gmod-ajax — JBrowse list

Re: [Gmod-ajax] next generation sequencing visualization

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

hmmm, I think you can easily construct situations where people might 
want to eyeball reads at the basepair level. Including insertions 
(which, fwiw, I think can be displayed a little more easily than per 
your email, Mitch -- e.g. as popups.)

Technically I think this comes down to a volume-of-data issue. Point 
being that you can already visualize short reads in aggregate, by 
generating a WIG plot of read density (easy) or by generating your own 
image track (almost as easy).

The only thing you currently cannot do is load a genome's worth of short 
reads into your web browser (nor would you want to do this). So, at the 
level of core tech, this comes down to how you deal with annotation 
tracks containing millions of features. The obvious answer being that 
you load them incrementally (e.g. in chunks [as we currently handle 
sequence] or by CGI range queries).

As an open source, developer-friendly project, we should be encouraging 
people (as a first resort) to make maximal use of the APIs and parts 
that we've already provided. That API should be extended only when it 
simply fails to meet a significant (empirical) demand.

So I think that I'd essentially agree with what Mitch said. Consider 
first what you can do using an image track (it might go further than you 
think -- e.g. you could display SNPs using a sequence logo) and whether 
it is at all possible that you could implement this yourself (obviously, 
with help from us).

At some point we will implement partial loading extensions that will 
allow you to eyeball high-volume feature tracks. But this will happen 
faster if you can demonstrate that you have already pushed back to your 
users with simpler (image-based) alternatives and they are, 
nevertheless, in need of a high-volume solution!

BTW, Sean Eddy has a discussion thread on next-gen sequencing challenges:
http://selab.janelia.org/people/eddys/blog/?p=86

Ian


Mitch Skinner wrote:
> Steve Taylor wrote:
>> Yes...but we really need a decent alignment viewer at the bp level to 
>> see SNPs etc. Can GBrowse display alignments in the panel?
>>   
> 
> The volume of data is large, right?  So why would someone want to 
> eyeball it?  Won't people be running programs to identify SNPs, rather 
> than trying to do it manually?
> 
> I worked with biologists for several years, so I know how much they like 
> to eyeball things.  But if the data volume is large, IMHO it's important 
> to push back and advocate automated analysis instead.  I'd hate to do a 
> lot of work only to find that after the initial burst of enthusiasm no 
> one used it.
> 
> Currently, there's an assumption built fairly widely into JBrowse (and 
> all other genome browsers as far as I know), which is that the 
> coordinate system defined by the reference sequence doesn't change on 
> the fly.  So it'll take a fair chunk of work to be able to show 
> insertions from resequencing.
> 
> On the other hand, if you're talking about viewing just a small region, 
> and you want to view it in alignment coordinates, and all of your data 
> is in aligment coordinates, then the JBrowse part of the work should be 
> easy to do.  We've talked about displaying per-base data (like sequence, 
> or a predicted RNA fold) in features; it's not implemented but it should 
> be straightforward to do.
> 
> Mitch

Re: [Gmod-ajax] next generation sequencing visualization

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

Steve Taylor wrote:
> Yes...but we really need a decent alignment viewer at the bp level to see SNPs etc. Can GBrowse display alignments in the panel?
>   

The volume of data is large, right?  So why would someone want to 
eyeball it?  Won't people be running programs to identify SNPs, rather 
than trying to do it manually?

I worked with biologists for several years, so I know how much they like 
to eyeball things.  But if the data volume is large, IMHO it's important 
to push back and advocate automated analysis instead.  I'd hate to do a 
lot of work only to find that after the initial burst of enthusiasm no 
one used it.

Currently, there's an assumption built fairly widely into JBrowse (and 
all other genome browsers as far as I know), which is that the 
coordinate system defined by the reference sequence doesn't change on 
the fly.  So it'll take a fair chunk of work to be able to show 
insertions from resequencing.

On the other hand, if you're talking about viewing just a small region, 
and you want to view it in alignment coordinates, and all of your data 
is in aligment coordinates, then the JBrowse part of the work should be 
easy to do.  We've talked about displaying per-base data (like sequence, 
or a predicted RNA fold) in features; it's not implemented but it should 
be straightforward to do.

Mitch

Re: [Gmod-ajax] next generation sequencing visualization

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

Mitch just added Sequence Tracks (which could be hacked to show 
alignments) and also plans to allow arbitrary text in features at 
base-resolution.

However, in order to load this many features you would need some work, 
hence my comments about incremental loading of NCLists.

