gmod-ajax — JBrowse list

Re: [Gmod-ajax] Genome browser

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

Hi Gary,

We'd be delighted to follow up with you and help you play with & extend
JBrowse, and would enthusiastically welcome you to the project!

I am CC'ing Mitch Skinner (lead JBrowse developer) and the gmod-ajax
mailing list (the main public forum for JBrowse discussions).

The main JBrowse site is
http://jbrowse.org/

There are links from there to the mailing list, our code repositories,
demos, our bug/feature trackers, etc.

Our imminent plans include opening up the JBrowse API with examples so
people can customize their own features, tracks, images, javascript
behavior etc.

Please do let us know how you get on,
Ian


Gary Churchill wrote:
> Thanks Kevin.  We will follow up on these leads.
> 
> All the best,
> 
> Gary
> 
> 
> On 9/15/09 12:17 AM, "Kevin White" <kp...@uc...> wrote:
> 
> Hi Gary
> 
> Actually we started a project but then realized that a CS group at Berkeley led by Ian Holmes was already working on this kind of a project. For our immediate purposes, implementing their new browser, JBrowse, and making modifications (or suggestions on improvement priorities to Ian's group) has worked pretty well.  If you have not taken a look at it already, I would suggest to do so.  It may have some of the features you are looking for already, or could be modified to do what you need.  I am ccing Ian here, as well as Bob Grossman who is the local faculty in Chicago on our Center grant who implemented Ian's browser.
> 
> Here are references to very recent papers from Ian's group and Bob's & mine.
> 
> JBrowse: A next-generation genome browser. Skinner ME <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Skinner%20ME%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Uzilov AV <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Uzilov%20AV%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Stein LD <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Stein%20LD%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Mungall CJ <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Mungall%20CJ%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> , Holmes IH <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Holmes%20IH%22%5BAutho
r%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DiscoveryPanel.Pubmed_RVAbstractPlus> . Genome Res. <javascript:AL_get(this,%20'jour',%20'Genome%20Res.');> 2009 Sep;19(9):1630-8. Epub 2009 Jul 1.
> Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. <http://www.ncbi.nlm.nih.gov/pubmed/19656951?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum>  Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP, Grossman RL. Bioinformatics. 2009 Aug 5.
> 
> To see our implementation of JBrowse, please check out this site:  https://www.cistrack.org/flynet/
> You can play around with our site to get a feel for at least one instance of it.
> 
> There are definitely improvements/features that we would like to see on JBrowse, but as far as an AJAX enabled genome browser this is the most advanced I know of and might be a good starting point.  What are some of the features you are thinking about?  For us, a parallel window with chromosome "cartoons" with annotation and dynamically selectable for browsing on the main browser would be pretty cool.  Might be useful for rapidly browsing different QTL for you guys.  Adding WIG files or nextgen sequencing peak calling or RNA calling  summaries as tracks (something we just need to do - I think JBrowse will already support this), is one of the high priorities on our local agenda.  Of course we are happy to share any tools, experience, etc... with you.  Obviously Ian's group did the heavy lifting already on the main browser infrastructure, for which we are extremely appreciative!
> 
> Kevin
> 
> 
> From: Gary Churchill [mailto:Gar...@ja...]
> Sent: Monday, September 14, 2009 3:51 PM
> To: kp...@uc...
> Cc: Keith Sheppard; Imogen Hurley; nn...@bs...
> Subject: Genome browser
> 
> Kevin,
> 
> We have been discussing strategies to develop an improved genome browser - inspired by Google Finance.  Keith Sheppard,  SE in my group, has come up with a plan to develop a genome using AJAX technology.  When it came up at group meeting, Imogen pointed out that you may have a similar plan already underway.
> 
> We would be happy to adopt your browser, or to contribute to its development, or to compare plans.  Which depends on how far along your browser development is.   It could be viewed as a cross-center cooperation.  And we'd like to improve on the browser we have.
> 
> Let me know if you are interested in pursuing this.
> 
> Best regards,
> 
> Gary
> 
> 

Re: [Gmod-ajax] many tracks per GFF file

[Giles V. <gv...@sa...>]

On 15 Sep 2009, at 09:41, Giles Velarde wrote:

>
> On 11 Sep 2009, at 17:19, Mitch Skinner wrote:
>
>> On 09/11/2009 07:23 AM, Giles Velarde wrote:
>>> My apologies for sending this on a Friday afternoon. Since this is  
>>> my
>>> first mail to the list let me say that JBrowse looks fantastic.
>>
>> Thanks!
>>
>>>   bin/flatfile-to-json.pl -gff
>>> /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/Lmjchr10.gff
>>> --autocomplete all --getType --getLabel --getSubs -- 
>>> subfeatureClasses
>>> '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' --getPhase
>>>
>>>   bin/generate-names.pl -v
>>>
>>> This works fine (see screenshot below). However I don't see quite  
>>> how
>>> to split things up into several tracks using this approach.Should I
>>> be
>>> using a config file to do that? If that's the case, does anyone have
>>> an example config file for specifying loading from GFF files? The
>>> provided example is for a DB.
>>
>> You have two options; one is to use flatfile-to-json.pl with the --
>> type
>> command line parameter.  That allows you to filter the GFF file for
>> specific feature types (you can have more than one --type option on
>> the
>> command line).  The other option is to use a config file.  The  
>> example
>> in docs/tutorial/conf_files uses the Bio::DB::SeqFeature::Store
>> "memory"
>> adaptor, which reads a flat file into memory and then acts as a DB.
>> That allows you to use a config file with a GFF source of features.
>>
>> If you use flatfile-to-json.pl, you probably also want to specify the
>> --cssclass, --tracklabel, and --key command line parameters.
>>
>> Hope this helps; I'm assuming you want to organize your tracks by
>> feature type.
>>
>> Mitch
>>
>
>
> Thanks, Mitch! I'll have a go.
>


