gmod-ajax — JBrowse list

[Gmod-ajax] Announcing the release ofJBrowse 1.3.0

[Robert B. <rb...@gm...>]

Hi all,

JBrowse version 1.3.0 has arrived!

We have a long list of improvements in this release, some of which have 
been a long time coming.  It’s full speed ahead from here: more major 
new features are just around the corner!

This release comes in two flavors: the “minimal” release 
(http://jbrowse.org/releases/JBrowse-1.3.0-min.zip - 2.0M) that includes 
only the software and documentation necessary to format your own data 
and run the browser, and the “full” release 
(http://jbrowse.org/releases/JBrowse-1.3.0-full.zip - 4.7M) that 
includes the developers’ test suite, more sample data files, and 
developer documentation.

One important note about browser support: as of this 1.3.0 release, 
JBrowse no longer supports Microsoft Internet Explorer 6.

Please see below for the full list of new features.

Rob

-- 
Robert Buels
Lead Developer
JBrowse - http://jbrowse.org


--------------------------------------

And now, the Big List of New Features (a.k.a. the release notes)!

1.3.0     2012-04-13 17:04:30 America/New_York

  * Added support for "rubberband" dynamic zooming, in which users can
    click and drag to select a region to zoom to.  Dragging on any
    scale bar, or shift-dragging on the main track pane, triggers a
    dynamic zoom.

  * Correcting a long-standing oversight, wiggle data tracks and
    feature histograms now have numerical y-axis scales that show the
    numerical values of the data.

  * Server-side data-formatting scripts now support a --compress option
    to compress (gzip) feature and sequence data to conserve server
    disk space.  Using this option requires some web server
    configuration.  Under Apache, AllowOverride FileInfo (or
    AllowOverride All) must be set for the JBrowse data directories in
    order to use the included .htaccess files, and mod_headers and
    mod_setenvif must be installed and enabled.  Under nginx a
    configuration snippet like the following should be included in the
    configuration:

       location ~* "\.(json|txt)z$" {
                add_header Content-Encoding  gzip;
                gzip off;
                types { application/json jsonz; }
       }

  * flatfile-to-json.pl: now much faster and more memory-efficient,
    especially for GFF3 files.  Remember that '###' directives are very
    important to have in large GFF3 files!  Also removed nonfunctional
    --extraData switch.

  * Added ability to turn off some JBrowse UI panels via URL arguments
    to the default index.html, or via arguments to the Browser
    constructor itself.  Can dynamically turn off the navigation box,
    the overview panel, and the track list, respectively.  When all of
    these are off, and if run in an iframe, JBrowse is running in an
    "embedded mode" that looks similar to the output of GBrowse's
    gbrowse_img script, with the exception that the view in this case
    is a fully functioning, scrollable and zoomable JBrowse.  See the
    GMOD wiki (http://gmod.org/wiki/JBrowse) for more on how to set up
    embedded mode.  Thanks to Julie Moon, a co-op student working at
    OICR, for this work!

  * Improved graphical look and feel.

  * Browser support for this release:
       * Google Chrome 18                perfect
       * Google Chrome 17                perfect
       * Mozilla Firefox 11.0            perfect
       * Mozilla Firefox 10.1            perfect
       * Mozilla Firefox 10.0.2          perfect
       * Mozilla Firefox 3.6.28          nonfunctional
       * Apple Safari 5.1.5 (Lion)       perfect
       * Microsoft Internet Explorer 9   perfect
       * Microsoft Internet Explorer 8   good
       * Microsoft Internet Explorer 7   minor problems
       * Microsoft Internet Explorer 6   not tested
       * KDE Konqueror 4.7.4             nonfunctional
       * KDE Konqueror 4.5.5             nonfunctional
       * Opera (all versions)            not tested

    NOTE: Internet Explorer 6 is no longer supported by JBrowse.

  * Added an automated-setup script, setup.sh, that tries to install
    Perl prerequisites, format Volvox example data, and install Wiggle
    and BAM support (fetching samtools from SVN if necessary)
    automatically.

  * Navigating to JBrowse with missing or malformed configuration or
    data will now bring up an error page with useful messages and links
    to help documentation, instead of a blank white page.

  * JBrowse data directories now include an Apache .htaccess in their
    root directory that, if mod_headers is installed and AllowOverride
    FileInfo or AllowOverride All is enabled, will emit the proper HTTP
    headers to allow cross-origin XHR requests for the data.

  * A new "Help" link in the upper right, or pressing "?" on the
    keyboard, brings up a "JBrowse Help" dialog box with basic usage
    information and links to more help information.

  * Arrowheads indicating strandedness are now drawn inside feature
    boundaries.

  * Clicking on the overview bar or the main scale bar now centers the
    view at the clicked position.  In addition, while holding down
    shift, clicking in the main track panel will also center the view
    at that position.

  * Added bin/remove-track.pl, a script to remove a track from a
    JBrowse data directory.  Run bin/remove-track.pl -? to see its
    documentation.

  * Added build instrumentation to support a JSDoc-based system of
    developer API documentation.  This documentation is still far from
    complete.

  * Ian Davis contributed code to add a view of the reverse strand of
    the sequence in the DNA track.  Thanks Ian!

  * Fixed bug in which, for some sequence chunk sizes, the DNA bases
    would display incorrectly.

  * Added minor gridlines to the main track view.

  * Fixed a long-standing off-by-one bug where the window could not be
    scrolled to view the last base in the reference sequence.

  * Coordinates displayed in the user interface are now 1-based closed
    coordinates, which are more familiar to most users.  Previously,
    the labels displayed interbase (i.e. 0-based half-open)
    coordinates.

  * NON-BACKWARDS-COMPATIBLE improvements to the JSON format used for
    track configuration, feature data, and image data
      - initial support for a new hook system for greater
        administrator-configurability of feature display
      - support for more than one level of subfeatures

  * Miscellaneous improvements and refactoring of data-formatting Perl
    code.

  * More detailed POD-based help documentation on all scripts

  * --tracklabel options to all scripts replaced with --trackLabel.

