gmod-ajax — JBrowse list

Re: [Gmod-ajax] jbrowse deep linking

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

Mitch Skinner wrote:
> No, this is currently implemented in index.html (take a look at 
> index.html to see how it works).  Andrew's "coordinates" is implemented 
> as "loc", which can be anything that you can put in the location box 
> (e.g., chrom:start..end, or a specific feature name/id if the feature 
> name/id is in a track that has "autocomplete" set).  And there's also a 
> "tracks" query parameter, which gets a comma-separated list of track 
> identifiers.
> 
> e.g.,
> http://jbrowse.org/ucsc/hg19/?loc=chr1:100417735..100505485&tracks=refseq_genes,human_mrnas


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.

Re: [Gmod-ajax] jbrowse deep linking

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

Just to clarify, this is not currently in the demo index.html page, but 
is in the JBrowse distribution (I was looking at the wrong file)

Mitch Skinner wrote:
> On 08/18/2009 10:24 AM, Ian Holmes wrote:
>>> I was hoping for something like
>>> http://www.jbrowse.org/ucsc/hg19/?coordinates=chr1:119777910-120173410&track=RefSeqGenes&track=CpGIslands&track=ORFeomeClones.
>>> Possible?
>>>
>> Currently the way to do this is via the Javascript API.
>>
> 
> No, this is currently implemented in index.html (take a look at 
> index.html to see how it works).  Andrew's "coordinates" is implemented 
> as "loc", which can be anything that you can put in the location box 
> (e.g., chrom:start..end, or a specific feature name/id if the feature 
> name/id is in a track that has "autocomplete" set).  And there's also a 
> "tracks" query parameter, which gets a comma-separated list of track 
> identifiers.
> 
> e.g.,
> http://jbrowse.org/ucsc/hg19/?loc=chr1:100417735..100505485&tracks=refseq_genes,human_mrnas
> 
> 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.
> 
> Mitch
> 
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Re: [Gmod-ajax] jbrowse deep linking

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

On 08/18/2009 10:24 AM, Ian Holmes wrote:
>> I was hoping for something like
>> http://www.jbrowse.org/ucsc/hg19/?coordinates=chr1:119777910-120173410&track=RefSeqGenes&track=CpGIslands&track=ORFeomeClones.
>> Possible?
>>
> Currently the way to do this is via the Javascript API.
>

No, this is currently implemented in index.html (take a look at 
index.html to see how it works).  Andrew's "coordinates" is implemented 
as "loc", which can be anything that you can put in the location box 
(e.g., chrom:start..end, or a specific feature name/id if the feature 
name/id is in a track that has "autocomplete" set).  And there's also a 
"tracks" query parameter, which gets a comma-separated list of track 
identifiers.

e.g.,
http://jbrowse.org/ucsc/hg19/?loc=chr1:100417735..100505485&tracks=refseq_genes,human_mrnas

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.

Mitch

Re: [Gmod-ajax] jbrowse deep linking

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

Hi Andrew,

> Is there an easy way to deep link to a specific view in JBrowse?  For 
> example, on your hg19 jbrowse demo, is there a way to link to exactly 
> this view (genomic position and selection of tracks)?
> 
> I was hoping for something like 
> http://www.jbrowse.org/ucsc/hg19/?coordinates=chr1:119777910-120173410&track=RefSeqGenes&track=CpGIslands&track=ORFeomeClones.  
> Possible?

Currently the way to do this is via the Javascript API. If you look at 
the source for the hg19 demo, you'll see a <script> block like this:

     <script type="text/javascript">
     /* <![CDATA[ */
            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo
                                });
            b.showTracks("DNA,gene,mRNA,noncodingRNA");
     /* ]]> */
     </script>



The two relevant methods of the Browser object are showTracks and 
navigateTo. (Note that this example already has a call to showTracks, 
but not navigateTo.) You probably want something like this after the 
call to the Browser constructor:


	b.showTracks("RefSeqGenes,CpGIslands,ORFeomeClones");
	b.navigateTo("chr1:119777910..120173410");


You can also pass these strings into the Browser constructor as defaults 
(see the Javascript code for documentation of this).

Although it isn't too hard to extract these strings from the URL (as in 
your permalinking example), we have avoided having the Browser object 
look directly at the URL, as it would be bad for embedding (one cannot 
know ahead of time which CGI parameters are used by the embedding 
application, and there is a possibility of a namespace clash).

Therefore, we currently leave this to the user to set up. We could use a 
tutorial explaining this.

For an example of both kinds of deep-linking, see the TWiki plugin, 
which allows deep-linking to specific features via the URL *or* a TWiki 
shortcut syntax.

Best wishes,
Ian

[Gmod-ajax] LookSeq: a browser-based (Ajax) viewer for deep sequencing data

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

http://view.ncbi.nlm.nih.gov/pubmed/19679872
http://www.sanger.ac.uk/Software/analysis/lookseq/

Re: [Gmod-ajax] pulling tracks off the local machine

[Michael L. <mfl...@fh...>]

On Fri, Aug 14, 2009 at 3:42 PM, Mitch Skinner
<mit...@be...>wrote:

