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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.
| + | <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"> | + | |
− | 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! ***35 characters or less*** -->
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− | == CMap Paper in Bioinformatics ==
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− | {{ImageRight|BionformaticsCover.gif|Bioinformatics||http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040}}
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− | A [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 paper] describing the [[CMap]] comparative map viewer is in the [http://bioinformatics.oxfordjournals.org/content/vol25/issue22/index.dtl current issue] of ''[http://bioinformatics.oxfordjournals.org/ Bioinformatics]'':
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− | : [http://bioinformatics.oxfordjournals.org/cgi/content/full/25/22/3040 CMap 1.01: a comparative mapping application for the Internet], by Ken Youens-Clark, [[User:Faga|Ben Faga]], Immanuel V. Yap, [[User:Lstein|Lincoln Stein]] and Doreen Ware.
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− | [[CMap]] is a web-based tool for displaying and comparing maps of any type and from any species. Users can compare an arbitrary number of maps, view pair-wise comparisons of known correspondences, and search for maps or for features by name, species, type and accession.
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− | See the [[CMap|CMap page]] to learn more. CMap will also be covered in the [http://www.intl-pag.org/18/18-gramene.html Gramene workshop] and in a poster at [[PAG 2010]].
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− | [[User:Clements|Dave Clements]]<br />
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− | [[GMOD Help Desk]]
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− | ''2009/11/14''
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− | == January 2010 GMOD Meeting ==
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− | {{ImageRight|Jan2010MtgLogo170.png|January 2010 GMOD Meeting||January 2010 GMOD Meeting}}
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− | <div style="font-size: 140%; text-align: center">[[January 2010 GMOD Meeting|Register for the January 2010 GMOD Meeting]]</div>
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− | I am pleased to announce that the [[January 2010 GMOD Meeting|January GMOD meeting]] will be taking place on January 14 and 15, 2010 in San Diego at the [[January 2010 GMOD Meeting#Lodging|Best Western Seven Seas]]
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− | (the same location as last year). Please see the [[January 2010 GMOD Meeting|meeting page]] for registration information.
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− | Please also take a moment to [[January 2010 GMOD Meeting#Agenda Proposals|add suggestions for the agenda]]. There is no registration fee for this meeting. However, there is limited space, so please register early.
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− | The proprietors of the Best Western have given us an excellent room rate, and extended it to the previous week, so that people attending the [[January 2010 GMOD Meeting|GMOD meeting]] and the [[PAG 2010|Plant and Animal Genome meeting]] before it may stay at the Best Western the entire time.
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− | Please direct follow up questions to the [https://lists.sourceforge.net/lists/listinfo/gmod-devel gmod-devel mailing list] ([mailto:gmod-devel@lists.sourceforge.net gmod-devel@lists.sourceforge.net]).
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− | Thanks and I look forward to seeing you in San Diego!
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− | [[User:Scott|Scott]]
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− | ''2009/11/13''
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− | == Long Term Database Funding ==
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− | You may have heard about [http://www.arabidopsis.org/doc/about/tair_funding/410 TAIR's funding situation]. Basically, their funding is being cut by 25% per year, starting in September 2010, and NSF is encouraging them to find alternative funding sources. This news was sent to the TAIR community (and posted on the [http://mailman.tairgroup.org/mailman/listinfo/biocurator Biocurator list]) on October 22. A day later the paper "[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Models for financial sustainability of biological databases and resources]" appeared in ''[http://database.oxfordjournals.org/ Database: The Journal of Biological Databases and Curation]''.
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− | All GMOD users need to give at least some thought to long term funding issues. A [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion thread on long term database funding] has now been started on the [http://biocurator.org International Society for Biocuration]'s (ISB) [http://biocurator.proboards.com/ forum site].
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− | {{ImageRight|TAIR_logo.gif|TAIR Funding Update and Discussion Forum||http://www.arabidopsis.org/doc/about/tair_funding/410}}
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− | [http://www.arabidopsis.org/ TAIR] asked people to do a couple things:
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− | # Cite TAIR in publications: as a reference, as a source of data in methods sections, and under acknowledgments.