Steve Taylor wrote:
> Hi Ian,
> 
>> PS as Jason Stajich just remarked to me, you can already generate a 
>> WIG track representing read depth at any given site.
> 
> Yes...but we really need a decent alignment viewer at the bp level to 
> see SNPs etc. Can GBrowse display alignments in the panel?
> 
> The closest I have seen on the web is LookSeq.
> 
> http://www.sanger.ac.uk/Software/analysis/lookseq/
> 
>>
>> Ian Holmes wrote:
>>> It has come up.... obviously this is very important.
>>>
>>> One approach would be to use this as the first test case for a plugin 
>>> image track (c.f. GBrowse glyphs).
> 
> Are you thinking of using existing GBrowse routines for this to generate 
> tiles (pre-rendered or on on the fly) like in the old Ajax GBrowse?
> 
> Steve
> 
>>>
>>> Another approach is to use this to motivate piecewise loading of 
>>> feature-rich tracks, and do layout (& rendering) on the client.
>>>
>>> Both are in tune with what we eventually want to do...
>>>
>>> As always, do please let us know if you're able to contribute to 
>>> either of these (the first, server-side approach is probably the most 
>>> easily addressed by non-core developers)
>>>
>>> I.
>>>
>>>
>>> Steve Taylor wrote:
>>>> Hi,
>>>>
>>>> Is anyone looking at a way of visualizing alignments from next 
>>>> generation sequencing in JBrowse?
>>>>
>>>> Kind regards and thanks,
>>>>
>>>> Steve
>>>> ------------------------------------------------------------------
>>>> Medical Sciences Division
>>>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>>>> Oxford University
>>>>
>>>> ------------------------------------------------------------------------------ 
>>>>
>>>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>>>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly 
>>>> and
>>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based 
>>>> development
>>>> software that enables intelligent coding and step-through debugging.
>>>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based 
>>> development
>>> software that enables intelligent coding and step-through debugging.
>>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] next generation sequencing visualization

[Steve T. <ste...@im...>]

Hi Ian,

> PS as Jason Stajich just remarked to me, you can already generate a WIG 
> track representing read depth at any given site.

Yes...but we really need a decent alignment viewer at the bp level to see SNPs etc. Can GBrowse display alignments in the panel?

The closest I have seen on the web is LookSeq.

http://www.sanger.ac.uk/Software/analysis/lookseq/

> 
> Ian Holmes wrote:
>> It has come up.... obviously this is very important.
>>
>> One approach would be to use this as the first test case for a plugin 
>> image track (c.f. GBrowse glyphs).

Are you thinking of using existing GBrowse routines for this to generate tiles (pre-rendered or on on the fly) like in the old Ajax GBrowse?

Steve

>>
>> Another approach is to use this to motivate piecewise loading of 
>> feature-rich tracks, and do layout (& rendering) on the client.
>>
>> Both are in tune with what we eventually want to do...
>>
>> As always, do please let us know if you're able to contribute to 
>> either of these (the first, server-side approach is probably the most 
>> easily addressed by non-core developers)
>>
>> I.
>>
>>
>> Steve Taylor wrote:
>>> Hi,
>>>
>>> Is anyone looking at a way of visualizing alignments from next 
>>> generation sequencing in JBrowse?
>>>
>>> Kind regards and thanks,
>>>
>>> Steve
>>> ------------------------------------------------------------------
>>> Medical Sciences Division
>>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>>> Oxford University
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>>> easily build your RIAs with Flex Builder, the Eclipse(TM)based 
>>> development
>>> software that enables intelligent coding and step-through debugging.
>>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>> ------------------------------------------------------------------------------ 
>>
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based 
>> development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] next generation sequencing visualization

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

PS as Jason Stajich just remarked to me, you can already generate a WIG 
track representing read depth at any given site.

Ian Holmes wrote:
> It has come up.... obviously this is very important.
> 
> One approach would be to use this as the first test case for a plugin 
> image track (c.f. GBrowse glyphs).
> 
> Another approach is to use this to motivate piecewise loading of 
> feature-rich tracks, and do layout (& rendering) on the client.
> 
> Both are in tune with what we eventually want to do...
> 
> As always, do please let us know if you're able to contribute to either 
> of these (the first, server-side approach is probably the most easily 
> addressed by non-core developers)
> 
> I.
> 
> 
> Steve Taylor wrote:
>> Hi,
>>
>> Is anyone looking at a way of visualizing alignments from next generation sequencing in JBrowse?
>>
>> Kind regards and thanks,
>>
>> Steve
>> ------------------------------------------------------------------
>> Medical Sciences Division
>> Weatherall Institute of Molecular Medicine/Sir William Dunn School
>> Oxford University
>>
>> ------------------------------------------------------------------------------
>> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] next generation sequencing visualization

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

It has come up.... obviously this is very important.

