gmod-ajax — JBrowse list

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[Mitch S. <mit...@be...>]

Hi, I'm sorry it's taken so long for me to get back to you.

This file is in the wiggle "bed" format, which UCSC now calls the 
"bedgraph" format.  That particular format (and not the other wiggle 
forms) is defined to use zero-based, half-open coordinates:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html

In other words, these lines in the file:

chr10   0       1       4
chr10   2       3       5

specify that there's a value of 4 at base 0, no data at base 1, and a 
value of 5 at base 2.  The "no data" at base 1 is what is giving you 
those blank spaces.

Just add 1 to the stop positions in your data, and the blank spaces will 
get filled in.  I attached a version of your original file where I've 
done this in order to show exactly what I mean.

Regards,
Mitch

CHAN, KENNETH 1 [AG/7721] wrote:
> Thanks Mitch, I found out that the low resolution problem does not
> happen in internet explorer (I used IE 6). But it occurs in google
> Chrome and Firefox.
>   The most problematic thing is not the resolution issue but the empty
> regions (the white vertical lines among the green bar that can be seen
> in the attachment) in the graph. I have manually checked the wig file.
> There should not be any empty regions. Would it be the problem in my
> data or a problem in wig-to-json.pl? Again, this is the command I used:
>
> ./bin/wig-to-json.pl --wig
> /bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
> overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
> "event_data/TS_76715/" --tracklabel Coverage
>
>
> Regards,
> Kenneth
>   

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Thanks Mitch, I found out that the low resolution problem does not
happen in internet explorer (I used IE 6). But it occurs in google
Chrome and Firefox.
  The most problematic thing is not the resolution issue but the empty
regions (the white vertical lines among the green bar that can be seen
in the attachment) in the graph. I have manually checked the wig file.
There should not be any empty regions. Would it be the problem in my
data or a problem in wig-to-json.pl? Again, this is the command I used:

./bin/wig-to-json.pl --wig
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
"event_data/TS_76715/" --tracklabel Coverage


Regards,
Kenneth



-----Original Message-----
From: Mitch Skinner [mailto:mit...@be...] 
Sent: Saturday, March 20, 2010 9:55 AM
To: CHAN, KENNETH 1 [AG/7721]
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and
the values didn't correspond to the values in wig file

CHAN, KENNETH 1 [AG/7721] wrote:
> Hi guys,
>   I encountered a strange result when using wig-to-json.pl. The
> quantitative track I got has a very low resolution and the values
> doesn't seem like corresponding to the wiggle file.

Hi, I haven't gotten a chance to reproduce this or look at it in detail 
yet, but I do have a quick answer to part of this:

Currently, JBrowse renders wiggle files up to one pixel per base 
(because that's the highest possible data density) and then uses the web

browser to stretch the images when the user is zoomed in closer than one

pixel per base.  On large genomes, this saves a lot of disk space and 
processing time compared to rendering images at higher resolutions.  
Plus, JBrowse allows for variable font sizes, so at the highest zoom 
level, different users will have different values for the number of 
pixels per base.  So even if we wanted to generate higher resolution 
images, we wouldn't be able to pick a scale factor for the highest zoom 
level that would work exactly for everyone; in many cases the web 
browser would still have to stretch or shrink the image.

Originally, the web browsers all used a scaling algorithm that kept the 
results crisp-looking, but more recently they've started to use a 
smoother (bicubic) scaling algorithm by default, and wiggle tracks 
started looking fuzzy in JBrowse when they're zoomed in all the way.

The web browsers have just started implementing switches that will allow

us to specify the old scaling method:
https://developer.mozilla.org/en/CSS/image-rendering

and writing the JBrowse code to set that value appropriately is on our 
to-do list (although if anyone wants to tackle it, that would be 
welcome; it should be simple to set the relevant CSS styles on the 
images in ImageTrack.js).

Mitch


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[Gmod-ajax] Add an extra link to jbrowse

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hello jbrowse developers,

  I tried to add an extra customized link to the jbrowser. I am not
familiar with javascript so I still couldn't do it properly. Can you
please let me know what I did wrong? The following shows my attempt:

-          Add a new input parameter to 'new Browser' function call in
the index.html:

o   var b = new Browser({

o         gbrowseLink: "http://serverABC/cgi-bin/gbrowse/chrm1",

o         containerID: "GenomeBrowser",

o         ...... 