Using the config file does indeed seem to be the best option for me. I  
ended up writing a little bash script :

rm -rf data
for file in /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/*.gff
do
     echo "processing GFF file? $file"
     ./bin/prepare-refseqs.pl -gff $file --conf conf.json
done
./bin/biodb-to-json.pl --conf conf.json
./bin/generate-names.pl -v



and used it with the following conf file :




{
   "description": "GFF Database",
   "db_adaptor": "Bio::DB::SeqFeature::Store",
   "db_args": { "-adaptor": "memory",
                "-dir": "/data/gv1/gff3-ftp/export_2009-09-14/ 
Lmajor/" },

   "TRACK DEFAULTS": {
     "class": "feature",
     "autocomplete": "all",
      "urlTemplate": "http://beta.genedb.org/NamedFeature? 
name={load_id}",
       "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
   },

   "tracks": [
     {
         "track" : "Gene",
         "feature": ["gene"],
         "key" : "Gene Span",
         "class": "dblhelix",
         "category": "Gene Model features"
     }
   ]
}


Thanks again, Mitch!
Giles




-- 
 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] many tracks per GFF file

[Giles V. <gv...@sa...>]

On 11 Sep 2009, at 17:19, Mitch Skinner wrote:

> On 09/11/2009 07:23 AM, Giles Velarde wrote:
>> My apologies for sending this on a Friday afternoon. Since this is my
>> first mail to the list let me say that JBrowse looks fantastic.
>
> Thanks!
>
>>    bin/flatfile-to-json.pl -gff
>> /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/Lmjchr10.gff
>> --autocomplete all --getType --getLabel --getSubs --subfeatureClasses
>> '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' --getPhase
>>
>>    bin/generate-names.pl -v
>>
>> This works fine (see screenshot below). However I don't see quite how
>> to split things up into several tracks using this approach.Should I  
>> be
>> using a config file to do that? If that's the case, does anyone have
>> an example config file for specifying loading from GFF files? The
>> provided example is for a DB.
>
> You have two options; one is to use flatfile-to-json.pl with the -- 
> type
> command line parameter.  That allows you to filter the GFF file for
> specific feature types (you can have more than one --type option on  
> the
> command line).  The other option is to use a config file.  The example
> in docs/tutorial/conf_files uses the Bio::DB::SeqFeature::Store  
> "memory"
> adaptor, which reads a flat file into memory and then acts as a DB.
> That allows you to use a config file with a GFF source of features.
>
> If you use flatfile-to-json.pl, you probably also want to specify the
> --cssclass, --tracklabel, and --key command line parameters.
>
> Hope this helps; I'm assuming you want to organize your tracks by
> feature type.
>
> Mitch
>


Thanks, Mitch! I'll have a go.





-- 
 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] many tracks per GFF file

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

On 09/11/2009 07:23 AM, Giles Velarde wrote:
> My apologies for sending this on a Friday afternoon. Since this is my
> first mail to the list let me say that JBrowse looks fantastic.

Thanks!

>     bin/flatfile-to-json.pl -gff
> /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/Lmjchr10.gff
> --autocomplete all --getType --getLabel --getSubs --subfeatureClasses
> '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' --getPhase
>
>     bin/generate-names.pl -v
>
> This works fine (see screenshot below). However I don't see quite how
> to split things up into several tracks using this approach.Should I be
> using a config file to do that? If that's the case, does anyone have
> an example config file for specifying loading from GFF files? The
> provided example is for a DB.

You have two options; one is to use flatfile-to-json.pl with the --type 
command line parameter.  That allows you to filter the GFF file for 
specific feature types (you can have more than one --type option on the 
command line).  The other option is to use a config file.  The example 
in docs/tutorial/conf_files uses the Bio::DB::SeqFeature::Store "memory" 
adaptor, which reads a flat file into memory and then acts as a DB. 
That allows you to use a config file with a GFF source of features.

If you use flatfile-to-json.pl, you probably also want to specify the 
--cssclass, --tracklabel, and --key command line parameters.

Hope this helps; I'm assuming you want to organize your tracks by 
feature type.

Mitch

[Gmod-ajax] many tracks per GFF file

[Giles V. <gv...@sa...>]

Hi,

My apologies for sending this on a Friday afternoon. Since this is my  
first mail to the list let me say that JBrowse looks fantastic.

I am trying to set it up to run off GFFs. Currently for each file I am  
doing:

	bin/prepare-refseqs.pl -gff /data/gv1/gff3-ftp/export_2009-09-10/ 
Lmajor/Lmjchr10.gff

	bin/flatfile-to-json.pl -gff /data/gv1/gff3-ftp/export_2009-09-10/ 
Lmajor/Lmjchr10.gff  --autocomplete all --getType --getLabel --getSubs  
--subfeatureClasses '{"CDS": "transcript-CDS", "exon": "transcript- 
exon"}' --getPhase

	bin/generate-names.pl -v

This works fine (see screenshot below). However I don't see quite how  
to split things up into several tracks using this approach.Should I be  
using a config file to do that? If that's the case, does anyone have  
an example config file for specifying loading from GFF files? The  
provided example is for a DB.

Please forgive me ignorance!

Thanks
Giles







-- 
 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] Fwd: Developmental RNA-Seq

[Steven E. B. <br...@co...>]

Thanks Ian.  It does seem possible that the ruler would render the 
blurriness just a minor annoyance and not a functional limitation; it's 
hard to tell with my current view.