  * New suite of integration tests, and some unit tests, for
    server-side Perl code.

  * Beginnings of a suite of Selenium-based integration tests for the
    front-end JavaScript code.

  * Support for Apple touch-based devices merged into normal
    index.html, so that the same link can be used regardless of the
    browsing platform.

  * Bug fixed in which non-stranded features do not display properly
    (a problem with the CSS styles).

[Gmod-ajax] Reminder: JBrowse conference call today, 2pm Pacific / 5pm Eastern

[Robert B. <rb...@gm...>]

Hello JBrowse users and developers,

As a reminder, we will have a JBrowse developers' conference call today 
(April 16th) at 2pm Pacific time / 5pm Eastern time.  Call details are 
below; we hope you will can join in.

Initial Agenda:

* Rob's progress report since last meeting (March 12)

* JBrowse 1.3.0 release just out!

* Plans for JBrowse 1.4.0

* JBrowse at BOSC

Of course, feel free to suggest additional agenda items either through 
email or during the call.

Call details:

1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
(The toll-free number from Thailand is 001800656911)
2. Enter access code 4867508#

Talk to you then!

Rob

----
Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

Re: [Gmod-ajax] bug or anything else? in jbrowse-1.2.2?

[Robert B. <rb...@gm...>]

Hi Dan,

Sorry for the slow reply.  I haven't been able to reproduce this using 
what you pasted.  If you are still having this problem, could you send 
me the files you're using so I can try with them?

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 03/26/2012 11:35 PM, Íõñõ wrote:
>
> Hello, jbrowse developer and maintainers:
> I'm constructing several simple track of long_peptide and
> short_peptide(it's defined myself actually).
> My gff3 file is like this:
> #------------------------------------------------------------------------------------------------------------------------------
> chrY Peptide HS_pepshort 14945644 14945707 . . .
> ID=103222;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=EQHDALEFFNSLVDSLDEALK
> chrY Peptide HS_pepshort 14951894 14951921 . . .
> ID=104018;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=FNDYFEFPR
> chrY Peptide HS_pepshort 14954256 14954298 . . .
> ID=104160;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=FSEYLLECPSAEVR
> chrY Peptide HS_pepshort 1496884 1496935 . . .
> ID=107084;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=KAEDLFQDAYYQSPETR
> chrY Peptide HS_pepshort 59252511 59252550 . . . Parent=108050;
> chrY Peptide HS_pepshort 59272371 59272385 . . . Parent=108050;
> chrY Peptide HS_peplong 59252511 59272385 . . .
> ID=108050;SPID=P51809;NPID=NP_005629;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=LELLIDKTENLVDSSVTFK
> chrY Peptide HS_pepshort 1496671 1496710 . . .
> ID=108588;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=LLDICAAMGLLEK
> chrY Peptide HS_pepshort 1496971 1497013 . . .
> ID=109297;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=LTACQVATAFNLSR
> chrY Peptide HS_pepshort 14952053 14952122 . . .
> ID=109439;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=LVGVLVHSGQASGGHYYSYIIQR
> chrY Peptide HS_pepshort 14958376 14958406 . . .
> ID=109615;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=LYSVVSQLIR
> chrY Peptide HS_pepshort 15028333 15028354 . . . Parent=111967;
> chrY Peptide HS_pepshort 15028429 15028440 . . . Parent=111967;
> chrY Peptide HS_peplong 15028333 15028440 . . .
> ID=111967;SPID=O15523;NPID=NP_004651;mol_type=peptide;organism=Homo
> sapiens;Chromosome=Y;peptide=SPILVATAVAAR
> #----------------------------------------------------------------------------------------------------------------------------------
> and my json conf file is like this:
> #----------------------------------------------------------------------------------------------------------------------------------
> ...
> {
> "track": "HS_Peplong",
> "feature": ["HS_peplong"],
> "class": "feature2",
> "key": "HS_PepLong",
> "subfeatures":true,
> "subfeature_classes":{
> "HS_Pepshort":"feature3"}
> },
> {
> "track": "HS_Pepshort",
> "feature": ["HS_pepshort"],
> "class": "feature5",
> "key": "HS_PepShort"
> }
> ...
> #----------------------------------------------------------------------------------------------------------------------------------
> But when I execute biodb-to-json.pl, it always throws a exception:
> #----------------------------------------------------------------------------------------------------------------------------------
> does'nt have a primary id:
> ...
> #----------------------------------------------------------------------------------------------------------------------------------
> I'm very confused that the exception warning string starts with a
> character '' (?it's null indeed). I've seen warning sentences of this
> type several times ,and It's usually have a substring like :'10008'
> doesn't have a pr! imary id...
> And what confuses me more...
> When I add a ";" at the end of lines in gff3 data file after
> "Parent=XXX", I execute biodb-to-json profile there is no warning or
> exception any more...It works! I don't know why in fact...
> But after appending ";" after "Parent=XXX" another problem came up. All
> the subfeatures in the tracks (HS_peplong) are lost...And I don't know
> why either...
> Is there something wrong with my files or anything else? Thanks for your
> answers and help.
> Dan
>
>
>
>
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Re: [Gmod-ajax] JBrowse tracks

[Robert B. <rb...@gm...>]

Hi Jerome,

Taking a look at this again, preparing for the 1.3.0 release in a few 
days.  Do you have a link to a JBrowse where I can see the sort of data 
you're dealing with that prompted this question about vertical track 
scrolling?

Rob

Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/10/2012 03:29 AM, Mariette wrote:
>
> Thanks for your answer, I did it,
> looking forward this feature,
>
> Jerome
>
>
>
> Le 09/02/2012 18:24, Robert Buels a écrit :
>> On 02/09/2012 11:12 AM, Mariette wrote:
>>> Yes, I'd like to offer to the user a view like IGV but in a web browser.
>>> (So the user can see all the reads)
>>
>> Yeah, I agree this would probably be a good feature for that.  Would
>> you mind adding it to the issue tracker at
>> http://github.com/GMOD/jbrowse/issues?
>>
>> In the mean time, have you considered converting your NGS alignments
>> to wiggle data that just shows the coverage?  Depending on what you're
>> using the data for, that can often be sufficient.
>>
>> Rob
>
>
> ------------------------------------------------------------------------------
> Virtualization&  Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

[Gmod-ajax] bug or anything else? in jbrowse-1.2.2?