-          Add the following bits to just before the "if
(params.bookmark)" in the "Browser.prototype.createNavBox" function in
the Browser.js file:

o       if (params.gbrowseLink) {

o           this.link = document.createElement("a");

o           this.link.appendChild(document.createTextNode("View in
gbrowse"));

o           this.link.href = params.gbrowseLink;

o           this.link.style.cssText = "float: right; clear";

o           navbox.appendChild(this.link);

o       }

o    

o
navbox.appendChild(document.createTextNode("\u00a0\u00a0\u00a0\u00a0"));

o    

By doing this, I could get the link 'View in gbrowse' next to the
original link, however, they are placed next to each other without
spacing.... What should be the proper way to add an extra customizable
link to the jbrowser? Thanks a lot.

 

Regards,

Kenneth

 


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[Gmod-ajax] HTML5/javascript/ajax transcriptome browser

[Anup P. <anu...@gm...>]

Dear GMOD users,

I have been working on genome/transcriptome browser for visualizing
next-generation sequencing data. tbrowse is HTML5/javascript/ajax
based browser designed to completely segregate data from
visualization, making development much easier, reducing the load on
servers and offering a much more interactive experience to users.

Currently the tool is focused at visualizing RNA-seq data. RNA-seq
data as genome tracks can help visualize spatial relationships between
expression and other genome annotations, but does a poor job of
visualizing change in expression over conditions. tbrowse offers both
a genome track visualization and also plots expression over samples.

The code and documentation are at http://code.google.com/p/tbrowse/
There is a demo at http://butler.fri.uni-lj.si/anup/tbrowse/

Anup Parikh

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[Mitch S. <mit...@be...>]

Mitch Skinner wrote:
> Currently, JBrowse renders wiggle files up to one pixel per base

I meant to say:

JBrowse renders wiggle files *at zoom levels* up to one pixel per base

Re: [Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[Mitch S. <mit...@be...>]

CHAN, KENNETH 1 [AG/7721] wrote:
> Hi guys,
>   I encountered a strange result when using wig-to-json.pl. The
> quantitative track I got has a very low resolution and the values
> doesn't seem like corresponding to the wiggle file.

Hi, I haven't gotten a chance to reproduce this or look at it in detail 
yet, but I do have a quick answer to part of this:

Currently, JBrowse renders wiggle files up to one pixel per base 
(because that's the highest possible data density) and then uses the web 
browser to stretch the images when the user is zoomed in closer than one 
pixel per base.  On large genomes, this saves a lot of disk space and 
processing time compared to rendering images at higher resolutions.  
Plus, JBrowse allows for variable font sizes, so at the highest zoom 
level, different users will have different values for the number of 
pixels per base.  So even if we wanted to generate higher resolution 
images, we wouldn't be able to pick a scale factor for the highest zoom 
level that would work exactly for everyone; in many cases the web 
browser would still have to stretch or shrink the image.

Originally, the web browsers all used a scaling algorithm that kept the 
results crisp-looking, but more recently they've started to use a 
smoother (bicubic) scaling algorithm by default, and wiggle tracks 
started looking fuzzy in JBrowse when they're zoomed in all the way.

The web browsers have just started implementing switches that will allow 
us to specify the old scaling method:
https://developer.mozilla.org/en/CSS/image-rendering

and writing the JBrowse code to set that value appropriately is on our 
to-do list (although if anyone wants to tackle it, that would be 
welcome; it should be simple to set the relevant CSS styles on the 
images in ImageTrack.js).

Mitch

Re: [Gmod-ajax] interesting arrowhead question

[Mitch S. <mit...@be...>]

On 03/17/2010 08:34 PM, Scott Cain wrote:
> Without double checking, I'd say I'm reasonably sure that the
> arrowheads are drawn inside the feature, such that the very point of
> the arrowhead is at the edge of the feature.
>    

I did some looking, and my current understanding is that in GBrowse it 
depends on the glyph.  For example, it looks like the transcript glyph 
draws them outside the feature (is this the latest code?  It's the 
Bio::Graphics SVN HEAD):

http://gmod.svn.sourceforge.net/viewvc/gmod/Bio-Graphics/trunk/lib/Bio/Graphics/Glyph/transcript.pm?view=markup#l_38

It looks to me like the $self->arrow calls are drawing outside the glyph 
bounds; also, the pad_left and pad_right subs take into account the 
arrow length.  It's a little complicated to follow because of the "flip" 
logic, though.

For the transcript2 glyph, it looks like it draws the arrowhead inside 
the feature unless the feature is too small for the arrowhead, in which 
case it draws it outside.

http://gmod.svn.sourceforge.net/viewvc/gmod/Bio-Graphics/trunk/lib/Bio/Graphics/Glyph/transcript2.pm?view=markup

Mitch

[Gmod-ajax] How to perform these features?