Steven

On Thu, 10 Sep 2009, Ian Holmes wrote:

> Yes, the blur is due to image rendering.
>
> It's certainly possible to fix, e.g. we could switch to a histogram built of 
> DIV elements, when you get to base resolution. (The image is mainly useful 
> for providing single-pixel resolution of WIG tracks, which is more important 
> when zoomed-out.)
>
> I suspect that with the vertical ruler (which is already on our list, but 
> this kind of feedback is invaluable in bumping it up towards the top) the 
> blurriness might be less of a critical problem, because the width of the blur 
> is actually small compared to the width of a base (but without the ruler, the 
> blur does make it harder to line up to individual bases by eye).
>
>
>
> Brenton Graveley wrote:
>> FYI - Steven's comments.  I haven't responded, but my understanding is that 
>> the blurriness at high magnification is a results of the image rendering? 
>> Not sure there is a solution...
>> 
>> Brent
>> 
>> 
>>> That does look fantastic.
>>> Two questions for high zoom to nucleotide level
>>> * Is there any way to not have wiggles get 'blurry' ?
>>> * Is there any way to have a vertical 'ruler' to see exactly what
>>>   base aligns with the tracks below?
>>> 
>>> Steven
>

Re: [Gmod-ajax] Fwd: Developmental RNA-Seq

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

On 09/10/2009 08:25 AM, Ian Holmes wrote:
>>> Two questions for high zoom to nucleotide level
>>> * Is there any way to not have wiggles get 'blurry' ?

Ah!  This is something I've been following.  The web browsers recently 
implemented the blurry scaling (because it looks nice in some contexts, 
though not in our case), and there was a backlash against it.  Now 
they're implementing a switch to turn it off; it'll be in firefox 3.6.  
A similar switch is also apparently implemented in internet explorer 7; 
something similar will probably also get implemented in Safari/Chrome if 
it hasn't been already.  Figuring out the mechanism in all the different 
browsers and setting it appropriately in JBrowse is definitely on the 
to-do list.

https://developer.mozilla.org/En/CSS/Image-rendering
https://bugzilla.mozilla.org/show_bug.cgi?id=423756
https://bugzilla.mozilla.org/show_bug.cgi?id=484150

>>> * Is there any way to have a vertical 'ruler' to see exactly what
>>>   base aligns with the tracks below?

This is also something we've talked about a bit; I've created ticket #44 
for this.

http://jbrowse.lighthouseapp.com/projects/23792-jbrowse/tickets/44-vertical-ruler

Mitch

Re: [Gmod-ajax] Fwd: Developmental RNA-Seq

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

Yes, the blur is due to image rendering.

It's certainly possible to fix, e.g. we could switch to a histogram 
built of DIV elements, when you get to base resolution. (The image is 
mainly useful for providing single-pixel resolution of WIG tracks, which 
is more important when zoomed-out.)

I suspect that with the vertical ruler (which is already on our list, 
but this kind of feedback is invaluable in bumping it up towards the 
top) the blurriness might be less of a critical problem, because the 
width of the blur is actually small compared to the width of a base (but 
without the ruler, the blur does make it harder to line up to individual 
bases by eye).



Brenton Graveley wrote:
> FYI - Steven's comments.  I haven't responded, but my understanding is 
> that the blurriness at high magnification is a results of the image 
> rendering?  Not sure there is a solution...
> 
> Brent
>  
> 
> 
>> That does look fantastic.
>> Two questions for high zoom to nucleotide level
>> * Is there any way to not have wiggles get 'blurry' ?
>> * Is there any way to have a vertical 'ruler' to see exactly what
>>   base aligns with the tracks below?
>>
>> Steven

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

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

I should also add that there's no reason someone couldn't port the
essential Perl scripts to Ruby. It's not something we plan to maintain
from here, but I think we'd all love to see that, and could offer
advice/help.

Ian Holmes wrote:
> Hi George,
> 
> Thanks for your interest in & kind comments about JBrowse.
> 
> Regarding your question, I'm afraid that currently we don't have any
> plans to port or maintain parallel implementations of the server
> components in other languages. The idea of a JavaScript implementation
> of the server algorithms is interesting, and a Ruby implementation would
> certainly be cool too. However JBrowse is a descendant of GBrowse and as
> such, will probably continue to use at least some Perl components for a
> while (if only to ensure a smooth GBrowse->JBrowse migration path).
> 
> It isn't too hard to call Perl scripts from Ruby, though -- right? Would
> there be any significant problem with doing that (other than having to
> install BioPerl)?
> 
> Best wishes,
> Ian
> 
> George Githinji wrote:
>> Hi,
>> Thanks for the efforts in developing Jbrowse.
>> Please I use  BioRuby for the bulk of my work, At the moment i would like to
>> embed a jbrowse viewer on a web page for a particular project I am are
>> working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
>> use for visualizing GFF files?
>>
>> Do I have to install bioperl? Are there plans to make Jbrowse bio-language
>> agnostic?
>>
>> Thanks!
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
>> trial. Simplify your report design, integration and deployment - and focus on 
>> what you do best, core application coding. Discover what's new with 
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

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

Hi George,

Thanks for your interest in & kind comments about JBrowse.

Regarding your question, I'm afraid that currently we don't have any
plans to port or maintain parallel implementations of the server
components in other languages. The idea of a JavaScript implementation
of the server algorithms is interesting, and a Ruby implementation would
certainly be cool too. However JBrowse is a descendant of GBrowse and as
such, will probably continue to use at least some Perl components for a
while (if only to ensure a smooth GBrowse->JBrowse migration path).

It isn't too hard to call Perl scripts from Ruby, though -- right? Would
there be any significant problem with doing that (other than having to
install BioPerl)?

Best wishes,
Ian

George Githinji wrote:
> Hi,
> Thanks for the efforts in developing Jbrowse.
> Please I use  BioRuby for the bulk of my work, At the moment i would like to
> embed a jbrowse viewer on a web page for a particular project I am are
> working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
> use for visualizing GFF files?
> 
> Do I have to install bioperl? Are there plans to make Jbrowse bio-language
> agnostic?
> 
> Thanks!
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

[George G. <geo...@gm...>]

Hi,
Thanks for the efforts in developing Jbrowse.
Please I use  BioRuby for the bulk of my work, At the moment i would like to
embed a jbrowse viewer on a web page for a particular project I am are
working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
use for visualizing GFF files?