One approach would be to use this as the first test case for a plugin 
image track (c.f. GBrowse glyphs).

Another approach is to use this to motivate piecewise loading of 
feature-rich tracks, and do layout (& rendering) on the client.

Both are in tune with what we eventually want to do...

As always, do please let us know if you're able to contribute to either 
of these (the first, server-side approach is probably the most easily 
addressed by non-core developers)

I.


Steve Taylor wrote:
> Hi,
> 
> Is anyone looking at a way of visualizing alignments from next generation sequencing in JBrowse?
> 
> Kind regards and thanks,
> 
> Steve
> ------------------------------------------------------------------
> Medical Sciences Division
> Weatherall Institute of Molecular Medicine/Sir William Dunn School
> Oxford University
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] next generation sequencing visualization

[Steve T. <ste...@im...>]

Hi,

Is anyone looking at a way of visualizing alignments from next generation sequencing in JBrowse?

Kind regards and thanks,

Steve
------------------------------------------------------------------
Medical Sciences Division
Weatherall Institute of Molecular Medicine/Sir William Dunn School
Oxford University

[Gmod-ajax] JBrowse basic installation/usage info

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

If you're interested in playing with the code, unfortunately there's 
almost no documentation and what we do have is mostly out of date.  
Until we have something better, I can offer the following:

The perl dependencies are JSON and bioperl (I've tested with 1.5 and 
1.6RC2); you'll get a performance boost if you also install JSON::XS.

I've attached the config file I've been using to test.

To get started, first run prepare-refseqs.pl to tell the browser about 
your refseqs.  Then, to tell the browser about your features, run either 
generate-json.pl (if you have an existing data source), or 
gff-to-json.pl (to generate tracks from GFF files).  I usually run the 
programs in bin/ from the jbrowse directory (the directory with 
index.html in it); the scripts have defaults that make it a bit easier 
that way.

After that, use generate-names.pl to gather each of the per-track name 
lists into the big tree that the browser uses for name/ID searching:
$ bin/generate-names.pl -v data/*/*/names.json

The C dependency (for wiggle tile generation) is libpng, with headers.  
There's a makefile for compiling wig2png.  I've been testing it with 
conservation data from UCSC:
http://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/
An example wig2png command line is:
$ bin/wig2png chr4.pp tiles data conservation4000 4000 100 255,255,255 
105,155,111
To tell the browser about your wiggle track, at the moment you have to 
edit data/trackInfo.js to add a section like this:

   {
      "url" : "data/{refseq}/conservation4000.json",
      "label" : "conservation",
      "type" : "ImageTrack",
      "key" : "Conservation"
   },


I hope to have a proper tutorial written up soon; I'll email the list 
when I have something.

Mitch

[Gmod-ajax] JBrowse code moved to GitHub

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

The code is now hosted at GitHub.  The source-browsing web interface is 
here:

http://github.com/jbrowse/jbrowse/tree/master

and you can clone (check out) the repository with:

git clone git://github.com/jbrowse/jbrowse.git


If you find git to be a barrier, you can also download .zip files from 
github (click on the "download" button).

Mitch

[Gmod-ajax] JBrowse progress, alpha release soon

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

Wow, it's been a while since we've had any list activity.  I guess we 
haven't really discussed JBrowse (the new name for our AJAX genome 
browser) on the list, so here's a brief summary of what we've implemented:

* getting feature data out of Bio::DasI and GFF files
* smooth panning/zooming from whole chromosome (refseq) to individual bases
* navigating directly to a given location
* remembering your location/zoom with cookies
* turning tracks on and off by dragging and dropping them
* subfeatures
* name/ID search
* quantitative (wiggle) tracks

If you haven't looked at the demo in a while, I encourage you to check 
it out:
http://genome.biowiki.org/

I think the next steps are:
* real sequence
* some actual documentation

Those should be done soon; after that we'll put out an alpha release.

Mitch

[Gmod-ajax] GMOD Meeting, January 15-16, 2009

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

Hello all,

The next GMOD Community Meeting (
http://gmod.org/wiki/January_2009_GMOD_Meeting) will be held January 15-16,
2009, in San Diego, California, immediately following the Plant and Animal
Genome (PAG 2009) conference.  If you are a GMOD user and/or developer, or
just want to learn more about GMOD then you are encouraged to attend.  See
the July 2008 GMOD Meeting page (http://gmod.org/wiki/July_2008_GMOD_Meeting)
for an idea of what goes on at a GMOD meeting.

