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Bio

JBrowse Configuration Guide

GMOD.org recent changes - Tue, 09/29/2020 - 22:48

‎Apache Configuration Note

← Older revision Revision as of 02:48, 30 September 2020 Line 1,168: Line 1,168:  If you are using the Apache web server, please be aware that the module <code>mime_magic</code> can cause BAM files to be served incorrectly.  Usually, the error in the web developer console will be something like "Not a BAM file".  Some packaged versions of Apache, particularly on Red Hat or CentOS-based systems, are configured with this module turned on by default.  We recommend you deactivate this Apache module for the server or directory used to serve JBrowse files.  If you do not want to deactivate this module for the entire server, try adding this line to your HTTPD config or .htaccess file: If you are using the Apache web server, please be aware that the module <code>mime_magic</code> can cause BAM files to be served incorrectly.  Usually, the error in the web developer console will be something like "Not a BAM file".  Some packaged versions of Apache, particularly on Red Hat or CentOS-based systems, are configured with this module turned on by default.  We recommend you deactivate this Apache module for the server or directory used to serve JBrowse files.  If you do not want to deactivate this module for the entire server, try adding this line to your HTTPD config or .htaccess file:       AddType application/octet-stream .bam .bami .bai      AddType application/octet-stream .bam .bami .bai  +  +In some cases the problem can also manifest in VCF tabix for example, you may also need to use  +  +    AddType application/octet-stream .gz  +    AddType application/octet-stream .tbi  +    AddEncoding dummy .gz .tbi  +  +Note that there may be some sideeffect related to downloading gz files from this, but it has been reported to fix jbrowse usage of tabix VCF. Let us know if you have other solutions     = Wiggle/BigWig Tracks (XYPlot, Density) = = Wiggle/BigWig Tracks (XYPlot, Density) = Colin Diesh
Categories: Bio

JBrowse FAQ

GMOD.org recent changes - Wed, 09/16/2020 - 11:23

‎What is the difference between CanvasFeatures and HTMLFeatures?

← Older revision Revision as of 15:23, 16 September 2020 Line 267: Line 267:     * CanvasFeatures are newer. * CanvasFeatures are newer. −* CanvasFeatures can support Gene glyphs, i.e., a gene with multiple transcripts are grouped together on the screen. In HTMLFeatures, you have to load at the &quot;transcript&quot; level, so this loses the gene level info (if you do try to load the --type gene, it will just load &quot;gene spans&quot;, but then it doesn't display the transcript subfeatures. not terrible, but not as cool as CanvasFeatures).+* CanvasFeatures can support Gene glyphs, i.e., a gene with multiple transcripts are grouped together on the screen. In HTMLFeatures, you have to load at the &quot;transcript&quot; level, so this loses the gene level info (if you do try to load the --type gene, it will just load &quot;gene spans&quot;, but then it doesn't display the transcript subfeatures. You have to use --type mRNA or similar with HTMLFeatures to see the transcripts!).  * CanvasFeatures are faster if your have a lot of data. * CanvasFeatures are faster if your have a lot of data. −* They can support more dynamic shapes (See the SashimiPlot plugin https://github.com/cmdcolin/sashimiplot for example of Arc track, or NeatCanvasFeatures for example of "intron hats")   * They have different configuration functions. All the "style" methods on CanvasFeatures can be callback functions, so you can have a dynamic callback for the feature color, label, etc. The "glyph" can also be a callback, so you can make a function to change to a box or diamond glyph depending on feature attributes.   * They have different configuration functions. All the "style" methods on CanvasFeatures can be callback functions, so you can have a dynamic callback for the feature color, label, etc. The "glyph" can also be a callback, so you can make a function to change to a box or diamond glyph depending on feature attributes.    * CanvasFeatures have better mouseovers. The HTMLFeatures mouseovers use the HTML title attribute which can only display plain text. On CanvasFeatures tracks, the mouseover it is a real tooltip that you can embed arbitrary HTML inside of. * CanvasFeatures have better mouseovers. The HTMLFeatures mouseovers use the HTML title attribute which can only display plain text. On CanvasFeatures tracks, the mouseover it is a real tooltip that you can embed arbitrary HTML inside of. Colin Diesh
Categories: Bio