Do I have to install bioperl? Are there plans to make Jbrowse bio-language
agnostic?

Thanks!

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

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

lfgu wrote:
> I will take your test dataset to descript this question.
>  
> The exact region for the second exon of rna-Apple3 genes in your volvox.gff3 file is 19000-19500.
>  
> When you press the zoom in button until you can see bases at DNA tracks,then you will find that the Figure for second exon structure in 
> Exonerate predictions tracks is not located from 19000 to 19500. 
>  
> The align between  DNA Tracks and Exonerate predictions tracks is not exact align at single base resolution, 
> there are several bases deviation.
>  
> I also check many cases on my own dataset, it is a pervasive phenomenon.

There are a few things going on here.  One is that some web browsers are 
less accurate than others; ticket #12 is for the JBrowse changes 
required to work around this, which I plan to work on soon (once the 
track density scalability work is done).  Firefox seems more accurate 
than other browsers, so right now you can get somewhat better results 
using that.  What browser are you using?

Another issue is one-based vs. zero-based; we haven't really talked 
about this, so maybe it's a good time to address it.  Currently, JBrowse 
uses interbase coordinates (also known as zero-based, half-open 
coordinates).  Interbase is what the UCSC browser, the chado database, 
and the BED file format use.  The GBrowse genome browser and the GFF 
file format use 1-based, fully closed coordinates.  So the feature that 
starts at "19000" in the GFF file starts one base before "19000" in JBrowse.

For comparison, I've attached screenshots the beginning of a particular 
exon in JBrowse, UCSC, and GBrowse (modENCODE) (the transcript is 
CG42358-RA).  While the numbering is different between the 1-based 
browser and the 0-based browsers, you can see that the DNA sequence and 
the exon boundary line up the same in all of them (with the exon 
starting at the cytosine).

Regards,
Mitch

JBrowse:


UCSC:


GBrowse:

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

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

Brenton Graveley wrote:
> This would be good. But I still think the best option is a dynamic 
> scaling based on the max/min in the viewing window even though I 
> realize it is difficult to implement. But perhaps having 3 different 
> scales of images such as 1-100, 1-1000 and 1-10000 would suffice for 
> most cases?

I hear you; I've been thinking about it off and on since you first 
proposed this, but I still don't entirely get it.  So I'd like to go 
into some detail, because I think the answers to these questions will 
help me understand the use case a bit better:

Suppose there is dynamic scaling.  Say you're looking at wiggle data in 
one region where the range of values is 1-100 (plotted, say, 100 pixels 
high), and variation between (say) 80 and 90 is relevant and interesting 
to you.  Now suppose you scroll a teeny bit to the right, and suddenly a 
data value of 10,000 becomes visible.  Then (because of the dynamic 
scaling) the scale changes so that the range of 1-10,000 is plotted on 
the same 100 pixel high region, and now your 80-90 variation is a .1 
pixel difference and is invisible.  Isn't that a problem?

If you're not actually interested in the 80-90 range, then you can plot 
on a 1-10,000 linear scale and be happy.  If you really are interested 
in both 80-90 and also in 8,000-9,000 then you can plot on a log scale 
and be happy.

Is there a specific situation where those two options aren't enough?  It 
seems to me that the point of plotting quantitative data in a genome 
browser is to compare values in one area to values in another area, so 
shouldn't you be able to plot your data all on the same scale?

If you want to call extra attention to really high values we could 
always color them differently or something.  Also, I think it makes 
sense to give the user the option to "zoom" in the y-direction in a 
limited sense.  But given how hard dynamic scaling would be to 
implement, I think it'll be a while before I get to it.  But again, it's 
open source--if someone wants to tackle it I'd be happy to talk about 
how to do it.

> Another feature that would be nice is a scale bar or number to easily 
> show the amount of sequence shown in the current window?

I was just looking at UCSC and I noticed they have both, and GBrowse 
shows the number of bases.  I added a ticket for this.

Regards,
Mitch

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

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

It's considerably more difficult, as the WIG track images are currently
rendered statically. A dynamic scaling would require more track metadata
and Javascript smarts, as opposed to the simpler server tweaks we have
been talking about. But it is do-able and I believe it is on our feature
tracker as something we plan to do.

The scale bar is a very good point; I think that is rather more urgent,
and I hope we'll have that soon

Cheers
I.

