gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse tracks

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

Thanks for your answer, I did it,
looking forward this feature,

Jerome



Le 09/02/2012 18:24, Robert Buels a écrit :
> On 02/09/2012 11:12 AM, Mariette wrote:
>> Yes, I'd like to offer to the user a view like IGV but in a web browser.
>> (So the user can see all the reads)
>
> Yeah, I agree this would probably be a good feature for that.  Would 
> you mind adding it to the issue tracker at 
> http://github.com/GMOD/jbrowse/issues?
>
> In the mean time, have you considered converting your NGS alignments 
> to wiggle data that just shows the coverage?  Depending on what you're 
> using the data for, that can often be sufficient.
>
> Rob

Re: [Gmod-ajax] JBrowse tracks

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

On 02/09/2012 11:12 AM, Mariette wrote:
> Yes, I'd like to offer to the user a view like IGV but in a web browser.
> (So the user can see all the reads)

Yeah, I agree this would probably be a good feature for that.  Would you 
mind adding it to the issue tracker at 
http://github.com/GMOD/jbrowse/issues?

In the mean time, have you considered converting your NGS alignments to 
wiggle data that just shows the coverage?  Depending on what you're 
using the data for, that can often be sufficient.

Rob

Re: [Gmod-ajax] JBrowse tracks

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

Hi Rob

Yes, I'd like to offer to the user a view like IGV but in a web browser.
(So the user can see all the reads)

Jerome






Le 09/02/2012 16:37, Robert Buels a écrit :
> Hi Mariette,
>
> I'm not sure of a way to do that with the current JBrowse.  Right now,
> scrolling is only for all tracks at once.
>
> What kind of data are you displaying?  NGS alignments with deep
> coverage?  Or something else?
>
> Rob
>
> On 02/06/2012 09:42 AM, Mariette wrote:
>> There is any way to make a JBrowse track size fixe and make it being
>> scrollable if there is too many information ?
>> There is a scrollbar for the whole jbrowse view, but it could be
>> convinient to have also one per piste to be able to
>> display several piste in the same screen.
> ------------------------------------------------------------------------------
> Virtualization&  Cloud Management Using Capacity Planning
> Cloud computing makes use of virtualization - but cloud computing
> also focuses on allowing computing to be delivered as a service.
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Re: [Gmod-ajax] JBrowse tracks

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

Hi Mariette,

I'm not sure of a way to do that with the current JBrowse.  Right now, 
scrolling is only for all tracks at once.

What kind of data are you displaying?  NGS alignments with deep 
coverage?  Or something else?

Rob

On 02/06/2012 09:42 AM, Mariette wrote:
> There is any way to make a JBrowse track size fixe and make it being
> scrollable if there is too many information ?
> There is a scrollbar for the whole jbrowse view, but it could be
> convinient to have also one per piste to be able to
> display several piste in the same screen.

[Gmod-ajax] April 2012 GMOD meeting registration open

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

Hello,

I am pleased to announce that registration is open for the April 2012
GMOD meeting  The cost for the meeting is $40 if you register before
March 7th and $50 after.  The meeting will be held April 5-6 at
Georgetown University in Washington DC, right after the Biocurator
meeting.  I am also pleased to announce that the keynote speaker will
be Deanna Church from the NCBI.  In addition to the main meeting,
there will be a Galaxy workshop the evening of April 5.

To register for the meeting, go to:

  http://gmod2012.eventbrite.com/

For more information on the meeting, go to:

  http://gmod.org/wiki/April_2012_GMOD_Meeting

If you would like to present at the meeting, or suggest a topic for
discussion, please feel free to add it to the meeting page, or email
me.  If you register before March 7th, you will be entered in a
drawing to get some GMOD swag from CafePress.

Thanks and see you in April,
Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] JBrowse tracks

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

Hi everyone,

There is any way to make a JBrowse track size fixe and make it being 
scrollable if there is too many information ?
There is a scrollbar for the whole jbrowse view, but it could be 
convinient to have also one per piste to be able to
display several piste in the same screen.

thanks for your reply,
Jerome

[Gmod-ajax] Fwd: Re: jbrowse loading times

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

Forwarding to list for the record.