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− | # Contribute to a [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion on the TAIR web site] about
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− | ## the bioinformatics needs of the ''Arabidopsis'' and wider plant biology communities and
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− | ## how resources like TAIR should be funded.
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− | The [http://www.arabidopsis.org/doc/about/tair_funding/410 discussion at TAIR] is now 19 pages long and contains mountains of praise for TAIR, and a few suggestions on alternative funding, including subscriptions, international and industrial support, and advertising. It also contains many statements that none of those options will work. The ''[http://database.oxfordjournals.org/cgi/content/full/2009/0/bap017 Database]'' paper discusses similar proposals, plus some others.
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− | If you are interested in long-term funding issues, I encourage you to participate in the [http://biocurator.proboards.com/index.cgi?board=fundingissues discussion at ISB]. If you use TAIR and want to see it funded, please [http://www.arabidopsis.org/doc/about/tair_funding/410 post a comment at the TAIR web site]. And, if you aren't already doing so, make it easy for your users to cite your database by including an easy to find "Citing this resource" link on your site.
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− | [[User:Clements|Dave Clements]]
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− | ''2009/11/06''
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− | == Two Openings at Bayer CropScience ==
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− | {{ImageRight|Logo_BayerCropScience.gif|Open positions at Bayer CropScience||http://www.mybayerjob.com/en}}
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− | '''1. BioAnalyst Scientist:'''
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− | You will provide support in various activities: [[Next Generation Sequencing]] (NGS) data analysis, expression data (microarrays) analysis, genomics and biological networks. The successful applicant should have a PhD or equivalent experience in (plant) genetics and/or genomics. Computer skills are not mandatory but knowledge of bioinformatics applications is required. Excellent communication skills and the ability to support and train researchers with genomics data analysis is essential.
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− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUE2NjQ4RkNFNjUwMDlBRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Scientist]
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− | '''2. BioAnalyst Researcher:'''
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− | You will support and foster the data management and analysis of [[Next Generation Sequencing]] (NGS) data (assembly, processing, development of analysis methods, pipelines, etc.). Candidates must be highly motivated to work on biological questions and flexible to interact with the various groups of the research center. They should have a degree (MSc or PhD) in computational biology, boinformatics, statistics or equivalent level of knowledge and possess some programming skills (e.g. [[Glossary#Perl|perl]] and/or python). The candidate should have a good background in (plant) genetics and/or genomics and/or molecular biology.
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− | More information: [https://mybayerjob.bayerbbs.com/sap(bD1lbiZjPTAwNQ==)/bc/bsp/sap/hrrcf_pinst_pbl/application.do?PARAM=UElOU1RfR1VJRD00QUI3NUU2MzIzRDcwMTEyRTEwMDgwMDAwQUJGRDkwRQ%3d%3d BioAnalyst Researcher]
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− | Operating language in the company is English.
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− | '''Interested in any of these positions?''' You can apply [http://www.mybayerjob.com/en here] or send your CV to [mailto:Laurent.viau@bayercropscience.com Laurent Viau]
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− | [[User:ErickAntezana|Erick Antezana]]
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− | ''2009/11/06''
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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 2 to visualize next generation sequencing (NGS) data]] is now available. The [[:Category:Tutorials|tutorial]] walks through how to configure the [[GBrowse]] 2 genome browser to display [[next generation sequencing]] (NGS) data using the [http://samtools.sourceforge.net SAMtools] GBrowse adaptor, Bio::DB::Sam. This tutorial was originally taught at the [[BA2009|Bioinformatics Australia 2009 (BA2009) GMOD Workshop]]. The tutorial includes a [[VMware]] image to work with and step-by-step instructions for visualizing the example human data that comes with the SAMtools package.
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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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− | A [[:Image:GBrowse_nextgen_poster.pdf|poster]] (by [[User:Scott|Scott Cain]]) demonstrating how to use the adaptor with ''GBrowse 1 and GBrowse 2'' is also available.