Brenton Graveley wrote:
> This would be good. But I still think the best option is a dynamic
> scaling based on the max/min in the viewing window even though I realize
> it is difficult to implement. But perhaps having 3 different scales of
> images such as 1-100, 1-1000 and 1-10000 would suffice for most cases?
> 
> Another feature that would be nice is a scale bar or number to easily
> show the amount of sequence shown in the current window?
> 
> Brent
> 
> Sent from my iPhone 3GS
> 
> On Sep 2, 2009, at 4:41 PM, Ian Holmes <ih...@be...> wrote:
> 
>> Thanks Yuri.
>>
>> Mitch, perhaps if the ratio V/R is small enough, where V is the variance
>> of the data and R=max-min is the range, the logarithmic option should be
>> triggered automatically?
>>
>> I.
>>
>> Yuri Bendana wrote:
>>> Hi Mitch,
>>> I've used the wiggle track in Gbrowse to plot read coverage and the log
>>> scaling was very useful because like you said the distribution can be
>>> wide
>>> (eg, 0-10k).
>>>
>>> yuri
>>>
>>> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner
>>> <mit...@be...>wrote:
>>>
>>>> Look in your JBrowse instance at chr05 around base 15377500:
>>>>
>>>>
>>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>>>
>>>>
>>>> Currently, JBrowse plots wiggle data on a linear scale, and by default
>>>> it uses the largest values in the wiggle file to define the top of the
>>>> plotted range. You have seen blank-looking images in the places you've
>>>> looked because most of your data values are much, much lower than the
>>>> maximum values in your dataset. They're so small in the plot that they
>>>> don't show up at all.
>>>>
>>>> Right now, one thing you could do is add a --min and --max parameter to
>>>> the wig-to-json.pl command line to specify the range of values to plot.
>>>> For example, if you specified --min 0 --max 100 then the plot would
>>>> show
>>>> values in that range, and values larger than that would be out-of-range
>>>> above the plot.
>>>>
>>>> We've also been talking about adding an option to plot on a logarithmic
>>>> vertical scale; would that work for your data? I've looked at
>>>> histograms
>>>> of some next-gen coverage data, and it seems like the distribution of
>>>> data values makes sense to plot on a logarithmic scale. But I think the
>>>> range of values that is most interesting depends on the biology, and
>>>> possibly on how the data is normalized; are you comparing this data to
>>>> some kind of control?
>>>>
>>>> Regards,
>>>> Mitch
>>>>
>>>> Lianfeng GU wrote:
>>>>> Hi prof Mitch:
>>>>>
>>>>> Thank you for your reply.
>>>>>
>>>>> After type "make" command in JBrowse root directory
>>>>>
>>>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
>>>>> see any figure in Col.wig track.
>>>>>
>>>>> You can check it by following website:
>>>>>
>>>>>
>>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>>
>>>>
>>>> [removed username and password because I'm cc-ing the mailing list.
>>>> -Mitch]
>>>>
>>>>> When i use your test dataset, the quantitative ("wiggle") tracks work
>>>>> well. You can see the Figure in wiggle tracks you can see it by
>>>>> following website:
>>>>>
>>>>>
>>>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>>
>>>>> The file of my Col.wig look like this:
>>>>>
>>>>> track type=bedGraph name="TopHat - read coverage"
>>>>> chr04 0 4051 0
>>>>> chr04 4051 4088 1
>>>>> chr04 4088 4090 14
>>>>> chr04 4090 4093 18
>>>>> chr04 4093 4094 20
>>>>> chr04 4094 4095 22
>>>>> chr04 4095 4096 24
>>>>> chr04 4096 4097 25
>>>>> chr04 4097 4126 28
>>>>> chr04 4126 4130 27
>>>>> chr04 4130 4153 28
>>>>> chr04 4153 4163 29
>>>>> chr04 4163 4165 16
>>>>> chr04 4165 4168 12
>>>>> chr04 4168 4169 10
>>>>>
>>>>> I donot know the reason that i cannot get any figure in wiggle tracks.
>>>>>
>>>>> Thank you for your suggestion and help.
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Lianfeng
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>>
>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>> 30-Day
>>>> trial. Simplify your report design, integration and deployment - and
>>>> focus
>>>> on
>>>> what you do best, core application coding. Discover what's new with
>>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> ------------------------------------------------------------------------------
>>>
>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>> ------------------------------------------------------------------------------
>>
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and
>> focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

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

This would be good. But I still think the best option is a dynamic  
scaling based on the max/min in the viewing window even though I  
realize it is difficult to implement. But perhaps having 3 different  
scales of images such as 1-100, 1-1000 and 1-10000 would suffice for  
most cases?

Another feature that would be nice is a scale bar or number to easily  
show the amount of sequence shown in the current window?

Brent

Sent from my iPhone 3GS

On Sep 2, 2009, at 4:41 PM, Ian Holmes <ih...@be...> wrote:

> Thanks Yuri.
>
> Mitch, perhaps if the ratio V/R is small enough, where V is the  
> variance
> of the data and R=max-min is the range, the logarithmic option  
> should be
> triggered automatically?
>
> I.
>
> Yuri Bendana wrote:
>> Hi Mitch,
>> I've used the wiggle track in Gbrowse to plot read coverage and the  
>> log
>> scaling was very useful because like you said the distribution can  
>> be wide
>> (eg, 0-10k).
>>
>> yuri
>>
>> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be... 
>> >wrote:
>>
>>> Look in your JBrowse instance at chr05 around base 15377500:
>>>
>>>
>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>>
>>> Currently, JBrowse plots wiggle data on a linear scale, and by  
>>> default
>>> it uses the largest values in the wiggle file to define the top of  
>>> the
>>> plotted range. You have seen blank-looking images in the places  
>>> you've
>>> looked because most of your data values are much, much lower than  
>>> the
>>> maximum values in your dataset. They're so small in the plot that  
>>> they
>>> don't show up at all.
>>>
>>> Right now, one thing you could do is add a --min and --max  
>>> parameter to
>>> the wig-to-json.pl command line to specify the range of values to  
>>> plot.
>>> For example, if you specified --min 0 --max 100 then the plot  
>>> would show
>>> values in that range, and values larger than that would be out-of- 
>>> range
>>> above the plot.
>>>
>>> We've also been talking about adding an option to plot on a  
>>> logarithmic
>>> vertical scale; would that work for your data? I've looked at  
>>> histograms
>>> of some next-gen coverage data, and it seems like the distribution  
>>> of
>>> data values makes sense to plot on a logarithmic scale. But I  
>>> think the
>>> range of values that is most interesting depends on the biology, and
>>> possibly on how the data is normalized; are you comparing this  
>>> data to
>>> some kind of control?
>>>
>>> Regards,
>>> Mitch
>>>
>>> Lianfeng GU wrote:
>>>> Hi prof Mitch:
>>>>
>>>> Thank you for your reply.
>>>>
>>>> After type "make" command in JBrowse root directory
>>>>
>>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i  
>>>> cannot
>>>> see any figure in Col.wig track.
>>>>
>>>> You can check it by following website:
>>>>
>>>>
>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>
>>> [removed username and password because I'm cc-ing the mailing  
>>> list. -Mitch]
>>>
>>>> When i use your test dataset, the quantitative ("wiggle") tracks  
>>>> work
>>>> well. You can see the Figure in wiggle tracks you can see it by
>>>> following website:
>>>>
>>>>
>>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>> The file of my Col.wig look like this:
>>>>
>>>> track type=bedGraph name="TopHat - read coverage"
>>>> chr04 0 4051 0
>>>> chr04 4051 4088 1
>>>> chr04 4088 4090 14
>>>> chr04 4090 4093 18
>>>> chr04 4093 4094 20
>>>> chr04 4094 4095 22
>>>> chr04 4095 4096 24
>>>> chr04 4096 4097 25
>>>> chr04 4097 4126 28
>>>> chr04 4126 4130 27
>>>> chr04 4130 4153 28
>>>> chr04 4153 4163 29
>>>> chr04 4163 4165 16
>>>> chr04 4165 4168 12
>>>> chr04 4168 4169 10
>>>>
>>>> I donot know the reason that i cannot get any figure in wiggle  
>>>> tracks.
>>>>
>>>> Thank you for your suggestion and help.
>>>>
>>>> Best wishes
>>>>
>>>> Lianfeng
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --- 
>>> --- 
>>> --- 
>>> --- 
>>> ------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>>> 2008 30-Day
>>> trial. Simplify your report design, integration and deployment -  
>>> and focus
>>> on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --- 
>> ---------------------------------------------------------------------
>>
>> --- 
>> --- 
>> --- 
>> ---------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>> 2008 30-Day
>> trial. Simplify your report design, integration and deployment -  
>> and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>
>>
>> --- 
>> ---------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
> --- 
> --- 
> --- 
> ---------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008  
> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