[王聃 <wan...@16...>]

Hello, jbrowse developer and maintainers:
I'm constructing several simple track of long_peptide and short_peptide(it's defined myself actually).
My gff3 file is like this:
#------------------------------------------------------------------------------------------------------------------------------
chrY    Peptide    HS_pepshort    14945644    14945707    .    .    .    ID=103222;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=EQHDALEFFNSLVDSLDEALK
chrY    Peptide    HS_pepshort    14951894    14951921    .    .    .    ID=104018;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=FNDYFEFPR
chrY    Peptide    HS_pepshort    14954256    14954298    .    .    .    ID=104160;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=FSEYLLECPSAEVR
chrY    Peptide    HS_pepshort    1496884    1496935    .    .    .    ID=107084;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=KAEDLFQDAYYQSPETR
chrY    Peptide    HS_pepshort    59252511    59252550    .    .    .    Parent=108050;
chrY    Peptide    HS_pepshort    59272371    59272385    .    .    .    Parent=108050;
chrY    Peptide    HS_peplong    59252511    59272385    .    .    .    ID=108050;SPID=P51809;NPID=NP_005629;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=LELLIDKTENLVDSSVTFK
chrY    Peptide    HS_pepshort    1496671    1496710    .    .    .    ID=108588;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=LLDICAAMGLLEK
chrY    Peptide    HS_pepshort    1496971    1497013    .    .    .    ID=109297;SPID=O95671;NPID=NP_004183;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=LTACQVATAFNLSR
chrY    Peptide    HS_pepshort    14952053    14952122    .    .    .    ID=109439;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=LVGVLVHSGQASGGHYYSYIIQR
chrY    Peptide    HS_pepshort    14958376    14958406    .    .    .    ID=109615;SPID=O00507;NPID=NP_004645;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=LYSVVSQLIR
chrY    Peptide    HS_pepshort    15028333    15028354    .    .    .    Parent=111967;
chrY    Peptide    HS_pepshort    15028429    15028440    .    .    .    Parent=111967;
chrY    Peptide    HS_peplong    15028333    15028440    .    .    .    ID=111967;SPID=O15523;NPID=NP_004651;mol_type=peptide;organism=Homo sapiens;Chromosome=Y;peptide=SPILVATAVAAR
#----------------------------------------------------------------------------------------------------------------------------------
and my json conf file is like this:
#----------------------------------------------------------------------------------------------------------------------------------
...
{
      "track": "HS_Peplong",
      "feature": ["HS_peplong"],
      "class": "feature2",
      "key": "HS_PepLong",
    "subfeatures":true,
    "subfeature_classes":{
    "HS_Pepshort":"feature3"
}
},
{
    "track": "HS_Pepshort",
      "feature": ["HS_pepshort"],
      "class": "feature5",
      "key": "HS_PepShort"
}
...
#----------------------------------------------------------------------------------------------------------------------------------
But when I execute biodb-to-json.pl, it always throws a exception:
#----------------------------------------------------------------------------------------------------------------------------------
 does'nt have a primary id:
...
#----------------------------------------------------------------------------------------------------------------------------------
I'm very confused that the exception warning string starts with a character '' (?it's null indeed). I've seen warning sentences of this type several times ,and It's usually have a substring like :'10008' doesn't have a primary id...
And what confuses me more...
When I add a ";" at the end of lines in gff3 data file after "Parent=XXX", I execute biodb-to-json profile there is no warning or exception any more...It works! I don't know why in fact...
But after appending ";" after "Parent=XXX" another problem came up. All the subfeatures in the tracks (HS_peplong) are lost...And I don't know why either...
Is there something wrong with my files or anything else? Thanks for your answers and help.
Dan

Re: [Gmod-ajax] Some questions about json conf files

[王聃 <wan...@16...>]

Thanks a lot , Rob.
Don


在 2012-03-26 04:47:17，"Robert Buels" <rb...@gm...> 写道： >On 03/25/2012 03:12 AM, 王聃 wrote: >> 1，I found that the track "Fingerprinted BACs" derived from example BAC >> in docs/tutorial/data_files/volvox.gff just showed a label. No matter >> how I edit the track configuration in volvox.json, it never showed me a >> complete track yet. I don't know why. > >This is a bug in the 1.2.1 release; features with no strand do not have  >CSS styles for display.  Release 1.2.2 is now available that fixes this  >issue, see http://jbrowse.org/jbrowse-1-2-2-released/ > >> 2, In the volvox.gff file there are many "example match" data lines >> there. And many lines with a different start and end share one common ID >> and name. Like seg15，there are about 15 segments named as "seg15". But >> in the jbrowse Alignments track, there is only one label as seg15 >> demonstrated clicked from the start: 39264 to the end: 48453. I don't >> know why. > >The Bio::DB::SeqFeature::Store::memory database backend, which is what  >the volvox.json example configuration uses, implicitly groups GFF3  >features that have the same Name attributes, similar to how the old GFF  >and GTF (a.k.a GFF2.5) formats worked.  This behavior is not strictly  >correct, but doesn't usually cause problems with standard GFF3 files,  >and is convenient for some users that have GFF3 files that are not very  >standards-compliant. > >Ro

Re: [Gmod-ajax] Some questions about json conf files

[Robert B. <rb...@gm...>]

On 03/25/2012 03:12 AM, Íõñõ wrote:
> 1£¬I found that the track "Fingerprinted BACs" derived from example BAC
> in docs/tutorial/data_files/volvox.gff just showed a label. No matter
> how I edit the track configuration in volvox.json, it never showed me a
> complete track yet. I don't know why.