-------- Original Message --------
Subject: 	Re: [Gmod-ajax] jbrowse loading times
Date: 	Tue, 31 Jan 2012 23:00:37 +0000
From: 	Alex Kalderimis <al...@in...>
To: 	rb...@gm...



Hi Rob,

Yeah, we're using the flat file processors to transform gff3 to the
processed json. As mentioned we were just wondering if we hadn't got
something very wrong.

I think we'll move to DAS in the future (it has the potential to
massively streamline our release process) - is there any chance of
jbrowse consuming DAS?

I will of course be happy to file this on github.

See you in DC.

Alex



-------- Original message --------
Subject: Re: [Gmod-ajax] jbrowse loading times
From: Robert Buels <rb...@gm...>
To: Alex Kalderimis <al...@in...>
CC:


Hi Alex,

By load times, you mean the JSON-formatting done on the server side,
using something like biodb-to-json.pl, right?

Yes, the current implementations of these tools are very, very
inefficient in many ways, particularly regarding their RAM usage. They
keep a lot of things in RAM, for example. It's definitely high on my
list of things to fix.

Could you file this as an issue in the tracker on GitHub so it doesn't
get lost?

Rob

On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
  > We've been doing some jbrowse loading, and experiencing extremely slow
  > load times. We're loading three tracks from all chromosomes of H.
  > sapiens and M. musculus, where we have about 3-4 million features on
  > each chromosomes (including SNPs). The load is taking days, and
  > consuming over 30GB of memory at peak - I seem to recall this being
  > quicker when we had fewer SNPs. What kinds of load times would you
  > expect for this kind of activity?
  >
  > Alex Kalderimis
  >
  >
------------------------------------------------------------------------------
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  > Metro Style Apps, more. Free future releases when you subscribe now!
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Re: [Gmod-ajax] jbrowse loading times

[Alex K. <al...@in...>]

Thanks for the advice - I'll certainly look into that option; I'll be sure to get back to you with my results.

Alex

-------- Original message --------
Subject: Re: [Gmod-ajax] jbrowse loading times 
From: Scott Cain <sc...@sc...> 
To: Alex Kalderimis <al...@in...> 
CC: "rb...@gm..." <rb...@gm...>,"gmo...@li..." <gmo...@li...> 

Alex,

While it would be crazy to push I into chado, putting it in a seqfeature::store database is not. I wouldn't be surprised if it were faster and less memory intensive overall if you did that. 

Scott

Sent from my iPhone

On Feb 1, 2012, at 5:48 PM, Alex Kalderimis <al...@in...> wrote:

>  Hi Scott, 
> 
> well, as you suspected, it is coming from flat files. Sadly making use of chado would require writing everything into chado from a built intermine - unlikely to happen...
> 
> I suspect when it comes to pushing the envelope with tools, we're seldom the user that tool developers have in mind.
> 
> Alex
> 
> 
> 
> -------- Original message --------
> Subject: Re: [Gmod-ajax] jbrowse loading times 
> From: Scott Cain <sc...@sc...> 
> To: Robert Buels <rb...@gm...> 
> CC: Alex Kalderimis <al...@in...>,"gmo...@li..." <gmo...@li...> 
> 
> 
> Alex,
> 
> What is the source for these loads?  If it's flat files, I would
> expect the behavior you're describing.  From Chado, I'd expect it to
> be slow, though not so much of a memory hog, but maybe so--I've never
> tried with that large of a data source.  I'd expect a
> Bio::DB::SeqFeature::Store data source to behave the best.
> 
> Nevertheless, Rob's right that the json conversion needs to be improved.
> 
> Scott
> 
> 
> On Tue, Jan 31, 2012 at 6:09 PM, Robert Buels <rb...@gm...> wrote:
> > Hi Alex,
> >
> > CCing the list on this reply.  By load times, you mean the
> > JSON-formatting done on the server side, using something like
> > biodb-to-json.pl, right?
> >
> > Yes, the current implementations of these tools are very, very
> > inefficient in many ways, particularly regarding their RAM usage.  They
> > keep a lot of things in RAM, for example.  It's definitely high on my
> > list of things to fix.
> >
> > Could you file this as an issue in the tracker on GitHub so it doesn't
> > get lost?
> >
> > Rob
> >
> > On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
> >> We've been doing some jbrowse loading, and experiencing extremely slow
> >> load times. We're loading three tracks from all chromosomes of H.
> >> sapiens and M. musculus, where we have about 3-4 million features on
> >> each chromosomes (including SNPs). The load is taking days, and
> >> consuming over 30GB of memory at peak - I seem to recall this being
> >> quicker when we had fewer SNPs. What kinds of load times would you
> >> expect for this kind of activity?
> >>
> >> Alex Kalderimis
> >>
> >> ------------------------------------------------------------------------------
> >> Keep Your Developer Skills Current with LearnDevNow!
> >> The most comprehensive online learning library for Microsoft developers
> >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> >> Metro Style Apps, more. Free future releases when you subscribe now!
> >> http://p.sf.net/sfu/learndevnow-d2d
> >> _______________________________________________
> >> Gmod-ajax mailing list
> >> Gmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>
> >
> >
> > ------------------------------------------------------------------------------
> > Keep Your Developer Skills Current with LearnDevNow!
> > The most comprehensive online learning library for Microsoft developers
> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> > Metro Style Apps, more. Free future releases when you subscribe now!
> > http://p.sf.net/sfu/learndevnow-d2d
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)     216-392-3087
> Ontario Institute for Cancer Research