You can register for the meeting at
http://gmod.org/wiki/January_2009_GMOD_Meeting_Registration.  Thanks to the
generous support of Doreen Ware and USDA-ARS, registration is *free*.  Space
is limited, so please register early (and it helps us plan).  Details on
lodging and other logistics will be forthcoming as the meeting gets closer.

If you have topics that you want covered at the meeting please add them to
the meeting page.

Please let the Help Desk know if you have any questions.

Thanks,

Dave C
GMOD Help Desk

Useful URLs:
http://gmod.org/wiki/January_2009_GMOD_Meeting
http://gmod.org/wiki/January_2009_GMOD_Meeting_Registration
http://gmod.org/wiki/PAG_2009 - GMOD @ PAG 2009
http://www.intl-pag.org/ - Plant and Animal Genome Meeting
http://gmod.org/wiki/July_2008_GMOD_Meeting - notes from prior meeting
http://gmod.org/wiki/2008_GMOD_Community_Survey#GMOD_Meetings

[Gmod-ajax] 2008 GMOD Community Survery: One Week Left!

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

Hello all,

If you haven't already done so, please take a few minutes to fill out
the first annual GMOD Community Survey:
 http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008

We'll be running the survey for one more week, until the end of
Friday, October 31.  If you are in the first 100 responders then you
will be enterred to win one of three GMOD T-shirts or mugs.

PLEASE NOTE:
1. There are *not* 50 pages of questions in the survey.  There are
only 38!  (I feel 24% better already!  ;-)  You'll be happy to know
that you will see only 8 pages, plus a page for each component you
use.
2. Your answers are not recorded until you hit "Submit" on the last
page, so please follow through to the last page.

Please take a few minutes to help improve and guide GMOD.  We really
do appreciate and welcome your feedback.

Thanks,

Dave C
GMOD Help Desk
--
Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
Fill out the the GMOD Community Survey NOW and win some GMOD Gear:
 http://gmod.org/wiki/GMOD_News#2008_GMOD_Community_Survey

[Gmod-ajax] 2008 GMOD Community Survery, or, Win a GMOD T-Shirt or Mug!

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

Hello all,

Please take a few minutes to fill out the first annual GMOD Community Survey:

  http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2008

We are asking all GMOD users and developers to provide input on how
GMOD is doing, and how it can be improved.  All questions are
optional, but please provide as much information as you can.  The
survey covers GMOD in general, and any GMOD components that you use
(and it only asks about components that you indicate you use).

*** Three randomly selected survey participants will receive the GMOD
T-shirt or mug of their choice (see
http://www.cafepress.com/GenericMOD/).  Names will be drawn from the
first 100 responses we receive, so get your response in early ***

Please contact the GMOD Help Desk <he...@gm...> if you have any questions.

Thank you,

The GMOD Team
http://gmod.org

-- 
Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ajax] webapp testing with selenium

[Seth C. <sjc...@be...>]

I've started seriously experimenting (using the firefox IDE plugin) with
selenium for webapp testing:

http://selenium.openqa.org/
http://selenium-ide.openqa.org/download.jsp

While it doesn't cover everything that one might want (I also imagine a
constantly changing interface at some points in development might gum
things up a bit), I've been very impressed with it so far. Before I
commit too much, I was wondering if anybody had any experiences with
this?

-Seth

[Gmod-ajax] haXe

[Seth C. <sjc...@be...>]

Does anybody have any experience with this language ( http://haxe.org )?
It seems to live somewhere between JavaScript and Java, with the promise
of being able to do everything in one language.

It seems to have a fairly large and recent set of libraries--among other
things, there is stuff for MySQL, XML, making an application server,
template engine, running under Apache, etc...:

http://haxe.org/tutos/mysql
http://haxe.org/tutos/xmlparse
http://haxe.org/tutos/client_server
http://haxe.org/mtwin/templo
http://haxe.org/tutos/mod_neko

I was surprised to find haxe and mod_neko ready to go in the Ubuntu
repositories, so I've tried both the Neko (command line and mod_neko)
and JS targets, and it seems to work as advertised--interesting to run
the same classes both in the browser and on the server.

The two biggest problems that I've noticed so far are that: 1) it is
"compiled" instead of interpreted, making development a little trickier
and 2) the language seems more constrained than JS, especially with
things like properties.

Anybody have any experiences or thoughts?

