gmod-ajax — JBrowse list

Re: [Gmod-ajax] JBrowse track groupings

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

Dear Mitch,

I have another feature request that I thought would be best to start  
on a separate thread.

One thing that would be very useful for users like me who have a lot  
of tracks s the ability to select entire groups of tracks to load at  
once instead of having to do it individually.  For instance, our  
modENCODE browser has 30 different RNA-Seq tracks from different  
timepoints throughout Drosophila development.  If there was a way to  
load all 12 embryonic time points at once it would be great.  Perhaps  
one way to do this would be to have a menu type thing on the left  
where you could have nested tracks.  So, perhaps you could have one  
track listed as "Development" and dragging this to the right would  
load all 30 time points.  Alternatively, there could be an arrow that  
you could click on and it would display the next set of groupings  
(e.g., Embryos, Larvae, Pupae, Adults).  Again, you could either drag  
one of these to the browser window to load the whole set or click on  
an arrow to show the next set of grouping (e.g., the individual tracks  
in each group).  I have absolutely no clue how easy or difficult  
something like this would be to implement, but it could be quite  
useful, especially since we will have many more tracks (~200 in the  
next year or so) to add to the browser.

Cheers,

Brent

Re: [Gmod-ajax] JBrowse wiggle file display - png

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

Hi Mitch,

Sorry to delay in responding about the vertical scaling issues.  As  
you mentioned in a previous email,  there are issues with dynamic and  
static scaling whether on a linear or log scale.  For instance, for  
some of our RNA-Seq datasets there are genes with hundreds of  
thousands of reads right next to a gene that is expressed at low  
levels.  What linear scaling allows you to do is see the full range.   
In a case like this, log scaling would help, but with such a dynamic  
range, even the low expressed genes would be very low.  The other  
thing about log scaling is that, at least to me, it is non-intuitive.   
The best thing would be something along the lines of what you mention  
- some type of "y-zooming".  This way, if you are interested in low  
expression of a certain segment in a region that also contains highly  
expressed genes, you could see it by zooming in.  Similarly, to see  
the real dynamic range, you could zoom out.

Nonetheless, I'll make a few tracks with linear scaling with a limit  
of 100 or so, linear scaling using the real max, and a log scale track  
and send some screenshot/links.

Cheers,

Brent



On Sep 29, 2009, at 6:51 AM, Mitch Skinner wrote:

> The short answer is; right now you can set the scale with the --min  
> and
> --max command line parameters.
>
> Sometime soon, we'll be implementing a log scale option.  Enabling the
> user to zoom vertically is something I'd like to do; there's a basic
> version of that that would be easy to implement (toggling between a
> "full" and "compressed" vertical axis is what I have in mind).  Would
> any of those things help in your case?
>
> Implementing a vertical scale indicator is definitely on the to-do  
> list.
>
> Brenton Gravely has been advocating making the vertical scale adjust  
> to
> the values in the visible region; I think that would be hard to
> implement so it's probably not going to happen near-term unless  
> someone
> wants to tackle it.
>
> I only have a basic understanding of exactly what people are using
> RNA-seq for.  So I'd like to know: in your case, how does the data
> answer a biological question?  If (say) one region has variation  
> between
> 100 and 200, and another region has variation between 100,000 and
> 200,000, are the 100-200 differences and the 100k-200k differences  
> both
> interesting?  In other words, what constitutes meaningful variation  
> your
> RNA-seq data?
>
> I keep asking these questions, and so far I haven't gotten an answer
> that has made it clear for me.  Maybe we're at an exploratory stage
> where the answers aren't clear in general?  I don't know.  It's  
> tough to
> make good UI decisions if the use case isn't clear.
>
> Mitch
>
> On 09/28/2009 01:24 PM, Shankar Ajay Subramanian wrote:
>> Hi,
>>
>> I'm a newbie to JBrowse and I was wondering if someone could help me
>> out with my question. I currently have a de novo genome assembly on
>> which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle
>> file (variableStep) has values that are in the range 1-275000. This
>> (huge) range of values is probably why most of the regions appear to
>> be without any reads/expression - the low values are probably not
>> rendered in the png image.
>>
>> I'm wondering if there's a solution to see the data at a better
>> resolution/scale. Are there options while converting to json that I
>> can use to make it appear better? Is dynamic scaling possible as a
>> user zooms in/out? Or should I do my own scaling/transposition before
>> I do the json conversion?
>>
>> Thanks,
>> Shankar
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry® Developer Conference in SF,  
>> CA
>> is the only developer event you need to attend this year. Jumpstart  
>> your
>> developing skills, take BlackBerry mobile applications to market  
>> and stay
>> ahead of the curve. Join us from November 9-12, 2009. Register  
>> now!
>> http://p.sf.net/sfu/devconf
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart  
> your
> developing skills, take BlackBerry mobile applications to market and  
> stay
> ahead of the curve. Join us from November 9-12, 2009. Register  
> now!
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Re: [Gmod-ajax] JBrowse wiggle file display - png

[Shankar A. S. <sha...@gm...>]

On Tue, Sep 29, 2009 at 9:02 AM, Mitch Skinner
<mit...@be...> wrote:
> On 09/29/2009 06:44 AM, Shankar Ajay Subramanian wrote:
>>
>> I circumvented the problem by converting my data to a log scale (base
>> 2), so the track looks like a set of jagged peaks that I expected to
>> see.
>>
>
> Did the log scale solve the problem for you?  In other words, does the log
> display convey all of the relevant variation, or is there some variation
> that you'd like to see but can't?