>  Hi, I'm sorry that I missed this message when it first came across the
> list.  I'm our lab's resident R advocate, so I'm definitely on board with
> your use case.
>
> I thought about it for a bit; I think you're right that trusting only the
> local host would address the security concerns.  But it only applies to the
> (relatively small group of) users who will run some kind of web server on
> the same machine as their web browser, right?  So I'm not sure how far it
> advances the ball.  And it's sort of a complicated story to tell users--"you
> can enter a url, but it has to be for your machine".
>
> I still think the right place to aggregate data is on the server (and not
> the client).  The user could enter an arbitrary URL, and then the server
> would get the data from there, process it, and send it to the user.  That
> should address your use case, right?  And also work for a large swath of
> other users, and address the security issues, and it wouldn't require users
> to have extra software running on their machines.
>
> I looked at the xmapbridge documentation, and it says:
> =====
> Importantly, all graph rendering is performed on the local machine so none
> of the underlying graph data is uploaded to the X:Map server to generate
> your graphs.
> =====
>
> I've been assuming that people would be willing to upload data to the
> server in order to visualize it in context with other genomic data.  So I'm
> interested in the reasons why the people who wrote xmapbridge felt that it
> was important not to upload data to the server.  Is it a confidentiality
> thing?  Or a data volume thing?  Or something else entirely?
>
> As far as I've seen, the set of people who will upload data to the server
> (or point the server toward a flat file or DAS source somewhere else on the
> web) is larger than the set of people who want to keep the data on their
> machine and can run all the necessary software locally.  Part of the point
> of JBrowse (as opposed to, say, IGB) is the assumption that people find it
> easier if they don't have to install software locally.  Perhaps you're happy
> running xmapbridge on your machine, but I imagine that you need to share
> your visualizations with the people you work with, and are they also
> R-savvy?
>
> So I plan to tackle the server-aggregation approach first.  We might work
> on this down the road, though.  And it's open source, so you can do whatever
> you like, of course.
>

The ability to share data is definitely one of the advantages of storing
data on the server. The xmapbridge approach is really more of a hybrid. The
local data stays on the local machine, and the shared/published data is
retrieved incrementally from the server. Now X:Map itself does not have any
upload capabilities, but that's beside the point.

The main use-case would be exploratory data analysis. The analyst wants to
visualize something but does not want to take the time to output the track
and upload it. If something interesting is found and needs to be shared,
then the effort can be invested to publish it on the server.

That said, I agree that hosting the data server-side should be the priority
for JBrowse. Thanks for your reply.

Michael


> Regards,
> Mitch
>
>
> On 07/23/2009 11:54 AM, Michael Lawrence wrote:
>
> Hi,
>
> Just heard about JBrowse. Love the interactivity.
>
> I would like to serve data from R, running on the local machine, to
> JBrowse. X:Map can already do this using the xmapbridge package. Basically,
> they use JSONP to communicate with a Java web server that interacts via the
> file system with R. I'd like to do something similar with JBrowse. I
> understand the security concerns, but perhaps the local host can be trusted?
> The user could enter URLs into JBrowse, and the data would be retrieved from
> a web server embedded in R.
>
> It would be great if JBrowse could support this.
>
> Thanks,
> Michael
>
> ------------------------------
>
> ------------------------------------------------------------------------------
>
>
> ------------------------------
>
> _______________________________________________
> Gmod-ajax mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>

Re: [Gmod-ajax] pulling tracks off the local machine

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

Hi, I'm sorry that I missed this message when it first came across the 
list.  I'm our lab's resident R advocate, so I'm definitely on board 
with your use case.

I thought about it for a bit; I think you're right that trusting only 
the local host would address the security concerns.  But it only applies 
to the (relatively small group of) users who will run some kind of web 
server on the same machine as their web browser, right?  So I'm not sure 
how far it advances the ball.  And it's sort of a complicated story to 
tell users--"you can enter a url, but it has to be for your machine".

I still think the right place to aggregate data is on the server (and 
not the client).  The user could enter an arbitrary URL, and then the 
server would get the data from there, process it, and send it to the 
user.  That should address your use case, right?  And also work for a 
large swath of other users, and address the security issues, and it 
wouldn't require users to have extra software running on their machines.

I looked at the xmapbridge documentation, and it says:
=====
Importantly, all graph rendering is performed on the local machine so 
none of the underlying graph data is uploaded to the X:Map server to 
generate your graphs.
=====

I've been assuming that people would be willing to upload data to the 
server in order to visualize it in context with other genomic data.  So 
I'm interested in the reasons why the people who wrote xmapbridge felt 
that it was important not to upload data to the server.  Is it a 
confidentiality thing?  Or a data volume thing?  Or something else entirely?

As far as I've seen, the set of people who will upload data to the 
server (or point the server toward a flat file or DAS source somewhere 
else on the web) is larger than the set of people who want to keep the 
data on their machine and can run all the necessary software locally.  
Part of the point of JBrowse (as opposed to, say, IGB) is the assumption 
that people find it easier if they don't have to install software 
locally.  Perhaps you're happy running xmapbridge on your machine, but I 
imagine that you need to share your visualizations with the people you 
work with, and are they also R-savvy?

So I plan to tackle the server-aggregation approach first.  We might 
work on this down the road, though.  And it's open source, so you can do 
whatever you like, of course.

Regards,
Mitch

On 07/23/2009 11:54 AM, Michael Lawrence wrote:
> Hi,
>
> Just heard about JBrowse. Love the interactivity.
>
> I would like to serve data from R, running on the local machine, to 
> JBrowse. X:Map can already do this using the xmapbridge package. 
> Basically, they use JSONP to communicate with a Java web server that 
> interacts via the file system with R. I'd like to do something similar 
> with JBrowse. I understand the security concerns, but perhaps the 
> local host can be trusted? The user could enter URLs into JBrowse, and 
> the data would be retrieved from a web server embedded in R.
>
> It would be great if JBrowse could support this.
>
> Thanks,
> Michael
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
>    
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    

Re: [Gmod-ajax] quantitative tracks

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

On 08/14/2009 01:48 AM, ambrose andongabo (RRes-Roth) wrote:
>
> Hello Mitch,
>
>                  I used JBrowse to display some data for scientist in 
> my lab.  This is comment from one of the scientist
>
> "It seems to behave a bit better when I restart the session.  I note 
> that the browser seems to remember the settings of which tracks etc 
> are chosen
>

Yeah, I've also encountered JBrowse bugs that were helped by refreshing 
the page.  Most of those have been fixed; it would helpful for us if 
people could take a screenshot of any weirdness they see and send it to 
us, with information about their browser and browser version and OS.  
That'll make it easier to track down and fix any remaining bugs.