This is a bug in the 1.2.1 release; features with no strand do not have 
CSS styles for display.  Release 1.2.2 is now available that fixes this 
issue, see http://jbrowse.org/jbrowse-1-2-2-released/

> 2, In the volvox.gff file there are many "example match" data lines
> there. And many lines with a different start and end share one common ID
> and name. Like seg15£¬there are about 15 segments named as "seg15". But
> in the jbrowse Alignments track, there is only one label as seg15
> demonstrated clicked from the start: 39264 to the end: 48453. I don't
> know why.

The Bio::DB::SeqFeature::Store::memory database backend, which is what 
the volvox.json example configuration uses, implicitly groups GFF3 
features that have the same Name attributes, similar to how the old GFF 
and GTF (a.k.a GFF2.5) formats worked.  This behavior is not strictly 
correct, but doesn't usually cause problems with standard GFF3 files, 
and is convenient for some users that have GFF3 files that are not very 
standards-compliant.

Rob

[Gmod-ajax] Some questions about json conf files

[王聃 <wan...@16...>]

Hello, everyone!
I'm always using the biodb-to-json perl script in bin directory to genenrate neccessary files in data. But today I found some problems: (volvox gff data and json configuration files in docs/tutorial/ as example ):
1，I found that the track "Fingerprinted BACs" derived from example BAC in docs/tutorial/data_files/volvox.gff just showed a label. No matter how I edit the track configuration in volvox.json, it never showed me a complete track yet. I don't know why.
2, In the volvox.gff file there are many "example match" data lines there. And many lines with a different start and end share one common ID and name. Like seg15，there are about 15 segments named as "seg15". But in the jbrowse Alignments track, there is only one label as seg15 demonstrated clicked from the start: 39264 to the end: 48453. I don't know why.
Thanks a lot.
Dan

Re: [Gmod-ajax] BED File

[Jawahar S. <gs...@sa...>]

Rob,
Many thanks.. Works perfectly! Thank you for your rapid response on this
issue.

Jawahar


On 22/03/2012 18:27, "Robert Buels" <rb...@gm...> wrote:

> Hi Jawahar,
> 
> OK, I just made a new hg19 tarball based on JBrowse 1.2.1 and posted it:
> 
> http://jbrowse.org/hg19-tarball-updated-to-jbrowse-1-2-1/
> 
> Does this work better?
> 
> Rob
> 
> On 03/22/2012 03:14 AM, Jawahar Swaminathan wrote:
>> Hi Robert,
>> I've managed to trace the problem back to my including the hg19-mini
>> tarball, which overwrote the jbrowse-1.2.1 js with that of version 1.1. What
>> I really wanted to do was to overlay my custom tracks on top of the existing
>> human genome annotation from your tarball download.
>> 
>> Re-installing jbrowser-1.2.1 and then copying over the data directory from
>> the tarball allows the inclusion of my custom bed file into jbrowse.
>> However, while all the labels for human annotation show up, there is really
>> no data associated with them. I've attached a screenshot to show you what I
>> mean. Any suggestion at all on what I could do?
>> 
>> So, is it possible to have a version 1.2.1 of jbrowse with data like you did
>> for version 1.1? That would be absolutely brilliant!
>> 
>> Thanks - Jawahar
>> 
>> 
>> On 22/03/2012 02:42, "Robert Buels"<rb...@gm...>  wrote:
>> 
>>> Hi Jawahar,
>>> 
>>> I haven't been able to reproduce this.  If you're still having this
>>> problem, could you load Carp::Always to force a backtrace and send that?
>>>    Something like this should do the trick:
>>> 
>>> perl -MCarp::Always bin/flatfile-to-json.pl --bed
>>> /Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel
>>> Decipher ‹key Decipher
>>> 
>>> You might need to install Carp::Always from CPAN first if you don't
>>> already have it.
>>> 
>>> Rob
>>> 
>>> 
>>> ----
>>> Robert Buels
>>> Lead Developer
>>> JBrowse Project, http://jbrowse.org
>>> 
>>> On 03/20/2012 08:01 AM, Jawahar Swaminathan wrote:
>>>> Hi
>>>> I¹m trying to include a BED file in a local install of jbrowse by using
>>>> bin/flatfile-to-json.pl and get a rather strange error.
>>>> 
>>>> bin/flatfile-to-json.pl --bed
>>>> /Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel
>>>> Decipher ‹key Decipher
>>>> 
>>>> chr1 915
>>>> Not an ARRAY reference at
>>>> /Users/gs9/Apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 217,
>>>> <GEN1>  line 11326.
>>>> 
>>>> This BED file contains only 3 tab-separated columns at the moment:
>>>> 
>>>> hrX 62351481 62546017
>>>> chr21 39156413 43816220
>>>> chr1 928301 1155984
>>>> chr14 20784119 21860987
>>>> chr19 33621788 35647292
>>>> 
>>>> And is read perfectly by the UCSC genome browser.
>>>> 
>>>> The error isn¹t exactly making it obvious where the problem is. I¹m
>>>> using version 1.2.1 of jbrowse.
>>>> 
>>>> Any suggestions?
>>>> 
>>>> Jawahar
>>>> 
>>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>>> Limited, a charity registered in England with number 1021457 and a compa
>>>> ny registered in England with number 2742969, whose registered office is
>>>> 2 15 Euston Road, London, NW1 2BE.
>>>> 
>>>> 
>>>> 
>>>> 
>> -----------------------------------------------------------------------------
>> >>
>> -
>>>> This SF email is sponsosred by:
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>>>> 
>>>> 
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>> 
>> --
>> Dr Jawahar Swaminathan
>> DECIPHER Project Manager
>> Wellcome Trust Sanger Institute
>> Wellcome Trust Genome Campus
>> Hinxton, Cambridge UK, CB10 1SA
>> Tel: +44 (0)1223 492392
>> Email: gan...@sa...
>> Helpdesk: dec...@sa...
>> Web: http://decipher.sanger.ac.uk



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] BED File

[Robert B. <rb...@gm...>]

Hi Jawahar,

OK, I just made a new hg19 tarball based on JBrowse 1.2.1 and posted it:

http://jbrowse.org/hg19-tarball-updated-to-jbrowse-1-2-1/

Does this work better?

