gmod-ajax — JBrowse list

Re: [Gmod-ajax] quantitative tracks

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

Dear Ambrose,

Currently there is no way to produce differentially-colored quantitative 
tracks exactly as you describe. A close approximation might be to 
generate a separate feature track for the exons, and view this alongside 
the quantitative track.

Best wishes,
Ian

ambrose andongabo (RRes-Roth) wrote:
> Hello Mitch,
> 
> I have this data 
> 
> File one
> "186497660","26815000","343","0.492",
> "186497660","26615000","343","0.543",
> "186497660","26215000","343","0.133",
> 
> File two
> "186497660","26815000","350","EX_pc-",
> "186497660","26615000","350","IN_pc+",
> "186497660","26215000","350","N   
> 
> The first file contains the data I used to designed my conservation track data. Well I passed the file and created the dot wig file. Now I intend to use the second file to color specific regions on my conservation track. There would be basically three main regions exons, introns and nothing represent in above lines as EX-pc- for exons, IN_pc for introns and N for nothing in that region.
> 
> Looking into your  wig-to-json.pl and wig2png.cc I can see that you use bgcolor and fgcolor. Is there any way I can modify these two files so that I can color my tracks depending on the value of each base.
> 
> Cheers
> 
> Ambrose
> 
> 
> Ambrose Andongabo Etenjeh
> 
> Centre for Mathematical and Computational Biology
> 
> Department of Biomathematics and Bioinformatics
> 
> Rothamsted Research
> 
> West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.
> 
> tel: 01582 763133 ext 2003 
> fax: 01582 467907 
> email: amb...@bb... 
> 
> Rothamsted Research is a company limited by guarantee, registered in England at the above address under the registration number 2393175 and a not for profit charity number 802038.
> 
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge  
> This is your chance to win up to $100,000 in prizes! For a limited time, 
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[Gmod-ajax] quantitative tracks

[ambrose a. (RRes-Roth) <amb...@bb...>]

Hello Mitch,

I have this data 

File one
"186497660","26815000","343","0.492",
"186497660","26615000","343","0.543",
"186497660","26215000","343","0.133",

File two
"186497660","26815000","350","EX_pc-",
"186497660","26615000","350","IN_pc+",
"186497660","26215000","350","N   

The first file contains the data I used to designed my conservation track data. Well I passed the file and created the dot wig file. Now I intend to use the second file to color specific regions on my conservation track. There would be basically three main regions exons, introns and nothing represent in above lines as EX-pc- for exons, IN_pc for introns and N for nothing in that region.

Looking into your  wig-to-json.pl and wig2png.cc I can see that you use bgcolor and fgcolor. Is there any way I can modify these two files so that I can color my tracks depending on the value of each base.

Cheers

Ambrose


Ambrose Andongabo Etenjeh

Centre for Mathematical and Computational Biology

Department of Biomathematics and Bioinformatics

Rothamsted Research

West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.

tel: 01582 763133 ext 2003 
fax: 01582 467907 
email: amb...@bb... 

Rothamsted Research is a company limited by guarantee, registered in England at the above address under the registration number 2393175 and a not for profit charity number 802038.

[Gmod-ajax] August 2009 GMOD Meeting

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

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

[Gmod-ajax] Some recent changes to the JBrowse command-line scripts

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

JBrowse work is ongoing, but I'd like to highlight a few specific recent 
changes, since they affect people who run JBrowse instances.

One big change was adding support for BED flat files; because of that, I 
changed the name of gff-to-json.pl to flatfile-to-json.pl.  Some of the 
command line arguments for that script have also changed; see the usage 
message for details.

Also, since a few people were confused about exactly how to run 
generate-names.pl, that script no longer needs any command line 
arguments.  It now figures out what files to operate on by itself.

Regards,
Mitch

[Gmod-ajax] WebGBrowse - a web server for GBrowse.