After you've taken a screenshot and sent us an email describing the 
problem (hopefully with an exact list of steps to reproduce it), though, 
refreshing the page will usually help.

> · I like the features so far -- the top level navigation seems v. 
> useful -- will it be possible to catch each end of the red bar and 
> stretch/shrink?
>

It's an interesting idea.  Currently, you can drag the red box to a 
different location, but you can't change its size by manipulating it 
directly.  Adding both mechanics (drag the box if you mousedown in the 
middle, and resize the box if you mousedown on the ends) is possible, 
but I think that might be confusing for the user if you get two 
different behaviors based on a few pixels difference in where the mouse 
comes down.

Of course, we could also just remove the current dragging mechanic and 
replace it with a resizing mechanic.  Resizing might be a more common 
operation than scrolling; it really depends on the user, though.  Is 
there something specific this user commonly does that would be easier to 
do by resizing the red box (as opposed to using the zoom buttons, or 
entering a base range in the text box)?

> · The track titles take up a lot of space and therefore make some 
> comparisons between tracks less easy. Could they be brought down and 
> possibly made optionally transparent?
>

I've avoided transparency in JBrowse because it can slow down scrolling 
(this is browser-, OS-, and hardware-dependent, though).  I suppose we 
could make the label font smaller, but this involves a tradeoff and 
different users (especially older users) will want that different ways.  
We'll keep this in mind for future changes, but right now there are a 
few things you can do:

One is to change the default font size in your web browser; JBrowse 
doesn't currently set the font size on anything because I wanted to 
respect the user's own settings.  Exactly how to do this varies; I've 
been meaning to write up a description of how to do it on different 
browsers and OSes.  On the machine I'm writing this on (firefox on 
linux), it's under Edit->Preferences, in the Content tab.

The other thing you can do is set up your own user CSS.  This is 
definitely more involved, and it requires you to read the JBrowse CSS 
and understand some of it, but it gives you a great deal of control over 
how JBrowse looks.  For firefox, creating a user CSS file is described here:
http://www.mozilla.org/unix/customizing.html#userContent

Specifically, you can add CSS for "div.track-label" (and, optionally 
"div.tracklist-label").  Then you can set font size, transparency, 
background color, padding, whatever you like.

Documenting this better is on the to-do list, but some of the CSS is 
going to get changed around (for example, I'm going to add a "jbrowse-" 
prefix to all the CSS classes) so I'm waiting until the code settles 
down a bit before documenting it.

> · We will ideally need the gene features colour-coded on the plots 
> (i.e. as I have below), as this really makes the interpretation so 
> much easier
>

We don't currently have code to do this, but you can render your own 
image track however you like, and incorporate those images into 
JBrowse.  You have to create a json file describing your image track 
(this gives the image tile width in pixels, and for each zoom level, it 
gives a URL prefix, height, and number of bases per image tile).  This 
isn't documented yet (it's ticket #27), but you can see how it works if 
you look in bin/wig-to-json.pl and src/wig2png.cc in the JBrowse 
distribution.

> · The scaling of individual tracks needs to be interactive. This would 
> require (i) baseline offset; (ii) switch between fixed range; variable 
> range and auto-fit range;
>

This is on the to-do list; I've added ticket #41:
http://jbrowse.lighthouseapp.com/projects/23792/tickets/41

Offset and fixed range should be pretty straightforward.  I can imagine 
a few different meanings for "auto-fit range", and it would be helpful 
to have a detailed description of what this means to you, and use case 
for where it would be useful.

> · Note that some datasets may be --ve to +ve, i.e. with x-axis 
> intersecting y at zero, but ranging from e.g. -1 to +1."
>

The current wiggle renderer handles this, but presenting the zero better 
is definitely on the to-do list.  If you want to add color-coding to a 
quantitative plot to indicate gene model boundaries, you're on your own 
for the moment, though.  If you can already create the plots, it should 
be reasonably straightforward to re-purpose them for JBrowse, and I'd be 
happy to answer questions about how to do that.

Regards,
Mitch

Re: [Gmod-ajax] how I set multiple reference sequences

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

On 08/08/2009 11:06 PM, du zhou wrote:
> In the tutorial, I know that I can set additional tracts by using 
> "biodb-to-json.pl" multiple times. Nevertheless, I have another 
> question that is it possible to delete tracks after config if I don't 
> like them in the future? Or I should rebuild a new Jbrowse html directory?
>

There's no program written to do it, but you can do it by hand.  You 
have to edit data/trackInfo.js to remove the relevant entry, and 
(optionally) delete all the directories:

data/tracks/*/<trackname>

Also,

On 08/07/2009 04:34 AM, du zhou wrote:
> I tried this "bin/prepare-refseqs.pl --gff 
> docs/tutorial/data_files/volvox.gff3 --refs gfftest", but it still 
> warned "found no ref seqs at bin/prepare-refseqs.pl line 199.".

Right, that won't work.  We don't currently have an example in the 
source tree that can be used to demonstrate that functionality.  I've 
attached a gff file that I've used to do this for fly.  I used it like this:

bin/prepare-refseqs.pl --gff ~/data/chroms.gff

> What are "ref seq names"? What are they use for? I am a bit confusing.

Chromosome names, usually, or contig names.  prepare-refseqs.pl uses the 
names to look up the reference sequence in the data source.

Hope that helps,
Mitch

Re: [Gmod-ajax] how I set multiple reference sequences

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

On 08/07/2009 02:14 AM, du zhou wrote:
> Thank you for reply.
> Yes, it works. One more question is that can I set the refseq without
> fasta files of DNA sequences? In other word, can I use the GFF file
> only as refseq?
> I tried ”bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3“, but it gave out "found no ref
> seqs at bin/prepare-refseqs.pl line 199.", and same happened when I
> tried "bin/prepare-refseqs.pl --gff
> docs/tutorial/data_files/volvox.gff3 --noseq"
> Thank you~

If you have a GFF file with sequence-region directives in it, you can
use that file with
bin/prepare-refseqs.pl --gff <file> --refs <comma-separated list of ref
seq names>

See the "Other Syntax" section of
http://www.sequenceontology.org/gff3.shtml
for details about sequence-region.