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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 Lövenich of [http://www.imsb.ethz.ch/ ETH Zürich]
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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/}}
| + | |
− | [http://www.modencode.org modENCODE] is [http://blog.modencode.org/?p=350 looking for a few consultants]. The project's aim is to discover and explore the genomes of ''C. elegans'' and ''D. melanogaster'', using new scientific strategies and new technologies for discovery.
| + | |
− | | + | |
− | Consultants will be responsible for interacting with several external research labs, as well as with internal software developers, to collect and collate experimental data
| + | |
− | of many different types. In addition to a strong background in biology, candidates must be knowledgeable in programming and/or software development. Candidates must also possess verbal and written communication skills, particularly for understanding requirements from biologists, and to productively work in a collaborative environment.
| + | |
− | | + | |
− | Please see the [http://blog.modencode.org/?p=350 complete job description] for details.
| + | |
− | | + | |
− | [http://www.modencode.org modENCODE] is a power GMOD user. The project uses [[GBrowse]], [[Chado]], [[InterMine]], [[JBrowse]], and [[GBrowse_syn]]. (See [[January 2009 GMOD Meeting#modENCODE: extending Chado, BIR-TAB, & GBrowse for automating data validation & display|Nicole Washington's talk]] at the [[January 2009 GMOD Meeting]] for some details on how they are used.)
| + | |
− | | + | |
− | | + | |
− | <span style="font-size: 120%">'''Gramene'''</span>
| + | |
− | | + | |
− | {{ImageRight|Gramene_logo180.jpg|Grameene Project Opening||http://news.gramene.org/}}
| + | |
− | | + | |
− | [http://www.gramene.org Gramene] has [http://news.gramene.org/?p=392 several bioinformatics openings] in the [http://www.science.oregonstate.edu/bpp/faculty/jaiswal/ Jaiswal lab] at Oregon State University.
| + | |
− | | + | |
− | The positions involve development and maintenance of the databases, software and analysis pipelines necessary for development of the Plant Gene Expression, biochemical and regulatory pathway networks, comparative genomics, text mining ([[Textpresso]]) and biological ontology projects. Gramene is a long-time GMOD user and is the home of the [[CMap]] comparative map viewer.
| + | |
− | | + | |
− | See [http://news.gramene.org/?p=392 the position announcement] for full details.
| + | |
− | | + | |
− | ''2009/10/02''
| + | |
− | | + | |
− | == GMOD @ Bioinformatics Australia ==
| + | |
− | | + | |
− | {{ImageRight|BA2009Logo.png|GMOD workshop at Bioinformatics Australia||BA2009}}
| + | |
− | There will be a half-day [[BA2009|pre-conference GMOD workshop]] on 28 October, 2009, at [http://www.ausbiotech2009.com.au/bia/bia-home Bioinformatics Australia (BA2009)]. The workshop will introduce [[GMOD Components]] for [[visualization]], [[annotation]], and data management, and the GMOD project as a whole. The workshop will also include a [[GBrowse]] demonstration with a worked example that includes [[next generation sequencing]] data.
| + | |
− | | + | |
− | Thanks to sponsorship from [http://www.bioplatforms.com/ Bioplatforms Australia] admission to the workshop is included in the conference registration fee.
| + | |
− | | + | |
− | Please see the [[BA2009|workshop page]] or [mailto:help@gmod.org contact the GMOD Help Desk] for more information.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/10/01''
| + | |
− | | + | |
− | == InterMine Data Warehouse Workshop ==
| + | |
− | | + | |
− | {{ImageRight|InterMine.png|InterMine Workshop|180|http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html}}
| + | |
− | | + | |
− | We are running another [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html InterMine workshop] in Cambridge, UK on November 16th-17th.
| + | |
− | | + | |
− | This is intended for software developers to learn the [[InterMine]] system. The two day course will step through creating a new Mine, integrating real data and deploying and customising the web application.
| + | |
− | | + | |
− | The course is free to attend, more details and sign up information
| + | |
− | are available on the [http://www.biomed.cam.ac.uk/gradschool/skills/intermine.html workshop page].
| + | |
− | | + | |
− | Please get in touch if you have any questions.