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hi all,

  There is a 'Link' at the right top corner of the browser. I would like
to change the link target. Is it possible to do it and how? (It's fine
for me to dig into the code if it is required.)

  I would also like to apply different background color or image to the
same track for different features which have different names or some
kind of differentiable ID or names. In gbrowse, I used perl callback to
do it. How do I do it in jbrowse?

  Can the configuration file control the behavior of the display? For
example, the height of a feature (eg. arrow head); controlling the level
of zooming for displaying the feature, etc.

  Are these gbrowse feature available in jbrowse?

-          "Draw target", "show mismatch".

-          Perform sequence translation.

-          Setting the "label density".

  Thanks a lot. 

 

Regards,

Kenneth

 


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[Gmod-ajax] wig-to-json.pl gives low resolution image and the values didn't correspond to the values in wig file

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hi guys,
  I encountered a strange result when using wig-to-json.pl. The
quantitative track I got has a very low resolution and the values
doesn't seem like corresponding to the wiggle file.
  I attached the wiggle file and the resulted picture after applied the
following command:

./bin/wig-to-json.pl --wig
/bifx/apache/htdocs/gbrowse2/databases/te_viewer/testing/TS_76715_CG_R_C
overage.wig --out "event_data/TS_76715/" --key "Reads Coverage" --tile
"event_data/TS_76715/" --tracklabel Coverage

  I noticed that the above command didn't generate the 'tiles' directory
in the "event_data/TS_76715" as I specified. If I took out the tile bit
(--tile "even_data/TS_76715"). The tile directory appears in the data
dir. I tried to copy the tile dir to the "event_data/TS_76715" manually
but the resolution didn't change. May I ask what the generated "tiles"
directory is for? And do you have any idea how I can fix this problem of
low resolution. Thanks.

Regards,
Kenneth

---------------------------------------------------------------------------------------------------------
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All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
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Re: [Gmod-ajax] interesting arrowhead question

[Scott C. <sc...@sc...>]

Without double checking, I'd say I'm reasonably sure that the
arrowheads are drawn inside the feature, such that the very point of
the arrowhead is at the edge of the feature.

Scott


On Wed, Mar 17, 2010 at 7:43 PM, Ian Holmes <ih...@be...> wrote:
> Mitch drew my attention to this recently-submitted lighthouse ticket:
>
> http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries
>
> In JBrowse we draw the arrowheads outside the feature. Robert Olson
> protests that they should be inside. Is there an established convention
> for this? How does GBrowse handle it?
>
> I.
>
> ------------------------------------------------------------------------------
> Download Intel&#174; Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] interesting arrowhead question

[Scott C. <sc...@sc...>]

Err, in case it wasn't obvious, I was referring to how GBrowse does it :-)

On Wed, Mar 17, 2010 at 11:34 PM, Scott Cain <sc...@sc...> wrote:
> Without double checking, I'd say I'm reasonably sure that the
> arrowheads are drawn inside the feature, such that the very point of
> the arrowhead is at the edge of the feature.
>
> Scott
>
>
> On Wed, Mar 17, 2010 at 7:43 PM, Ian Holmes <ih...@be...> wrote:
>> Mitch drew my attention to this recently-submitted lighthouse ticket:
>>
>> http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries
>>
>> In JBrowse we draw the arrowheads outside the feature. Robert Olson
>> protests that they should be inside. Is there an established convention
>> for this? How does GBrowse handle it?
>>
>> I.
>>
>> ------------------------------------------------------------------------------
>> Download Intel&#174; Parallel Studio Eval
>> Try the new software tools for yourself. Speed compiling, find bugs
>> proactively, and fine-tune applications for parallel performance.
>> See why Intel Parallel Studio got high marks during beta.
>> http://p.sf.net/sfu/intel-sw-dev
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Thanks Mitch for the detailed reply.
  Previously I thought biodb-to-json.pl will automatically treat the
first line in volvox.gff3 (ctgA example ........ Name=ctgA) as the
reference sequence similar to gbrowse so no prepare-refseqs.pl is
required when directly converting the config file. Anyway, I was wrong. 
 Just tried the 'git pull', but showed 'Failed to find a valid git
directory'. That's not important anyway.
 For other users' reference, after I used prepare-refseqs.pl and
biodb-to-json.pl. Since I used the --out parameter to specify a new
output location, I needed to manually modify the index.html file so that
it points to the correct location of refSeqs.js and trackInfo.js.

  Thank the whole jbrowse developing team for developing such a nice UI.
Hope it will continue to be successful and provide richer features and
functionalities in the soon future.