I'll document that better, and maybe add an example file to make it
easier to demonstrate how to use it. You're right that the example GFF
file that we currently have doesn't work for that use.

I added that functionality originally because I wanted it for testing,
but I'm interested in real use cases. Is there no sequence for your
organism? Or are your users just not interested in the sequence? What
data are you starting from, and what format is it in?

Regards,
Mitch

Re: [Gmod-ajax] how I set multiple reference sequences

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

On 08/06/2009 07:55 PM, du zhou wrote:
> My problem is that presuming that I have three fasta files
> representing three chromosomes, and how I set these reference
> sequences (using bin/prepare-refseqs.pl ?) ?

Hello,

You can just run bin/prepare-refseqs.pl three times, once for each fasta
file. I added some code to handle this case better in mid-June; if your
JBrowse is older than that, then pull the current version.

Please let us know if it works for you; if it doesn't then there may be
a bug.

Mitch

[Gmod-ajax] how I set multiple reference sequences

[du z. <adu...@gm...>]

Hi, here is my question. As mentioned in the tutorial use the command "$
bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa" to set
reference sequences.
My problem is that presuming that I have three fasta files representing
three chromosomes, and how I set these reference sequences (using
bin/prepare-refseqs.pl ?) ?
And what else config files should I prepared for these three refseq?
Thank you~

-- 
杜舟 (name in Chinese)
Zhou Du (name in English)
PhD candidate in Bioinformatics
College of Biological Sciences
China Agricultural University
Beijing, China
Lab phone: +86-(010)-62731214

[Gmod-ajax] pulling tracks off the local machine

[Michael L. <mfl...@fh...>]

Hi,

Just heard about JBrowse. Love the interactivity.

I would like to serve data from R, running on the local machine, to JBrowse.
X:Map can already do this using the xmapbridge package. Basically, they use
JSONP to communicate with a Java web server that interacts via the file
system with R. I'd like to do something similar with JBrowse. I understand
the security concerns, but perhaps the local host can be trusted? The user
could enter URLs into JBrowse, and the data would be retrieved from a web
server embedded in R.

It would be great if JBrowse could support this.

Thanks,
Michael

Re: [Gmod-ajax] JBrowse feature requests

[Bernhard S. <Ber...@ep...>]

I have signed up for a lighthouse account and am watching the tickets of 
interest to me. Should we move these comments/discussions there? For the 
moment, I've inserted a few comments in the cited text below.

Bernhard

On 07/23/2009 07:42 AM, Mitch Skinner wrote:
> To add a little bit to what Ian said:
>
> Fabrice David wrote:
>    
>> Zooming in/out dynamically in the web browser would require to
>> generate images for the different levels... As a suggestion, would it
>> be possible to create JSON (transformed into SVG in the browser)
>> instead of an image; like for the gene density view? Then, users could
>> custom both the resolution (bin size), scale and range dynamically.
>> But I guess there is a problem of performance doing this way?
>>      
>
> Yes, the reason we're using pre-rendered images is for performance, and
> also to support Internet Explorer (which doesn't have SVG).  The web
> browser is able to scale (and offset) pre-rendered images on the client
> side though, which is something I'd like to implement at some point.
> But that scaling couldn't switch between log and linear scales.
>
>    
>> In the case of superposed tracks, we should probably avoid confusion
>> having multiple scales; and assume that values in the different tracks
>> are directly comparable. Then, indeed, if the different tracks have
>> not the same scale/range, we should notice it easily having
>> superimposed and unreadable scales. But, this is less true for the
>> type of display (if we use the min or the max to display the histogram
>> - ticket #35). Then we could be comparing tracks that are actually not
>> comparable. Thus, it should be probably useful to set constraints
>> about which tracks can be superposed in TrackInfo.js. Following these
>> constraints people could superimpose or not tracks by drag-and-drop.
>>      
>
> Well, I could imagine data sources with different scales that you might
> want to compare.  Say, comparing microarray expression data with RNA-seq
> expression data, maybe.  I don't know if people would really want to do
> that, but I do think that people might want to compare tracks with
> different scales.  My main concern is about how those differences ought
> to be reflected in the user interface.
>
> I think we can wait until we start implementing this functionality to
> make some of these decisions, though.
>
>    

I actually have someone doing exactly what you mention here -- comparing 
rna-seq to expression data from tiling arrays.
As you say, the important thing is that the user notices the differences 
in scales. However, brings up an additional problem. Should the user be 
able to apply different y-axis zoom factors to different superimposed 
tracks? In the rna-seq/tilin array example, this would be useful.

>> However, there is still a problem about superimposing several images:
>> the z-index matters. As Bernhard proposed, you could use
>> semi-transparency for the foreground, and/or maybe also add another
>> option to render the tracks as single lines instead of histograms;
>> allowing the comparison of more than 2 tracks. What do you think about
>> this?
>>      
>
> Yes, the z-index matters, but setting the z-index should be do-able,
> although it might require some changes to the way ImageTrack.js.  Or
> maybe I'm misunderstanding the problem you're talking about?
>
> One issue will be semi-transparency support in IE 6; we'll have to do
> some experiments to see what (if anything) works there.
>
> By "render the tracks as single lines instead of histograms", you mean
> using color to indicate the quantitative value?  That's definitely high
> on the to-do list (ticket #7).  That will probably get done before
> superimposing tracks.
>    

What is meant here is to have a line plot instead of a bar plot. (i.e. 
just the upper border of the current solid surface in each plot)

> Mitch
>    

Re: [Gmod-ajax] JBrowse feature requests

[Mitch S. <mi...@ar...>]

To add a little bit to what Ian said:

Fabrice David wrote:
> Zooming in/out dynamically in the web browser would require to 
> generate images for the different levels... As a suggestion, would it 
> be possible to create JSON (transformed into SVG in the browser) 
> instead of an image; like for the gene density view? Then, users could 
> custom both the resolution (bin size), scale and range dynamically. 
> But I guess there is a problem of performance doing this way?