Cheers,

-Seth

Re: [Gmod-ajax] AJAX Gbrowse - problem rendering tiles for EST reads

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

Adam Davis wrote:
> The "wo oo" part was me inserting prints into generate-tiles.pl  to 
> find the point at which it hangs.  Here is the code from that file, 
> starting at line 255:
> The print statement I inserted actually gets cut off halfway through, 
> which is odd.  It always cuts off in the same place too.
>
> print
>    " There are $num_tracks tracks, $num_zooms zoom levels total\n",
>    
> "-------------------------------------------------------------------------\n"; 
>
> print " wo\noo\noo"; 
> <---------------------------------------------------------------------------------------Here 
> is the print I inserted

Thanks for the detailed reply.

Hmmm, I probably need to spend some time reading the code and thinking,
but off the top of my head I have some information that might help.  The
wo\noo\noo gets cut off before the last oo because the output is line
buffered; your last oo does get output to some buffer, but the program
gets stuck before the oo makes it any further than that.

So it might seem like the program is getting stuck in the middle of your
print statement, but it's actually further down than that.  You could
try moving the print further down, and/or you could also try running
generate-tiles with strace:
strace ./generate-tiles.pl <all your generate-tiles.pl arguments>
I'm assuming you're using linux.  Strace will probably generate a lot of
output, and we'd be interested in the last few screenfuls of it.

Whenever something hangs on linux and it's not using any CPU (it isn't,
right?) it's usually waiting on some kind of IO; best guess is the
database.  We've tried to use Bio::DB similarly to the way regular
GBrowse does, so that we'll be compatible with existing GBrowse setups,
but I think we have to do some things differently, and this is probably
due to one of those.

One of the things we do differently from regular GBrowse is that we deal
with an entire landmark (chromosome/scaffold/contig/whatever) of data at
a time (to do layout).  So the hang may just be the database churning,
trying to gather all the data that we're asking for.  How many reads are
on scaffold_1?

I expected some difficulty scaling with some plant genomes, which I've
heard are huge, but I thought the individual chromosomes weren't much
bigger than (say) human, so I was hoping we'd be okay.  But if my guess
is right then we need to do some more scaling work.

Mitch

Re: [Gmod-ajax] AJAX Gbrowse - problem rendering tiles for EST reads

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

It's tough to say; I don't know of a reason why this wouldn't work, and 
I'm sure there are lots of possibilities for what's going on.  So I'd 
like to go through a bit of troubleshooting, if you don't mind answering 
some questions.

1.  What output (if any) do you get when you try to generate tiles?
2.  Can you generate tiles for other kinds of features?
3.  What database are you using (Bio::DB:GFF, 
Bio::DB::SeqFeature::Store, Chado, ?)
4.  What versions of Bioperl and GBrowse are you using?

Thanks,
Mitch

Davis, Adam Christiaan wrote:
> I have been having problems getting the tile generator to generate tiles for EST reads.  I have them set up with EST DNA fasta files so that when zoomed in it displays the DNA with insertions/deletions and mismatches.  It all displays perfectly fine in gbrowse, but when I try to generate tiles, it hangs and never even starts the entire landmark view.  I tried disabling the DNA display when zoomed in, but it still wouldnt generate.  I'm wondering if it has to do with having the GFF file set up to utilize the DNA fasta file for the EST reads.  For all of this, I loaded everything into database first, then generated tiles after checking that it displayed properly in gbrowse.  Here are some example lines from my EST gff file
>
> scaffold_45     est     match   753297  756343  .       +       .       Target EST:CACW5781.b1 1 905
> scaffold_30     est     match   563618  564742  .       -       .       Target EST:CACW6759.g1 1 742
> scaffold_2      est     match   1281895 1282741 .       -       .       Target EST:CACW11451.g1 1 863
> scaffold_68     est     match   160772  161720  .       +       .       Target EST:CACW4784.g2 1 725
> scaffold_45     est     HSP     753297  753324  .       +       .       Target EST:CACW5781.b1 1 28
> scaffold_45     est     HSP     753463  753501  .       +       .       Target EST:CACW5781.b1 29 67
> scaffold_45     est     HSP     753854  753979  .       +       .       Target EST:CACW5781.b1 68 193
> scaffold_45     est     HSP     754933  755079  .       +       .       Target EST:CACW5781.b1 194 340
> scaffold_45     est     HSP     755505  755688  .       +       .       Target EST:CACW5781.b1 341 524
> scaffold_45     est     HSP     755963  756343  .       +       .       Target EST:CACW5781.b1 525 905
> scaffold_30     est     HSP     563618  564293  .       +       .       Target EST:CACW6759.g1 1 675
> scaffold_30     est     HSP     564676  564742  .       +       .       Target EST:CACW6759.g1 676 742
> scaffold_2      est     HSP     1281895 1282741 .       -       .       Target EST:CACW11451.g1 1 863
> scaffold_68     est     HSP     161163  161720  .       -       .       Target EST:CACW4784.g2 1 560
> scaffold_68     est     HSP     160772  160936  .       -       .       Target EST:CACW4784.g2 561 725
>
> And here is the track in my conf file:
> [EST]
> feature      = match:est
> glyph        = segments
> label_position = left
> draw_target   = 1
> show_mismatch = 1
> fontcolor = blue
> mismatch_color = red
> true_target = 1
> realign = 1
> bgcolor      = white
> fgcolor =  black
> key          = ESTs
>
> [EST:1000]
> label_position = top
>
> I have tried commenting out most of the track settings trying to make it just a generic track, and it still doesnt work, which is why I think it has to do with the GFF file formatting.
>
> If anyone can possibly provide any insight as to why I can't get the tiles to generate (or if it just isn't supported), I would greatly appreciate it.
>
> -Adam Davis
>
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>   