It seems to be working well so far. I have to yet compare it with
another track. Will let you know if I run into some trouble.

>
>> The use case that you described (100 vs 200 and 100k vs 200k) both
>> constitute interesting differences since there is a two-fold
>> difference between the min and max for the two regions.
>
> Can there be 100-200 variation and also 100k-200k variation within the same
> region?  If so, are both of those still interesting?
>
> Or do large fluctuations tend to happen only between widely separated areas?
>

I think I'll have to answer this rather circuitously. If that were to
were, it would definitely be interesting. It's tough to say if both
those variations in one region is something one might see. Sorry, if
the answer sounds silly.

>>  In my
>> particular case, if I were to compare two conditions/experiments (say,
>> pre- and post-treatment) where a particular region varies between
>> 1-500 (which is no doubt "interesting"), I'm unable to see this
>> difference on the browser currently, since the threshold to have a
>> data point displayed with my data range (1-200k) is ~1000. I suppose
>> vertical scaling will help fix this. Correct me if I am wrong.
>>
>
> I think it should help, yes.
>
>> I don't know if I answered your question, but I'd be happy to answer
>> any further questions that you might have in making improvements.
>>
>
> You did answer my questions, thanks.  Once we get to implementing the log
> scaling and vertical scale bar and vertical zooming in JBrowse, it would be
> helpful to get feedback on how well those things work for you.

Definitely, I presume you'll post a message to list informing us on upgrades.

>
> Thanks,
> Mitch
>

Re: [Gmod-ajax] JBrowse wiggle file display - png

[Shankar A. S. <sha...@gm...>]

Hi Mitch,

I circumvented the problem by converting my data to a log scale (base
2), so the track looks like a set of jagged peaks that I expected to
see.

Looking through the code very briefly it appears as though that
JBrowse precomputes png images for wiggle tracks at different zoom
levels. If that's the case, you're absolutely right, it's a tough task
to adjust the scale to values in the visible region (akin to the UCSC
genome browser).

The use case that you described (100 vs 200 and 100k vs 200k) both
constitute interesting differences since there is a two-fold
difference between the min and max for the two regions. In my
particular case, if I were to compare two conditions/experiments (say,
pre- and post-treatment) where a particular region varies between
1-500 (which is no doubt "interesting"), I'm unable to see this
difference on the browser currently, since the threshold to have a
data point displayed with my data range (1-200k) is ~1000. I suppose
vertical scaling will help fix this. Correct me if I am wrong.

I don't know if I answered your question, but I'd be happy to answer
any further questions that you might have in making improvements.

Regards,
Shankar

On Tue, Sep 29, 2009 at 5:51 AM, Mitch Skinner
<mit...@be...> wrote:
> The short answer is; right now you can set the scale with the --min and
> --max command line parameters.
>
> Sometime soon, we'll be implementing a log scale option.  Enabling the
> user to zoom vertically is something I'd like to do; there's a basic
> version of that that would be easy to implement (toggling between a
> "full" and "compressed" vertical axis is what I have in mind).  Would
> any of those things help in your case?
>
> Implementing a vertical scale indicator is definitely on the to-do list.
>
> Brenton Gravely has been advocating making the vertical scale adjust to
> the values in the visible region; I think that would be hard to
> implement so it's probably not going to happen near-term unless someone
> wants to tackle it.
>
> I only have a basic understanding of exactly what people are using
> RNA-seq for.  So I'd like to know: in your case, how does the data
> answer a biological question?  If (say) one region has variation between
> 100 and 200, and another region has variation between 100,000 and
> 200,000, are the 100-200 differences and the 100k-200k differences both
> interesting?  In other words, what constitutes meaningful variation your
> RNA-seq data?
>
> I keep asking these questions, and so far I haven't gotten an answer
> that has made it clear for me.  Maybe we're at an exploratory stage
> where the answers aren't clear in general?  I don't know.  It's tough to
> make good UI decisions if the use case isn't clear.
>
> Mitch
>
> On 09/28/2009 01:24 PM, Shankar Ajay Subramanian wrote:
>> Hi,
>>
>> I'm a newbie to JBrowse and I was wondering if someone could help me
>> out with my question. I currently have a de novo genome assembly on
>> which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle
>> file (variableStep) has values that are in the range 1-275000. This
>> (huge) range of values is probably why most of the regions appear to
>> be without any reads/expression - the low values are probably not
>> rendered in the png image.
>>
>> I'm wondering if there's a solution to see the data at a better
>> resolution/scale. Are there options while converting to json that I
>> can use to make it appear better? Is dynamic scaling possible as a
>> user zooms in/out? Or should I do my own scaling/transposition before
>> I do the json conversion?
>>
>> Thanks,
>> Shankar
>>
>> ------------------------------------------------------------------------------
>> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart your
>> developing skills, take BlackBerry mobile applications to market and stay
>> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
>> http://p.sf.net/sfu/devconf
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Information about how to build demo server (fly and human)

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

On 09/18/2009 03:53 AM, Motokazu Ishikawa wrote:
> If you could provide information about how to build demo server (fly and
> human) on your web site, it will greatly help me to do my work.
> Especially, I want to see contents of each data files (gff, bed).
>    

This is a description of the fly part.  The human part is more 
complicated; it involved downloading BED files from UCSC's table browser 
and then processing them with flatfile-to-json.pl.