Yes, the reason we're using pre-rendered images is for performance, and 
also to support Internet Explorer (which doesn't have SVG).  The web 
browser is able to scale (and offset) pre-rendered images on the client 
side though, which is something I'd like to implement at some point.  
But that scaling couldn't switch between log and linear scales.

> In the case of superposed tracks, we should probably avoid confusion 
> having multiple scales; and assume that values in the different tracks 
> are directly comparable. Then, indeed, if the different tracks have 
> not the same scale/range, we should notice it easily having 
> superimposed and unreadable scales. But, this is less true for the 
> type of display (if we use the min or the max to display the histogram 
> - ticket #35). Then we could be comparing tracks that are actually not 
> comparable. Thus, it should be probably useful to set constraints 
> about which tracks can be superposed in TrackInfo.js. Following these 
> constraints people could superimpose or not tracks by drag-and-drop.

Well, I could imagine data sources with different scales that you might 
want to compare.  Say, comparing microarray expression data with RNA-seq 
expression data, maybe.  I don't know if people would really want to do 
that, but I do think that people might want to compare tracks with 
different scales.  My main concern is about how those differences ought 
to be reflected in the user interface.

I think we can wait until we start implementing this functionality to 
make some of these decisions, though.

> However, there is still a problem about superimposing several images: 
> the z-index matters. As Bernhard proposed, you could use 
> semi-transparency for the foreground, and/or maybe also add another 
> option to render the tracks as single lines instead of histograms; 
> allowing the comparison of more than 2 tracks. What do you think about 
> this?

Yes, the z-index matters, but setting the z-index should be do-able, 
although it might require some changes to the way ImageTrack.js.  Or 
maybe I'm misunderstanding the problem you're talking about?

One issue will be semi-transparency support in IE 6; we'll have to do 
some experiments to see what (if anything) works there.

By "render the tracks as single lines instead of histograms", you mean 
using color to indicate the quantitative value?  That's definitely high 
on the to-do list (ticket #7).  That will probably get done before 
superimposing tracks.

Mitch

Re: [Gmod-ajax] JBrowse and mysql

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

Aarti Venkat wrote:
> I am trying to use JBrowse to display certain information about honey 
> bee genes that I have stored in a database named BlastData in mysql.I 
> ran the prepare-refseqs script with a configuration file that I 
> made.Its giving some errors saying DBD::mysql::st execute failed: 
> Table 'BlastData.meta' doesn't exist.

Hi Aarti,

Your config file snippet looks right to me.  So unfortunately I think I 
have to start with the dumb questions before we get to the interesting ones.

The BlastData database is a Bio::DB::SeqFeature::Store database, right?  
Is it on the same machine as the one you're running the JBrowse scripts 
on?  (if not, change your dsn to 
"dbi:mysql:database=BlastData;host=<host>")  Is there a table named 
"meta" in the BlastData database?

$ mysql -uxxx -p
mysql> use BlastData;
mysql> show tables;

Does the user in your config file have select permissions on the tables 
in BlastData?  You can check this with the "SHOW GRANTS" command in mysql.

If you haven't seen it already, you might find the config file I used 
for my fly demo useful.   It's here:
http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json

Also, some random guesses about what *might* be problematic:

* old bioperl (JBrowse needs 1.6)
* mixed upper and lower case in the database name (probably fine but 
sometimes it bites you)

Mitch

>
> {
> "description": "Honey Bee Genome",
> "db_adaptor": "Bio::DB::SeqFeature::Store",
> "db_args": {
>                  "-adaptor": "DBI::mysql",
>                 "-dsn":"dbi:mysql:BlastData",
>                "-user": "xxx",
>                "-pass": "xxx"}
> }

[Gmod-ajax] JBrowse and mysql

[Aarti V. <aa...@gm...>]

Hi Mitch,

I am trying to use JBrowse to display certain information about honey bee
genes that I have stored in a database named BlastData in mysql.I ran the
prepare-refseqs script with a configuration file that I made.Its giving some
errors saying DBD::mysql::st execute failed: Table 'BlastData.meta' doesn't
exist.

The start of the configuration file looks like this:

{
"description": "Honey Bee Genome",
"db_adaptor": "Bio::DB::SeqFeature::Store",
"db_args": {
                 "-adaptor": "DBI::mysql",
                "-dsn":"dbi:mysql:BlastData",
               "-user": "xxx",
               "-pass": "xxx"}
}

Guess the adaptor and args to mysql isnt right?Can you let me know how to
connect to mysql db and fetch info frm it?

Thanks!
-- 
Aarti Venkat
Graduate Student
Crop Sciences-Bioinformatics
UIUC
Mike Ditka <http://www.brainyquote.com/quotes/authors/m/mike_ditka.html>  -
"If God had wanted man to play soccer, he wouldn't have given us arms."

Re: [Gmod-ajax] JBrowse feature requests

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

Hi David, I'm ccing this discussion to the gmod-ajax list as some of it 
may be of general interest.

Fabrice David wrote:
> Hello Mitch,
> 
> Thank you very much for your quick reply!
> 
> On Jul 19, 2009, at 5:22 AM, Mitch Skinner wrote:
> 
>> Hello!  I'm always excited when people show interest in JBrowse.  Thanks
>> for being specific with your feedback; I've replied in more detail below:
>>
>> Bernhard Sonderegger wrote:
>>> A y-axis for quantitative tracks (.wig data). The absence of y-axis
>>> label and scale in the display and the absence of configuration
>>> options to select the range and to choose between logarithmic or
>>> linear scales makes it difficult to compare certain types of data.
>>
>> The JBrowse administrator can use the wiggle-processing program's --min
>> and --max command-line options to set the range of the image, and the
>> --height option to set the pixel height.  Or did you mean an option for
>> the end user to set the scale in their web browser?
> 
> Yes, --min and --max options should be sufficient to set the range.
> Zooming in/out dynamically in the web browser would require to generate 
> images for the different levels... As a suggestion, would it be possible 
> to create JSON (transformed into SVG in the browser) instead of an 
> image; like for the gene density view? Then, users could custom both the 
> resolution (bin size), scale and range dynamically. But I guess there is 
> a problem of performance doing this way?