Regards,
Kenneth



-----Original Message-----
From: Mitch Skinner [mailto:mit...@be...] 
Sent: Thursday, March 18, 2010 2:48 AM
To: CHAN, KENNETH 1 [AG/7721]
Cc: gmo...@li...
Subject: Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but
no track was outputted

Did you run prepare-refseqs.pl?

Also, I think that vmware image has git installed, so it might help to 
go into
/var/www/jbrowse/
and run "git pull" to update that jbrowse installation.

Also, by default, the "data" directory is created as a subdirectory of 
the working directory that the scripts are run from, and (by default) 
the index.html file expects the "data" directory to be in the same 
directory as the index.html file.  So if you run the scripts from the 
"jbrowse" directory (i.e., if you run them like: bin/prepare-refseqs.pl)

then you can just use the defaults, otherwise use the --out parameter to

specify the location of the data directory.

Hope this helps,
Mitch

On 03/17/2010 09:26 AM, CHAN, KENNETH 1 [AG/7721] wrote:
> Hello all,
>    I downloaded the VMware ('Ending Image' in
> http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
> configuration file (volvox_conf.json) to json. However no track was
> outputted by the following steps:
> - go to '/var/www/jbrowse/docs/tutorial/conf_files'
> - change the db_args attribute to point to the correct data directory:
> "-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
> - in the same conf_files directory and type:
> ../../../bin/biodb-to-json.pl --conf volvox.json
> - it created directories 'data/tracks', but somehow nothing is in both
> dir or sub-dir.
>
> Did I do anything wrong or missed out any crucial steps? (I was
> expecting the biodb-to-json.pl will generate all tracks in the config
> file directly.)
> Thanks.
>
> Regards,
> Kenneth
>
>
------------------------------------------------------------------------
---------------------------------
> This e-mail message may contain privileged and/or confidential
information, and is intended to be received only by persons entitled to
receive such information. If you have received this e-mail in error,
please notify the sender immediately. Please delete it and all
attachments from any servers, hard drives or any other media. Other use
of this e-mail by you is strictly prohibited.
>
>
> All e-mails and attachments sent and received are subject to
monitoring, reading and archival by Monsanto, including its
subsidiaries. The recipient of this e-mail is solely responsible for
checking for the presence of "Viruses" or other "Malware". Monsanto,
along with its subsidiaries, accepts no liability for any damage caused
by any such code transmitted by or accompanying this e-mail or any
attachment.
>
------------------------------------------------------------------------
---------------------------------
>
>
>
------------------------------------------------------------------------
------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    



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[Gmod-ajax] interesting arrowhead question

[Ian H. <ih...@be...>]

Mitch drew my attention to this recently-submitted lighthouse ticket:

http://jbrowse.lighthouseapp.com/projects/23792/tickets/54-arrowheads-are-outside-feature-boundaries

In JBrowse we draw the arrowheads outside the feature. Robert Olson
protests that they should be inside. Is there an established convention
for this? How does GBrowse handle it?

I.

Re: [Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

[Mitch S. <mit...@be...>]

Did you run prepare-refseqs.pl?

Also, I think that vmware image has git installed, so it might help to 
go into
/var/www/jbrowse/
and run "git pull" to update that jbrowse installation.

Also, by default, the "data" directory is created as a subdirectory of 
the working directory that the scripts are run from, and (by default) 
the index.html file expects the "data" directory to be in the same 
directory as the index.html file.  So if you run the scripts from the 
"jbrowse" directory (i.e., if you run them like: bin/prepare-refseqs.pl) 
then you can just use the defaults, otherwise use the --out parameter to 
specify the location of the data directory.

Hope this helps,
Mitch

On 03/17/2010 09:26 AM, CHAN, KENNETH 1 [AG/7721] wrote:
> Hello all,
>    I downloaded the VMware ('Ending Image' in
> http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
> configuration file (volvox_conf.json) to json. However no track was
> outputted by the following steps:
> - go to '/var/www/jbrowse/docs/tutorial/conf_files'
> - change the db_args attribute to point to the correct data directory:
> "-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
> - in the same conf_files directory and type:
> ../../../bin/biodb-to-json.pl --conf volvox.json
> - it created directories 'data/tracks', but somehow nothing is in both
> dir or sub-dir.
>
> Did I do anything wrong or missed out any crucial steps? (I was
> expecting the biodb-to-json.pl will generate all tracks in the config
> file directly.)
> Thanks.
>
> Regards,
> Kenneth
>
> ---------------------------------------------------------------------------------------------------------
> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.
>
>
> All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
> ---------------------------------------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    

[Gmod-ajax] using biodb-to-json.pl on volvox_conf.json but no track was outputted

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hello all,
  I downloaded the VMware ('Ending Image' in
http://gmod.org/wiki/JBrowse_Tutorial) and tried to convert the
configuration file (volvox_conf.json) to json. However no track was
outputted by the following steps:
- go to '/var/www/jbrowse/docs/tutorial/conf_files'
- change the db_args attribute to point to the correct data directory:
"-dir": "/var/www/jbrowse/docs/tutorial/data_files" },
- in the same conf_files directory and type:
../../../bin/biodb-to-json.pl --conf volvox.json
- it created directories 'data/tracks', but somehow nothing is in both
dir or sub-dir.