Re: [Gmod-ajax] jbrowse loading times

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

Alex,

While it would be crazy to push I into chado, putting it in a seqfeature::store database is not. I wouldn't be surprised if it were faster and less memory intensive overall if you did that. 

Scott

Sent from my iPhone

On Feb 1, 2012, at 5:48 PM, Alex Kalderimis <al...@in...> wrote:

>  Hi Scott, 
> 
> well, as you suspected, it is coming from flat files. Sadly making use of chado would require writing everything into chado from a built intermine - unlikely to happen...
> 
> I suspect when it comes to pushing the envelope with tools, we're seldom the user that tool developers have in mind.
> 
> Alex
> 
> 
> 
> -------- Original message --------
> Subject: Re: [Gmod-ajax] jbrowse loading times 
> From: Scott Cain <sc...@sc...> 
> To: Robert Buels <rb...@gm...> 
> CC: Alex Kalderimis <al...@in...>,"gmo...@li..." <gmo...@li...> 
> 
> 
> Alex,
> 
> What is the source for these loads?  If it's flat files, I would
> expect the behavior you're describing.  From Chado, I'd expect it to
> be slow, though not so much of a memory hog, but maybe so--I've never
> tried with that large of a data source.  I'd expect a
> Bio::DB::SeqFeature::Store data source to behave the best.
> 
> Nevertheless, Rob's right that the json conversion needs to be improved.
> 
> Scott
> 
> 
> On Tue, Jan 31, 2012 at 6:09 PM, Robert Buels <rb...@gm...> wrote:
> > Hi Alex,
> >
> > CCing the list on this reply.  By load times, you mean the
> > JSON-formatting done on the server side, using something like
> > biodb-to-json.pl, right?
> >
> > Yes, the current implementations of these tools are very, very
> > inefficient in many ways, particularly regarding their RAM usage.  They
> > keep a lot of things in RAM, for example.  It's definitely high on my
> > list of things to fix.
> >
> > Could you file this as an issue in the tracker on GitHub so it doesn't
> > get lost?
> >
> > Rob
> >
> > On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
> >> We've been doing some jbrowse loading, and experiencing extremely slow
> >> load times. We're loading three tracks from all chromosomes of H.
> >> sapiens and M. musculus, where we have about 3-4 million features on
> >> each chromosomes (including SNPs). The load is taking days, and
> >> consuming over 30GB of memory at peak - I seem to recall this being
> >> quicker when we had fewer SNPs. What kinds of load times would you
> >> expect for this kind of activity?
> >>
> >> Alex Kalderimis
> >>
> >> ------------------------------------------------------------------------------
> >> Keep Your Developer Skills Current with LearnDevNow!
> >> The most comprehensive online learning library for Microsoft developers
> >> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> >> Metro Style Apps, more. Free future releases when you subscribe now!
> >> http://p.sf.net/sfu/learndevnow-d2d
> >> _______________________________________________
> >> Gmod-ajax mailing list
> >> Gmo...@li...
> >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> >>
> >
> >
> > ------------------------------------------------------------------------------
> > Keep Your Developer Skills Current with LearnDevNow!
> > The most comprehensive online learning library for Microsoft developers
> > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> > Metro Style Apps, more. Free future releases when you subscribe now!
> > http://p.sf.net/sfu/learndevnow-d2d
> > _______________________________________________
> > Gmod-ajax mailing list
> > Gmo...@li...
> > https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 
> 
> 
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

