventbrite by June 20th 2016. Early bird registration ends May 21.

For those who would like to present a talk or poster, the meeting registration form includes a section for submitting the presentation title and abstract.

If you have any suggestions or requests for the meeting, please contact the GMOD help desk.


Posted to the GMOD News on 2016/04/04

Please Support EcoCyc

EcoCyc, the E. coli information resource and one of the resources offered by the Pathway Tools group, is in need of letters of support from the community after receiving a poor grant review, which could result in a complete loss of funding on July 1st, 2014. If you are a user of EcoCyc, please consider writing a short letter in support of this vital resource. The deadline for letters is May 26th, 2014.

From the Pathway Tools website

ECOCYC FUNDING CRISIS -- DEADLINE MAY 26

EcoCyc received a very unfavorable grant review in February 2014. We are in discussions with the NIH to resolve this situation.

EcoCyc's usage has steadily increased. We made very strong progress on our challenging aims from the current grant period, and the project has produced many publications. EcoCyc received excellent reviews on previous grant applications. Furthermore, the needs of the prokaryotic research community for the content and software tools offered by EcoCyc have never been higher.

In the worst case, we will lose all funding on July 1, 2014 and be forced to re-apply. Even in the best case, we may receive a crippling funding cut that causes us to fall behind in its manual literature curation effort, and requires us to lay off experienced curation staff until funding can be obtained.

These events could seriously undermine EcoCyc, end the project altogether, or force us to begin charging usage fees.

To maintain EcoCyc as the free, up to date, and high-quality resource that you depend on, please tell the NIH what EcoCyc means to your research. Please click the button below to submit a PDF letter of support on institutional letterhead, or a short support statement, explaining the importance of EcoCyc.

We ask all regular users to submit; a short statement will take less than two minutes of your time. Students and post-docs, please ask your lab head to submit in addition to your submission.

More information on what to write and where to submit letters is available at the Pathway Tools website.


Posted to the GMOD News on 2014/05/21

June 2014 WebApollo Hackathon

Berkeley Bioinformatics Open-Source Projects (BBOP) invites you to join us this summer for a WebApollo Hackathon at Lawrence Berkeley National Laboratory, California.

When: Monday, June 2 - 6, 2014

Where: Lawrence Berkeley National Laboratory. Building 74 (B74), Room 104. 1 Cyclotron Rd, Berkeley, CA 94720

What: five days of intensive, collaborative WebApollo development!

For five days developers will work on new features of interest to their research communities, improve existing features, and collaborate on developing features of interest to other colleagues.

Participants should:

  • be able to set up their own WebApollo server before arriving in Berkeley, including Postgres, Tomcat, etc.
  • code comfortably in JavaScript (client) and Java (server).

What will we do while we are there? You tell us! Send your suggestions for feature development, your questions, and any additional comments to apollo [dash] dev [at] lists [dot] lbl [dot] gov

Registration is free of charge, but tickets are required. Register online!

Participants are responsible for arranging travel and accommodation on their own.

More details: WebApollo Hackathon information

via Monica Munoz-Torres


Posted to the GMOD News on 2014-04-22

Applications Open for GMOD Online Training

GMOD will be holding its first online training course for those interested in the set up and use of GMOD components.

The course will be held from Monday 19th May to Friday 23rd May 2014, and will cover core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database.

If you are interested in attending, please see GMOD Online Training 2014 for more information and to submit your application.


Posted to the GMOD News on 2014-03-31

Canto Workshop at Biocuration 2014

GMOD will be running a workshop at Biocuration 2014 to demonstrate the use of Canto, on Wednesday 9th April in the afternoon. Canto is a literature curation tool that allows users to create functional annotations for genes and gene products using OBO (ontology) terms. Canto will soon be added to GMOD in the Cloud, and this workshop will show participants how to get a GMOD in the Cloud instance up and running--it takes less than ten minutes!--and how to use Canto for literature curation.

We will have more information closer to the time.


Posted to the GMOD News on 2014/03/25

Tripal 2.0a released

The Tripal Development Team is pleased to announce an alpha release of Tripal 2.0 for Drupal 7. This release is expected to have bugs and there is some functionality still under development. However, this release is made to help early adopters of Tripal for Drupal 7. Reports of bugs or other issues are highly welcomed. Below are available resources for Tripal 2.0a

   Download Instructions
   New Functionality
   Installation and Tutorial
   Tripal 2.0 API site
   Tripal Mailing List
   Tripal Developer's Mailing List

The Installation tutorial is still under development but should have enough information for complete installation of Tripal v2.0a as well as loading of organisms and features.