Did I do anything wrong or missed out any crucial steps? (I was
expecting the biodb-to-json.pl will generate all tracks in the config
file directly.)
Thanks.

Regards,
Kenneth

---------------------------------------------------------------------------------------------------------
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Re: [Gmod-ajax] How to remove a track

[Ian H. <ih...@be...>]

Hi Kenneth,

Currently the easiest way to do this is to edit the file 
data/trackInfo.js (where 'data' is your dataRoot directory). Within this 
file you will see one clause like the following for each track:

    {
       "url" : "data/tracks/{refseq}/sts_markers/trackData.json",
       "type" : "FeatureTrack",
       "label" : "sts_markers",
       "key" : "STS Markers"
    },

Just delete that clause and the track will disappear. We do clearly need 
  a script to do this, and I've added a request ticket for that.

best, Ian


CHAN, KENNETH 1 [AG/7721] wrote:
> Hi all,
>   Can anyone tell me how to delete a track completely in JBrowse?
>   I tried to delete the track directory (eg. TrackToBeDelete) in the
> path of jbrowse/data/tracks/RefSeq/ TrackToBeDelete. However, in the
> jbrowse the track name is still there, only the actual data is not
> displaying. It seems to me that the track information is recorded in the
> browserRoot level instead of the dataRoot level, doesn't it? How can I
> remove a track completely? Thanks in advance.
> 
> Regards,
> Kenneth
> 
> ---------------------------------------------------------------------------------------------------------
> This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.
> 
> 
> All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
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> 
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[Gmod-ajax] How to remove a track

[CHAN, K. 1 [AG/7721] <ken...@mo...>]

Hi all,
  Can anyone tell me how to delete a track completely in JBrowse?
  I tried to delete the track directory (eg. TrackToBeDelete) in the
path of jbrowse/data/tracks/RefSeq/ TrackToBeDelete. However, in the
jbrowse the track name is still there, only the actual data is not
displaying. It seems to me that the track information is recorded in the
browserRoot level instead of the dataRoot level, doesn't it? How can I
remove a track completely? Thanks in advance.

Regards,
Kenneth

---------------------------------------------------------------------------------------------------------
This e-mail message may contain privileged and/or confidential information, and is intended to be received only by persons entitled to receive such information. If you have received this e-mail in error, please notify the sender immediately. Please delete it and all attachments from any servers, hard drives or any other media. Other use of this e-mail by you is strictly prohibited.


All e-mails and attachments sent and received are subject to monitoring, reading and archival by Monsanto, including its subsidiaries. The recipient of this e-mail is solely responsible for checking for the presence of "Viruses" or other "Malware". Monsanto, along with its subsidiaries, accepts no liability for any damage caused by any such code transmitted by or accompanying this e-mail or any attachment.
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Re: [Gmod-ajax] Representation of exons and introns with jbrowse OK

[Isabelle L. <isa...@ve...>]