Re: [Gmod-ajax] jbrowse loading times

[Alex K. <al...@in...>]

 Hi Scott, 

well, as you suspected, it is coming from flat files. Sadly making use of chado would require writing everything into chado from a built intermine - unlikely to happen...

I suspect when it comes to pushing the envelope with tools, we're seldom the user that tool developers have in mind.

Alex

-------- Original message --------
Subject: Re: [Gmod-ajax] jbrowse loading times 
From: Scott Cain <sc...@sc...> 
To: Robert Buels <rb...@gm...> 
CC: Alex Kalderimis <al...@in...>,"gmo...@li..." <gmo...@li...> 

Alex,

What is the source for these loads?  If it's flat files, I would
expect the behavior you're describing.  From Chado, I'd expect it to
be slow, though not so much of a memory hog, but maybe so--I've never
tried with that large of a data source.  I'd expect a
Bio::DB::SeqFeature::Store data source to behave the best.

Nevertheless, Rob's right that the json conversion needs to be improved.

Scott


On Tue, Jan 31, 2012 at 6:09 PM, Robert Buels <rb...@gm...> wrote:
> Hi Alex,
>
> CCing the list on this reply.  By load times, you mean the
> JSON-formatting done on the server side, using something like
> biodb-to-json.pl, right?
>
> Yes, the current implementations of these tools are very, very
> inefficient in many ways, particularly regarding their RAM usage.  They
> keep a lot of things in RAM, for example.  It's definitely high on my
> list of things to fix.
>
> Could you file this as an issue in the tracker on GitHub so it doesn't
> get lost?
>
> Rob
>
> On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
>> We've been doing some jbrowse loading, and experiencing extremely slow
>> load times. We're loading three tracks from all chromosomes of H.
>> sapiens and M. musculus, where we have about 3-4 million features on
>> each chromosomes (including SNPs). The load is taking days, and
>> consuming over 30GB of memory at peak - I seem to recall this being
>> quicker when we had fewer SNPs. What kinds of load times would you
>> expect for this kind of activity?
>>
>> Alex Kalderimis
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)        216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] jbrowse loading times

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

Alex,

What is the source for these loads?  If it's flat files, I would
expect the behavior you're describing.  From Chado, I'd expect it to
be slow, though not so much of a memory hog, but maybe so--I've never
tried with that large of a data source.  I'd expect a
Bio::DB::SeqFeature::Store data source to behave the best.

Nevertheless, Rob's right that the json conversion needs to be improved.

Scott


On Tue, Jan 31, 2012 at 6:09 PM, Robert Buels <rb...@gm...> wrote:
> Hi Alex,
>
> CCing the list on this reply.  By load times, you mean the
> JSON-formatting done on the server side, using something like
> biodb-to-json.pl, right?
>
> Yes, the current implementations of these tools are very, very
> inefficient in many ways, particularly regarding their RAM usage.  They
> keep a lot of things in RAM, for example.  It's definitely high on my
> list of things to fix.
>
> Could you file this as an issue in the tracker on GitHub so it doesn't
> get lost?
>
> Rob
>
> On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
>> We've been doing some jbrowse loading, and experiencing extremely slow
>> load times. We're loading three tracks from all chromosomes of H.
>> sapiens and M. musculus, where we have about 3-4 million features on
>> each chromosomes (including SNPs). The load is taking days, and
>> consuming over 30GB of memory at peak - I seem to recall this being
>> quicker when we had fewer SNPs. What kinds of load times would you
>> expect for this kind of activity?
>>
>> Alex Kalderimis
>>
>> ------------------------------------------------------------------------------
>> Keep Your Developer Skills Current with LearnDevNow!
>> The most comprehensive online learning library for Microsoft developers
>> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
>> Metro Style Apps, more. Free future releases when you subscribe now!
>> http://p.sf.net/sfu/learndevnow-d2d
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] installed but the page shows nothing

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

I do have a restricted umask set (077). Regardless, I think it will be
probably nice to add a line in the tutorial page because this may be a
common pitfall for users. Thanks!