[Gmod-ajax] AJAX Gbrowse - problem rendering tiles for EST reads

[Davis, A. C. <da...@mu...>]

I have been having problems getting the tile generator to generate tiles fo=
r EST reads.  I have them set up with EST DNA fasta files so that when zoom=
ed in it displays the DNA with insertions/deletions and mismatches.  It all=
 displays perfectly fine in gbrowse, but when I try to generate tiles, it h=
angs and never even starts the entire landmark view.  I tried disabling the=
 DNA display when zoomed in, but it still wouldnt generate.  I'm wondering =
if it has to do with having the GFF file set up to utilize the DNA fasta fi=
le for the EST reads.  For all of this, I loaded everything into database f=
irst, then generated tiles after checking that it displayed properly in gbr=
owse.  Here are some example lines from my EST gff file

scaffold_45     est     match   753297  756343  .       +       .       Tar=
get EST:CACW5781.b1 1 905
scaffold_30     est     match   563618  564742  .       -       .       Tar=
get EST:CACW6759.g1 1 742
scaffold_2      est     match   1281895 1282741 .       -       .       Tar=
get EST:CACW11451.g1 1 863
scaffold_68     est     match   160772  161720  .       +       .       Tar=
get EST:CACW4784.g2 1 725
scaffold_45     est     HSP     753297  753324  .       +       .       Tar=
get EST:CACW5781.b1 1 28
scaffold_45     est     HSP     753463  753501  .       +       .       Tar=
get EST:CACW5781.b1 29 67
scaffold_45     est     HSP     753854  753979  .       +       .       Tar=
get EST:CACW5781.b1 68 193
scaffold_45     est     HSP     754933  755079  .       +       .       Tar=
get EST:CACW5781.b1 194 340
scaffold_45     est     HSP     755505  755688  .       +       .       Tar=
get EST:CACW5781.b1 341 524
scaffold_45     est     HSP     755963  756343  .       +       .       Tar=
get EST:CACW5781.b1 525 905
scaffold_30     est     HSP     563618  564293  .       +       .       Tar=
get EST:CACW6759.g1 1 675
scaffold_30     est     HSP     564676  564742  .       +       .       Tar=
get EST:CACW6759.g1 676 742
scaffold_2      est     HSP     1281895 1282741 .       -       .       Tar=
get EST:CACW11451.g1 1 863
scaffold_68     est     HSP     161163  161720  .       -       .       Tar=
get EST:CACW4784.g2 1 560
scaffold_68     est     HSP     160772  160936  .       -       .       Tar=
get EST:CACW4784.g2 561 725

And here is the track in my conf file:
[EST]
feature      =3D match:est
glyph        =3D segments
label_position =3D left
draw_target   =3D 1
show_mismatch =3D 1
fontcolor =3D blue
mismatch_color =3D red
true_target =3D 1
realign =3D 1
bgcolor      =3D white
fgcolor =3D  black
key          =3D ESTs

[EST:1000]
label_position =3D top

I have tried commenting out most of the track settings trying to make it ju=
st a generic track, and it still doesnt work, which is why I think it has t=
o do with the GFF file formatting.

If anyone can possibly provide any insight as to why I can't get the tiles =
to generate (or if it just isn't supported), I would greatly appreciate it.

-Adam Davis

[Gmod-ajax] hacker firefox extensions

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

http://www.darkreading.com/document.asp?doc_id=136029

Re: [Gmod-ajax] Test DWR-Ajax

[Seth C. <sjc...@lb...>]

I'm not really familiar with the DWR framework, but looking at the
webpage, I assume that the problem is that since it is a Java integrated
framework, it doesn't give you much opportunity to handle the JavaScript
code in isolation (like with rhino).