Hi Ian,

Thank you,
My configuration file was badly written
Now It's OK
I see exons

best wishes,
Isabelle


Ian Holmes wrote:
> Hi Isabelle,
>
> Yes - subfeatures can be used to display exon/intron structure.
>
> The GFF file corresponding to the example config file 'volvox.json' 
> that you included (full path docs/tutorial/conf_files/volvox.json) is 
> in docs/tutorial/data_files/volvox.gff3. The corresponding sequence 
> file is docs/tutorial/data_files/volvox.fa.
>
> There is currently no way to modify the height of a track except by 
> hacking the javascript yourself (so, no configuration-level way to do 
> it).
>
> best wishes,
> Ian
>
> Isabelle Luyten wrote:
>> Hello,
>>
>> I am very interested in your tool jbrowse.
>>
>> But I am not safe to use all its possibilities.
>>
>> I have 2 questions:
>>
>> 1)  I want to show exon-intron strucutre of mRNA.
>>
>> I ask the same question as Motokazu Ishikawa, but I did not find 
>> answer to his question under this site:
>>
>> Under http: // mailarchive / forum.php sourceforge.net/? 
>> Forum_name=gmod-ajax
>>    [ Gmod-ajax ] Subfeature were not shown      Motokazu Ishikawa < 
>> m.ishikawa@is >      1      2009-10-16 00:44
>>
>> Could I have the file GFF corresponding In the following tracks? 
>> (volvox.json)
>>
>>     {
>>       "track": "CDS",
>>       "feature": ["CDS:predicted", "mRNA:exonerate"],
>>       "class": "cds",
>>       "phase": 1,
>>       "key": "Predicted genes",
>>       "category": "Genes"
>>     },
>>     {
>>       "track": "Transcript",
>>       "feature": ["mRNA:exonerate"],
>>       "description": 1,
>>       "class": "transcript",
>>       "subfeatures": true,
>>       "subfeature_classes": {
>>         "CDS": "transcript-CDS",
>>         "UTR": "transcript-UTR"
>>       },
>>       "arrowheadClass": "transcript-arrowhead",
>>       "key": "Exonerate predictions",
>>       "category": "Genes"
>>     },
>>
>>
>> Do sub-features well serve to display introns and exons for example, 
>> or otherwise to which are of use you they?
>>
>> 2) I have sometimes 100 in 200 elements for a track (ex ESTs)
>>
>> How to decrease the height of these tracks?
>> Is it with the NClists?
>> Can you give me an example or give me the Web address where I can 
>> find it?
>>
>> Best regards
>>


-- 
Isabelle

--------------------------------------
isa...@ve...
INRA-URGI:
Unité de Recherche Génomique Info
Centre de Recherche de Versailles-Grignon
01 30 83 38 30
--------------------------------------

Re: [Gmod-ajax] Subfeature were not shown

[Ian H. <ih...@be...>]

Hi Motokazu,

Sorry for the delay in answering this - somehow we missed it.

Do you still need help with this? If so can you supply the command-line 
usage?

best wishes
Ian

Motokazu Ishikawa wrote:
> I want to show exon-intron strucutre of mRNA. mRNA shape (gray arrow)
> can successfully be shown, but subfeatures (UTR and CDS) weren't shown
> on on it. Any subfeature-*.json file weren't created under data/tracks
> directory. Could you give me some advices ?
> 
> GFF3 file and config file are belows.
> 
> ** GFF3 file
> 
> chr22 hg18_refGene gene 49288242 49293001 . - . ID=gene:NM_033200;
> Name=gene:NM_033200;Note=NM_033200
> chr22 hg18_refGene mRNA 49288242 49293001 . - . ID=mRNA:NM_033200.1;
> Name=mRNA:NM_033200.1; Parent=gene:NM_033200; Index=1
> chr22 hg18_refGene five_prime_UTR 49292971 49293001 . - .
> ID=five_prime_UTR:NM_033200.1.1; Name=five_prime_UTR:NM_033200.1.1;
> Parent=mRNA:NM_033200.1
> chr22 hg18_refGene CDS 49292877 49292970 . - 0 ID=CDS:NM_033200.1.2;
> Name=CDS:NM_033200.1.2; Parent=mRNA:NM_033200.1
> 
> 
> ** conf file
> 
> {
> "description": "ucsc tracks",
> "db_adaptor": "Bio::DB::SeqFeature::Store",
> "db_args": { "-adaptor": "memory",
> "-dir": "stage/ucsc" },
> "TRACK DEFAULTS": {
> "class": "feature",
> "autocomplete": "all"
> },
> "tracks": [
> {
> "track": "ucsc_gene",
> "key": "ucsc Gene Span",
> "feature": ["gene"],
> "autocomplete": "all",
> "class": "feature2",
> "category": "Gene Model features",
> "urlTemplate": "http://flybase.org/cgi-bin/fbidq.html?{load_id}",
> "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
> },
> {
> "track": "ucsc_mRNA",
> "feature": ["mRNA"],
> "autocomplete": "alias",
> "subfeatures": true,
> "key": "ucsc mRNA",
> "class": "transcript",
> "subfeature_classes": {
> "CDS": "transcript-CDS",
> "five_prime_UTR": "transcript-five_prime_UTR",
> "three_prime_UTR": "transcript-three_prime_UTR"
> },
> "arrowheadClass": "transcript-arrowhead",
> "clientConfig": {
> "histScale":5
> },
> "urlTemplate":
> "http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term={load_id}",
> "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
> },
> {
> "track": "ucsc_snp",
> "feature": ["point_mutation"],
> "key": "ucsc Mutation: point mutation",
> "class": "feature",
> "category": "Mapped features"
> }
> ]
> }
> 
> 

Re: [Gmod-ajax] Representation of exons and introns with jbrowse

[Ian H. <ih...@be...>]

Hi Isabelle,

Yes - subfeatures can be used to display exon/intron structure.