| + | |
− | | + | |
− | Regards,
| + | |
− | | + | |
− | [mailto:richard@flymine.org Richard Smith]
| + | |
− | | + | |
− | ''2009/09/29''
| + | |
− | | + | |
− | == Tripal: A Web Front End for Chado ==
| + | |
− | | + | |
− | {{ImageRight|TripalLogo.jpg|Tripal|200|Tripal}}
| + | |
− | [[Tripal]] is a new web front end for [[Chado]] databases and is now a part of GMOD. Tripal is a collection of [http://www.drupal.org Drupal] modules initially developed by the [http://www.genome.clemson.edu/ Clemson University Genomics Institute (CUGI)]. Tripal is already powering several web sites, including the [http://www.marinegenomics.org Marine Genomics Project] and [http://www.fagaceae.org/ Fagaceae Genomics Web].
| + | |
− | | + | |
− | Tripal supports Drupal themes, page content and look and feel customization, materialized views, searching, and job management out of the box.
| + | |
− | | + | |
− | Tripal can be downloaded from the GMOD [[SVN]] repository. Tripal (already!) has an extensive [[Media:TripalUsersGuideJune2009.pdf|User's Guide]] and a [[Tripal Tutorial|tutorial]] to help users install, configure and extend Tripal.
| + | |
− | | + | |
− | If you use or are considering using [[Chado]], please take a look at [[Tripal]].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/28''
| + | |
− | | + | |
− | == Reactome User Survey ==
| + | |
− | | + | |
− | Reactome is committed to providing access to high-quality pathway information and helpful data analysis tools. With this in mind, we are actively soliciting comments from the research community in order to assess community needs. We are interested to hear about your experience with Reactome, and would like to know a bit about your background and research interests so that we can continue to improve the Reactome site and tools.
| + | |
− | | + | |
− | You can access the survey at [http://www.surveymonkey.com/s.aspx?sm=Ph5q56zmGkqVabn9QNfemw_3d_3d SurveyMonkey]
| + | |
− | | + | |
− | Thank you for taking part.
| + | |
− | | + | |
− | Robin Haw
| + | |
− | Manager of Reactome Outreach
| + | |
− | Outreach [at] reactome.org
| + | |
− | http://www.reactome.org
| + | |
− | | + | |
− | Posted by [[User:Scott|Scott Cain]]
| + | |
− | | + | |
− | ''2009/9/28''
| + | |
− | | + | |
− | == DIYA: Do It Yourself Annotator ==
| + | |
− | | + | |
− | {{ImageRight|DIYALogo.png|DIYA|100|DIYA}}
| + | |
− | [[DIYA]], the ''Do It Yourself Annotator'' is now officially a part of GMOD. DIYA is a modular and configurable open source pipeline framework, written in Perl, used (initially) for the rapid [[annotation]] of microbial genome sequences. The software is currently used to take nucleotide sequence contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in [[GFF]] format. Current development seeks to integrate DIYA with the [http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS AMOS] collection of assembly tools.
| + | |
− | | + | |
− | DIYA [http://sourceforge.net/projects/diyg/ resides in Sourceforge], where it has [http://sourceforge.net/mail/?group_id=205628 mailing lists] and a [http://sourceforge.net/apps/wordpress/diyg/ blog], and uses [http://sourceforge.net/apps/trac/diyg/ Trac] for development tracking. DIYA is stable and version 1.0 has been released.
| + | |
− | | + | |
− | DIYA is part of the ''[http://sourceforge.net/projects/diyg/ Do It Yourself Genomics (DIYG) Project]''. Developers of DIYA (and DIYG) include Andrew Stewart and [[User:Bosborne|Brian Osborne]] (formerly of the [[GMOD Help Desk]]). The DIYA community is looking for interested developers to contribute to DIYA. See the [[DIYA]] page for more.