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

http://www.ncbi.nlm.nih.gov/pubmed/19357095?dopt=Abstract

SUMMARY: The Generic Genome Browser (GBrowse) is one of the most widely
used tools for visualizing genomic features along a reference sequence.
However, the installation and configuration of GBrowse is not trivial
for biologists. We have developed a web server, WebGBrowse that allows
users to upload genome annotation in the GFF3 format, configure the
display of each genomic feature by simply using a web browser, and
visualize the configured genomic features with the integrated GBrowse
software. AVAILABILITY: WebGBrowse is accessible via
http://webgbrowse.cgb.indiana.edu/ and the system is also freely
available for local installations. Contact: do...@in....

Re: [Gmod-ajax] 2009 GMOD Summer Schools - Americas and Europe

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

Hello all,

***The application deadline for both GMOD summer schools is April 6,
one week from now.***

GMOD Summer School - Americas will be held 16-19 July at the National
Evolutionary Synthesis Center (NESCent), in Durham, NC, USA.  Student
tuition is free.  See
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas

GMOD Summer School - Europe will be held 3-6 August at the University
of Oxford, in Oxford, UK.  This is a part of GMOD Europe 2009, which
includes the next GMOD Meeting.  Student tuition is £95.  See
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe

Please contact the GMOD Help Desk (he...@gm...) if you have questions.

We hope to see you in Durham or Oxford,

Dave C.

On Mon, Mar 16, 2009 at 10:54 AM, Dave Clements, GMOD Help Desk
<gmo...@go...> wrote:
> Hello all,
>
> GMOD is offering two Summer Schools in 2009, one on each side of the
> Atlantic. GMOD Summer Schools
> (http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to
> the GMOD project and include several days of hands-on training on how
> to install, configure and administer GMOD tools.  The 2008 GMOD Summer
> School was a great success with 25 students from 4 countries in
> attendance.
>
> Americas, 16-19 July
> - at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA
> - Student tuition is free, thanks to NIH grant 1R01HG004483-01.
>  - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
>
> Europe, 3-6 August
>  - at the University of Oxford, Oxford, United Kingdom
>  - Part of GMOD Europe 2009, which includes the next GMOD Meeting
>  - Student tuition is £75
>  - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
>
> The schools will feature training on these GMOD components:
> * GBrowse - the most widely installed genome viewer on the web
> * Chado - a modular and extensible database schema
> * Apollo - genome annotation editor
> * BioMart - biological data warehouse system
> * GBrowse_syn - a GBrowse based synteny viewer
> * JBrowse - a brand new Web 2.0 genome browser
> * Artemis-Chado Integration (Europe only)
> * MAKER - Genome annotation pipeline (Americas only)
> * Tripal - Web front end for Chado (Americas only)
>
> Applications for the 2009 GMOD Summer Schools are now being accepted.
>
> ***The deadline for applications is the end of the day, April 6.***
>
> Enrollment is limited to 25 participants in each course.  If
> applications exceed capacity (and we expect they will) then applicants
> will be picked based on the strength of their application.  Applicants
> will be notified of their admission status by mid April.
>
> Please contact the GMOD Help Desk if you have any questions.
>
> Thanks,
>
> Dave Clements
> GMOD Help Desk
> he...@gm...
>
> http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
> http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
> http://gmod.org/wiki/GMOD_Europe_2009
>

[Gmod-ajax] JBrowse tutorial

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

http://biowiki.org/view/JBrowse/QuickTutorial

Re: [Gmod-ajax] Jbrowse on mac os 10.5

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

iphan wrote:
> It looks like my problem was an apache issue (apart from the bioperl issue).  I just unpacked the tarball from github and it works like a charm.  Apologies for wasting your time.
>   

Your penance is to occasionally answer an OS X related question on the 
mailing list :)

> This creates a track that shows the invidual CDSs, as expected, but it also displays an element that spans the entire chromosome (see attachment). How do I only display the CDSs without hacking into the json output? Is there something like a 'skip top parent feature' option?
>   

There isn't currently such an option; at the moment what you can do is 
create a config file using the Bio::DB::SeqFeature::Store memory adapter 
and use biodb-to-json.pl instead.  You can look at the example config 
file in docs/tutorial/conf_files/volvox.json to get an idea of how it 
should look.