Rob

On 03/22/2012 03:14 AM, Jawahar Swaminathan wrote:
> Hi Robert,
> I've managed to trace the problem back to my including the hg19-mini
> tarball, which overwrote the jbrowse-1.2.1 js with that of version 1.1. What
> I really wanted to do was to overlay my custom tracks on top of the existing
> human genome annotation from your tarball download.
>
> Re-installing jbrowser-1.2.1 and then copying over the data directory from
> the tarball allows the inclusion of my custom bed file into jbrowse.
> However, while all the labels for human annotation show up, there is really
> no data associated with them. I've attached a screenshot to show you what I
> mean. Any suggestion at all on what I could do?
>
> So, is it possible to have a version 1.2.1 of jbrowse with data like you did
> for version 1.1? That would be absolutely brilliant!
>
> Thanks - Jawahar
>
>
> On 22/03/2012 02:42, "Robert Buels"<rb...@gm...>  wrote:
>
>> Hi Jawahar,
>>
>> I haven't been able to reproduce this.  If you're still having this
>> problem, could you load Carp::Always to force a backtrace and send that?
>>    Something like this should do the trick:
>>
>> perl -MCarp::Always bin/flatfile-to-json.pl --bed
>> /Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel
>> Decipher ‹key Decipher
>>
>> You might need to install Carp::Always from CPAN first if you don't
>> already have it.
>>
>> Rob
>>
>>
>> ----
>> Robert Buels
>> Lead Developer
>> JBrowse Project, http://jbrowse.org
>>
>> On 03/20/2012 08:01 AM, Jawahar Swaminathan wrote:
>>> Hi
>>> I¹m trying to include a BED file in a local install of jbrowse by using
>>> bin/flatfile-to-json.pl and get a rather strange error.
>>>
>>> bin/flatfile-to-json.pl --bed
>>> /Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel
>>> Decipher ‹key Decipher
>>>
>>> chr1 915
>>> Not an ARRAY reference at
>>> /Users/gs9/Apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 217,
>>> <GEN1>  line 11326.
>>>
>>> This BED file contains only 3 tab-separated columns at the moment:
>>>
>>> hrX 62351481 62546017
>>> chr21 39156413 43816220
>>> chr1 928301 1155984
>>> chr14 20784119 21860987
>>> chr19 33621788 35647292
>>>
>>> And is read perfectly by the UCSC genome browser.
>>>
>>> The error isn¹t exactly making it obvious where the problem is. I¹m
>>> using version 1.2.1 of jbrowse.
>>>
>>> Any suggestions?
>>>
>>> Jawahar
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a compa
>>> ny registered in England with number 2742969, whose registered office is
>>> 2 15 Euston Road, London, NW1 2BE.
>>>
>>>
>>>
>>>
> ----------------------------------------------------------------------------->>
> -
>>> This SF email is sponsosred by:
>>> Try Windows Azure free for 90 days Click Here
>>> http://p.sf.net/sfu/sfd2d-msazure
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> --
> Dr Jawahar Swaminathan
> DECIPHER Project Manager
> Wellcome Trust Sanger Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge UK, CB10 1SA
> Tel: +44 (0)1223 492392
> Email: gan...@sa...
> Helpdesk: dec...@sa...
> Web: http://decipher.sanger.ac.uk

Re: [Gmod-ajax] BED File

[Robert B. <rb...@gm...>]

Hi Jawahar,

I haven't been able to reproduce this.  If you're still having this 
problem, could you load Carp::Always to force a backtrace and send that? 
  Something like this should do the trick:

perl -MCarp::Always bin/flatfile-to-json.pl --bed 
/Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel 
Decipher —key Decipher

You might need to install Carp::Always from CPAN first if you don't 
already have it.

Rob


----
Robert Buels
Lead Developer
JBrowse Project, http://jbrowse.org

On 03/20/2012 08:01 AM, Jawahar Swaminathan wrote:
> Hi
> I’m trying to include a BED file in a local install of jbrowse by using
> bin/flatfile-to-json.pl and get a rather strange error.
>
> bin/flatfile-to-json.pl --bed
> /Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel
> Decipher —key Decipher
>
> chr1 915
> Not an ARRAY reference at
> /Users/gs9/Apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 217,
> <GEN1> line 11326.
>
> This BED file contains only 3 tab-separated columns at the moment:
>
> hrX 62351481 62546017
> chr21 39156413 43816220
> chr1 928301 1155984
> chr14 20784119 21860987
> chr19 33621788 35647292
>
> And is read perfectly by the UCSC genome browser.
>
> The error isn’t exactly making it obvious where the problem is. I’m
> using version 1.2.1 of jbrowse.
>
> Any suggestions?
>
> Jawahar
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a compa
> ny registered in England with number 2742969, whose registered office is
> 2 15 Euston Road, London, NW1 2BE.
>
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] BED File

[Jawahar S. <gs...@sa...>]

Hi
I¹m trying to include a BED file in a local install of jbrowse by using
bin/flatfile-to-json.pl and get a rather strange error.

bin/flatfile-to-json.pl --bed
/Volumes/nfs/DECIPHER/genomemaps/decipher_bed_new.txt --tracklabel Decipher
‹key Decipher

chr1    915
Not an ARRAY reference at
/Users/gs9/Apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 217,
<GEN1> line 11326.

This BED file contains only 3 tab-separated columns at the moment:

hrX    62351481        62546017
chr21   39156413        43816220
chr1    928301  1155984
chr14   20784119        21860987
chr19   33621788        35647292

And is read perfectly by the UCSC genome browser.

The error isn¹t exactly making it obvious where the problem is. I¹m using
version 1.2.1 of jbrowse.

Any suggestions?