AGR GFF

AGR GFF uploads - Wed, 08/19/2020 - 04:35
[{"id":49639,"s3Path":"3.1.1/GFF/FB/GFF_FB_0.gff","md5Sum":"c445f7e02c6276bf562ba54957235f01","valid":true,"uploadDate":1594225375895,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":44,"name":"FB","description":"Fly Base"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_FB.gff"},{"id":49064,"s3Path":"3.1.0/GFF/MGI/GFF_MGI_6.gff","md5Sum":"e589458fc69cebff5ba13d8030930a17","valid":true,"uploadDate":1594151565673,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000},{"id":15544,"releaseVersion":"3.1.0","releaseDate":1593993600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":45,"name":"MGI","description":"Mouse Genome Database"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_MGI.gff"},{"id":48186,"s3Path":"3.1.1/GFF/WB/GFF_WB_0.gff","md5Sum":"e0e675ce51c81ad05db68759bfacb79f","valid":true,"uploadDate":1594117851138,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":47,"name":"WB","description":"Worm Base"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_WB.gff"},{"id":50580,"s3Path":"3.1.1/GFF/RGD/GFF_RGD_0.gff","md5Sum":"29614c08b3280dfd418434688e0b17d4","valid":true,"uploadDate":1594317019628,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":42,"name":"RGD","description":"Rat Genome Database"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_RGD.gff"},{"id":56656,"s3Path":"3.1.1/GFF/HUMAN/GFF_HUMAN_1.gff","md5Sum":"f56647fe51b625d83ebf3109841974e8","valid":true,"uploadDate":1596642161972,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":43,"name":"HUMAN","description":"Human"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_HUMAN.gff"},{"id":41039,"s3Path":"3.1.0/GFF/ZFIN/GFF_ZFIN_1.gff","md5Sum":"f646cfd544f9d637e798b6419619ccdf","valid":true,"uploadDate":1591761356189,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000},{"id":15544,"releaseVersion":"3.1.0","releaseDate":1593993600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":46,"name":"ZFIN","description":"Zebrafish Information Network"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_ZFIN.gff"},{"id":48990,"s3Path":"3.1.1/GFF/SGD/GFF_SGD_0.gff","md5Sum":"c42ff08528bd8cfdf02a5a0ccc577eda","valid":true,"uploadDate":1594148743172,"releaseVersions":[{"id":40635,"releaseVersion":"3.1.1","releaseDate":1596067200000},{"id":15546,"releaseVersion":"3.2.0","releaseDate":1603065600000}],"dataType":{"id":23,"name":"GFF","description":"Gene Features File","fileExtension":"gff","dataSubTypeRequired":true,"validationRequired":false},"dataSubType":{"id":48,"name":"SGD","description":"Saccharomyces Genome Database"},"stableURL":"https://fms.alliancegenome.org/api/data/download/GFF_SGD.gff"}]
Categories: Bio

gmod.org is DOWN, 1596377281

GMOD.org status - Sun, 08/02/2020 - 10:35
Categories: Bio

gmod.org is DOWN, 1596370081

GMOD.org status - Sun, 08/02/2020 - 08:35
Categories: Bio

gmod.org is DOWN, 1596362881

GMOD.org status - Sun, 08/02/2020 - 06:35
Categories: Bio

gmod.org is DOWN, 1596355681

GMOD.org status - Sun, 08/02/2020 - 04:35
Categories: Bio

gmod.org is DOWN, 1596348481

GMOD.org status - Sun, 08/02/2020 - 02:35
Categories: Bio

gmod.org is DOWN, 1596341281

GMOD.org status - Sun, 08/02/2020 - 00:35
Categories: Bio

gmod.org is DOWN, 1596334081

GMOD.org status - Sat, 08/01/2020 - 22:35
Categories: Bio

gmod.org is DOWN, 1596326881

GMOD.org status - Sat, 08/01/2020 - 20:35
Categories: Bio

gmod.org is DOWN, 1596319681

GMOD.org status - Sat, 08/01/2020 - 18:35
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gmod.org is DOWN, 1596312496

GMOD.org status - Sat, 08/01/2020 - 16:35
Categories: Bio

gmod.org is DOWN, 1596161281

GMOD.org status - Fri, 07/31/2020 - 00:05
Categories: Bio

gmod.org is DOWN, 1596154081

GMOD.org status - Thu, 07/30/2020 - 21:35
Categories: Bio

gmod.org is DOWN, 1595023681

GMOD.org status - Fri, 07/17/2020 - 18:35
Categories: Bio

User:RobertBuels

GMOD.org recent changes - Tue, 07/07/2020 - 15:37

← Older revision Revision as of 19:37, 7 July 2020 Line 1: Line 1:  [[Image:Rbuels and pretty flowers.jpg|300px]] [[Image:Rbuels and pretty flowers.jpg|300px]]    −'''Robert Buels''' is a bioinformatics software developer currently living in Cambridge, Massachusetts.  From 2004 to 2012, he worked at the [http://solgenomics.net Sol Genomics Network], an clade-oriented database for the Solanaceae and other plants.+'''Robert Buels''' is a bioinformatics software developer currently living in Seattle, Washington.  From 2004 to 2012, he worked at the [http://solgenomics.net Sol Genomics Network], an clade-oriented database for the Solanaceae and other plants.     From January 2012 to March 2014, he was the lead developer on the [[JBrowse]] project. From January 2012 to March 2014, he was the lead developer on the [[JBrowse]] project.     In March 2014, Rob moved to a role as a software developer on the Knowledge Informatics team at [http://foundationmedicine.com Foundation Medicine]. In March 2014, Rob moved to a role as a software developer on the Knowledge Informatics team at [http://foundationmedicine.com Foundation Medicine].  +  +Starting in 2018, Rob became the technical lead for the JBrowse 2 development team.     [http://twitter.com/rbuels rbuels tweets] [http://twitter.com/rbuels rbuels tweets] RobertBuels
Categories: Bio

gmod.org is OK,

GMOD.org status - Mon, 06/15/2020 - 12:35
Categories: Bio

gmod.org is DOWN, 1592230081

GMOD.org status - Mon, 06/15/2020 - 11:05
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gmod.org is DOWN, 1592222881

GMOD.org status - Mon, 06/15/2020 - 08:35
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