The GFF file corresponding to the example config file 'volvox.json' that 
you included (full path docs/tutorial/conf_files/volvox.json) is in 
docs/tutorial/data_files/volvox.gff3. The corresponding sequence file is 
docs/tutorial/data_files/volvox.fa.

There is currently no way to modify the height of a track except by 
hacking the javascript yourself (so, no configuration-level way to do it).

best wishes,
Ian

Isabelle Luyten wrote:
> Hello,
> 
> I am very interested in your tool jbrowse.
> 
> But I am not safe to use all its possibilities.
> 
> I have 2 questions:
> 
> 1)  I want to show exon-intron strucutre of mRNA.
> 
> I ask the same question as Motokazu Ishikawa, but I did not find answer 
> to his question under this site:
> 
> Under http: // mailarchive / forum.php sourceforge.net/? 
> Forum_name=gmod-ajax
>    [ Gmod-ajax ] Subfeature were not shown      Motokazu Ishikawa < 
> m.ishikawa@is >      1      2009-10-16 00:44
> 
> Could I have the file GFF corresponding In the following tracks? 
> (volvox.json)
> 
>     {
>       "track": "CDS",
>       "feature": ["CDS:predicted", "mRNA:exonerate"],
>       "class": "cds",
>       "phase": 1,
>       "key": "Predicted genes",
>       "category": "Genes"
>     },
>     {
>       "track": "Transcript",
>       "feature": ["mRNA:exonerate"],
>       "description": 1,
>       "class": "transcript",
>       "subfeatures": true,
>       "subfeature_classes": {
>         "CDS": "transcript-CDS",
>         "UTR": "transcript-UTR"
>       },
>       "arrowheadClass": "transcript-arrowhead",
>       "key": "Exonerate predictions",
>       "category": "Genes"
>     },
> 
> 
> Do sub-features well serve to display introns and exons for example, or 
> otherwise to which are of use you they?
> 
> 2) I have sometimes 100 in 200 elements for a track (ex ESTs)
> 
> How to decrease the height of these tracks?
> Is it with the NClists?
> Can you give me an example or give me the Web address where I can find it?
> 
> Best regards
> 

[Gmod-ajax] Representation of exons and introns with jbrowse

[Isabelle L. <isa...@ve...>]

Hello,

I am very interested in your tool jbrowse.

But I am not safe to use all its possibilities.

I have 2 questions:

1)  I want to show exon-intron strucutre of mRNA.

I ask the same question as Motokazu Ishikawa, but I did not find answer 
to his question under this site:

Under http: // mailarchive / forum.php sourceforge.net/? 
Forum_name=gmod-ajax
   [ Gmod-ajax ] Subfeature were not shown      Motokazu Ishikawa < 
m.ishikawa@is >      1      2009-10-16 00:44

Could I have the file GFF corresponding In the following tracks? 
(volvox.json)

    {
      "track": "CDS",
      "feature": ["CDS:predicted", "mRNA:exonerate"],
      "class": "cds",
      "phase": 1,
      "key": "Predicted genes",
      "category": "Genes"
    },
    {
      "track": "Transcript",
      "feature": ["mRNA:exonerate"],
      "description": 1,
      "class": "transcript",
      "subfeatures": true,
      "subfeature_classes": {
        "CDS": "transcript-CDS",
        "UTR": "transcript-UTR"
      },
      "arrowheadClass": "transcript-arrowhead",
      "key": "Exonerate predictions",
      "category": "Genes"
    },


Do sub-features well serve to display introns and exons for example, or 
otherwise to which are of use you they?

2) I have sometimes 100 in 200 elements for a track (ex ESTs)

How to decrease the height of these tracks?
Is it with the NClists?
Can you give me an example or give me the Web address where I can find it?

Best regards

-- 
Isabelle

--------------------------------------
isa...@ve...
INRA-URGI:
Unité de Recherche Génomique Info
Centre de Recherche de Versailles-Grignon
01 30 83 38 30
--------------------------------------

Re: [Gmod-ajax] installing multiple browsers on a single server

[James C. <ca...@gm...>]

On 1 March 2010 20:36, Brenton Graveley <brg...@gm...> wrote:
> Hi Mitch,
>
> I have a question about how you recommend installing browsers for multiple organisms on a  single server?  I am currently doing this by installing JBrowse in separate folders on the server, but this seems inefficient since I have multiple copies of the source code that each browser is using.  What is the best way of doing this?