Jawahar




-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 

 Limited, a charity registered in England with number 1021457 and a 
 compa
ny registered in England with number 2742969, whose registered 
 office is 2
15 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] using jbrowse to visualize protein annotation

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

SGD (yeastgenome.org) used to have a "Protein browser" that used
GBrowse to display protein domains on a protein.  They just used
protein coordinates rather than DNA coordinates, and GBrowse didn't
care (GBrowse did have the ability to rename the coordinate space, so
it didn't label the x axis "kb" or the like).  I bet you could do the
same thing with JBrowse.

Scott


On Thu, Mar 15, 2012 at 11:17 AM, Robert Buels <rb...@gm...> wrote:
> Hi Guy,
>
> I myself don't know if anybody has done this, but I think it would
> probably work.  And if it doesn't work, I can probably fix it so that it
> will work in the 1.3.0 release, which will be pretty soon.
>
> Try just making a fasta file of protein sequences and some GFF or BED
> files that define features on them, and try loading them the same as you
> would genomic data.
>
> Let me know how it goes, and if you run into any problems.
>
> Rob
>
> ----
> Robert Buels
> Lead Developer
> JBrowse Project, http://jbrowse.org
>
>
>
> On 03/14/2012 01:13 PM, Guy Yachdav wrote:
>> Dear Jbrowse devs and maintainers,
>>
>> I am maintaining the PredictProtein service (www.predictprotein.org
>> <http://www.predictprotein.org>) provided by Burkhard Rost's group in
>> Munich, Germany. The service provides protein feature annotation for
>> almost a dozen different protein features. Most of the predicted
>> features are position based, either two or multiple state predictions
>> and in most cases are also expressed with a prediction confidence value.
>> To visualize our annotation we are using our in-house javascript library
>> called jBio (http://jbio.sourceforge.net/). Unfortunately. that project
>> is no longer maintained and we decided to use some off-the-shelf
>> solution if possible.
>>
>> I liked the capability and simplicity of jBrowse. Most of the existing
>> features like adding and removing tracks, zooming and panning fit our
>> needs. However when I looked at the process of preparing the data to be
>> rendered and displayed by jBrowse, i saw that the scripts are mostly
>> DNA-centric. My question is then - can jBrowse be easily adapted to the
>> protein world? are there such plans. Was it done by anyone else before?
>>
>> Thanks for your help,
>> Guy
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF email is sponsosred by:
>> Try Windows Azure free for 90 days Click Here
>> http://p.sf.net/sfu/sfd2d-msazure
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
> _______________________________________________
> 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] using jbrowse to visualize protein annotation

[Robert B. <rb...@gm...>]

Hi Guy,

I myself don't know if anybody has done this, but I think it would 
probably work.  And if it doesn't work, I can probably fix it so that it 
will work in the 1.3.0 release, which will be pretty soon.

Try just making a fasta file of protein sequences and some GFF or BED 
files that define features on them, and try loading them the same as you 
would genomic data.

Let me know how it goes, and if you run into any problems.

Rob

----
Robert Buels
Lead Developer
JBrowse Project, http://jbrowse.org



On 03/14/2012 01:13 PM, Guy Yachdav wrote:
> Dear Jbrowse devs and maintainers,
>
> I am maintaining the PredictProtein service (www.predictprotein.org
> <http://www.predictprotein.org>) provided by Burkhard Rost's group in
> Munich, Germany. The service provides protein feature annotation for
> almost a dozen different protein features. Most of the predicted
> features are position based, either two or multiple state predictions
> and in most cases are also expressed with a prediction confidence value.
> To visualize our annotation we are using our in-house javascript library
> called jBio (http://jbio.sourceforge.net/). Unfortunately. that project
> is no longer maintained and we decided to use some off-the-shelf
> solution if possible.
>
> I liked the capability and simplicity of jBrowse. Most of the existing
> features like adding and removing tracks, zooming and panning fit our
> needs. However when I looked at the process of preparing the data to be
> rendered and displayed by jBrowse, i saw that the scripts are mostly
> DNA-centric. My question is then - can jBrowse be easily adapted to the
> protein world? are there such plans. Was it done by anyone else before?
>
> Thanks for your help,
> Guy
>
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Displaying dense data

[Robert B. <rb...@gm...>]

Hi Kurt,

As far as I can tell, you have done everything right so far.  This is 
probably some kind of bug in JBrowse, but I need a little more 
information to figure out what the problem is.

Is this site public?  Do you have a URL where I can see this problem 
happening?

If there is no where I can look at it, do you have any javascript error 
messages in your browser when this happens?  Depending on what browser 
you are using, these messages will usually come up as a little 
exclamation point or X in the lower right corner of the browser window.

Rob


On 03/15/2012 09:50 AM, Kurt Canobi wrote:
> Hello
>
> I'm trying to load datasets into JBrowse using flatfile-to-json.pl
> <http://flatfile-to-json.pl> - the data is very dense in some points
> where there may be multiple features at a single base position. The data
> seems to load in okay but all I get in the JBrowse display is a big
> block where the features should be (see attached image). I've successful
> loaded other tracks (albeit that had much less data) in the same way so
> I can't figure out where I'm going wrong. Is there a specific way of
> loading in dense data? I've tried converting to bed format but have the
> same problem. See below for the commands that I'm running and also a
> snippet of one of the gff3 files, I've also attached a screenshot of
> what I'm getting.
>
> I'm completely out of ideas as to what might be wrong so if anyone can
> help it would be very much appreciated!
>
> Thanks
>
> Kurt
>
>
> ./bin/flatfile-to-json.pl <http://flatfile-to-json.pl> --gff
> ../jbrowse_data/test.gff3 --tracklabel test1 --key "test1"
> ./bin/generate-names.pl <http://generate-names.pl> --verbose
>
> chr1    dbsnp    snp    10144    10145    .    +    .    ID=rs144773400
> chr1    dbsnp    snp    10228    10229    .    +    .    ID=rs143255646
> chr1    dbsnp    snp    10233    10234    .    +    .    ID=rs145599635
> chr1    dbsnp    snp    10247    10248    .    +    .    ID=rs148908337
> chr1    dbsnp    snp    10254    10255    .    +    .    ID=rs140194106
> chr1    dbsnp    snp    10290    10291    .    +    .    ID=rs145427775
> chr1    dbsnp    snp    10326    10327    .    +    .    ID=rs112750067
> chr1    dbsnp    snp    10329    10330    .    +    .    ID=rs150969722
> chr1    dbsnp    snp    10433    10433    .    +    .    ID=rs56289060
> chr1    dbsnp    snp    10439    10440    .    +    .    ID=rs112155239
> chr1    dbsnp    snp    10439    10440    .    +    .    ID=rs112766696
> chr1    dbsnp    snp    10439    10440    .    +    .    ID=rs138941843
> chr1    dbsnp    snp    10491    10492    .    +    .    ID=rs55998931
>
>
>
>
> ------------------------------------------------------------------------------
> This SF email is sponsosred by:
> Try Windows Azure free for 90 days Click Here
> http://p.sf.net/sfu/sfd2d-msazure
>
>
>
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] using jbrowse to visualize protein annotation