In the GFF, is the chromosome specified using a #sequence-region 
directive or as a GFF line? 
I think that makes a difference although I'm not entirely sure.  Also, 
I've been thinking about adding a command line option to gff-to-json.pl 
that tells it to only process features of a given type.  Would that do 
what you want?

Sorry those CDS images look so awful; they were just an experiment a 
while ago and I never went back and cleaned them up and made them 
consistent.  I don't really know much about how the annotation process 
works, so I've been wondering how often people want to look at CDSs 
outside of gene models.  Do you get CDS features before the gene models 
have been created?

Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello Mitch

It looks like my problem was an apache issue (apart from the bioperl issue).
I just unpacked the tarball from github and it works like a charm. Apologies
for wasting your time.

I have one question: I am creating one track from a GFF file at a time, e.g.
a CDS track:

./bin/gff-to-json.pl -gff lmajor_chr1.gff3 --cssclass feature --tracklabel
CDS --featlabel

This creates a track that shows the invidual CDSs, as expected, but it also
displays an element that spans the entire chromosome (see attachment). How
do I only display the CDSs without hacking into the json output? Is there
something like a 'skip top parent feature' option?


Thanks

Isabelle

On 3/18/09 7:51 PM, "Mitch Skinner" <mit...@be...> wrote:

> iphan wrote:
>> installing the latest jbrowse using the tar and the zip file fails because it
>> looks like the dnd directory is missing from the archives: Apache returns the
>> error
>> 
>> File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
>> http://localhost/~iphan/jbrowse/index.html
>>   
> 
> Two questions:
> * The zip file you're using is the one from github, right?
> 
> * Does the HTML (index.html) file have a reference to jbrowse_dojo.js?
> Also, there should be a jbrowse_dojo.js file in the jslib/dojo directory.
> 
> I used the dojo custom build tools to create a js file (jbrowse_dojo.js)
> that should include all of the JBrowse dojo dependencies, including
> dnd.  That change should make the whole thing a lot faster to load; I've
> tested it with firefox and I think IE but not with safari so far; I'll
> check that later tonight.
> 
> As always, if I can look at the installation over the internet I can
> probably diagnose things faster, although given that it's your laptop I
> can see how that would be tough to do.
> 
>> I don't have git, so would very much appreciate it if I could use the
>> alternative downloads.
>>   
> 
> The tar and zip files from github should be the same as what's in the
> git repository, the last time I tried it, it was the same but I haven't
> checked it lately.  When we make a release I'll also put a zip file on
> jbrowse.org.
> 
> Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

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

iphan wrote:
> installing the latest jbrowse using the tar and the zip file fails because it looks like the dnd directory is missing from the archives: Apache returns the error
>
> File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
> http://localhost/~iphan/jbrowse/index.html
>   

Two questions:
* The zip file you're using is the one from github, right?

* Does the HTML (index.html) file have a reference to jbrowse_dojo.js?  
Also, there should be a jbrowse_dojo.js file in the jslib/dojo directory.

I used the dojo custom build tools to create a js file (jbrowse_dojo.js) 
that should include all of the JBrowse dojo dependencies, including 
dnd.  That change should make the whole thing a lot faster to load; I've 
tested it with firefox and I think IE but not with safari so far; I'll 
check that later tonight.

As always, if I can look at the installation over the internet I can 
probably diagnose things faster, although given that it's your laptop I 
can see how that would be tough to do.

> I don't have git, so would very much appreciate it if I could use the alternative downloads.
>   

The tar and zip files from github should be the same as what's in the 
git repository, the last time I tried it, it was the same but I haven't 
checked it lately.  When we make a release I'll also put a zip file on 
jbrowse.org.

Mitch

Re: [Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello Mitch

installing the latest jbrowse using the tar and the zip file fails because
it looks like the dnd directory is missing from the archives: Apache returns
the error

File does not exist: /Users/iphan/Sites/jbrowse/jslib/dojo/dnd, referer:
http://localhost/~iphan/jbrowse/index.html

I've tested the old jbrowse and that works fine, so I know I've got all
dependencies sorted out.