Have two index.htmls, in the browser construction point to different
locations for dataRoot but one location for browserRoot:

eg:
           var b = new Browser({
                                   containerID: "GenomeBrowser",
                                   refSeqs: refSeqs,
                                   trackData: trackInfo,
                                   defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                                   location: queryParams.loc,
                                   tracks: queryParams.tracks,
                                   bookmark: bookmarkCallback,
                                   browserRoot: CODE_PATH,
                                   dataRoot: DATA_PATH
                               });

James

[Gmod-ajax] installing multiple browsers on a single server

[Brenton G. <brg...@gm...>]

Hi Mitch, 

I have a question about how you recommend installing browsers for multiple organisms on a  single server?  I am currently doing this by installing JBrowse in separate folders on the server, but this seems inefficient since I have multiple copies of the source code that each browser is using.  What is the best way of doing this?

Thanks,

Brent

Re: [Gmod-ajax] GMOD Logo Program

[Dave C. G. H. D. <he...@gm...>]

Hello all,

This is a reminder that the deadline for applications to the GMOD Logo
Program (http://gmod.org/wiki/GMOD_Logo_Program) is March 1, one week from
today.

See the program wiki page (http://gmod.org/wiki/GMOD_Logo_Program) and below
for details.  Please let me know if you have any questions.

Thanks,

Dave C.

PS: And the deadline for applying to 2010 GMOD Summer School Americas is
TODAY!  See http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas for
details.

On Thu, Feb 4, 2010 at 9:29 AM, Dave Clements, GMOD Help Desk <he...@gm...
> wrote:

> Hello all,
>
> Need a logo that tells people what your web site, database or GMOD
> component is about?  If your resource needs a logo then the GMOD Logo
> Program (http://gmod.org/wiki/GMOD_Logo_Program) can help.
>
>
> I am pleased to announce the first call for participation in the GMOD
> Logo Program. This program is for GMOD users and developers that would
> like have a custom designed logo for their web site, database or GMOD
> component. The program pairs GMOD community members with students in
> advanced design classes at colleges and universities.  This spring we
> will be working with a class at Linn-Benton Community College.
> Participants will meet several times (remotely) over a 3 week period,
> with the end result being a new logo for your resource.
>
> Participation is limited to non-profits, and costs US$75. If you are
> interested, please see http://gmod.org/wiki/GMOD_Logo_Program for
> additional details and requirements, and an application form. The
> program is accepting applications until March 1.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
> PS: This program was inspired by ZFIN's success with its logo (see
> http://zfin.org).  ZFIN's excellent logo was created by working with a
> design class at the University of Oregon.
>
> --
> Please keep responses on the list!
> http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/GMOD_Logo_Program
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] 2010 GMOD Summer School - Americas

[Dave C. G. H. D. <he...@gm...>]

Hello all,

This is a reminder that the deadline for applying to the 2010 GMOD
Summer School - Americas is the end of the day on Monday, February 22,
which is now less than a week away.  Any applications received after
that will automatically be placed on the waiting list.

Admission is competitive and is based on the strength of the
application, especially the statement of interest.  See
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas for additional
information.

Thanks,

Dave Clements

On Fri, Jan 29, 2010 at 2:01 PM, Dave Clements, GMOD Help Desk
<he...@gm...> wrote:
> Hello all,
>
> I am pleased to announce that we are now accepting applications for:
>
>   2010 GMOD Summer School - Americas
>     6-9 May 2010
>     NESCent, Durham, NC, USA
>     http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> This will be a hands-on multi-day course aimed at teaching new GMOD
> users/administrators how to get GMOD Components up and running. The
> course will introduce participants to the GMOD project and then focus
> on installation, configuration and integration of popular GMOD
> Components. The course will be held May 6-9, at NESCent in Durham, NC.
>
> These components will be covered:
>    * Apollo - genome annotation editor
>    * Chado - a modular and extensible database schema
>    * Galaxy - workflow system
>    * GBrowse - the Generic Genome Browser
>    * GBrowse_syn - A generic synteny browser
>    * JBrowse - genome browser
>    * MAKER - genome annotation pipeline
>    * Tripal - web front end for Chado
>
> The deadline for applying is the end of Friday, February 22. Admission
> is competitive and is based on the strength of the application
> (especially the statement of interest). In 2009 there were over 50
> applications for the 25 slots. Any applications received after the
> deadline will be placed on the waiting list.
>
> See the course page for details and an application link:
>  http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
>
> PS: We are also investigating holding a GMOD course in the
> Asia/Pacific region, sometime this fall. Watch the GMOD mailing lists
> and the GMOD News page/RSS feed for updates.
> --
> Please keep responses on the list!
> http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/GMOD_News
> Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback