gmod-ajax — JBrowse list

[Gmod-ajax] 2011 GMOD Spring Training, March 8-12

[Dave C. G. H. D. <he...@gm...>]

Applications are now being accepted for the 2011 GMOD Spring Training
course a five-day hands-on school aimed at teaching new GMOD
administrators how to install, configure and integrate popular GMOD
components. The course will be held March 8-12 at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, as
part of GMOD Americas 2011.

Links:
   * http://gmod.org/wiki/2011_GMOD_Spring_Training
   * http://gmod.org/wiki/GMOD_Americas_2011
   * http://www.nescent.org/

These components will be covered:
   * Apollo - genome annotation editor
   * Chado - biological database schema
   * Galaxy - workflow system
   * GBrowse - genome viewer
   * GBrowse_syn - synteny viewer
   * GFF3 - genome annotation file format and tools
   * InterMine - biological data mining system
   * JBrowse - next generation genome browser
   * MAKER - genome annotation pipeline
   * Tripal - web front end to Chado databases

The deadline for applying is the end of Friday, January 7, 2011.
Admission is competitive and is based on the strength of the
application, especially the statement of interest. The 2010 school had
over 60 applicants for the 25 slots. Any application received after
deadline will be automatically placed on the waiting list.

The course requires some knowledge of Linux as a prerequisite. The
registration fee will be $265 (only $53 per day!). There will be a
limited number of scholarships available.

This may be the only GMOD School offered in 2011. If you are
interested, you are strongly encouraged to apply by January 7.

Thanks,

Dave Clements
--
http://gmod.org/wiki/GMOD_Americas_2011
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] refseqs

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

Hi Anja,

I'm not sure what you're asking.  In GFF, the text in the first column
is called the reference sequence, and is what all of the features that
are displayed in a genome browser are displayed on (that is, the
features are in reference to them).  With genomes that are well
sequenced and annotated, the reference sequence is usually a
chromosome, but contig, BAC or transcript are also used as reference
sequences.

Does that help?

Scott


On Mon, Nov 29, 2010 at 9:27 AM, Anja Friedrich
<fri...@ho...> wrote:
> Hi all,
>
> can someone please explain me what the reference sequence is good for?
>
> Cheers,
> Anja
>
> ------------------------------------------------------------------------------
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-- 
------------------------------------------------------------------------
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] [Gmodevohackathon] New Proposed Mailing lists

[Ben H. <hi...@ge...>]

thirded
On Dec 2, 2010, at 10:08 AM, Sheldon McKay wrote:

> I think #2 would be a good idea.  No objections to #1.
>
> Sheldon
>
> Sheldon McKay, PhD
> Scientific Lead, iPlant Collaborative
> BIO5 Institute, University of Arizona
> Email: mc...@em...
> Google Voice:  (203) 701-9204
>
>
> On Tue, Nov 30, 2010 at 5:30 PM, Dave Clements  
> <cle...@ne...> wrote:
> Hello all,
>
> Several action items came out of the recent GMOD Evo Hackathon,  
> including the possible creation of new email lists.  I'm CC'ing this  
> to every GMOD list that I think might care about the topics for the  
> proposed new lists:
>
> Proposed New Lists
> 1. Phenotype, Population, and Natural Diversity (PhenPopDiv, PPGaND?)
> 2. Comparative Genomics and Phylogeny (CompGenPhylo)?
>
> Both of the proposed lists are about research areas, rather than  
> specific components.  For example, anything about phenotypes, be it  
> storing them (Chado, InterMine, BioMart), visualizing them (GBrowse,  
> JBrowse, Tripal, ...), or anything else, would be appropriate for  
> the PhenPopDiv list.
>
> This is both a strength and a weakness.  If you care about one of  
> these research areas then you would now have a place to go to post  
> questions and information.  However, if you care specifically and  
> only about, say, Phylogeny in Chado, then it is no longer clear  
> where you should send emails.  The safest option would be to post to  
> both gmod-schema and to CompGenPhylo.
>
> I think the advantages of the lists outweigh the drawbacks.   
> However, I'd like community input before doing anything.
>
> If you have opinions or suggested revisions (large or small), please  
> respond.
>
> Thanks,
>
> Dave C
>
> -- 
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>
> _______________________________________________
> Gmodevohackathon mailing list
> Gmo...@ne...
> https://lists.nescent.org/mailman/listinfo/gmodevohackathon
>
> _______________________________________________
> Gmodevohackathon mailing list
> Gmo...@ne...
> https://lists.nescent.org/mailman/listinfo/gmodevohackathon

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hi...@ge...

Re: [Gmod-ajax] [Gmodevohackathon] New Proposed Mailing lists

[Sheldon M. <she...@gm...>]

I think #2 would be a good idea.  No objections to #1.

Sheldon

Sheldon McKay, PhD
Scientific Lead, iPlant Collaborative
BIO5 Institute, University of Arizona
Email: mc...@em...
Google Voice:  (203) 701-9204


On Tue, Nov 30, 2010 at 5:30 PM, Dave Clements <cle...@ne...> wrote:

> Hello all,
>
> Several action items came out of the recent GMOD Evo Hackathon, including
> the possible creation of new email lists.  I'm CC'ing this to every GMOD
> list that I think might care about the topics for the proposed new lists:
>
> *Proposed New Lists*
> 1. Phenotype, Population, and Natural Diversity (PhenPopDiv, PPGaND?)
> 2. Comparative Genomics and Phylogeny (CompGenPhylo)?
>
> Both of the proposed lists are about research areas, rather than specific
> components.  For example, anything about phenotypes, be it storing them
> (Chado, InterMine, BioMart), visualizing them (GBrowse, JBrowse, Tripal,
> ...), or anything else, would be appropriate for the PhenPopDiv list.
>
> This is both a strength and a weakness.  If you care about one of these
> research areas then you would now have a place to go to post questions and
> information.  However, if you care specifically and only about, say,
> Phylogeny in Chado, then it is no longer clear where you should send emails.
>  The safest option would be to post to both gmod-schema and to CompGenPhylo.
>
> I think the advantages of the lists outweigh the drawbacks.  However, I'd
> like community input before doing anything.
>
> If you have opinions or suggested revisions (large or small), please
> respond.
>
> Thanks,
>
> Dave C
>
> --
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>
> _______________________________________________
> Gmodevohackathon mailing list
> Gmo...@ne...
> https://lists.nescent.org/mailman/listinfo/gmodevohackathon
>

[Gmod-ajax] New Proposed Mailing lists

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

Hello all,

Several action items came out of the recent GMOD Evo Hackathon, including
the possible creation of new email lists.  I'm CC'ing this to every GMOD
list that I think might care about the topics for the proposed new lists:

*Proposed New Lists*
1. Phenotype, Population, and Natural Diversity (PhenPopDiv, PPGaND?)
2. Comparative Genomics and Phylogeny (CompGenPhylo)?

Both of the proposed lists are about research areas, rather than specific
components.  For example, anything about phenotypes, be it storing them
(Chado, InterMine, BioMart), visualizing them (GBrowse, JBrowse, Tripal,
...), or anything else, would be appropriate for the PhenPopDiv list.

This is both a strength and a weakness.  If you care about one of these
research areas then you would now have a place to go to post questions and
information.  However, if you care specifically and only about, say,
Phylogeny in Chado, then it is no longer clear where you should send emails.
 The safest option would be to post to both gmod-schema and to CompGenPhylo.

I think the advantages of the lists outweigh the drawbacks.  However, I'd
like community input before doing anything.

If you have opinions or suggested revisions (large or small), please
respond.

Thanks,

Dave C

-- 
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback

[Gmod-ajax] A GMOD "virtual issue" in the journal Database

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

Hello,

I recently had a chat with one of the editors of the journal Database
(http://database.oxfordjournals.org/), an open access journal whose
aim for publications lines up very nicely with the goals of GMOD.
During this discussion, the idea of a GMOD "virtual issue" came up,
and it is one that I am very excited about.  Therefore, I'm reaching
out to you (the GMOD community) for ideas as well as commitments to
write peer reviewed articles for this publication.  Articles can be
about theory, tutorial or community.  I expect at least one each
papers about Chado at a minimum (that is, there very well may be more
papers just about Chado).  Please feel free to respond either to me
personally or to the mailing list that you are subscribed to that got
this message to you if you'd like to discuss this further.

The virtual issue approach that Database takes is very appealing, in
that the submitted papers do not need to be in by a certain cutoff
date, as this is not going to put into a "dead tree" form :-)  So, the
virtual issue can be created at any point, either when there is just
one paper, or when there is a critical mass (which we would have
control over), and more papers can be added to it at any time.  An
example of a Database virtual issue is the one they created for the
biocurator meeting last year:

  http://www.oxfordjournals.org/our_journals/databa/biocuration_virtual_issue.html

I look forward to your ideas and commitments!
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] refseqs

[Anja F. <fri...@ho...>]

Hi all, 

can someone please explain me what the reference sequence is good for?

Cheers, 
Anja
 		 	   		  

Re: [Gmod-ajax] Perl agnostic Jbrowse?

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

Hi George,

The official answer to this is that we would like to evolve the json format a little longer before we stabilize and formally document it. However, unofficially, and if you don't mind building on top of a format that will almost certainly change over the next 12 months before settling down, perhaps you & I could work together to get just enough documentation to meet your needs.

-Ian (by phone)

On Nov 23, 2010, at 10:55 PM, George Githinji <geo...@gm...> wrote:

> Hi Mitch,
> Sorry I was not specific enough. What I would want to do is to take
> advantage of the jbrowse javascript framework or rendering system to
> display data on a webpage without necessarily having to setup and
> install Jbrowse as an application.
> 
> For example say I have a website that i have developed using
> python/django or Ruby/Ruby on Rails, can I use Jbrowse javascript
> framework or API to render my data, as long as i can  generate  a JSON
> output?
> 
> 
> On Wed, Nov 17, 2010 at 11:20 PM, Mitch Skinner
> <mit...@be...> wrote:
>> On 11/16/2010 09:23 PM, George Githinji wrote:
>>> 
>>> Are there plans to decouple jbrowse from perl?
>> 
>> Could you be more specific about what you want to do?
>> 
>> Mitch
>> 
> 
> 
> 
> -- 
> ---------------
> Sincerely
> George
> KEMRI/Wellcome-Trust Research Program
> Skype: george_g2
> Blog: http://biorelated.wordpress.com/
> 
> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> Tap into the largest installed PC base & get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] touchJBrowse.js

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

Wow - this is neat!

It would be fantastic if we could zoom in and out using pinch
gestures, just like on an Ipad or iPhone.

Best,

Ann

On Tue, Nov 23, 2010 at 1:15 PM, Brian O'Connor <bri...@gm...> wrote:
> Hi,
>
> I'd really like to get JBrowse working on the iPad as seen in this video:
>
> http://www.youtube.com/watch?v=FMVtxTt6KCg
>
> Can someone (Juan?) provide guidance on how to do this?  Or, if it's
> complicated, maybe a tarball of browser that's been configured to work
> as in the demo?  I noticed the touchJBrowse.js javascript has been
> checked in a couple months ago but it looks like this isn't simply an
> include-this-js-and-it-will-just-work sort of thing.
>
> Thanks very much, I'm looking forward to getting this to work.
> There's a lot of excitement around standardizing on the browser in my
> group and this is the last missing piece to make that happen.
>
> --Brian
>
> ------------------------------------------------------------------------------
> Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> Tap into the largest installed PC base & get more eyes on your game by
> optimizing for Intel(R) Graphics Technology. Get started today with the
> Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
> http://p.sf.net/sfu/intelisp-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Hg19 tarball problem

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

Thanks for the report, and nice job figuring the whole thing out.  I ran 
your python script on the hg19mini data, and I ran generate-names.pl on 
the result, and created a new hg19mini tarball:

http://jbrowse.org/releases/data/ucsc/hg19mini-2.tar.gz

Mitch

On 11/23/2010 10:21 PM, Chris Tandiono wrote:
> I'm having (or rather, had) a problem with the hg19mini tarball 
> available on jbrowse.org <http://jbrowse.org>; it looks like the 
> format for each track's names.json is not what's being expected by 
> generate-names.pl <http://generate-names.pl>.
>
> Of course, I do see that this fix: 
> https://github.com/jbrowse/jbrowse/commit/6bd8bfcf81389bc188414b18af3935053a585c42
>
> has already been made. Either way I though someone might be interested 
> in this Python script which attempts to convert from the broken format 
> to the expected format.
>

Re: [Gmod-ajax] Perl agnostic Jbrowse?

[George G. <geo...@gm...>]

Hi Mitch,
Sorry I was not specific enough. What I would want to do is to take
advantage of the jbrowse javascript framework or rendering system to
display data on a webpage without necessarily having to setup and
install Jbrowse as an application.

For example say I have a website that i have developed using
python/django or Ruby/Ruby on Rails, can I use Jbrowse javascript
framework or API to render my data, as long as i can  generate  a JSON
output?


On Wed, Nov 17, 2010 at 11:20 PM, Mitch Skinner
<mit...@be...> wrote:
> On 11/16/2010 09:23 PM, George Githinji wrote:
>>
>> Are there plans to decouple jbrowse from perl?
>
> Could you be more specific about what you want to do?
>
> Mitch
>



-- 
---------------
Sincerely
George
KEMRI/Wellcome-Trust Research Program
Skype: george_g2
Blog: http://biorelated.wordpress.com/

[Gmod-ajax] Hg19 tarball problem

[Chris T. <chr...@be...>]

Hi,

I'm having (or rather, had) a problem with the hg19mini tarball available on jbrowse.org; it looks like the format for each track's names.json is not what's being expected by generate-names.pl.

Of course, I do see that this fix: https://github.com/jbrowse/jbrowse/commit/6bd8bfcf81389bc188414b18af3935053a585c42

has already been made. Either way I though someone might be interested in this Python script which attempts to convert from the broken format to the expected format.

Chris

[Gmod-ajax] touchJBrowse.js

[Brian O'C. <bri...@gm...>]

Hi,

I'd really like to get JBrowse working on the iPad as seen in this video:

http://www.youtube.com/watch?v=FMVtxTt6KCg

Can someone (Juan?) provide guidance on how to do this?  Or, if it's
complicated, maybe a tarball of browser that's been configured to work
as in the demo?  I noticed the touchJBrowse.js javascript has been
checked in a couple months ago but it looks like this isn't simply an
include-this-js-and-it-will-just-work sort of thing.

Thanks very much, I'm looking forward to getting this to work.
There's a lot of excitement around standardizing on the browser in my
group and this is the last missing piece to make that happen.

--Brian

Re: [Gmod-ajax] bases overlapping

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

On 11/16/2010 09:23 PM, George Githinji wrote:
> Are there plans to decouple jbrowse from perl?

Could you be more specific about what you want to do?

Mitch

Re: [Gmod-ajax] bases overlapping

[George G. <geo...@gm...>]

Hi,
Thanks for an excellent tool!
Are there plans to decouple jbrowse from perl?


george

Re: [Gmod-ajax] bases overlapping

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

Hi,

Sorry I've taken so long to get back to you.  I've been trying to 
reproduce this, but I haven't been able to.  Is this jbrowse instance on 
the internet somewhere, where I can look at it?  Also, what version of 
chromium?

Mitch

On 10/21/2010 05:23 AM, Andrea Malossini wrote:
> Hi,
>
> sometimes the bases in the main sequence seem to partially overlap
> (see the attchment). Is that a known problem or a browser specific
> problem?
> Currently I'm using chromium.
>
> Thanks
> Andrea
>
>
> ------------------------------------------------------------------------------
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Re: [Gmod-ajax] Adding links to features

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

If you're using flatfile-to-json.pl to process your gff file, then 
adding these two command-line arguments should do it:

--extraData '{"note": "sub {$_[0]->attributes(\"Note\")}"}' 
--urlTemplate '{note}'

Mitch

On 11/16/2010 08:05 AM, Shelly Cole wrote:
> Hello
>
> I am fairly new to jbrowse and would like to ask for your help in 
> customizing by browser.
> I am using a gff file where the note field contains a url, and I would 
> like each feature to link to the url in its note field.
> how can I accomplish this?
>
> Thank you
>
> Shelly Cole
>
>
> ------------------------------------------------------------------------------
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> standards for HTML5, CSS3, SVG 1.1,  ECMAScript5, and DOM L2&  L3.
> Spend less time writing and  rewriting code and more time creating great
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[Gmod-ajax] Adding links to features

[Shelly C. <she...@ho...>]

Hello

I am fairly new to jbrowse and would like to ask for your help in customizing by browser.
I am using a gff file where the note field contains a url, and I would like each feature to link to the url in its note field.
how can I accomplish this?

Thank you

Shelly Cole
 		 	   		  

Re: [Gmod-ajax] hg19 demo download

[Brian O'C. <bri...@gm...>]

Awesome, you are a life saver!

Everyone I've shown this browser to loves it.  It really works well.
You guys should be very proud of the work you've done!

--Brian

On Thu, Nov 11, 2010 at 6:19 PM, Ian Holmes <ih...@be...> wrote:
> Hi Brian,
>
> Some of the data is here (not sequence yet I'm afraid, we can prepare a
> bigger tarball with sequence if you desperately need it)
>
> http://jbrowse.org/?cat=7
>
> Best, Ian
>
> Brian O'Connor wrote:
>>
>> Hi,
>>
>> I think you literally just posted this yesterday but would it be
>> possible to download the hg19 demo you have pre-configured and ready
>> to go?  I've been asked to quickly setup a genome browser for hg19,
>> JBrowse is awesome so I naturally want to use it, but it would save
>> time to have the pre-configured hg19 demo ready to go.
>>
>> Thanks for your help.  I'm looking forward to using this browser!
>>
>> --Brian O'Connor
>>
>>
>> ------------------------------------------------------------------------------
>> Centralized Desktop Delivery: Dell and VMware Reference Architecture
>> Simplifying enterprise desktop deployment and management using
>> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
>> client virtualization framework. Read more!
>> http://p.sf.net/sfu/dell-eql-dev2dev
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] hg19 demo download

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

Hi Brian,

Some of the data is here (not sequence yet I'm afraid, we can prepare a 
bigger tarball with sequence if you desperately need it)

http://jbrowse.org/?cat=7

Best, Ian

Brian O'Connor wrote:
> Hi,
> 
> I think you literally just posted this yesterday but would it be
> possible to download the hg19 demo you have pre-configured and ready
> to go?  I've been asked to quickly setup a genome browser for hg19,
> JBrowse is awesome so I naturally want to use it, but it would save
> time to have the pre-configured hg19 demo ready to go.
> 
> Thanks for your help.  I'm looking forward to using this browser!
> 
> --Brian O'Connor
> 
> ------------------------------------------------------------------------------
> Centralized Desktop Delivery: Dell and VMware Reference Architecture
> Simplifying enterprise desktop deployment and management using
> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end
> client virtualization framework. Read more!
> http://p.sf.net/sfu/dell-eql-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] hg19 demo download

[Brian O'C. <bri...@gm...>]

Hi,

I think you literally just posted this yesterday but would it be
possible to download the hg19 demo you have pre-configured and ready
to go?  I've been asked to quickly setup a genome browser for hg19,
JBrowse is awesome so I naturally want to use it, but it would save
time to have the pre-configured hg19 demo ready to go.

Thanks for your help.  I'm looking forward to using this browser!

--Brian O'Connor

Re: [Gmod-ajax] Development status

[David B. <dav...@gm...>]

Dear Ian,

I'm sorry if I mis-communicated myself. I'm sure you're all doing your
best and I greatly appreciate your efforts for the benift of the
community. It's the genuine excitement about JBrowse that makes me
keep a close eye on it and hope it will develop faster.

We are currently using JBrowse only internally, for testing purposes
and in-house use. Our PI won't leave our current, public browsers
until we can get most of the basic functionality to work on JBrowse
too. I will be more than happy to share our running JBrowse server as
soon as possible!

Dave

On Tue, Nov 9, 2010 at 10:59 PM, Ian Holmes <ih...@be...> wrote:
> Dear David,
>
> We have been posting more-or-less monthly to the blog at jbrowse.org and, in
> these posts, have advertised the fact that we are now releasing jbrowse
> tarballs on a quarterly basis. So you can expect the next release in
> December.
>
> There have been several commits to github over the last month. The last was
> on 10/18. Please be aware that there are several branches, so if you do not
> see activity on the master branch, you could try one of the others
> (currently evohack, for the ongoing GMOD Evo hackathon, and jsongen-refactor
> for some work towards the next release). Note also that some development
> happens in git repos away from github.com, so just because you haven't seen
> any commits for a week or two, doesn't mean nothing is happening.
>
> I'm sorry if quarterly releases, monthly blog posts and regular github
> commits aren't enough activity for you, but that's really about as much as
> we can support right now - and actually I think it's quite a respectable
> level of activity (far from the "neglect" you allude to). So I'm not sure
> what your expectations are.
>
> It's great that you have many feature requests; so do a lot of users! There
> is a long list at jbrowse.lighthouseapp.com. Have you entered your requests
> there, or checked to see whether they overlap with other requests?
>
> We are continually looking for ways to raise jbrowse's profile and
> potentially secure new streams of funding, so that we can ramp up
> development. In order to do this, it is very helpful to have examples of
> working jbrowse instances, so as to demonstrate that jbrowse is useful to
> the community. In this context, I would ask that if you have any examples of
> jbrowse running, please do share them on this list. I would be happy to then
> post them on the jbrowse.org blog.
>
> Best wishes,
> Ian
>
> On 11/9/10 12:27 PM, David Breimann wrote:
>>
>> Dear JBrowse developers,
>>
>> I would greatly appreciate if you could drop a short note about
>> development status and the tentative schedule for the availability of
>> new features in the near future.
>>
>> Just a (personal) reminder - what I'm missing the most are:
>> - Displaying numerical values on WIG tracks (scale and show-as-you-point)
>> - Customize pop-out baloons for features (as in GBrowse)
>> - Choosing glyphs/color of glyph using feature-specific data (so we
>> can have different glyphs in the same track, e.g. according to some
>> comment in the relevant GFF3 line).
>>
>> I hope development is going well -- it's hard to tell since
>> jbrowse.org and the git repository seem a bit neglected.
>>
>> Keep up the good work!
>>
>> Dave
>>
>>
>> ------------------------------------------------------------------------------
>> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
>> David G. Thomson, author of the best-selling book "Blueprint to a
>> Billion" shares his insights and actions to help propel your
>> business during the next growth cycle. Listen Now!
>> http://p.sf.net/sfu/SAP-dev2dev
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] Development status