I don't have git, so would very much appreciate it if I could use the
alternative downloads.

Thanks,

Isabelle


On 3/15/09 2:29 AM, "Mitch Skinner" <mit...@be...> wrote:

> iphan wrote:
>> I've managed to install Jbrowse on my linux box, but somehow the tricks that
>> worked there don't seem to apply to the Mac. What are the minimal set of
>> Gbrowse libraries required for Jbrowse?
>>   
> 
> JBrowse perl dependencies are:
> 
> ========
> (required)
> bioperl 1.6
> JSON
> 
> (optional; gives you a performance boost)
> JSON::XS
> ========
> 
> You can get JSON and JSON::XS from CPAN.
> 
> Also, if you want to display wiggle files, you need libpng with headers;
> I don't know what the story is on OS X here, probably Ian can tell you.
> All I know is that some of my friends have had more success with
> macports than fink (not with JBrowse specifically but in general), but
> that information is a bit old.  You also need a C++ compiler, but it
> sounds like you've got that already.
> 
> And that's all.  Specifically, you *don't* need a GBrowse installation.
> It was the case a long time ago that you did, so there may be a page
> somewhere on biowiki.org that still says you do.  If so, please point it
> out; I thought we either deleted those or marked them as obsolete.
> 
> Mitch

[Gmod-ajax] 2009 GMOD Summer Schools - Americas and Europe

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

Hello all,

GMOD is offering two Summer Schools in 2009, one on each side of the
Atlantic. GMOD Summer Schools
(http://gmod.org/wiki/GMOD_Summer_School) introduce new GMOD users to
the GMOD project and include several days of hands-on training on how
to install, configure and administer GMOD tools.  The 2008 GMOD Summer
School was a great success with 25 students from 4 countries in
attendance.

Americas, 16-19 July
- at the National Evolutionary Synthesis Center (NESCent), Durham, NC, USA
- Student tuition is free, thanks to NIH grant 1R01HG004483-01.
 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas

Europe, 3-6 August
 - at the University of Oxford, Oxford, United Kingdom
 - Part of GMOD Europe 2009, which includes the next GMOD Meeting
 - Student tuition is £75
 - http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe

The schools will feature training on these GMOD components:
* GBrowse - the most widely installed genome viewer on the web
* Chado - a modular and extensible database schema
* Apollo - genome annotation editor
* BioMart - biological data warehouse system
* GBrowse_syn - a GBrowse based synteny viewer
* JBrowse - a brand new Web 2.0 genome browser
* Artemis-Chado Integration (Europe only)
* MAKER - Genome annotation pipeline (Americas only)
* Tripal - Web front end for Chado (Americas only)

Applications for the 2009 GMOD Summer Schools are now being accepted.

***The deadline for applications is the end of the day, April 6.***

Enrollment is limited to 25 participants in each course.  If
applications exceed capacity (and we expect they will) then applicants
will be picked based on the strength of their application.  Applicants
will be notified of their admission status by mid April.

Please contact the GMOD Help Desk if you have any questions.

Thanks,

Dave Clements
GMOD Help Desk
he...@gm...

http://gmod.org/wiki/2009_GMOD_Summer_School_-_Americas
http://gmod.org/wiki/2009_GMOD_Summer_School_-_Europe
http://gmod.org/wiki/GMOD_Europe_2009

Re: [Gmod-ajax] Jbrowse on mac os 10.5

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

iphan wrote:
> I've managed to install Jbrowse on my linux box, but somehow the tricks that
> worked there don't seem to apply to the Mac. What are the minimal set of
> Gbrowse libraries required for Jbrowse?
>   

JBrowse perl dependencies are:

========
(required)
bioperl 1.6
JSON

(optional; gives you a performance boost)
JSON::XS
========

You can get JSON and JSON::XS from CPAN.

Also, if you want to display wiggle files, you need libpng with headers; 
I don't know what the story is on OS X here, probably Ian can tell you.  
All I know is that some of my friends have had more success with 
macports than fink (not with JBrowse specifically but in general), but 
that information is a bit old.  You also need a C++ compiler, but it 
sounds like you've got that already.