-hl

On Wed, Feb 1, 2012 at 9:05 AM, Robert Buels <rb...@gm...> wrote:

> Hi Heewook,
>
> Please remember keep the gmod-ajax CCed on replies, so there's a public
> record that other people can find to help with their problems.
>
> prepare-refseqs.pl doesn't do any permissions changing that I'm aware of,
> it will create files with the default permissions for the user it's running
> under (i.e. according to that user's umask).  Do you have a restricted
> umask set?
>
> Rob
>
>
>
> On 01/31/2012 07:55 PM, Heewook Lee wrote:
>
>> Rob,
>>
>> I actually found out why it wasn't loading. When "bin/prepare-refseqs.pl
>> <http://prepare-refseqs.pl>" is called, it creates a directory called
>>
>> data along with a couple of .js files and a directory(seq). The problem
>> rises from the permission. when the script runs it creats the data
>> directory with 700 then .js files in the directory with 600. And nothing
>> is mentioned in the tutorial that the user has to set up the permission
>> for these files.
>>
>>
>> I have a quick suggestion for you regarding this. I think it will work
>> for a broader group of people if you actually document in the tutorial
>> that the user has to change the directory and file permissions for these
>> newly created files upon running the scripts or you can modify the
>> script so that it will set the permission automatically when it is
>> called in your next release. Thank you!
>>
>> best -hl
>>
>>
>>
>> On Tue, Jan 31, 2012 at 5:50 PM, Robert Buels <rb...@gm...
>> <mailto:rb...@gm...>> wrote:
>>
>>    Hi Heewok,
>>
>>    Do you see any errors in your web server's logs, like 404 (not
>>    found) errors?
>>
>>    Rob
>>
>>
>>    On 01/24/2012 02:32 AM, Heewook Lee wrote:
>>
>>        Hi,
>>
>>        I installed the jbrowse along with all the prerequisites on the
>>        tutorial
>>        page. followed the exact same commands(using the volvox data
>>        that comes
>>        with the tarball). When I load the page on my web browser, all i
>>        see is
>>        just a blank page. When i click on view source from the browser,
>>        I see
>>        exactly what's on index.html. so the webserver seems to be
>>        working. Can
>>        somebody help? Thanks!
>>
>>
>>
>>
>>
>>        ------------------------------**__----------------------------**
>> --__------------------
>>
>>        Keep Your Developer Skills Current with LearnDevNow!
>>        The most comprehensive online learning library for Microsoft
>>        developers
>>        is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5,
>>        CSS3, MVC3,
>>        Metro Style Apps, more. Free future releases when you subscribe
>> now!
>>        http://p.sf.net/sfu/__**learndevnow-d2d<http://p.sf.net/sfu/__learndevnow-d2d>
>>        <http://p.sf.net/sfu/**learndevnow-d2d<http://p.sf.net/sfu/learndevnow-d2d>
>> >
>>
>>
>>
>>        ______________________________**___________________
>>        Gmod-ajax mailing list
>>        Gmo...@li...urceforge.__**net
>>        <mailto:Gmod-ajax@lists.**sourceforge.net<Gmo...@li...>
>> >
>>        https://lists.sourceforge.net/**__lists/listinfo/gmod-ajax<https://lists.sourceforge.net/__lists/listinfo/gmod-ajax>
>>        <https://lists.sourceforge.**net/lists/listinfo/gmod-ajax<https://lists.sourceforge.net/lists/listinfo/gmod-ajax>
>> >
>>
>>
>>
>>
>

Re: [Gmod-ajax] installed but the page shows nothing

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

Hello Heewook,

Sorry I didn't see this email sooner.  I'd guess that the
prepare-refseqs step didn't go as it's supposed to.  Can you try doing
that again and make sure that the results  end up in the the
appropriate "data" directory in your jbrowse directory?