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

Thanks Yuri.

Mitch, perhaps if the ratio V/R is small enough, where V is the variance
of the data and R=max-min is the range, the logarithmic option should be
triggered automatically?

I.

Yuri Bendana wrote:
> Hi Mitch,
> I've used the wiggle track in Gbrowse to plot read coverage and the log
> scaling was very useful because like you said the distribution can be wide
> (eg, 0-10k).
> 
> yuri
> 
> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be...>wrote:
> 
>> Look in your JBrowse instance at chr05 around base 15377500:
>>
>>
>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>
>> Currently, JBrowse plots wiggle data on a linear scale, and by default
>> it uses the largest values in the wiggle file to define the top of the
>> plotted range. You have seen blank-looking images in the places you've
>> looked because most of your data values are much, much lower than the
>> maximum values in your dataset. They're so small in the plot that they
>> don't show up at all.
>>
>> Right now, one thing you could do is add a --min and --max parameter to
>> the wig-to-json.pl command line to specify the range of values to plot.
>> For example, if you specified --min 0 --max 100 then the plot would show
>> values in that range, and values larger than that would be out-of-range
>> above the plot.
>>
>> We've also been talking about adding an option to plot on a logarithmic
>> vertical scale; would that work for your data? I've looked at histograms
>> of some next-gen coverage data, and it seems like the distribution of
>> data values makes sense to plot on a logarithmic scale. But I think the
>> range of values that is most interesting depends on the biology, and
>> possibly on how the data is normalized; are you comparing this data to
>> some kind of control?
>>
>> Regards,
>> Mitch
>>
>> Lianfeng GU wrote:
>>> Hi prof Mitch:
>>>
>>> Thank you for your reply.
>>>
>>> After type "make" command in JBrowse root directory
>>>
>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
>>> see any figure in Col.wig track.
>>>
>>> You can check it by following website:
>>>
>>>
>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>
>> [removed username and password because I'm cc-ing the mailing list. -Mitch]
>>
>>> When i use your test dataset, the quantitative ("wiggle") tracks work
>>> well. You can see the Figure in wiggle tracks you can see it by
>>> following website:
>>>
>>>
>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>> The file of my Col.wig look like this:
>>>
>>> track type=bedGraph name="TopHat - read coverage"
>>> chr04 0 4051 0
>>> chr04 4051 4088 1
>>> chr04 4088 4090 14
>>> chr04 4090 4093 18
>>> chr04 4093 4094 20
>>> chr04 4094 4095 22
>>> chr04 4095 4096 24
>>> chr04 4096 4097 25
>>> chr04 4097 4126 28
>>> chr04 4126 4130 27
>>> chr04 4130 4153 28
>>> chr04 4153 4163 29
>>> chr04 4163 4165 16
>>> chr04 4165 4168 12
>>> chr04 4168 4169 10
>>>
>>> I donot know the reason that i cannot get any figure in wiggle tracks.
>>>
>>> Thank you for your suggestion and help.
>>>
>>> Best wishes
>>>
>>> Lianfeng
>>>
>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Yuri B. <yrb...@gm...>]

Hi Mitch,
I've used the wiggle track in Gbrowse to plot read coverage and the log
scaling was very useful because like you said the distribution can be wide
(eg, 0-10k).

yuri

On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be...>wrote:

> Look in your JBrowse instance at chr05 around base 15377500:
>
>
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>
> Currently, JBrowse plots wiggle data on a linear scale, and by default
> it uses the largest values in the wiggle file to define the top of the
> plotted range. You have seen blank-looking images in the places you've
> looked because most of your data values are much, much lower than the
> maximum values in your dataset. They're so small in the plot that they
> don't show up at all.
>
> Right now, one thing you could do is add a --min and --max parameter to
> the wig-to-json.pl command line to specify the range of values to plot.
> For example, if you specified --min 0 --max 100 then the plot would show
> values in that range, and values larger than that would be out-of-range
> above the plot.
>
> We've also been talking about adding an option to plot on a logarithmic
> vertical scale; would that work for your data? I've looked at histograms
> of some next-gen coverage data, and it seems like the distribution of
> data values makes sense to plot on a logarithmic scale. But I think the
> range of values that is most interesting depends on the biology, and
> possibly on how the data is normalized; are you comparing this data to
> some kind of control?
>
> Regards,
> Mitch
>
> Lianfeng GU wrote:
> > Hi prof Mitch:
> >
> > Thank you for your reply.
> >
> > After type "make" command in JBrowse root directory
> >
> > i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
> > see any figure in Col.wig track.
> >
> > You can check it by following website:
> >
> >
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>
> [removed username and password because I'm cc-ing the mailing list. -Mitch]
>
> > When i use your test dataset, the quantitative ("wiggle") tracks work
> > well. You can see the Figure in wiggle tracks you can see it by
> > following website:
> >
> >
> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
> >
> > The file of my Col.wig look like this:
> >
> > track type=bedGraph name="TopHat - read coverage"
> > chr04 0 4051 0
> > chr04 4051 4088 1
> > chr04 4088 4090 14
> > chr04 4090 4093 18
> > chr04 4093 4094 20
> > chr04 4094 4095 22
> > chr04 4095 4096 24
> > chr04 4096 4097 25
> > chr04 4097 4126 28
> > chr04 4126 4130 27
> > chr04 4130 4153 28
> > chr04 4153 4163 29
> > chr04 4163 4165 16
> > chr04 4165 4168 12
> > chr04 4168 4169 10
> >
> > I donot know the reason that i cannot get any figure in wiggle tracks.
> >
> > Thank you for your suggestion and help.
> >
> > Best wishes
> >
> > Lianfeng
> >
> >
> >
> >
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

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

Look in your JBrowse instance at chr05 around base 15377500:

http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921

Currently, JBrowse plots wiggle data on a linear scale, and by default
it uses the largest values in the wiggle file to define the top of the
plotted range. You have seen blank-looking images in the places you've
looked because most of your data values are much, much lower than the
maximum values in your dataset. They're so small in the plot that they
don't show up at all.

Right now, one thing you could do is add a --min and --max parameter to
the wig-to-json.pl command line to specify the range of values to plot.
For example, if you specified --min 0 --max 100 then the plot would show
values in that range, and values larger than that would be out-of-range
above the plot.

We've also been talking about adding an option to plot on a logarithmic
vertical scale; would that work for your data? I've looked at histograms
of some next-gen coverage data, and it seems like the distribution of
data values makes sense to plot on a logarithmic scale. But I think the
range of values that is most interesting depends on the biology, and
possibly on how the data is normalized; are you comparing this data to
some kind of control?

Regards,
Mitch

Lianfeng GU wrote:
> Hi prof Mitch:
>
> Thank you for your reply.
>
> After type "make" command in JBrowse root directory
>
> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
> see any figure in Col.wig track.
>
> You can check it by following website:
>
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html

[removed username and password because I'm cc-ing the mailing list. -Mitch]

> When i use your test dataset, the quantitative ("wiggle") tracks work
> well. You can see the Figure in wiggle tracks you can see it by
> following website:
>
> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>
> The file of my Col.wig look like this:
>
> track type=bedGraph name="TopHat - read coverage"
> chr04 0 4051 0
> chr04 4051 4088 1
> chr04 4088 4090 14
> chr04 4090 4093 18
> chr04 4093 4094 20
> chr04 4094 4095 22
> chr04 4095 4096 24
> chr04 4096 4097 25
> chr04 4097 4126 28
> chr04 4126 4130 27
> chr04 4130 4153 28
> chr04 4153 4163 29
> chr04 4163 4165 16
> chr04 4165 4168 12
> chr04 4168 4169 10
>
> I donot know the reason that i cannot get any figure in wiggle tracks.
>
> Thank you for your suggestion and help.
>
> Best wishes
>
> Lianfeng
>
>
>
>

Re: [Gmod-ajax] jbrowse deep linking

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

Mitch Skinner wrote:
> All of which is to say: I think JBrowse (the embed-ee) should implement 
> the UI.  We could stick a button with a chain-link icon somewhere in the 
> area where the navigation buttons (and the big trapezoid) are, say.  And 
> the embedder could pass a bookmark callback in to the Browser 
> constructor that would take a Browser object as an argument and return a 
> URL string (using the visibleTracks and visibleRegion methods).  Then 
> the embed-ee could take that callback and use it when the icon is 
> clicked.  We could also omit the icon if there was no bookmark callback 
> passed in.
>   

Okay, this is now implemented and pushed to the github master branch, 
and the dmel and human hg19 demos are updated.

Mitch

Re: [Gmod-ajax] jbrowse deep linking

[Andrew S. <as...@gn...>]

Bummer, it looks like BioGPS is a bit behind -- lagging on hg18.  Once
we do our next data update, we'll add a link to the jbrowse demo...