And that's all.  Specifically, you *don't* need a GBrowse installation.  
It was the case a long time ago that you did, so there may be a page 
somewhere on biowiki.org that still says you do.  If so, please point it 
out; I thought we either deleted those or marked them as obsolete.

Mitch

[Gmod-ajax] Jbrowse on mac os 10.5

[iphan <isa...@sb...>]

Hello


I've managed to install Jbrowse on my linux box, but somehow the tricks that
worked there don't seem to apply to the Mac. What are the minimal set of
Gbrowse libraries required for Jbrowse?

Installing GD with Fink was the only step that worked (see big rant below).

Is there a pre-packaged Gbrowse perl library that I can just download and
put in my PERL5LIB path to get Jbrowse running?

That would really make my day!

Thanks,

Isabelle


<big rant>
I've spent several hours trying to install Gbrowse on my mac (10.5.6) and
can't get it to go past the blasted cpan nightmare. Sorry, had to let my
frustration out. I really hate cpan with a vengance, and it probably knows
it ;-)

Errors are inconsistent: cpan can't install either LWP, or Harness, or GD,
or Compress::Zlib. I've first tried to execute the Gbrowse installer without
any options. It crashes with:

Force getting a BioPerl nightly build; the most recent release is too old

*** Installing BioPerl ***
Downloading bioperl-live...
Can't locate LWP.pm in @INC (@INC contains:
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1)
at /System/Library/Perl/Extras/5.8.8/LWP/Simple.pm line 37.

I tried to install LWP from cpan and get:
Can't make directory /Users/iphan/.cpan/build/YAML-0.68 read+writeable:
Operation not permitted at /System/Library/Perl/5.8.8/CPAN.pm line 966

I understand that error means I shouldn't have run the gbrowse installer
script with 'sudo', but since it won't run otherwise, what the hell am I
supposed to do??! Manually do a chmod of .cpan after each installer crash?

 I've tried pre-installing Bioperl 7 times, from the tarball, from cpan,
from cvs, version 1.6.0, 1.5.x version, dev version (guess that's the same
as downloading from cvs?), bioperl-live. None of them seem to play with the
Gbrowse perl installer:

*** (back in Bioperl Build.PL) ***
Cannot chdir() back to /Users/iphan/.cpan/build/BioPerl-1.6.0: No such file
or directory at Bio/Root/Build.pm line 461.
Couldn't run Build.PL:
/System/Library/Perl/Extras/5.8.8/Module/Build/Compat.pm line 200.
Running make test
  Make had some problems, maybe interrupted? Won't test
Running make install
  Make had some problems, maybe interrupted? Won't install

</big rant>

Re: [Gmod-ajax] next generation sequencing visualization

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

Steve Taylor wrote:
> In addition an alignment display would be useful for viewing 
> conservation across species at the base pair level and is already part 
> of the UCSC browser.

This part we can almost do now.  The client-side work for showing 
sequence is done, although there's currently no mechanim for 
insertions.  The client side sequence stuff was written with the ref seq 
in mind; for alignments, gaps are easy to represent, and display, but 
insertions would need more work to do something like UCSC does.

It ought to be straightforward, though.  It's the short-read stuff 
that's more of a challenge, although with the incremental feature 
loading that Ian was talking about it should be do-able, as long as the 
density of reads isn't too ungodly high.  We have to do incrememtal 
loading anyway for other kinds of dense tracks.

Actually, what is a reasonable (rough estimate) upper bound on the read 
density?  Is this something we can expect to change over time?  Also, 
does anyone have some data I could test with?