Scott


On Tue, Jan 24, 2012 at 2:32 AM, Heewook Lee <he...@um...> wrote:
> Hi,
>
> I installed the jbrowse along with all the prerequisites on the tutorial
> page. followed the exact same commands(using the volvox data that comes with
> the tarball). When I load the page on my web browser, all i see is just a
> blank page. When i click on view source from the browser, I see exactly
> what's on index.html. so the webserver seems to be working. Can somebody
> help? Thanks!
>
>
>
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

Re: [Gmod-ajax] jbrowse loading times

[Gregg H. <gre...@gm...>]

One of the goals of the WebApollo project (annotation editor built on top
of JBrowse) is to add support for DAS.  Currently we're doing that in a
roundabout way via server-side middleware which translates DAS to JBrowse
JSON on the fly, and which helps us get around point-of-origin security
restrictions.  But now that many DAS servers support CORS (cross-origin
resource sharing), which allows a Javascript client to access data from
non-origin sites, it may make sense to look at adding direct client-side
support for parsing DAS.  If we go that route there are currently several
Javascript DAS clients and libraries available, so we might be able to
adapt existing code.

Gregg

On Tue, Jan 31, 2012 at 3:08 PM, Robert Buels <rb...@gm...> wrote:

> On 01/31/2012 06:00 PM, Alex Kalderimis wrote:
> > I think we'll move to DAS in the future (it has the potential to
> > massively streamline our release process) - is there any chance of
> > jbrowse consuming DAS?
>
> This has been talked about off and on.  I don't have a thorough enough
> command of the codebase yet to know how hard it would be to do this, but
> I suspect it wouldn't be easy.
>
> Anybody else on this list super-interested in DAS support?
>
> Rob
>
>
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Re: [Gmod-ajax] jbrowse loading times

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

Hi Alex,

CCing the list on this reply.  By load times, you mean the 
JSON-formatting done on the server side, using something like 
biodb-to-json.pl, right?

Yes, the current implementations of these tools are very, very 
inefficient in many ways, particularly regarding their RAM usage.  They 
keep a lot of things in RAM, for example.  It's definitely high on my 
list of things to fix.

Could you file this as an issue in the tracker on GitHub so it doesn't 
get lost?

Rob

On 01/31/2012 09:55 AM, Alex Kalderimis wrote:
> We've been doing some jbrowse loading, and experiencing extremely slow
> load times. We're loading three tracks from all chromosomes of H.
> sapiens and M. musculus, where we have about 3-4 million features on
> each chromosomes (including SNPs). The load is taking days, and
> consuming over 30GB of memory at peak - I seem to recall this being
> quicker when we had fewer SNPs. What kinds of load times would you
> expect for this kind of activity?
>
> Alex Kalderimis
>
> ------------------------------------------------------------------------------
> Keep Your Developer Skills Current with LearnDevNow!
> The most comprehensive online learning library for Microsoft developers
> is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3,
> Metro Style Apps, more. Free future releases when you subscribe now!
> http://p.sf.net/sfu/learndevnow-d2d
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>

Re: [Gmod-ajax] jbrowse loading times

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

On 01/31/2012 06:00 PM, Alex Kalderimis wrote:
> I think we'll move to DAS in the future (it has the potential to
> massively streamline our release process) - is there any chance of
> jbrowse consuming DAS?

This has been talked about off and on.  I don't have a thorough enough 
command of the codebase yet to know how hard it would be to do this, but 
I suspect it wouldn't be easy.

Anybody else on this list super-interested in DAS support?

Rob

[Gmod-ajax] jbrowse loading times

[Alex K. <al...@in...>]

We've been doing some jbrowse loading, and experiencing extremely slow
load times. We're loading three tracks from all chromosomes of H.
sapiens and M. musculus, where we have about 3-4 million features on
each chromosomes (including SNPs). The load is taking days, and
consuming over 30GB of memory at peak - I seem to recall this being
quicker when we had fewer SNPs. What kinds of load times would you
expect for this kind of activity?