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Chado in RDF: OpenFlyData ==
| + | |
− | | + | |
− | {{ImageRight|RDF_icon_96.gif|RDF||http://gmod.org/wiki/August_2009_GMOD_Meeting#Linked_Data_for_GMOD_Databases}}
| + | |
− | | + | |
− | The [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|OpenFlyData project has ported the FlyBase Chado database]] and several other ''Drosophila'' gene expression databases to the [http://www.w3.org/RDF/ Resource Description Framework (RDF)]. Each source database has a separate [http://en.wikipedia.org/wiki/Triplestore RDF store], and [http://openflydata.org/ OpenFlyData] provides both a browser and a programmatic [http://www.w3.org/TR/rdf-sparql-query/ SPARQL-based] interface to each. Source databases include the [[Chado]] database from [[:Category:FlyBase|FlyBase]], [http://www.fruitfly.org/ BDGP], [http://www.flyatlas.org/ FlyAtlas] and [http://www.fly-ted.org/ FlyTED].
| + | |
− | | + | |
− | Transforming databases into RDF can be an effective way to merge these data, and does not require mapping everything to a central [[Glossary#RDBMS|relational]] [[Glossary#Schema|schema]]. The common graph-based data model facilitates the reuse of RDF data published by other projects, with fewer constraints on the kind of questions you can ask.
| + | |
− | | + | |
− | For more on [http://openflydata.org/OpenFlyData OpenFlyData], see the [[August 2009 GMOD Meeting#Linked Data for GMOD Databases|''Linked Data for GMOD Databases'']] presentation from the [[August 2009 GMOD Meeting]], and the [http://openflydata.org OpenFlyData web site].
| + | |
− | | + | |
− | [[User:JunZhao|Jun Zhou]] and [[User:Clements|Dave Clements]]
| + | |
− | | + | |
− | ''2009/09/23''
| + | |
− | | + | |
− | == Bioinformatics Position at SpBase ==
| + | |
− | | + | |
− | {{ImageRight|SpBaseLogo.png|Position at SpBase||http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az}}
| + | |
− | | + | |
− | The [http://www.spbase.org Sea Urchin Model Organism database (SpBase)] has an opening for a Bioinformatician. From the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az position announcement]:
| + | |
− | <div class="indent">The computation group supporting the Sea Urchin Model Organism database, SpBase, is seeking a highly motivated individual to take responsibility for collecting, organizing and displaying gene expression information at all life stages of the purple sea urchin ''Strongylocentrotus purpuratus''. The individual will work with existing computer code as well as develop new software. A particular challenge of the project is to move data from various sourves and of various types to a common framework for presentation and manipulation by the user.</div>
| + | |
− | | + | |
− | See the [http://www2.recruitingcenter.net/clients/CalTech/publicjobs/controller.cfm?jbaction=JobProfile&Job_Id=15519&esid=az job posting] for more on the position. Please contact [mailto:acameron@caltech.edu Andy Cameron] if you have questions about the position.
| + | |
− | | + | |
− | SpBase uses several [[GMOD Components]], including [[GBrowse]], [[Apollo]], [[BioMart]], and [[Chado]].
| + | |
− | | + | |
− | [[User:Clements|Dave C.]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/09/22''
| + | |
− | | + | |
− | == 2009 GMOD Community Survey ==
| + | |
− | <div style="float:right">
| + | |
− | {|
| + | |
− | | {{#icon: GMODMug150x150.jpg|GMOD Mug|100|}}
| + | |
− | | {{#icon: TShirtThumb.jpg|GMOD T Shirt||}}
| + | |
− | |}
| + | |
| </div> | | </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">⇒</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|||}} </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">⇒</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.
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− | | + | |
− | | + | |
− | 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.
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− | | + | |
− | 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]].
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− | | + | |
− | 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]].
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− | | + | |
− | GBrowse can be installed with the [[GBrowse Install HOWTO|GBrowse netinstaller]].
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− | | + | |
− | 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].
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− | | + | |
− | 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]].
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− | | + | |
− | 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
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− | | + | |
− | [[User:Scott|Scott]]
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− | | + | |
− | ''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.
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− | | + | |
− | 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.
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− | | + | |
− | 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.
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− | | + | |
− | [mailto:mki101@uri.edu Marian Goldsmith], [mailto:a.papanicolaou@ex.ac.uk Alexie Papanicolaou], and [mailto:flegeai@rennes.inra.fr Fabrice Legeai].
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− | | + | |
− | ''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.
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− | | + | |
− | 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 £50.