Mitch

Re: [Gmod-ajax] next generation sequencing visualization

[Jason S. <ja...@bi...>]

> As an example a popular program is called maq to align Illumina  
> reads to a reference sequence. A useful visualization is its  
> 'pileup' output which shows a vertical output with the reference  
> sequence, orientation of reads and base changes. In my experience  
> Maqviewer doesn't seem to work on some of the systems I tried (due  
> to some GTK issues) and reports from people that have got it working  
> say its pretty basic. I run a core group and getting things running  
> on everyone's desktops (which usually means in a browser) saves  
> everyone's time...
>
Tools like EagleView from the MarthLab http://bioinformatics.bc.edu/marthlab/EagleView 
  are really appropriate for this too.

> In addition an alignment display would be useful for viewing  
> conservation across species at the base pair level and is already  
> part of the UCSC browser.

The per base conservation can come from wiggle-style plotting I would  
think is already a good way to solve this.

>
> Maybe the back end could use SAM/BAM format to store the alignments http://samtools.sourceforge.net/ 
>  which appears to be a useful emerging standard. Note there is a  
> ASCII viewer as part of the package
> which I'll check out.
>
> 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  
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> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Gmod-ajax mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Jason Stajich
ja...@bi...

Re: [Gmod-ajax] next generation sequencing visualization

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

Hi Mitch,

>> 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?

Yes, but there will often be a need to eyeball low level data.

> 
> 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.

I agree this is maybe too much to do now though it is going to be have to be thought about at some stage since there will be many 'reference' genomes. I'd be happy just to see 'simple' alignments for 
now:-).

> 
> 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.


As an example a popular program is called maq to align Illumina reads to a reference sequence. A useful visualization is its 'pileup' output which shows a vertical output with the reference sequence,
orientation of reads and base changes. In my experience Maqviewer doesn't seem to work on some of the systems I tried (due to some GTK issues) and reports from people that have got it working say its 
pretty basic. I run a core group and getting things running on everyone's desktops (which usually means in a browser) saves everyone's time...

In addition an alignment display would be useful for viewing conservation across species at the base pair level and is already part of the UCSC browser.

Maybe the back end could use SAM/BAM format to store the alignments http://samtools.sourceforge.net/ which appears to be a useful emerging standard. Note there is a ASCII viewer as part of the package 
which I'll check out.

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

Re: [Gmod-ajax] next generation sequencing visualization

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

Ian Holmes wrote:
> Incidentally, in case it's not clear, I think that dealing with next-gen 
> sequencing data is a **crucial** issue for JBrowse. Any pushback from us 
> about high-volume feature tracks is simply about the best short-term way 
> to achieve this (innovative visualization strategies, vs simply scaling 
> up the idea of a clickable feature track).

Well, for my part, the pushback is mainly about clarifying the use 
cases.  I'm not saying that short reads aren't important, but so far I 
haven't seen anyone really articulate the detailed use cases that one 
would need to make good implementation decisions.

Use cases so far -

1.  Andrew is a computational biologist.  He's writing software to 
process short-read data, and he'd like to eyeball the input and output 
of his program.  Does it matter to him if he's looking at alignment 
coordinates or genomic coordinates?  How much genomic context does he 
need/want to see?  Does he care about a zoomed-out view (e.g., to see 
what fraction of the genome has been covered) or a zoomed-in view (e.g., 
to check for off-by-one errors), or both?

2. Elmer the Eyeballer is a biologist.  He wants to get a good gut feel 
for his short-read data, because the gut is the source of the hypotheses 
that one then proceeds to pull from one's rear.  Does he also want to 
use the tool to monitor his resequencing progress?  When he's looking at 
SNPs, is he identifying them manually, or looking at the output of a 
SNP-identifying tool?  If the latter, does he just need to see the SNPs 
or is the original read context important?  If a large number of reads 
are identical, does he need to see each individual one?  Also, the same 
questions as for Andrew: zoomed out/zoomed in, genomic context, 
coordinate system, etc.

Sorry for the snark.  I really do care about Elmer.  It's just not 
immediately clear to me that Elmer wouldn't be better served by an 
alignment viewer.  Does he want a web-based aligment viewer, or (again) 
is it important to include other genomic information?

Or more generally: what kinds of questions are people trying to answer 
when they're eyeballing short read data?