[Guy Y. <gya...@gm...>]

Dear Jbrowse devs and maintainers, 

I am maintaining the PredictProtein service (www.predictprotein.org) provided by Burkhard Rost's group in Munich, Germany. The service provides protein feature annotation for almost a dozen different protein features. Most of the predicted features are position based, either two or multiple state predictions and in most cases are also expressed with a prediction confidence value. To visualize our annotation we are using our in-house javascript library called jBio (http://jbio.sourceforge.net/). Unfortunately. that project is no longer maintained and we decided to use some off-the-shelf solution if possible. 

I liked the capability and simplicity of jBrowse. Most of the existing features like adding and removing tracks, zooming and panning fit our needs. However when I looked at the process of preparing the data to be rendered and displayed by jBrowse,  i saw that the scripts are mostly DNA-centric. My question is then - can jBrowse be easily adapted to the protein world? are there such plans. Was it done by anyone else before?

Thanks for your help, 
Guy
 

[Gmod-ajax] Minutes: JBrowse conference call, March 12th, 2012

[Robert B. <rb...@gm...>]

Hi all,

Here are the minutes for the JBrowse conference call held just now.  The 
next meeting is scheduled for April 16, 2012 at 2pm US Pacific / 5pm US 
Eastern time.

--------------

ATTENDANCE
-----------

Rob Buels
Scott Cain
Chris Childers
Ian Holmes
Ed Lee
Gregg Helt
Lincoln Stein


MINUTES
---------

Rob progress report: Lots of bug fixes, several new feature
enhancements since last month.  In no particular order:

   - jbrowse_img merged in, thanks to Julie Moon
   - 1.3.0 release scheduled for before the GMOD meeting
   - fixed a number of bugs
   - changed all numbers in the user interface to be in one-based
     coordinates
   - added more gridlines in the main view
   - contribution of reverse-complemented DNA sequence by Ian Davis
   - added developer documentation to build system
   - more Selenium integration tests, refactored integration tests to
     be fairly well-written Python.
   - extensive work on formalizing JavaScript API for JBrowse data
     backends
   - issue tracker organized (http://github.com/gmod/jbrowse/issues),
     with milestones for the 1.3.0 and 2.0.0 releases.

Discussion of adding a "flip plus/minus" button to JBrowse.  Rob
agrees it's a good feature, asked Greg to add it to the bug tracker.

Ian says that high-value data sets need to be formatted with the new
release.

Contact Ian Durham at EBI for getting large datasets of modENCODE data
to format with JBrowse.

Lincoln points out that JBrowse really needs the ability to make
cross-origin requests to data sets.  Decouple the code from the data
sets.

Gregg has some experimental support for loading BAM data directly with
HTTP byte range requests.  Uses HTML5 binary-format support.  When
merged into master, will need to make sure that it degrades gracefully
on browsers that don't support typed arrays.

During Rob's visit, need to codify and formalize the API for JBrowse
data backends.

Gregg noticed that in the new layout, the arrowheads are not taken
into account when laying out features.  Rob pointed out that
https://github.com/GMOD/jbrowse/issues/41 is related to this.  Some
discussion about this, Rob says he will put the arrowheads inside the
feature boundaries.

Gregg notes that WebApollo is going into a code freeze soon, as a
first beta release that collaborators will actually use.

Next meeting scheduled for: April 16, 2pm Pacific / 5pm Eastern

Re: [Gmod-ajax] refSeqs & trackInfo

[Robert B. <rb...@gm...>]

That's a good question.  I still don't have a complete list of all the 
things that need to go in the next release, but I'm working on getting 
that together.

Rob

On 03/02/2012 03:10 AM, Mariette wrote:
>
> Thanks Rob for your answer!
>
> When do you think the new vesion will be released ?
> (It's just to know if I have to implement something to make jbrowse work
> with the current version)
>
> Jerome
>
>
>
> Le 01/03/2012 18:12, Robert Buels a écrit :
>> Hi Jerome,
>>
>> In JBrowse 1.2.1, the data/refSeqs.js and data/trackInfo.js must be
>> included in the index.html.
>>
>> In the coming release, however, this will be passable as a parameter
>> to the JBrowse object.
>>
>> Rob
>>
>> On 03/01/2012 11:28 AM, Mariette wrote:
>>> Hi everyone,
>>>
>>> I have hard time to understand how is managed the refSeqs& the
>>> trackInfo params when building a jbrowse object.
>>> I'd like to set the path to the js but it's not working. There is any
>>> way to provide the right path to the js file other than
>>> including it inside the html page ?
>>>
>>> thanks for your reply,
>>> Jerome
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> Virtualization& Cloud Management Using Capacity Planning
>>> Cloud computing makes use of virtualization - but cloud computing
>>> also focuses on allowing computing to be delivered as a service.
>>> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>
>

[Gmod-ajax] Reminder: JBrowse conference call, March 12th, 2pm Pacific / 5pm Eastern

[Robert B. <rb...@gm...>]

Hello JBrowse users and developers,

As a reminder, the next JBrowse developers' conference call will be held 
on Monday, March 12, at 2pm Pacific time / 5pm Eastern time / .  Call 
details are below; we hope you will can join in.