Posted to the GMOD News on 2014/02/27

Precompiled Ontologies in Chado

Eric Rasche and the Center for Phage Technology at Texas A&M University are making Chado database dumps of precompiled ontologies publicly available to save other Chado users the time and hassle of downloading and compiling the ontologies themselves.

Go to the download site.

The ontologies currently available are:

  • Chado Feature Properties
  • Gene Ontology
  • Plant Ontology
  • Relationship Ontology
  • Sequence Ontology

These are updated weekly; the workflow is as follows:

  • clone Chado from SVN
  • build
  • load ontologies
  • dump database as SQL
  • upload to a publicly accessible webserver

Please contact Eric if you are interested in having other ontologies added to the dumps, other builds with different (sub)sets of ontologies, or archived copies of schemas over time.

Note that none of the Chado-related scripts are installed, and the GMOD conf files are not created in GMOD_ROOT. For remote access (e.g., via Artemis), and tools that do not make use of GMOD_ROOT locally, this is not a problem.


Posted to the GMOD News on 2014/02/20

GCC2014 Registration is Open

We are pleased to announce that Early Registration and Talk and Poster Abstract Submission are now open for the 2014 Galaxy Community Conference (GCC2014).

GCC2014 will be held at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States, from June 30 through July 2, 2014. GCC2014 starts with a Training Day featuring five parallel tracks, each with three, two and half hour long workshops. There are 13 different topics spanning the full Galactic spectrum of topics. Take a look!

Early registration is now open. Register early and avoid paying 70% more for regular registration costs.  Early registration is very affordable, with combined registration (Training Day + main meeting) starting at $140 for post-docs and students. Registration is capped this year at 250 participants, and we expect to hit that limit. Registering early assures you a place at the conference and also a spot in the Training Day workshops you want to attend.

You can also book affordable conference housing at the same time you register. See the conference Logistics page for details on this and other housing options.

Abstract submission for both oral presentations and posters is also open.  Abstract submission for oral presentations closes April 4, while poster submission closes April 25. Poster authors will be notified of acceptance status within two weeks of submission, while presentation authors will be notified no later than May2.  Please consider presenting your work. If you are dealing with big biological data, then this meeting wants to hear about your work.

The GigaScience "Galaxy: Data Intensive and Reproducible Research" series announced for the last conference has published its first papers, and is continuing to take submissions for this year's meeting and beyond. BGI is also continuing to cover the article processing charges until the end of the year, and for more information see their latest update.

Thanks, and hope to see you in Baltimore!

The http:GCC2014 Organizing Committee


Posted to the GMOD News on 2014/02/14

GMOD Paper Cuts, Feb 10th, 2014

__NOFACTBOX__

GMOD Paper Cuts is a periodic selection of choice cuts from the scientific literature featuring interesting, exciting, or otherwise eye-catching GMOD-related work.

If you would like a paper to appear in GMOD Paper Cuts, please email the details to the GMOD helpdesk. Ideally the paper should be in an open-access publication so that anyone can read it.

For more GMOD and GMOD-related papers, and to contribute your own GMOD-related publications, join our Mendeley group.


Finding the missing honey bee genes: lessons learned from a genome upgrade [1]

The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes.

Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data.

Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.

Interesting findings from the new assembly of the honey bee genome, including many more genes than were found in the initial assembly. The Hymenoptera Genome Database uses numerous GMOD resources, including MAKER for automated genome annotation, JBrowse and GBrowse for sequence browsing, and WebApollo for community genome annotation.


Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila [2]