One thing that you could do is introduce your testing functions into the
HTML of the page directly, and then have it crawl around in the DOM
firing events. It would take some trial and error to get right, and
might be difficult to maintain as your Java code changes, but it would
give you full access to the generated code.

There are also things like: http://www.croczilla.com/jssh/ , but would
only work for mozilla.

I've never tried it, but the debuggers like venkmann and drosera might
also allow you insert code.

-Seth


On Tue, 2007-09-11 at 19:24 -0300, Samuel Cardoso wrote:
> Hi,
> 
> I would like to test my Ajax applications, is there any solution?
> The problem is that i'm using DWR Ajax, i just can't use some basic
> test functions because this framework is too high level.
> 
> Thanks for any help!
> 
> Samuel Cardoso
> sam...@gm...
> 
> -------------------------------------------------------------------------
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[Gmod-ajax] Test DWR-Ajax

[Samuel C. <sam...@gm...>]

Hi,

I would like to test my Ajax applications, is there any solution?
The problem is that i'm using DWR Ajax, i just can't use some basic
test functions because this framework is too high level.

Thanks for any help!

Samuel Cardoso
sam...@gm...

[Gmod-ajax] JSUnit+Ajax

[Samuel C. <sam...@gm...>]

Hi,

Is there any way to test my AJAX applications? I'm trying to use JSUnit, but
i can't get to any place!
Really thanks for any help!

-- 
Samuel Cardoso
Ciencia da Computacao - DCC/UFMG

Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

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

Yes, I think that if you provide the ability to represent arbitrary sets 
of features (which the divbrowser was clearly born to do) and an API 
that is mashup/plugin friendly, then we could inch our way towards 
something like this without forgetting that the G in GBrowse stands for 
Generic -- i.e. without doing something that is too specific to one 
particular database.

And yes, I am guiltier than anyone of tossing random ideas into the mix 
  -- really this is blue-sky discussion and should not be confused with 
the more modest, concrete & well-defined goals that we have put in 
writing elsewhere (in our proposal to NIH, on the wiki, etc.)




Chris Mungall wrote:
> On Aug 24, 2007, at 5:41 PM, Mitch Skinner wrote:
> 
>> Ian Holmes wrote:
>>> How would this compare with existing systems e.g. Ensembl MART?
>>>
>> I've only spent a bit of time with it, but I don't see a way to  
>> view the
>> results of a biomart query in the genome browser, which is what I was
>> thinking.  In addition to creating new tracks by uploading, we could
>> allow people to create tracks by defining queries.  It should be easy
>> for us to track how popular these are, so there's a natural connection
>> to the points and feedback/recognition items from the game/webapp  
>> article.
>>
>> Also, while you can specify a list of IDs to biomart, that requires  
>> the
>> user to manage their own collection.  We could certainly make  
>> collection
>> management a lot easier (e.g., an "add this to my collection"  
>> button on
>> feature popups).  Centralizing collections also makes them easier to
>> share (like the "post your hotlist" thing, with individual features
>> instead of tracks).
> 
> I like this idea, but in the interests of not seeing us diverge too  
> far from the core plan I'd like to place this in the context of a  
> wider architecture.
> 
> I think GBrowse-ajax should make the assumption that we will soon  
> live in an ideal bioinformatics nation where data sources will expose  
> powerful query interfaces - MART, InterMine, or more ontology-based  
> schemes - through some appropriate HTTP API or RESTful architecture.
> 
> GBrowse should provide a way of slurping a bunch of feature IDs and  
> showing them in an appropriate way. Or, conversely, a way of  
> exporting a bunch of IDs, perhaps from a ROI.
> 
> So long as gbrowse is mashup/plugin friendly then it should be  
> possible to wrap this functionality in the way you describe.
> 
>> In addition to having a nice query building UI like biomart does, I
>> think it makes sense to expose something lower level, like (say) raw
>> SPARQL.  Most biologists won't use it, but if we make it easy for more
>> advanced users to share their queries with other people then it's  
>> still
>> pretty useful IMO.
> 
> SPARQL is fairly limited. However, it is the standard query language  
> for RDF.
> 
> You can assume that a SPARQL wrapper for Chado will be available  
> sometime in the next half of year or so. We've already done this for  
> the GO database[1]. Again, I think GBrowse should just worry about  
> accepting lists of IDs and/or regions - this would be the main point  
> of contact. Some enterprising semweb fan will then hopefully cobble  
> together a non-horrible SPARQL interface that pipes the results into  
> a GBrowse display.
> 
>> But these are all just random ideas.  Mainly, I wanted to ask for help
>> translating game ideas into stuff that relates more concretely to what
>> we're doing.
>>
>> Mitch
>>
>> ---------------------------------------------------------------------- 
>> ---
>> This SF.net email is sponsored by: Splunk Inc.
>> Still grepping through log files to find problems?  Stop.
>> Now Search log events and configuration files using AJAX and a  
>> browser.
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>> _______________________________________________
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>>
> 
> 
> -------------------------------------------------------------------------
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Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