I downloaded the GFF files from flybase; this is the current release as 
of this writing:

ftp://ftp.flybase.net/releases/current/dmel_r5.21/gff/

I installed bioperl 1.6 and the JSON and JSON::XS modules from CPAN.

I loaded the gff files into a mysql database by going into the directory 
with the GFF files and running this command:

$ bp_seqfeature_load.pl --dsn=dbi:mysql:dmel_5_15 --adaptor=DBI::mysql 
--fast --create dmel-*

(my database was named dmel_5_15 because 5.15 was the latest release 
when I did this; you'll probably want to name yours something else)

I used this JBrowse config file:

http://jbrowse.org/code/jbrowse-master/docs/examples/config/Dmel.json

(you'll want to change the description and db_args to reflect your data)

I downloaded the JBrowse code and placed it where the HTTP server would 
serve it (in my case, under /var/www/html).  Then (from the jbrowse 
directory) I did this to prepare the sequence data:

$ bin/prepare-refseqs.pl --conf ~/Dmel.json --refs 2L,2R,3L,3R,4,X

(the config file was in my home directory; in general, you want this to 
be somewhere other than the jbrowse directory, because it contains 
information on how to access your database, which you usually want to 
keep secret)

Then, once prepare-refseqs.pl was finished, I ran this (also within the 
jbrowse directory):

$ bin/biodb-to-json.pl --conf ~/JBrowseConfig.js

Then I ran generate-names to make the features searchable:

$ bin/generate-names.pl

And that should be it.

Mitch

Re: [Gmod-ajax] JBrowse wiggle file display - png

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

On 09/29/2009 06:44 AM, Shankar Ajay Subramanian wrote:
> I circumvented the problem by converting my data to a log scale (base
> 2), so the track looks like a set of jagged peaks that I expected to
> see.
>    

Did the log scale solve the problem for you?  In other words, does the 
log display convey all of the relevant variation, or is there some 
variation that you'd like to see but can't?

> The use case that you described (100 vs 200 and 100k vs 200k) both
> constitute interesting differences since there is a two-fold
> difference between the min and max for the two regions.

Can there be 100-200 variation and also 100k-200k variation within the 
same region?  If so, are both of those still interesting?

Or do large fluctuations tend to happen only between widely separated areas?

>   In my
> particular case, if I were to compare two conditions/experiments (say,
> pre- and post-treatment) where a particular region varies between
> 1-500 (which is no doubt "interesting"), I'm unable to see this
> difference on the browser currently, since the threshold to have a
> data point displayed with my data range (1-200k) is ~1000. I suppose
> vertical scaling will help fix this. Correct me if I am wrong.
>    

I think it should help, yes.

> I don't know if I answered your question, but I'd be happy to answer
> any further questions that you might have in making improvements.
>    

You did answer my questions, thanks.  Once we get to implementing the 
log scaling and vertical scale bar and vertical zooming in JBrowse, it 
would be helpful to get feedback on how well those things work for you.

Thanks,
Mitch

Re: [Gmod-ajax] question about link to Jbrowse from other databases

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

On 09/22/2009 07:13 PM, du zhou wrote:
> Hi everyone. I have used Jbrowse for a while, it is really attractive.
> My question is about how to link to Jbrowse from other sites. I found
> a similar question of jbrowse deep link already existed in the mail
> list. However, I still have no idea what can I do now?
> What exactly should I do to achieve this (and both my database and
> Jbrowse are in intranet)? Is there a detailed tuturial about this job?

One way to do this has been implemented, but it hasn't been documented
yet because I plan to change it. So as long as you know it can change,
this is what you can do now:

Here's an example link:

http://jbrowse.org/genomes/dmel/?loc=X:4814624..4821114&tracks=DNA,gene,cDNA,hitsGenomic_ncRna_v22_dmel_r5_lgOddsCutoff_uniq,mRNA

There are two URL parameters here, "loc" and "tracks". "loc" can be
anything that you might put into the location box, like
"X:4814624..4821114" or a feature name/ID. "tracks" is a comma-separated
list of track identifiers.

So if your other database has information on the location of the
features you want to link to, you can put that location into the "loc"
URL parameter in your links.

Hope this helps,
Mitch

Re: [Gmod-ajax] Using multiple glyphs per track

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

On 09/23/2009 08:13 PM, David Rosenberg wrote:
>    From what I can see, there is no 'easy' way to use multiple glyphs
> per track in the current implementation (something I am interested in
> doing).  Is this something you plan to implement?
>    

This is definitely something that we've been talking about and that we 
plan to do.  This is what I've thought about this so far:

The main question in my mind is what callbacks we should allow for.  The 
possibilities I've been thinking about are callbacks that take the 
feature data as an argument and return:

* an HTML element (or just the element type, e.g., "div" or "a")
* a CSS class
* some CSS style text (e.g., "background-color: red")

Can anyone think of other things that people might want to customize 
with a callback?

One potential complication is that people could do things in these 
callbacks that would throw off FeatureTracks's layout code (e.g., by 
breaking FeatureTrack's current assumption that all features are the 
same height).

Once we implement this, then we should probably reimplement some of the 
current functionality (like how feature elements are usually "div"s but 
become "a"s if there's a urlTemplate) in terms of default callbacks.

Mitch

Re: [Gmod-ajax] Couldn't execute flatfile-to-json.pl

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

Hello,

It looks like we should add an example to the tutorial for using 
flatfile-to-json.pl, and flatfile-to-json.pl probably needs some changes 
or at least more helpful error messages.

Could you send your gff file and your data/refSeqs.js file?  That should 
help me reproduce the problem you're seeing.

Thanks,
Mitch

On 09/24/2009 06:06 AM, Adhemar wrote:
> Hi All,
> I'm a newbie on using jbrowse and I'm quite excited with its
> functionalities.
> The installation ran smoothly and it's working 100% if I follow the
> 'Getting Started With JBrowse' tutorial.
> The thing is that I couldn't create a new jbrowse instance using a GFF
> file.
> It's not working even with the example file (volvox.gff).
> I wonder if you could help me figure out what's going on.
> My PC is a Fedora 11 i386 + bioperl 1.6 + JSON 2.15.
> Here is the error message:
>
> [localuser@localhost temp]$ bin/flatfile-to-json.pl -gff file.gff
> --autocomplete all
>
> working on seq Seq1
>
> -------------------- EXCEPTION --------------------
> MSG: segment() called in a scalar context but multiple features match.
> Either call in a list context or narrow your search using the -types or
> -class arguments
>
> STACK Bio::DB::SeqFeature::Store::segment
> /usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:1298
> STACK toplevel bin/flatfile-to-json.pl:152
> -------------------------------------------
>
>
> Thanks in advance.
> Adhemar
>    

Re: [Gmod-ajax] tracks with empties

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

On 09/27/2009 03:16 PM, Giles Velarde wrote:
> I had a look over the weekend (see patch below). This turned out to be 
> a little bit more complicated than I thought because if I tried to 
> just do something simple in the error handler like
>
>     this.setLoaded();
>
> data structures weren't initialized properly and errors ensued. I got 
> around this by faking an empty track inside the error handler and 
> passing it onto loadSuccess(). Not being familiar with JBrowse, I 
> don't know if this is the best way to do it, but it seems to work for me.

Cool!  It's great to see people getting into the code.  What you did was 
the first thing I thought of doing, but I wanted to solve the problem 
for ImageTrack as well.  This is what I just committed to the master branch:

http://github.com/jbrowse/jbrowse/commit/6e7f2e8940ccb3fa6bf2c79db499121289d67fe6

It adds yet another bit of state to the Track class, which I usually try 
to avoid; on the other hand, it saves us from having to maintain a 
proper fake empty track.

Hopefully I don't sound like I'm dismissing what you did; I'm really 
happy when I get patches, but I thought about it and decided I wanted to 
go in a different direction.

Regards,
Mitch

Re: [Gmod-ajax] tracks with empties

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

On 29 Sep 2009, at 13:31, Mitch Skinner wrote:

> On 09/27/2009 03:16 PM, Giles Velarde wrote:
>> I had a look over the weekend (see patch below). This turned out to  
>> be a little bit more complicated than I thought because if I tried  
>> to just do something simple in the error handler like
>>
>>    this.setLoaded();
>>
>> data structures weren't initialized properly and errors ensued. I  
>> got around this by faking an empty track inside the error handler  
>> and passing it onto loadSuccess(). Not being familiar with JBrowse,  
>> I don't know if this is the best way to do it, but it seems to work  
>> for me.
>
> Cool!  It's great to see people getting into the code.  What you did  
> was the first thing I thought of doing, but I wanted to solve the  
> problem for ImageTrack as well.  This is what I just committed to  
> the master branch:
>
> http://github.com/jbrowse/jbrowse/commit/6e7f2e8940ccb3fa6bf2c79db499121289d67fe6
>
> It adds yet another bit of state to the Track class, which I usually  
> try to avoid; on the other hand, it saves us from having to maintain  
> a proper fake empty track.
>
> Hopefully I don't sound like I'm dismissing what you did; I'm really  
> happy when I get patches, but I thought about it and decided I  
> wanted to go in a different direction.
>
> Regards,
> Mitch

No worries, Mitch. I am just scratching its surface right now, and was  
well aware that was probably a better way.
Glad it's fixed! Will try it out asap.
Cheers,
Giles



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

Re: [Gmod-ajax] JBrowse wiggle file display - png

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

The short answer is; right now you can set the scale with the --min and 
--max command line parameters.

Sometime soon, we'll be implementing a log scale option.  Enabling the 
user to zoom vertically is something I'd like to do; there's a basic 
version of that that would be easy to implement (toggling between a 
"full" and "compressed" vertical axis is what I have in mind).  Would 
any of those things help in your case?

Implementing a vertical scale indicator is definitely on the to-do list.

Brenton Gravely has been advocating making the vertical scale adjust to 
the values in the visible region; I think that would be hard to 
implement so it's probably not going to happen near-term unless someone 
wants to tackle it.

I only have a basic understanding of exactly what people are using 
RNA-seq for.  So I'd like to know: in your case, how does the data 
answer a biological question?  If (say) one region has variation between 
100 and 200, and another region has variation between 100,000 and 
200,000, are the 100-200 differences and the 100k-200k differences both 
interesting?  In other words, what constitutes meaningful variation your 
RNA-seq data?

I keep asking these questions, and so far I haven't gotten an answer 
that has made it clear for me.  Maybe we're at an exploratory stage 
where the answers aren't clear in general?  I don't know.  It's tough to 
make good UI decisions if the use case isn't clear.

Mitch

On 09/28/2009 01:24 PM, Shankar Ajay Subramanian wrote:
> Hi,
>
> I'm a newbie to JBrowse and I was wondering if someone could help me
> out with my question. I currently have a de novo genome assembly on
> which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle
> file (variableStep) has values that are in the range 1-275000. This
> (huge) range of values is probably why most of the regions appear to
> be without any reads/expression - the low values are probably not
> rendered in the png image.
>
> I'm wondering if there's a solution to see the data at a better
> resolution/scale. Are there options while converting to json that I
> can use to make it appear better? Is dynamic scaling possible as a
> user zooms in/out? Or should I do my own scaling/transposition before
> I do the json conversion?
>
> Thanks,
> Shankar
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry® Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9-12, 2009. Register now!
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>    

[Gmod-ajax] JBrowse wiggle file display - png

[Shankar A. S. <sha...@gm...>]

Hi,

I'm a newbie to JBrowse and I was wondering if someone could help me
out with my question. I currently have a de novo genome assembly on
which I'd like to overlay wiggle tracks from RNA-seq data. The wiggle
file (variableStep) has values that are in the range 1-275000. This
(huge) range of values is probably why most of the regions appear to
be without any reads/expression - the low values are probably not
rendered in the png image.

I'm wondering if there's a solution to see the data at a better
resolution/scale. Are there options while converting to json that I
can use to make it appear better? Is dynamic scaling possible as a
user zooms in/out? Or should I do my own scaling/transposition before
I do the json conversion?

Thanks,
Shankar

Re: [Gmod-ajax] tracks with empties

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

On 23 Sep 2009, at 19:21, Mitch Skinner wrote:

> On 09/23/2009 02:58 AM, Giles Velarde wrote:
>> Should it be possible to make the Loading message time out? I guess  
>> it would then display a wholly blank track, which would be accurate  
>> in this case. The disadvantage of that approach is for users with  
>> poor connections, where timeouts happen more often, and where blank  
>> tracks would then appear even though the data is there on the server.
>
> If there's no file, then the client should be getting a 404 HTTP  
> error code.  And it should be straightforward to add an error  
> handler to the code that loads the individual tracks.  That should  
> handle the no-file case without requiring a timeout.  I'll send a  
> message to the list when I have something.
>
> Mitch

Thanks Mitch,

I had a look over the weekend (see patch below). This turned out to be  
a little bit more complicated than I thought because if I tried to  
just do something simple in the error handler like

	this.setLoaded();

data structures weren't initialized properly and errors ensued. I got  
around this by faking an empty track inside the error handler and  
passing it onto loadSuccess(). Not being familiar with JBrowse, I  
don't know if this is the best way to do it, but it seems to work for  
me.

All the Best,
Giles


 From f2406d7e65c65fb98553b197eec0107db7c49c08 Mon Sep 17 00:00:00 2001
From: Giles Velarde <gv...@sa...>
Date: Sun, 27 Sep 2009 12:24:39 +0100
Subject: [PATCH] added an error handler to FeatureTrack to handle  
tracks with no features

---
  js/FeatureTrack.js |   27 ++++++++++++++++++++++++++-
  1 files changed, 26 insertions(+), 1 deletions(-)

diff --git a/js/FeatureTrack.js b/js/FeatureTrack.js
index 40ea281..d05e587 100644
--- a/js/FeatureTrack.js
+++ b/js/FeatureTrack.js
@@ -27,12 +27,37 @@ function FeatureTrack(trackMeta, url, refSeq,  
browserParams) {
      var curTrack = this;
      dojo.xhrGet({url: curTrack.baseUrl + url,
  		 handleAs: "json",
-		 load: function(o) { curTrack.loadSuccess(o); }
+		 load: function(o) { curTrack.loadSuccess(o); },
+		 error: function(o) { curTrack.loadFail(o); }
  	});
  }

  FeatureTrack.prototype = new Track("");

+FeatureTrack.prototype.loadFail = function(error) {
+    if (error.status == "404")
+    {
+        console.log(this.trackMeta.label + " not loaded due to  
missing JSON file, creating an 'empty' track... ");
+        var trackInfo = {
+            "subfeatureClasses":null,
+            "headers": 
["start","end","strand","id","name","phase","type","load_id"],
+            "featureCount":0,
+            "featureNCList":[],
+            "key": this.trackMeta.key,
+            "className":"",
+            "clientConfig":null,
+            "rangeMap":[],
+            "arrowheadClass":null,
+            "subfeatureHeaders":["start","end","strand","id","type"],
+            "label": this.trackMeta.label,
+            "type": this.trackMeta.type,
+            "sublistIndex":0
+        };
+        this.loadSuccess(trackInfo);
+    }
+}
+
+
  FeatureTrack.prototype.loadSuccess = function(trackInfo) {
      var startTime = new Date().getTime();
      this.count = trackInfo.featureCount;
-- 
1.5.6.3



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] Couldn't execute flatfile-to-json.pl

[Adhemar <az...@gm...>]

Hi All,
I'm a newbie on using jbrowse and I'm quite excited with its 
functionalities.
The installation ran smoothly and it's working 100% if I follow the 
'Getting Started With JBrowse' tutorial.
The thing is that I couldn't create a new jbrowse instance using a GFF 
file.
It's not working even with the example file (volvox.gff).
I wonder if you could help me figure out what's going on.
My PC is a Fedora 11 i386 + bioperl 1.6 + JSON 2.15.
Here is the error message:

[localuser@localhost temp]$ bin/flatfile-to-json.pl -gff file.gff 
--autocomplete all

working on seq Seq1

-------------------- EXCEPTION --------------------
MSG: segment() called in a scalar context but multiple features match.
Either call in a list context or narrow your search using the -types or 
-class arguments

STACK Bio::DB::SeqFeature::Store::segment 
/usr/local/lib/perl5/site_perl/5.10.0/Bio/DB/SeqFeature/Store.pm:1298
STACK toplevel bin/flatfile-to-json.pl:152
-------------------------------------------


Thanks in advance.
Adhemar

Re: [Gmod-ajax] tracks with empties

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

Thanks, Mitch!

On 23 Sep 2009, at 19:21, Mitch Skinner wrote:

> On 09/23/2009 02:58 AM, Giles Velarde wrote:
>> Should it be possible to make the Loading message time out? I guess  
>> it would then display a wholly blank track, which would be accurate  
>> in this case. The disadvantage of that approach is for users with  
>> poor connections, where timeouts happen more often, and where blank  
>> tracks would then appear even though the data is there on the server.
>
> If there's no file, then the client should be getting a 404 HTTP  
> error code.  And it should be straightforward to add an error  
> handler to the code that loads the individual tracks.  That should  
> handle the no-file case without requiring a timeout.  I'll send a  
> message to the list when I have something.
>
> Mitch



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] Using multiple glyphs per track

[David R. <ros...@uc...>]

 From what I can see, there is no 'easy' way to use multiple glyphs  
per track in the current implementation (something I am interested in  
doing).  Is this something you plan to implement?

I have come up with a short-term solution (hack) to this problem  
through modifying the FeatureTrack.js file.

	here's a diff of my addition:


--- FeatureTrack.js	2009-09-23 21:04:08.000000000 -0500
+++ FeatureTrack.old.js	2009-09-23 15:42:15.000000000 -0500
@@ -363,32 +363,6 @@
              featDiv.className = "minus-" + className; break;
          }

-
-        var cnvReTester = /^CNV-.*$/;
-        if (feature[name].search(cnvReTester) == 0) {
-            var fSlots = feature[name].split(/-/);
-            if (fSlots[1].charAt(0) == '1') { // i.e. is CNV
-                if ((fSlots[1].charAt(1) * 1) < 2) { // i.e. is  
deletion
-                    featDiv.className = 'deletion' +  
fSlots[1].charAt(1);
-                } else {
-                    featDiv.className = 'duplication' +  
fSlots[1].charAt(1);
-                }
-            } else if (fSlots[1].charAt(0) == '2') { // i.e. is probe
-                switch (fSlots[1].charAt(1)) {
-                case '1':
-                    featDiv.className = 'snpprobe'; break;
-                case '2':
-                    featDiv.className = 'exonprobe'; break;
-                case '3':
-                    featDiv.className = 'gapprobe'; break;
-                }
-            }
-        };
-
-
-
-
-
      if ((phase !== undefined) && (feature[phase] !== null))
          featDiv.className = featDiv.className + feature[phase];



As you can see, I wrote it specifically to address my particular  
needs, although it could easily be 'generalized' to allow for any  
javascript callback using the 5 features stored in the json data.




David M. Rosenberg
University of Chicago
Committee on Neurobiology
947 E 58th St. MC 0928
Chicago, IL 60637

(773) 299-8740

ros...@uc...
http://www.palmerlab.org/Members/rosenbergdm

Re: [Gmod-ajax] 2009 GMOD Community Survey

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

Hello all,

This is a final reminder that the 2009 GMOD Survey (and your chance to
win GMOD gear) closes in two days, at the end of Friday, September 25.
 If you haven't already done so, please take a few minutes to fill out
the survey at:

  http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009


And, if you have an interest in automatic text mining & publication
curation tools such as Textpresso, the Biocurator community is running
a survey on that topic at

  http://www.surveymonkey.com/s.aspx?sm=3tfC_2fq3h2bxoncUJES_2fjtg_3d_3d

This survey was spawned by the "Text Mining for the BioCuration
Workflow" workshop at the 2009 Biocuration Conference.  See
http://projects.eml.org/sdbv/events/BiocurationMeeting/workshop1.html.
 (And, no, there is no free stuff, but it is a good cause.)

Thanks,

Dave C.

On Wed, Sep 16, 2009 at 5:06 PM, Dave Clements, GMOD Help Desk
<gmo...@go...> wrote:
> Hello all,
>
> Please take a few minutes to fill out the 2009 GMOD Community Survey
> and your name will be entered to win a free GMOD T-shirt or mug!  This
> year's survey focuses on genome and comparative genomics visualization
> (and is much shorter than the 2008 survey). We are asking all GMOD
> users and developers to provide feedback.
>
>  http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009
>
> Three randomly selected survey participants will receive the GMOD
> T-shirt or mug of their choice. Names will be drawn from the first 100
> responses, so get your response in early. The survey closes at the end
> of the day on September 25.
>
> Please contact the GMOD Help Desk if you have any questions.
>
> Thanks,
>
> Dave C
> GMOD Help Desk
>
> --
> * Please keep responses on the list!
> * Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
> * GMOD News: http://gmod.org/wiki/GMOD_News
>



-- 
* Please keep responses on the list!
* Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
* GMOD News: http://gmod.org/wiki/GMOD_News

Re: [Gmod-ajax] tracks with empties

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

On 09/23/2009 02:58 AM, Giles Velarde wrote:
> Should it be possible to make the Loading message time out? I guess it 
> would then display a wholly blank track, which would be accurate in 
> this case. The disadvantage of that approach is for users with poor 
> connections, where timeouts happen more often, and where blank tracks 
> would then appear even though the data is there on the server.

If there's no file, then the client should be getting a 404 HTTP error 
code.  And it should be straightforward to add an error handler to the 
code that loads the individual tracks.  That should handle the no-file 
case without requiring a timeout.  I'll send a message to the list when 
I have something.

Mitch

[Gmod-ajax] tracks with empties

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

Hello JBrowsers,

I have encountered a situation where if the GFF file in question does  
not have features of a certain type, but JBrowse is configured to show  
these, then the track gets stuck with a "Loading..." (see screenshot).  
It looks like it's making a request to a json file that's not there in  
this case. e.g. :

gv1@ubuntu:~/code/jbrowse_config$ ls /var/www/jbrowsers/jbrowse/data/ 
tracks/Lmjchr1
Exon  Gene  Polypeptide  Repeats
gv1@ubuntu:~/code/jbrowse_config$ ls /var/www/jbrowsers/jbrowse/data/ 
tracks/Lmjchr10
Exon  Gene  Polypeptide  Pseudogenics  Repeats

In the chromosome 10, there are some tracks labelled as pseudogenics.  
In chromosome 1, there aren't. Because in this situation I am loading  
a lot of GFF files, there are bound to be ones that don't have some of  
the features specified in the config file.

Should it be possible to make the Loading message time out? I guess it  
would then display a wholly blank track, which would be accurate in  
this case. The disadvantage of that approach is for users with poor  
connections, where timeouts happen more often, and where blank tracks  
would then appear even though the data is there on the server.

Another option might be to create a blank files with empty data  
structures in them, but I guess that depends on how the js handles  
empties.

All the Best,
Giles





-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] question about link to Jbrowse from other databases

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

Hi everyone. I have used Jbrowse for a while, it is really attractive.
My question is about how to link to Jbrowse from other sites. I found a
similar question of jbrowse deep link already existed in the  mail list.
However, I still have no idea what can I do now?
What exactly should I do to achieve this (and both my database and Jbrowse
are in intranet)?  Is there a detailed tuturial about this job?
Thanks a lot~

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

Re: [Gmod-ajax] Information about how to build demo server (fly and human)

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

Hi Motokazu,

Some resources that might help
* http://gmod.org/wiki/GFF3 - the GFF3 file format.
* http://gbrowse.org  will (probably) have links to GFF3 files for fly and human
* http://jbrowse.org/code/jbrowse-master/docs/config.html talks about
the config file.

Hope this helps,

Dave C.

On Fri, Sep 18, 2009 at 3:53 AM, Motokazu Ishikawa
<m.i...@is...> wrote:
> Currently, I am trying to setup my own jbrowse server.. But I haven't
> manage it, because I don't know how to write configuration file and
> content of gff, bed files.
>
> If you could provide information about how to build demo server (fly and
> human) on your web site, it will greatly help me to do my work.
> Especially, I want to see contents of each data files (gff, bed).
>
> thanks in advance.
>
> --
> Osaka University
> Graduate School of Information Science and Technology
> Motokazu Ishikawa
> E-mail: m.i...@is...
> Web:    http://www-mats.ist.osaka-u.ac.jp/
>
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

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

[Gmod-ajax] Information about how to build demo server (fly and human)

[Motokazu I. <m.i...@is...>]

Currently, I am trying to setup my own jbrowse server.. But I haven't
manage it, because I don't know how to write configuration file and
content of gff, bed files.