The gene density histogram is actually built of DIV elements, not SVG 
primitives. I believe Internet Explorer cannot render SVGs without a plugin.

Since an early stage we considered implementing the WIGgle (i.e. 
quantitative) tracks in the same way as the gene density histograms. 
Probably this would have been easier... I remember a discussion between 
myself, Mitch and Lincoln Stein at CSHL in 2007...

The drawback is the resolution is not very good: if you put thousands of 
pixel-wide DIVs on the page (as you would need in order to get 
resolution comparable to the PNG images we currently use to display 
quantitative tracks) then the browser gets pretty slow, especially if 
you try to display many such tracks.

For various reasons, we also considered it an important proof of concept 
to have clientside code to display arbitrary chromosome-length images as 
tracks (broken up into managably-sized tile PNGs).

So these were the reasons that our initial implementation of 
quantitative tracks used static images, rather than dynamically 
generated content.

We want to encourage a diversity of track types and styles, however 
(just as GBrowse does), and writing up documentation (so that others can 
add track types) is high on our list.

To take your example, it would certainly be cool to have the an option 
to render quantitative tracks using DIV histograms (just like the gene 
density tracks). For one thing, this would definitely be one way to make 
it easier to implement dynamic behavior (track overlay, track 
subtraction/comparison, dynamic resizing)

I would really encourage you to put these sorts of feature requests 
straight into the lighthouse feature- and bug-tracking system. We would 
like discussions like this to be persistent, and benefit from the 
ongoing accumulation of comments, so that a feature request becomes 
finely-honed by the hive mind often before any code is written. Tracking 
systems can do that, but email is less good for it.

I don't believe you need a lighthouse account to create a ticket (though 
I haven't tried) -- in any case it's easy to get an account.

Thanks so much for your feedback -- as I hope is clear from the above, 
we value it highly.

Cheers!
Ian


>> I've also added some new tickets to our  bug tracking system:
>>
>> * log scale rendering option is now ticket #33
>> * y-axis display is now ticket #34
>>
>>> When zooming out, narrow peaks sometimes shrink in height. It appears
>>> that the algorithm used to generate the track images takes the average
>>> value across a bin of genomic positions to calculate the hight of each
>>> (1 pixel wide) bar in the display instead of using the maximum. It
>>> would be nice to have an option to select the max.
>>
>> I agree; this is ticket #35.  I intend to add both min and max, and
>> possibly display all three at the same time.
>>
>>
>>> Comparing tracks by displaying them side-by-side is not always
>>> sufficient to reveal differences between highly similar tracks. An
>>> additional action to allow superposition of two pre-calculated tracks
>>> would be helpful. This would of course require the background of the
>>> pre-calculated images to be fully transparent and the foreground to be
>>> partially transparent. Transparency is supported by the .png format so
>>> the substance of implementing this feature would involve the drag-and
>>> drop action to superpose tracks.
>>
>> This is ticket #36.  So far, I've avoided using transparency because it
>> slowed down panning and zooming (significantly, on some platforms), but
>> if transparency only occurs in specific situations and the user can turn
>> it off (by un-superposing the tracks) that should be fine.  Or, web
>> browser technology may advance enough that my speed concerns will go
>> away.  Either way, this functionality clearly serves a need by helping
>> users compare tracks to each other.
>>
>> Do you think it's okay to superpose two tracks that have different
>> scales?  We could certainly just superpose the tracks as-is and call it
>> done, possibly including displaying more than one axis.  But it would be
>> difficult to try and match the axes of the two tracks (e.g., by scaling
>> and offsetting them), especially if one of them was logarithmic and the
>> other linear.
> 
> In the case of superposed tracks, we should probably avoid confusion 
> having multiple scales; and assume that values in the different tracks 
> are directly comparable. Then, indeed, if the different tracks have not 
> the same scale/range, we should notice it easily having superimposed and 
> unreadable scales. But, this is less true for the type of display (if we 
> use the min or the max to display the histogram - ticket #35). Then we 
> could be comparing tracks that are actually not comparable. Thus, it 
> should be probably useful to set constraints about which tracks can be 
> superposed in TrackInfo.js. Following these constraints people could 
> superimpose or not tracks by drag-and-drop.
> However, there is still a problem about superimposing several images: 
> the z-index matters. As Bernhard proposed, you could use 
> semi-transparency for the foreground, and/or maybe also add another 
> option to render the tracks as single lines instead of histograms; 
> allowing the comparison of more than 2 tracks. What do you think about 
> this?
> 
>>
>>
>>> Thanks for your feed-back on my suggestions, and keep up the good work
>>> developing JBrowse.
>>
>> Thanks!
>>
>> Mitch
> 
> 
> Thanks again to have added these tickets!
> Have a nice week-end,
> 
> Fabrice

Re: [Gmod-ajax] is there any tutorial for build a Jbrowse for display microarray data?

[李道丰 <li...@gm...>]

Hi Mitch,

thank you very much for your response
i use BLAT to map the probe sets to the chromosome,so genrated the .psl file
i also found the wiggle file format is suite for display microarray data
what stoped me is where to start
now i got the .psl file generated by BLAT contains probe set locations in
chromosomes
log2 transformed expression value of each probe set of 3 different time
points
i want to use a MySQL database backend
could you give me some hit tell me step by step operation (also good if not
very detail)
sorry if my quest brings trouble to you

Best Regards.