[Chris M. <cj...@fr...>]

On Aug 24, 2007, at 5:41 PM, Mitch Skinner wrote:

> Ian Holmes wrote:
>> How would this compare with existing systems e.g. Ensembl MART?
>>
>
> I've only spent a bit of time with it, but I don't see a way to  
> view the
> results of a biomart query in the genome browser, which is what I was
> thinking.  In addition to creating new tracks by uploading, we could
> allow people to create tracks by defining queries.  It should be easy
> for us to track how popular these are, so there's a natural connection
> to the points and feedback/recognition items from the game/webapp  
> article.
>
> Also, while you can specify a list of IDs to biomart, that requires  
> the
> user to manage their own collection.  We could certainly make  
> collection
> management a lot easier (e.g., an "add this to my collection"  
> button on
> feature popups).  Centralizing collections also makes them easier to
> share (like the "post your hotlist" thing, with individual features
> instead of tracks).

I like this idea, but in the interests of not seeing us diverge too  
far from the core plan I'd like to place this in the context of a  
wider architecture.

I think GBrowse-ajax should make the assumption that we will soon  
live in an ideal bioinformatics nation where data sources will expose  
powerful query interfaces - MART, InterMine, or more ontology-based  
schemes - through some appropriate HTTP API or RESTful architecture.

GBrowse should provide a way of slurping a bunch of feature IDs and  
showing them in an appropriate way. Or, conversely, a way of  
exporting a bunch of IDs, perhaps from a ROI.

So long as gbrowse is mashup/plugin friendly then it should be  
possible to wrap this functionality in the way you describe.

> In addition to having a nice query building UI like biomart does, I
> think it makes sense to expose something lower level, like (say) raw
> SPARQL.  Most biologists won't use it, but if we make it easy for more
> advanced users to share their queries with other people then it's  
> still
> pretty useful IMO.

SPARQL is fairly limited. However, it is the standard query language  
for RDF.

You can assume that a SPARQL wrapper for Chado will be available  
sometime in the next half of year or so. We've already done this for  
the GO database[1]. Again, I think GBrowse should just worry about  
accepting lists of IDs and/or regions - this would be the main point  
of contact. Some enterprising semweb fan will then hopefully cobble  
together a non-horrible SPARQL interface that pipes the results into  
a GBrowse display.

> But these are all just random ideas.  Mainly, I wanted to ask for help
> translating game ideas into stuff that relates more concretely to what
> we're doing.
>
> Mitch
>
> ---------------------------------------------------------------------- 
> ---
> This SF.net email is sponsored by: Splunk Inc.
> Still grepping through log files to find problems?  Stop.
> Now Search log events and configuration files using AJAX and a  
> browser.
> Download your FREE copy of Splunk now >>  http://get.splunk.com/
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Article: Using game design to build the next Digg or Flickr

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

Ian Holmes wrote:
> How would this compare with existing systems e.g. Ensembl MART?
>

I've only spent a bit of time with it, but I don't see a way to view the 
results of a biomart query in the genome browser, which is what I was 
thinking.  In addition to creating new tracks by uploading, we could 
allow people to create tracks by defining queries.  It should be easy 
for us to track how popular these are, so there's a natural connection 
to the points and feedback/recognition items from the game/webapp article.

Also, while you can specify a list of IDs to biomart, that requires the 
user to manage their own collection.  We could certainly make collection 
management a lot easier (e.g., an "add this to my collection" button on 
feature popups).  Centralizing collections also makes them easier to 
share (like the "post your hotlist" thing, with individual features 
instead of tracks).

In addition to having a nice query building UI like biomart does, I 
think it makes sense to expose something lower level, like (say) raw 
SPARQL.  Most biologists won't use it, but if we make it easy for more 
advanced users to share their queries with other people then it's still 
pretty useful IMO.

But these are all just random ideas.  Mainly, I wanted to ask for help 
translating game ideas into stuff that relates more concretely to what 
we're doing.

Mitch