I keep asking questions not because I doubt the value of the enterprise, 
but just because I'd like someone to explain it to me in more detail (or 
point me toward a nice review, or help me find a good person to talk to 
about it).  Well, to be honest, I do wonder if it'll be useful in a 
longer term sense.  Does anyone still look at Sanger sequencing traces?  
Once the base-calling algorithms were debugged, how much did people care 
about the underlying trace data?

Mitch

Re: [Gmod-ajax] next generation sequencing visualization

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

Ann Loraine wrote:
> http://bowtie-bio.sourceforge.net/index.shtml
>
> My lab is using it in combination with another program from the
> Salzberg lab titled Top Hat, which aims to solve the "how do we map
> short reads across introns" problem.
>   

I skimmed the web pages for bowtie (Burrows-Wheeler!  very cool) and top 
hat.  Does top hat generate its bed and wig output in alignment coords 
or refseq coords?  What do you currently do with the top hat output?

Mitch

Re: [Gmod-ajax] next generation sequencing visualization

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

Dave Clements wrote:
> Mitch/Ian: does JBrowse support semantic browsing a la GBrowse, where 
> you can specify thresholds for switching from one view to the other?


In a sense, yes.  As you zoom in, the track for displaying features 
switches from showing a feature density histogram, to showing individual 
features, to showing features with labels and subfeatures.  There's 
currently not a general mechanism for switching from one kind of view to 
another (e.g., from a wiggle (image) track to a feature track); the 
feature track uses its knowledge about the number of features to choose 
the zoom thresholds where it makes those transitions, so those 
transitions are currently all implemented in FeatureTrack.

But it should be reasonably straightforward to add a new kind of track 
that switches between ImageTrack and FeatureTrack at a set threshold.

Mitch

Re: [Gmod-ajax] next generation sequencing visualization

[Dave C. <cle...@ne...>]

Hello all,

Here's my 2¢ worth.

At the PAG meeting in January almost everyone I saw that was talking about
next-gen sequencing data showed detailed alignments.  My reaction was
similar to Mitch's: Why?  However, I am sympathetic to Andrew's arguments.
There's no substitute for spot checking through eye-balling.

The folks I'm working with at Oregon on some high-throughput data are using
MAQ for alignments and they seem happy with it.  See
http://maq.sourceforge.net/.  They do visualization of the alignments in
Maqviewer.  By the time it makes it into GBrowse (where I come in) it's all
been summarized.  GBrowse supports symantic zooming which would let you go
from WIG to individual alignments (although I haven't tried showing the
alignments yet).  I'll see what I can figure out in the next week or so.

Mitch/Ian: does JBrowse support semantic browsing a la GBrowse, where you
can specify thresholds for switching from one view to the other?

Also, I'm doing a workshop on using GMOD tools for next gen data in a few
weeks.  If you have something in JBrowse you would like me to show, please
let me know.  I suspect it would make a wizzy demo.

Dave C.


On Wed, Mar 11, 2009 at 7:42 PM, Ann Loraine <alo...@gm...> wrote:

> FYI ..
>
> Here is a link to a short read alignment tool you might like to try,
> if you haven't already:
>
> http://bowtie-bio.sourceforge.net/index.shtml
>
> My lab is using it in combination with another program from the
> Salzberg lab titled Top Hat, which aims to solve the "how do we map
> short reads across introns" problem.
>
> All the best,
>
> Ann Loraine
>
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
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Re: [Gmod-ajax] next generation sequencing visualization

[Ann L. <alo...@gm...>]

FYI ..

Here is a link to a short read alignment tool you might like to try,
if you haven't already:

http://bowtie-bio.sourceforge.net/index.shtml

My lab is using it in combination with another program from the
Salzberg lab titled Top Hat, which aims to solve the "how do we map
short reads across introns" problem.

All the best,

Ann Loraine

Re: [Gmod-ajax] next generation sequencing visualization

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

Could all of this be handled by a combination of:

WIG track (for showing density of reads, and/or read start/endpoints)
Sequence track (for showing SNPs)
GFF/BED track (for showing deletions and insertions, and maybe SNPs)

If so, then aren't we really talking about a small raft of server 
scripts, as opposed to a fundamental change?