Don't forget, the transition to US Daylight Saving Time is on the Sunday 
before the call.

Initial Agenda:

* Rob's progress report since last meeting (Feb 13)

* Set working priorities for Rob's visit to Berkeley March 18 - 27.

      - Rob's initial suggestion: that week, prioritize merging, then
        refactoring JBrowse and WebApollo code so that broadly-applicable
        features are merged into JBrowse master, and WebApollo is a true
        layer on top of JBrowse.

Of course, feel free to suggest additional agenda items either through 
email or during the call.

Call details:

1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
(The toll-free number from Thailand is 001800656911)
2. Enter access code 4867508#

Talk to you then!

Rob
----
Robert Buels
JBrowse Lead Developer

Re: [Gmod-ajax] Cannot open jbrowse.org

[Robert B. <rb...@gm...>]

Hi Dan,

That's very unfortunate.  You can also download the JBrowse releases 
from https://github.com/GMOD/jbrowse/tags.  Does that work for you?

Rob

On 03/07/2012 10:49 PM, Íõñõ wrote:
> Hello, everyone!
> I'm a jbrowse user from Chinese mainland. As the restricted connection
> to the Internet of our goverment, some .org websites cannot be
> connected, jbrowse included...Can some developers put the latest and
> updated jbrowse software files on sourceforge Generic Model Organism
> Database Project <https://sourceforge.net/projects/gmod/> please? I saw
> a lot of GMOD software tools there...
> Thanks a lot!
> Wang Dan
>
>
> ------------------------------------------------------------------------
> Èý°Ë½Ú£¬ÍøÒ×΢²©ÌæÄÐÈËÉìÔ©£¡
> <http://pub.t.163.com/special/weibotupian/3838.html?from=mail>
>
>
>
> ------------------------------------------------------------------------------
> Virtualization&  Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
> http://www.accelacomm.com/jaw/sfnl/114/51521223/
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] Cannot open jbrowse.org

[王聃 <wan...@16...>]

Hello, everyone!
  I'm a jbrowse user from Chinese mainland. As the restricted connection to the Internet of our goverment, some .org websites cannot be connected, jbrowse included...Can some developers put the latest and updated jbrowse software files on sourceforge Generic Model Organism Database Project please? I saw a lot of GMOD software tools there...
  Thanks a lot!
Wang Dan

[Gmod-ajax] April GMOD meeting early registration

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

Hello,

This is a reminder that there is only a little over two days left to
get in on early registration for the April 2012 GMOD meeting.  In
addition to getting a $10 discount on the registration fee, you will
be entered in a drawing to get a GMOD coffee cup or T-shirt.  There
are some very good speakers and topics lined up for the meeting; I'm
looking forward to a good one.  Please see:

  http://gmod.org/wiki/April_2012_GMOD_Meeting

for more information on the meeting, and to:

  http://gmod2012.eventbrite.com/

to register for the meeting.  I look forward to seeing you next month.

Scott


-- 
------------------------------------------------------------------------
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] setting up jbrowse with a bacterial reference genome

[Heewook L. <he...@um...>]

Thanks!

-hl

On Fri, Mar 2, 2012 at 10:12 AM, Robert Buels <rb...@gm...> wrote:

> On 02/29/2012 06:45 PM, Heewook Lee wrote:
>
>> Right now, i am using triangle from genome.css to display a SNP and when
>> you zoom all the way in(1bp-resolution), the triangle will turn
>> into isosceles trapezoid because it takes up 2bp.
>>
>
> I looked into this 2-base issue, and I think it's caused by the fact that
> the triangle glyph is implemented with a hackish CSS trick involving border
> widths, and this turns out not to work very well for single-base features.
>  Try using a different glyph for your SNPs. "dblhelix" might be an OK one.
>
> As for the interbase (i.e. 0-based half-open) coordinates issue, I have a
> ticket open to show everything in the user interface as 1-based
> coordinates.  It's https://github.com/GMOD/**jbrowse/issues/74<https://github.com/GMOD/jbrowse/issues/74>.
>  I'm actually working on that right now, since it's both important and a
> relatively easy fix.
>
> Rob
>

Re: [Gmod-ajax] setting up jbrowse with a bacterial reference genome

[Robert B. <rb...@gm...>]

On 02/29/2012 06:45 PM, Heewook Lee wrote:
> Right now, i am using triangle from genome.css to display a SNP and when
> you zoom all the way in(1bp-resolution), the triangle will turn
> into isosceles trapezoid because it takes up 2bp.

I looked into this 2-base issue, and I think it's caused by the fact 
that the triangle glyph is implemented with a hackish CSS trick 
involving border widths, and this turns out not to work very well for 
single-base features.  Try using a different glyph for your SNPs. 
"dblhelix" might be an OK one.

As for the interbase (i.e. 0-based half-open) coordinates issue, I have 
a ticket open to show everything in the user interface as 1-based 
coordinates.  It's https://github.com/GMOD/jbrowse/issues/74.  I'm 
actually working on that right now, since it's both important and a 
relatively easy fix.

Rob

Re: [Gmod-ajax] refSeqs & trackInfo

[Mariette <jma...@to...>]

Thanks Rob for your answer!

When do you think the new vesion will be released ?
(It's just to know if I have to implement something to make jbrowse work 
with the current version)

Jerome



Le 01/03/2012 18:12, Robert Buels a écrit :
> Hi Jerome,
>
> In JBrowse 1.2.1, the data/refSeqs.js and data/trackInfo.js must be 
> included in the index.html.
>
> In the coming release, however, this will be passable as a parameter 
> to the JBrowse object.
>
> Rob
>
> On 03/01/2012 11:28 AM, Mariette wrote:
>> Hi everyone,
>>
>> I have hard time to understand how is managed the refSeqs&  the
>> trackInfo params when building a jbrowse object.
>> I'd like to set the path to the js but it's not working. There is any
>> way to provide the right path to the js file other than
>> including it inside the html page ?
>>
>> thanks for your reply,
>> Jerome
>>
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