We and others recently demonstrated that the readily programmable CRISPR/Cas9 system can be used to edit the Drosophila genome. However, most applications to date have relied on aberrant DNA repair to stochastically generate frame-shifting indels and adoption has been limited by a lack of tools for efficient identification of targeted events. Here we report optimized tools and techniques for expanded application of the CRISPR/Cas9 system in Drosophila through homology-directed repair (HDR) with double-stranded DNA (dsDNA) donor templates that facilitate complex genome engineering through the precise incorporation of large DNA sequences including screenable markers. Using these donors, we demonstrate the replacement of a gene with exogenous sequences and the generation of a conditional allele. To optimize efficiency and specificity, we generated transgenic flies that express Cas9 in the germline, and directly compared HDR and off-target cleavage rates of different approaches for delivering CRISPR components. We also investigated HDR efficiency in a mutant background previously demonstrated to bias DNA repair towards HDR. Finally, we developed a web-based tool that identifies CRISPR target sites and evaluates their potential for off-target cleavage using empirically rooted rules. Overall, we have found that injection of a dsDNA donor and guide RNA-encoding plasmids into vasa-Cas9 flies yields the highest efficiency HDR, and that target sites can be selected to avoid off-target mutations. Efficient and specific CRISPR/Cas9-mediated HDR opens the door to a broad array of complex genome modifications and greatly expands the utility of CRISPR technology for Drosophila research.

CRISPR is one of the most exciting recent technological advancements of the past couple of years. This paper reports new techniques and tools for using the CRISPR/Cas9 system for complex genome engineering. For more information, see the flyCRISPR website.


Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress [3]

Brachypodium distachyon is a close relative of many important cereal crops. Abiotic stress tolerance has a significant impact on productivity of agriculturally important food and feedstock crops. Analysis of the transcriptome of Brachypodium after chilling, high-salinity, drought, and heat stresses revealed diverse differential expression of many transcripts. Weighted Gene Co-Expression Network Analysis revealed 22 distinct gene modules with specific profiles of expression under each stress. Promoter analysis implicated short DNA sequences directly upstream of module members in the regulation of 21 of 22 modules. Functional analysis of module members revealed enrichment in functional terms for 10 of 22 network modules. Analysis of condition-specific correlations between differentially expressed gene pairs revealed extensive plasticity in the expression relationships of gene pairs. Photosynthesis, cell cycle, and cell wall expression modules were down-regulated by all abiotic stresses. Modules which were up-regulated by each abiotic stress fell into diverse and unique gene ontology GO categories. This study provides genomics resources and improves our understanding of abiotic stress responses of Brachypodium.

Check out the JBrowse-powered Brachypodium web genome browser and other resources on the new Brachypodium website!


Analyses of Hypomethylated Oil Palm Gene Space[4]

Demand for palm oil has been increasing by an average of ~8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

The newly-sequenced oil palm genome used the MAKER automated annotation pipeline. The oil palm is one of a number of genomics projects taking off in Malaysia at the moment. Perfect timing for a GMOD workshop!


Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian [5]

The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies.

[...]

The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”

Information and resources for the newly-sequenced cnidarian E. lineata; all genomic data is publicly available at EdwardsiellaBase, and can be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse.


Happy reading!


  1. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-86
  2. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1534.2Fgenetics.113.160713
  3. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0087499
  4. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1371.2Fjournal.pone.0086728
  5. Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-15-71
Disclaimer: the papers included in this feature are for your entertainment and edification only. Inclusion does not imply an endorsement of the material or any association between the authors and the GMOD project.


Posted to the GMOD News on 2014/02/10

News Archives

The GMOD News Archives lists all news items since autumn 2007.

Adding a News Item

Note: If you don't want to do this yourself, please send the item to the GMOD Help Desk and we will post it for you.

GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the GMOD News and GMOD News Archives pages, and in the news tracker on the home page.

Short Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • Please make News Item Title be as short as possible, and no more 35 characters at most.
  2. Enter the text of your news item.
    • The first link in the news item should point to the page/URL you want the RSS feed to link to.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
{{NewsItem|yyyy/mm/dd}}

Longer Instructions

Please follow these guidelines when adding a news item.

  1. Create a new page named "News/News Item Title".
    • Please make News Item Title be as short as possible, and no more 35 characters at most.
    • The page must start with News/, otherwise it won't be picked by the RSS news feed.
  2. Enter the text of your news item.
    • Make the news item succinct.
    • Do not start the item with a MediaWiki header ("== Header ==").
      • It won't render very well. You should be able to avoid headers altogether.
    • The first link in the news item should point to the page/URL you want the RSS feed to link to.
      • For example, the first link in a news item about Chado could point to the Chado page.
    • You can include images in your news item. See preexisting news items for what markup to use to do this.
  3. Preview / save your changes. Edit and save the page until the news item looks like you want.
  4. Once you are happy with how the item looks, insert this line at the end of it:
    {{NewsItem|yyyy/mm/dd}}
    Where yyyy/mm/dd is the current date. This line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour.
  5. Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.
    • Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line:
    {{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}