Andrew Uzilov wrote:
> 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 have actually found the genome browser to be very useful in debugging such 
> automated approaches.  It is frequently much easier to look through the output 
> of your program visually, in the genome browser, to spot off-by-1 errors and 
> such, than it is to write debug code to get the same answer.  Software 
> developers would greatly benefit from visualizing the output of their code in 
> the browser, even if the data set is gigantic.
> 
> The whole power of genome browsers is that a picture is worth 1000 words, and 
> visual correlation is easier than looking at tab-delimited debugging logs.
> 
>> 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.
> 
> In defense of the biologists, eyeballing the data is crucial to forming new 
> hypotheses.  And they're not just doing it because it's all they know how to do, 
> but it is important in building personal priors.  You want to have an 
> expectation of some sort before you design and run a large-scale automated 
> analysis.  This is especially true if you are moving into genomics territory so 
> poorly understood that you might not even know what to expect, so you have click 
> around a bit to get an idea.
> 
> This is something I try to teach my students in a graduate computational 
> genomics class.  So many of them run into writing algorithms based on bad 
> assumptions because they haven't even LOOKED at the initial data.  And then they 
> wonder why their accuracy is poor.  Genomics has a lot to learn from 
> low-throughput biology.
> 
>> 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.
> 
> Yeah, that's a tough one.  UCSC has a "solution" in their conservation (multiple 
> genome alignment) track where they put little tick marks where the insertion in 
> the "other" (non-reference) genome occurs, so you don't have to space out the 
> reference genome.  You can't see the inserted sequence unless you click out to a 
> separate page, but it is a simple solution that is decent.
> 
> Cheers,
> Andrew
> 
> 
> 
>> 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
>>
>> ------------------------------------------------------------------------------
>> 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.
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Re: [Gmod-ajax] next generation sequencing visualization

[Andrew U. <and...@gm...>]

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 have actually found the genome browser to be very useful in debugging such 
automated approaches.  It is frequently much easier to look through the output 
of your program visually, in the genome browser, to spot off-by-1 errors and 
such, than it is to write debug code to get the same answer.  Software 
developers would greatly benefit from visualizing the output of their code in 
the browser, even if the data set is gigantic.

The whole power of genome browsers is that a picture is worth 1000 words, and 
visual correlation is easier than looking at tab-delimited debugging logs.

> 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.

In defense of the biologists, eyeballing the data is crucial to forming new 
hypotheses.  And they're not just doing it because it's all they know how to do, 
but it is important in building personal priors.  You want to have an 
expectation of some sort before you design and run a large-scale automated 
analysis.  This is especially true if you are moving into genomics territory so 
poorly understood that you might not even know what to expect, so you have click 
around a bit to get an idea.

This is something I try to teach my students in a graduate computational 
genomics class.  So many of them run into writing algorithms based on bad 
assumptions because they haven't even LOOKED at the initial data.  And then they 
wonder why their accuracy is poor.  Genomics has a lot to learn from 
low-throughput biology.

> 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.

Yeah, that's a tough one.  UCSC has a "solution" in their conservation (multiple 
genome alignment) track where they put little tick marks where the insertion in 
the "other" (non-reference) genome occurs, so you don't have to space out the 
reference genome.  You can't see the inserted sequence unless you click out to a 
separate page, but it is a simple solution that is decent.

Cheers,
Andrew



> 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
> 
> ------------------------------------------------------------------------------
> 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
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Re: [Gmod-ajax] next generation sequencing visualization

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

Incidentally, in case it's not clear, I think that dealing with next-gen 
sequencing data is a **crucial** issue for JBrowse. Any pushback from us 
about high-volume feature tracks is simply about the best short-term way 
to achieve this (innovative visualization strategies, vs simply scaling 
up the idea of a clickable feature track). It is NOT meant to minimize 
the importance of next-gen sequencing data in genome browsers!


Ian Holmes wrote:
> 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
> 
> ------------------------------------------------------------------------------
> 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
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