On Tue, Jul 14, 2009 at 11:54 PM, Mitch Skinner
<mit...@be...>wrote:

>  On 07/13/2009 08:46 PM, 李道丰 wrote:
>
> some settings of Jbrowse is same to Gbrowse by Lincoln Stein?
>
>
> The settings related to setting up a data source for feature data are the
> same.  But beyond that, the JBrowse configuration values are different, and
> the syntax of the config file is different.
>
>  *display microarray probe sets locations on the chorosome*
>
>
> What format is this data in?  So far, we've worked mainly with feature data
> in GFF and BED formats; if you can get your input data into one of those
> formats, then we can definitely help you.
>
>  *display corresponding expression value of each probe set*
>
>
> What format is this data in?  For quantitative data, JBrowse currently
> supports the wiggle file format:
> http://genome.ucsc.edu/goldenPath/help/wiggle.html
>
>  *searchable probe sets*
>
>
> You mean, searchable by ID?  This is controlled by the "autocomplete"
> setting in the config file (for biodb-to-json.pl) or the "autocomplete"
> command-line parameter for flatfile-to-json.pl.
>
>  *clicked probe sets linked to an outer database*
>
>
> This is controlled by the "urltemplate" config file setting or command-line
> parameter.  The Dmel demo config file has an example of this:
> http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json
>
>  additionlly, in the currentlly version of Jbrowse,click an item would
> popup an window- -
> can i replace that behaviour with others like balloon tips?
>
>
> This is one of the things on our to-do list.  You can do it now if you want
> to modify the javascript code yourself; in js/FeatureTrack.js, in the
> loadSuccess method, there's some code to set a property of the track, called
> onFeatureClick.  Changing that method will change what happens when a user
> clicks on a feature.
>
> Regards,
> Mitch
>



-- 
Daofeng Li,PhD Candidate
China Agricultural University

Re: [Gmod-ajax] is there any tutorial for build a Jbrowse for display microarray data?

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

On 07/13/2009 08:46 PM, 李道丰 wrote:
> some settings of Jbrowse is same to Gbrowse by Lincoln Stein? 

The settings related to setting up a data source for feature data are 
the same.  But beyond that, the JBrowse configuration values are 
different, and the syntax of the config file is different.

> /display microarray probe sets locations on the chorosome/

What format is this data in?  So far, we've worked mainly with feature 
data in GFF and BED formats; if you can get your input data into one of 
those formats, then we can definitely help you.

> /display corresponding expression value of each probe set/

What format is this data in?  For quantitative data, JBrowse currently 
supports the wiggle file format:
http://genome.ucsc.edu/goldenPath/help/wiggle.html

> /searchable probe sets/

You mean, searchable by ID?  This is controlled by the "autocomplete" 
setting in the config file (for biodb-to-json.pl) or the "autocomplete" 
command-line parameter for flatfile-to-json.pl.

> /clicked probe sets linked to an outer database/

This is controlled by the "urltemplate" config file setting or 
command-line parameter.  The Dmel demo config file has an example of this:
http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json

> additionlly, in the currentlly version of Jbrowse,click an item would 
> popup an window- -
> can i replace that behaviour with others like balloon tips?

This is one of the things on our to-do list.  You can do it now if you 
want to modify the javascript code yourself; in js/FeatureTrack.js, in 
the loadSuccess method, there's some code to set a property of the 
track, called onFeatureClick.  Changing that method will change what 
happens when a user clicks on a feature.

Regards,
Mitch

Re: [Gmod-ajax] August 2009 GMOD Meeting

[Dave C. G. H. D. <gmo...@go...>]

Hello all,

Just a reminder that the August 2009 GMOD Meeting is being held 6-7
August, in Oxford, UK.  With a little over 3 weeks to go, the meeting
is now 40% full.  All remaining space is available on a first come
first served basis, and I encourage you to register now, before all
open slots are taken.  (The January meeting was completely full.)

You can register at http://gmod.org/wiki/August_2009_GMOD_Meeting.

Please let me know if you have any questions.

Cheers,

Dave C.


On Wed, Jul 1, 2009 at 1:41 PM, Dave Clements, GMOD Help
Desk<gmo...@go...> wrote:
> Hello all,
>
> The next GMOD meeting will be held 6-7 August, at the University of
> Oxford, in Oxford, United Kingdom. Registration is now open. Space is
> available on a first come, first served basis and there is room for 55
> attendees. The meeting cost is £50.  See
> http://gmod.org/wiki/August_2009_GMOD_Meeting to register
>
> As with previous GMOD meetings, this meeting will have a mixture of
> project, component, and user talks. The agenda is driven by attendee
> suggestions, and you are encouraged to add your suggestions now (see
> http://gmod.org/wiki/August_2009_GMOD_Meeting#Agenda_Suggestions).
>
> For examples of what happens at a GMOD meeting, see the writeups of
> the January 2009, July 2008, or any other previous meeting (see
> http://gmod.org/wiki/Meetings). GMOD meetings are an excellent way to
> meet other GMOD developers and users and to learn (and affect) what's
> coming in the project.
>
> Please join us in Oxford this August,
>
> Dave Clements
> GMOD Help Desk
>
> Note: Unless you have applied to and been admitted to the Summer
> School, don't you dare register for it. The registration web site will
> let you do this, but bureaucratic hellishness will ensue.
>
> --
> * Learn more about GMOD at: ISMB/ECCB: http://www.iscb.org/ismbeccb2009/
>   (BioMart, Chado, Galaxy, InterMine)
> * Please keep responses on the list!
> * Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
* Register now for the August GMOD Meeting:
http://gmod.org/wiki/August_2009_GMOD_Meeting
* Please keep responses on the list!
* Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ajax] is there any tutorial for build a Jbrowse for display microarray data?