Alex Kalderimis

[Gmod-ajax] installed but the page shows nothing

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

Hi,

I installed the jbrowse along with all the prerequisites on the tutorial
page. followed the exact same commands(using the volvox data that comes
with the tarball). When I load the page on my web browser, all i see is
just a blank page. When i click on view source from the browser, I see
exactly what's on index.html. so the webserver seems to be working. Can
somebody help? Thanks!

[Gmod-ajax] Minutes from JBrowse meeting, 1/9/12

[Robert B. <rm...@co...>]

Minutes mostly by Nomi Harris, with some edits and expansions by Rob.

Attendees
----------

Rob, Scott, Nomi, Suzi, Lincoln, Chris C., Ed

Minutes
----------

Rob's official start day is probably tomorrow (waiting for official 
documents).
Working on an integration test suite in Selenium (had to do it in 
Python--not quite as nice as the Perl testing stuff). (This includes 
some UI testing--Selenium lets you do this by basically launching a 
browser that you can remote-control.)
First will integrate Natalie Fox's faceted track selected
Then will work on merging in Mitch's JSON refactoring stuff. Hopes to 
have that done before PAG.

There's an intern named Julie Moon working with Lincoln on documentation 
of URL API (for purposes of embedding) and will work out a mechanism for 
turning off the JBrowse controls, so that people will be able to embed 
static JBrowse shots in web pages that let the user move around only in 
very limited ways.

Rob is going to PAG and was planning to fly home the morning of the 
19th. It may be hard for him to arrange to stay longer to join us for 
part of the WebApollo Hackathon, but he will see what he can do.

Some discussion about folding, packing, and overlay of tracks and
subtracks.  The overlay option makes features no longer bump
eachother, but overlay eachother.  This is especially useful for
multiple wiggle tracks.

Suzi asked: Lincoln mentioned about moving tracks to overlay each other, 
and also how it would be nice to have the ability to do set operations 
(union, etc.) on tracks. Where is this on your priority list?
Rob said it's on his radar but he's not sure what the priority is. We 
should talk to Ian about that.
Suzi: What does the UCSC browser offer in terms of set operations?
Lincoln: UCSC has various "packing" operations (full/squished/compact) 
that control how collision control works. There's a new packing 
operation called overlay (or something like that) with a transparency 
value, so that instead of bumping each other, features are superimposed 
on each other with transparency. This is useful for wiggle tracks--can 
put them into a sort of merged profile.
Suzi: Is it dynamic?
Lincoln: No--not integrated with drag.
Lincoln: It would be great if you could dump tracks on top of each 
other, and if you did that, it could pop up a menu to let you do set 
operations.
Suzi: Yes, and you might want to create a new track and put your new 
composed track into it.
We will talk to Gregg about this (he implemented something like this in 
IGB.)

Ed: Tracks are listed in order they appear in the configuration file. He 
added something to allow you to sort the track order.
Suzi: Would like to revisit different ways to index tracks. Don't like 
the labels. Would like to have track information/controls aligned with 
the tracks.
Ed: We once had a discussion about having track labels float to the left 
so they don't use up real estate.

Suzi: Would the work Gregg did on making features show the individual 
bases be useful in JBrowse?
(Currently in JBRowse, the DNA track shows up if you zoom in enough, but 
you don't see bases in other tracks.)
Ed: Well, this is most useful when editing, but could also be nice if 
you saw bases when you zoomed in enough. Right now, though, it only 
shows DNA sequence when you select a feature, so if we wanted to show 
bases in JBrowse, would have to either (1) add WebApollo's selection 
capability to JBrowse (which might be useful anyway), or (2) show bases 
in all tracks once you zoom in enough.
Rob: It would make sense to add both selection and more basepair-showing 
capability to core JBrowse.


Hackathon objective: add ability to get data from Chado into 
JBrowse/WebApollo. This will greatly increase the number of datasources 
that JBrowse/WebApollo will have access to. (Can already read UCSC and 
GFF3.)

[Gmod-ajax] JBrowse conference call, January 9th, 2pm Pacific

[Robert B. <rm...@co...>]

Hello JBrowse users and developers,

The next JBrowse developers' conference call will be held on Monday, 
January 9 at 2pm Pacific time.  Call details are below; we hope you will 
join in.