Cheers,
-andrew

> -----Original Message-----
> From: Ian Holmes [mailto:ih...@be...]
> Sent: Tuesday, August 18, 2009 12:37 PM
> To: Andrew Su
> Cc: Mitch Skinner; <gmo...@li...>
> Subject: Re: [Gmod-ajax] jbrowse deep linking
> 
> Absolutely!
> 
> -Ian (via phone; please excuse brevity/typos)
> 
> On Aug 18, 2009, at 12:32 PM, "Andrew Su" <as...@gn...> wrote:
> 
> > Fantastic, thanks guys...  I see now how that's set up from the
> github
> > version of index.html.
> >
> > Is it okay to link to your demo version of hg19 (as a plugin from
> > http://biogps.gnf.org)?  If you'd rather we not, that's fine, we'll
> > work
> > on getting our own instance set up.
> >
> > Cheers,
> > -andrew
> >
> >> -----Original Message-----
> >> From: Mitch Skinner [mailto:mit...@be...]
> >> Sent: Tuesday, August 18, 2009 11:14 AM
> >> To: Ian Holmes
> >> Cc: Andrew Su; gmo...@li...
> >> Subject: Re: [Gmod-ajax] jbrowse deep linking
> >>
> >> On 08/18/2009 11:06 AM, Ian Holmes wrote:
> >>> So, to be clear: the above URL works, but it does NOT work in the
> >> same
> >>> way that the index.html file in the distribution works. (So,
> looking
> >>> at jbrowse.org/ucsc/hg19/index.html will not actually be much
use.)
> >> We
> >>> need to update the demo.
> >>>
> >>
> >> Oops, right, I'll update the demos.
> >>
> >> Mitch

Re: [Gmod-ajax] jbrowse deep linking

[Andrew S. <as...@gn...>]

Fantastic, thanks guys...  I see now how that's set up from the github
version of index.html.

Is it okay to link to your demo version of hg19 (as a plugin from
http://biogps.gnf.org)?  If you'd rather we not, that's fine, we'll work
on getting our own instance set up.  

Cheers,
-andrew

> -----Original Message-----
> From: Mitch Skinner [mailto:mit...@be...]
> Sent: Tuesday, August 18, 2009 11:14 AM
> To: Ian Holmes
> Cc: Andrew Su; gmo...@li...
> Subject: Re: [Gmod-ajax] jbrowse deep linking
> 
> On 08/18/2009 11:06 AM, Ian Holmes wrote:
> > So, to be clear: the above URL works, but it does NOT work in the
> same
> > way that the index.html file in the distribution works. (So, looking
> > at jbrowse.org/ucsc/hg19/index.html will not actually be much use.)
> We
> > need to update the demo.
> >
> 
> Oops, right, I'll update the demos.
> 
> Mitch

Re: [Gmod-ajax] jbrowse deep linking

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

Absolutely!

-Ian (via phone; please excuse brevity/typos)

On Aug 18, 2009, at 12:32 PM, "Andrew Su" <as...@gn...> wrote:

> Fantastic, thanks guys...  I see now how that's set up from the github
> version of index.html.
>
> Is it okay to link to your demo version of hg19 (as a plugin from
> http://biogps.gnf.org)?  If you'd rather we not, that's fine, we'll  
> work
> on getting our own instance set up.
>
> Cheers,
> -andrew
>
>> -----Original Message-----
>> From: Mitch Skinner [mailto:mit...@be...]
>> Sent: Tuesday, August 18, 2009 11:14 AM
>> To: Ian Holmes
>> Cc: Andrew Su; gmo...@li...
>> Subject: Re: [Gmod-ajax] jbrowse deep linking
>>
>> On 08/18/2009 11:06 AM, Ian Holmes wrote:
>>> So, to be clear: the above URL works, but it does NOT work in the
>> same
>>> way that the index.html file in the distribution works. (So, looking
>>> at jbrowse.org/ucsc/hg19/index.html will not actually be much use.)
>> We
>>> need to update the demo.
>>>
>>
>> Oops, right, I'll update the demos.
>>
>> Mitch

Re: [Gmod-ajax] jbrowse deep linking

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

On 08/18/2009 11:09 AM, Ian Holmes wrote:
> Since the "embedder" in this case is the index.html file, which 
> extracts the parameters from the URL, presumably the natural way to do 
> this is to add a "Bookmark" link to the index.html file, that extracts 
> the 'loc' and 'tracks' params using the Browser's visibleTracks and 
> visibleRegion method?

Certainly, that's one natural way to do it.  But currently, the 
JBrowse-controlled HTML element takes up the whole viewport.  So there's 
currently no place for the index.html file to put a "bookmark" link.  I 
like it that way because it means that as much space as possible is 
dedicated to the actual genomic features, which I think is the right 
priority.  If, say, we added a bookmark link above the 
JBrowse-controlled HTML element and made that HTML element smaller, then 
there would be a significant amount of wasted space at the top of the 
viewport (a big blank region to the side of the bookmark link).

Plus, if the bookmarking user experience is the same in multiple 
embedders (say, click on a bookmark link, get a URL), then I think the 
UI should be the same regardless of embedder.

All of which is to say: I think JBrowse (the embed-ee) should implement 
the UI.  We could stick a button with a chain-link icon somewhere in the 
area where the navigation buttons (and the big trapezoid) are, say.  And 
the embedder could pass a bookmark callback in to the Browser 
constructor that would take a Browser object as an argument and return a 
URL string (using the visibleTracks and visibleRegion methods).  Then 
the embed-ee could take that callback and use it when the icon is 
clicked.  We could also omit the icon if there was no bookmark callback 
passed in.

Mitch

Re: [Gmod-ajax] jbrowse deep linking

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

On 08/18/2009 11:06 AM, Ian Holmes wrote:
> So, to be clear: the above URL works, but it does NOT work in the same 
> way that the index.html file in the distribution works. (So, looking 
> at jbrowse.org/ucsc/hg19/index.html will not actually be much use.) We 
> need to update the demo.
>

Oops, right, I'll update the demos.

Mitch

Re: [Gmod-ajax] jbrowse deep linking

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

Mitch Skinner wrote:
> Implementing a nice way for users to generate those URLs is still a 
> to-do, though.  Actually, it's a bit harder since we made this the 
> responsibility of the embedder.  But I have an idea for how to do it.

Since the "embedder" in this case is the index.html file, which extracts 
the parameters from the URL, presumably the natural way to do this is to 
add a "Bookmark" link to the index.html file, that extracts the 'loc' 
and 'tracks' params using the Browser's visibleTracks and visibleRegion 
method?

At least, that's how I thought we were going to do it...