[李道丰 <li...@gm...>]

Dear list owners and members,

i had try to build a genome browse by Jbrowse for display my micorarray data
i also read almost all docs in jbrowse.org and accompalished with the
software package
in my understanding. some settings of Jbrowse is same to Gbrowse by Lincoln
Stein?
but i am confused on how to use my own data on Jbrowse
i had setup the Jbowser using the example data ctgA
Could anyone provide some guides for me to finish the following job:
**
*display microarray probe sets locations on the chorosome*
*display corresponding expression value of each probe set*
*searchable probe sets*
*clicked probe sets linked to an outer database*


additionlly, in the currentlly version of Jbrowse,click an item would popup
an window- -
can i replace that behaviour with others like balloon tips?

Thanks in advance for any clues on my problem

Warm Regards.

-- 
Daofeng Li,PhD Candidate
China Agricultural University

Re: [Gmod-ajax] Jbrowse track from external URL?

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

Mitch Skinner wrote:
> If you want something today, you could 
> just run your own JBrowse server and aggregate other people's data and 
> the standard annotation tracks yourself.  If you do that, you might also 
> be able to use Ian's TWiki plugin to allow other people to upload their 
> own data; I'm not sure if he considers it a proof-of-concept or 
> production-ready.

The TWiki plugin should work, but it requires some knowledge of how to
configure & administer a TWiki system, and also some (hopefully minimal)
education of users in how to operate a TWiki in general, and this plugin
in particular.

You should be aware that the user interface for the wiki plugin is less
intuitive than JBrowse (it looks like a genome browser embedded in a
wiki, so there is a bit of clutter)

Also, validation of user input is almost nonexistent (also true of the
command-line scripts, but more of a problem in a user-facing system)

In these ways it's a proof-of-concept system, but it should also work.

See the following ticket regarding input format validation:
http://jbrowse.lighthouseapp.com/projects/23792-jbrowse/tickets/28


As Mitch noted, the currently-supported interface to JBrowse is the
server scripts; we hope to document the JSON before too long, so that
people can extend JBrowse themselves, but we'd like to retain some
flexibility for now.

Re: [Gmod-ajax] Jbrowse track from external URL?

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

On 07/08/2009 09:24 AM, Caroline wrote:
> I've just had a quick look at JBrowse - am I right in thinking that it
> expects JSON-formatted feature data? Is there a definition of the data
> format anywhere?
>    

The use case of including external data in JBrowse is an important one 
and I'm very keen on making it work, but there are a bunch of caveats:

You're right that the javascript client does expect JSON-formatted 
feature data, but I've been treating the JSON format as an internal 
implementation detail rather than a public interface.  As JBrowse 
development has progressed, I've been changing the specifics of what's 
in the JSON, and I'd like to continue to have the freedom to do that for 
at least a little while longer.

The public interface for getting data into JBrowse is from an 
implementation of the bioperl Bio::DasI interface (like Bio::DB::GFF, 
Bio::DB::SeqFeature::Store, or Bio::DB:Das::Chado) or from flatfiles 
(GFF or BED, currently).  JBrowse includes perl scripts for generating 
the JSON from those sources.

If I'm understanding you correctly, you're suggesting that the JBrowse 
javascript client could get data directly from outside servers.  That 
won't work exactly that way, though, because a javascript client can't 
get data from more than one server (this is a security restriction 
imposed by the web browsers).  We could theoretically get around that 
restriction if the datasources each served some javascript glue code 
(the "mashup" approach), but that means we'd have to completely trust 
each data source, and that makes me uncomfortable.  ("mashups are 
self-inflicted cross-site-scripting attacks", is the way Doug Crockford 
puts it)

The mashup approach might work okay for plain JBrowse as it is right 
now, but if someone embedded JBrowse in an application that involved 
logging in, and allowed arbitrary external URLs, then that approach 
would be a huge security hole.

Instead, the web browser should (in my opinion) be getting everything 
from a single server.  That server might get data from other servers, 
though (some people distinguish "mashup in the browser" from "mashup in 
the server"; this would be the latter).  So I've been thinking about 
writing a proxy to convert external URL sources (with, say, DAS or 
flatfiles) into JBrowse's JSON.  The proxy would run on a JBrowse 
server, get data from an external URL, convert it, and then serve it to 
the client.

It should be pretty straightforward to glue an external-URL front end to 
JBrowse's JSON-generating code.  The JSON-generating code expects a 
chromosome's worth of data at a time, though, so that approach might not 
scale well to very large feature sets.  How many features (per 
chromosome) would be in a given track for you?

On the other hand, large feature sets might be okay as long as the 
server serving them (and our hypothetical external-URL front end) 
supports HTTP caching (conditional GETs) properly.  Then the conversion 
work would only have to be done when the data changes.  Still, the 
JSON-generating code is implemented using bioperl, so there would still 
be some scalability issues.  In that case, an implementation in another 
language is certainly a possibility.

I'm probably not going to be able to get to that for a month or two, 
though (maybe more).  If someone else wants to tackle it, I'd be happy 
to help and answer questions.  If you want something today, you could 
just run your own JBrowse server and aggregate other people's data and 
the standard annotation tracks yourself.  If you do that, you might also 
be able to use Ian's TWiki plugin to allow other people to upload their 
own data; I'm not sure if he considers it a proof-of-concept or 
production-ready.

Regards,
Mitch

[Gmod-ajax] Jbrowse track from external URL?

[Caroline <Car...@kc...>]

Hi,

I've just had a quick look at JBrowse - am I right in thinking that it
expects JSON-formatted feature data? Is there a definition of the data
format anywhere?  

We are generating lots of ChIPseq data and we want to visualise it
alongside other people's data and standard annotation tracks. I was
thinking of storing our data (aligned reads and called peaks) in say
BAM, or BioHDF and wrapping it in a REST API to which you could make GET
requests like http://whatever.com/experimentname/chr/start/end and get
back appropriately formatted feature data. How easy would it be to get
JBrowse to let users register a feature-server like this as a track and
have it call the server for the feature data as required? Does this even
seem like a sensible approach?

Cheers,
Cass