If you could provide information about how to build demo server (fly and
human) on your web site, it will greatly help me to do my work.
Especially, I want to see contents of each data files (gff, bed).

thanks in advance.

-- 
Osaka University
Graduate School of Information Science and Technology
Motokazu Ishikawa
E-mail: m.i...@is...
Web:    http://www-mats.ist.osaka-u.ac.jp/

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

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

On 15 Sep 2009, at 14:49, Giles Velarde wrote:

>
> On 15 Sep 2009, at 09:41, Giles Velarde wrote:
>
>>
>> On 11 Sep 2009, at 17:19, Mitch Skinner wrote:
>>
>>> On 09/11/2009 07:23 AM, Giles Velarde wrote:
>>>> My apologies for sending this on a Friday afternoon. Since this  
>>>> is my
>>>> first mail to the list let me say that JBrowse looks fantastic.
>>>
>>> Thanks!
>>>
>>>>  bin/flatfile-to-json.pl -gff
>>>> /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/Lmjchr10.gff
>>>> --autocomplete all --getType --getLabel --getSubs -- 
>>>> subfeatureClasses
>>>> '{"CDS": "transcript-CDS", "exon": "transcript-exon"}' --getPhase
>>>>
>>>>  bin/generate-names.pl -v
>>>>
>>>> This works fine (see screenshot below). However I don't see quite  
>>>> how
>>>> to split things up into several tracks using this approach.Should I
>>>> be
>>>> using a config file to do that? If that's the case, does anyone  
>>>> have
>>>> an example config file for specifying loading from GFF files? The
>>>> provided example is for a DB.
>>>
>>> You have two options; one is to use flatfile-to-json.pl with the --
>>> type
>>> command line parameter.  That allows you to filter the GFF file for
>>> specific feature types (you can have more than one --type option on
>>> the
>>> command line).  The other option is to use a config file.  The  
>>> example
>>> in docs/tutorial/conf_files uses the Bio::DB::SeqFeature::Store
>>> "memory"
>>> adaptor, which reads a flat file into memory and then acts as a DB.
>>> That allows you to use a config file with a GFF source of features.
>>>
>>> If you use flatfile-to-json.pl, you probably also want to specify  
>>> the
>>> --cssclass, --tracklabel, and --key command line parameters.
>>>
>>> Hope this helps; I'm assuming you want to organize your tracks by
>>> feature type.
>>>
>>> Mitch
>>>
>>
>>
>> Thanks, Mitch! I'll have a go.
>>
>
>
> Using the config file does indeed seem to be the best option for me.  
> I ended up writing a little bash script :
>
> rm -rf data
> for file in /data/gv1/gff3-ftp/export_2009-09-10/Lmajor/*.gff
> do
>    echo "processing GFF file? $file"
>    ./bin/prepare-refseqs.pl -gff $file --conf conf.json
> done
> ./bin/biodb-to-json.pl --conf conf.json
> ./bin/generate-names.pl -v
>
>
>
> and used it with the following conf file :
>
>
>
>
> {
>  "description": "GFF Database",
>  "db_adaptor": "Bio::DB::SeqFeature::Store",
>  "db_args": { "-adaptor": "memory",
>               "-dir": "/data/gv1/gff3-ftp/export_2009-09-14/ 
> Lmajor/" },
>
>  "TRACK DEFAULTS": {
>    "class": "feature",
>    "autocomplete": "all",
>     "urlTemplate": "http://beta.genedb.org/NamedFeature? 
> name={load_id}",
>      "extraData": {"load_id": "sub {shift->attributes(\"load_id\");}"}
>  },
>
>  "tracks": [
>    {
>        "track" : "Gene",
>        "feature": ["gene"],
>        "key" : "Gene Span",
>        "class": "dblhelix",
>        "category": "Gene Model features"
>    }
>  ]
> }
>
>
> Thanks again, Mitch!
> Giles
>
>


Hi All,

Just wanted to report that I am getting a lot of

print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 597, <GEN4> line 1423.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1423.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1456.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1489.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1523.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1556.
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN4> line 1589.
.........
print() on closed filehandle GEN2 at /usr/local/share/perl/5.10.0/Bio/ 
DB/SeqFeature/Store/memory.pm line 599, <GEN38> line 11008.

on the console when running

	./bin/biodb-to-json.pl --conf conf.json

Other than that, everything seems to be working with the GFF building...

Best,
Giles





-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

[Gmod-ajax] 2009 GMOD Community Survey

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

Hello all,

Please take a few minutes to fill out the 2009 GMOD Community Survey
and your name will be entered to win a free GMOD T-shirt or mug!  This
year's survey focuses on genome and comparative genomics visualization
(and is much shorter than the 2008 survey). We are asking all GMOD
users and developers to provide feedback.

  http://survey.oit.duke.edu/ViewsFlash/servlet/viewsflash?cmd=page&pollid=NESCent!GMODUserSurvey2009

Three randomly selected survey participants will receive the GMOD
T-shirt or mug of their choice. Names will be drawn from the first 100
responses, so get your response in early. The survey closes at the end
of the day on September 25.

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

Thanks,

Dave C
GMOD Help Desk

-- 
* Please keep responses on the list!
* Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
* GMOD News: http://gmod.org/wiki/GMOD_News