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

Dear David,

We have been posting more-or-less monthly to the blog at jbrowse.org 
and, in these posts, have advertised the fact that we are now releasing 
jbrowse tarballs on a quarterly basis. So you can expect the next 
release in December.

There have been several commits to github over the last month. The last 
was on 10/18. Please be aware that there are several branches, so if you 
do not see activity on the master branch, you could try one of the 
others (currently evohack, for the ongoing GMOD Evo hackathon, and 
jsongen-refactor for some work towards the next release). Note also that 
some development happens in git repos away from github.com, so just 
because you haven't seen any commits for a week or two, doesn't mean 
nothing is happening.

I'm sorry if quarterly releases, monthly blog posts and regular github 
commits aren't enough activity for you, but that's really about as much 
as we can support right now - and actually I think it's quite a 
respectable level of activity (far from the "neglect" you allude to). So 
I'm not sure what your expectations are.

It's great that you have many feature requests; so do a lot of users! 
There is a long list at jbrowse.lighthouseapp.com. Have you entered your 
requests there, or checked to see whether they overlap with other requests?

We are continually looking for ways to raise jbrowse's profile and 
potentially secure new streams of funding, so that we can ramp up 
development. In order to do this, it is very helpful to have examples of 
working jbrowse instances, so as to demonstrate that jbrowse is useful 
to the community. In this context, I would ask that if you have any 
examples of jbrowse running, please do share them on this list. I would 
be happy to then post them on the jbrowse.org blog.

Best wishes,
Ian

On 11/9/10 12:27 PM, David Breimann wrote:
> Dear JBrowse developers,
>
> I would greatly appreciate if you could drop a short note about
> development status and the tentative schedule for the availability of
> new features in the near future.
>
> Just a (personal) reminder - what I'm missing the most are:
> - Displaying numerical values on WIG tracks (scale and show-as-you-point)
> - Customize pop-out baloons for features (as in GBrowse)
> - Choosing glyphs/color of glyph using feature-specific data (so we
> can have different glyphs in the same track, e.g. according to some
> comment in the relevant GFF3 line).
>
> I hope development is going well -- it's hard to tell since
> jbrowse.org and the git repository seem a bit neglected.
>
> Keep up the good work!
>
> Dave
>
> ------------------------------------------------------------------------------
> The Next 800 Companies to Lead America's Growth: New Video Whitepaper
> David G. Thomson, author of the best-selling book "Blueprint to a
> Billion" shares his insights and actions to help propel your
> business during the next growth cycle. Listen Now!
> http://p.sf.net/sfu/SAP-dev2dev
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] Development status

[David B. <dav...@gm...>]

Dear JBrowse developers,

I would greatly appreciate if you could drop a short note about
development status and the tentative schedule for the availability of
new features in the near future.

Just a (personal) reminder - what I'm missing the most are:
- Displaying numerical values on WIG tracks (scale and show-as-you-point)
- Customize pop-out baloons for features (as in GBrowse)
- Choosing glyphs/color of glyph using feature-specific data (so we
can have different glyphs in the same track, e.g. according to some
comment in the relevant GFF3 line).

I hope development is going well -- it's hard to tell since
jbrowse.org and the git repository seem a bit neglected.

Keep up the good work!

Dave

[Gmod-ajax] bases overlapping

[Andrea M. <and...@un...>]

Hi,

sometimes the bases in the main sequence seem to partially overlap
(see the attchment). Is that a known problem or a browser specific
problem?
Currently I'm using chromium.

Thanks
Andrea