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− | | + | |
− | 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.
| + | |
− | | + | |
− | June will be a busy month for GMOD outreach. If you can't make it to this meeting, there will also be [[#GMOD Workshops at SMBE, AGS|GMOD workshops]] at [http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27 SMBE] and the [http://www.k-state.edu/agc/symp2009/seminar.html Arthropod Genomics Symposium].
| + | |
− | | + | |
− | [[User:Clements|Dave Clements]]<br />
| + | |
− | [[GMOD Help Desk]]
| + | |
− | | + | |
− | ''2009/05/19''
| + | |
− | <endFeed />
| + | |
− | | + | |
− | = [[GMOD News Archives|News Archives]] =
| + | |
− | | + | |
− | Items more than 6 months old are available in the [[GMOD News Archives]].
| + | |
− | | + | |
− | = Adding a News Item =
| + | |
− | | + | |
− | '''Note:''' If you don't want to do this on your own, please send the item to the [mailto:help@gmod.org GMOD Help Desk] and we will post it for you.
| + | |
− | | + | |
− | This page generates both an RSS feed and updates the GMOD News list on the [[Main Page|home page]]. Therefore, please follow these guidelines when adding a news item.
| + | |
− | # Edit the [[#News Items|News Items]] section of this page. This will allow you to see how big your news item title is, compared to existing news items. | + | |
− | # Add your news item immediately after the <tt><nowiki><startFeed /></nowiki></tt> tag.
| + | |
− | # Title
| + | |
− | #* '''Use a short title. Titles should be small enough to fit on a single line in the GMOD News list on the [[Main Page|home page]]'''.
| + | |
− | #* Place the title in a second level heading: <tt>== Your Title ==</tt>
| + | |
− | # News Text
| + | |
| #* Make the news item succinct. | | #* Make the news item succinct. |
− | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' | + | #* Do not start the item with a MediaWiki header ("== Header =="). |
− | #* End the news item with your name and the date in the format ''YYYY/MM/DD''. | + | #** It won't render very well. You should be able to avoid headers altogether. |
− | # Preview your changes | + | #* '''The first link in the news item should point to the page/URL you want the RSS feed to link to. |
− | #* Check the table of contents. Is the title no longer than any previous title? Is the title at the same depth as the other news item titles?
| + | #** For example, the first link in a news item about [[Chado]] could point to the [[Chado]] page.''' |
− | #* Check the news item. Does the text look good, does it look like the other news items, and does the first link point to where you want it to? | + | #* You can include images in your news item. See [[:Category:News Items|preexisting news items]] for what markup to use to do this. |
− | #* '''Make sure that your MediaWiki markup (links, italics, etc.) is correct.''' The MediaWiki extension that lists news items on the [[Main Page|home page]] is temperamental. Incorrect markup can lead to garbage on the home page. | + | # Preview / save your changes. Edit and save the page until the news item looks like you want. |
− | #* Revise until you like it and then save it.
| + | # Once you are happy with how the item looks, insert this line at the end of it: |
− | | + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd}}</nowiki></pre> |
− | Once you have saved the page, a link to the new item will show up on the home page in about an hour. (Why the delay? It uses an RSS feed of this page and it queries the feed infrequently.) | + | #: Where ''yyyy/mm/dd'' is the current date. This line will cause it to be added to the GMOD News RSS feed. The item will show up in the feed within an hour. |
| + | # '''Once you have added the NewsItem template and saved the page, try to avoid editing the page after that.''' |
| + | #* Every edit results in the news item being reposted to the RSS feed. If you do need to update an item later on, you may do so, but please also update the NewsItem line: |
| + | #: <pre><nowiki>{{NewsItem|yyyy/mm/dd, updated yyyy/mm/dd}}</nowiki></pre> |
| | | |
− | [[Category:GMOD Community]] | + | [[Category:GMOD_Community]] |
News that is relevant to the GMOD user and developer communities. This page only shows recent news; to see all news items since autumn 2007, go to the GMOD News Archives. See also the GMOD Calendar and Events List.
GMOD news items are wiki pages with the prefix "News/". Creating a news item will automatically add it to the RSS feed, which appears on the GMOD News and GMOD News Archives pages, and in the news tracker on the home page.
Please follow these guidelines when adding a news item.
Please follow these guidelines when adding a news item.