Call details:

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

Talk to you then!

Rob
----
Robert Buels
JBrowse Lead Developer (as of this month)

Re: [Gmod-ajax] JBrowse conference call, December 12th, 2pm Pacific

[Robert B. <rm...@co...>]

Sure, will do.

On 12/12/2011 03:02 PM, Lincoln Stein wrote:
> Sorry I missed this!
>
> In future, could you cc the announcements to my assistant,
> Ren...@oi... <mailto:Ren...@oi...>?

Re: [Gmod-ajax] JBrowse conference call, December 12th, 2pm Pacific

[Lincoln S. <lin...@gm...>]

Sorry I missed this!

In future, could you cc the announcements to my assistant,
Ren...@oi...?

Lincoln

On Friday, December 9, 2011, Robert Buels <rm...@co...> wrote:
> Hello JBrowse users and developers,
>
> The next JBrowse developers' conference call will be held on Monday,
December 12 at 2pm Pacific time.  Call details are below; we hope you will
join in.
>
> Call details:
>
> 1. Dial Toll-Free Number: 866-740-1260 (U.S. & Canada)
> (The toll-free number from Thailand is 001800656911)
> 2. Enter access code 4867508#
>
> Talk to you then!
>
> Rob
>
>

Re: [Gmod-ajax] JBrowse conference call, December 12th, 2pm Pacific

[Robert B. <rm...@co...>]

Hi all,

Good to talk with you!  Here are the minutes from the meeting.

Rob


Attendance
-------------
Nomi Harris
Gregg Helt
Ed Lee
Chris Childers
Scott Cain
Tyra Wolfsberg
Ian Holmes
Sheldon McKay

Minutes
------------

Rob reports that he will be giving a JBrowse presentation at PAG.

Scott says the GMOD meeting in April is right after the BioCuration
meeting in Georgetown. Gregg and Ed will be at the BioCuration
meeting, so maybe they can just stay for the GMOD meeting.

Gregg asked Tyra about how she is using JBrowse at NHGRI.  Tyra says
she is using JBrowse for a novel genome they are sequencing.

Tyra had a question about JBrowse's current behavior when lists of
tracks to display are specified in the URL (and passed into the
Browser constructor as the 'tracks' parameter).  Currently, that
passed parameter overrides the list of displayed tracks in the user's
cookie, there was some discussion about whether the two lists should be
unioned instead, rather than one overriding the other.  The
conclusion was that this might be too complex.

Tyra also had a use case for displaying the genotypes of polymorphisms
in the genome.  JBrowse doesn't currently have functionality for doing
this; there was discussion about GBrowse's allele_tower glyph, which
sounds like it does this.  Some methods for accomplishing this in a
JBrowse installation were discussed; the feature roadmap for JBrowse
includes giving it the ability to use GBrowse glyphs in some fashion,
and that should help with this.

Gregg and Ed outlined for Tyra a bit about some of the things that
they are working on the WebApollo branch, such as context menus and
other experimental features, some of which they hope to role into the
main JBrowse branch.

Ian will be giving a talk at a European bioinformatics meeting next
week.

Rob is going to be starting as the primary JBrowse developer in
January.

Next Meeting
--------------
January 9, 2012, 2pm PST

[Gmod-ajax] Deadline to apply for GMOD Workshop in Český Krumlov, Czech Republic extended

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

Hello,

The Special Topics workshop on GMOD that is being held in conjunction
with the Workshop on Genomics in Český Krumlov, Czech Republic has had
its application deadline extended to December 15.  If you or someone
you know might be interested in this 3 day workshop offered January
23-25, please see:

  http://evomics.org/workshops/workshop-on-genomics/2012-genomics-cesky-krumlov/2012/

for more information.  I hope to see you in the Czech Republic next month.

Scott


-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

[Gmod-ajax] JBrowse conference call, December 12th, 2pm Pacific

[Robert B. <rm...@co...>]

Hello JBrowse users and developers,

The next JBrowse developers' conference call will be held on Monday, 
December 12 at 2pm Pacific time.  Call details are below; we hope you 
will join in.

Call details:

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

Talk to you then!

Rob