gmod-ajax — JBrowse list

Re: [Gmod-ajax] is this mailing list still works

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

Thanks for saying so; my silence on the mailing list been a combination 
of being sick, travel, and trying to finish this imminent JBrowse 
release (including fixing one of the issues you found).  I'll be 
catching up on email once the release is out (the next few days).

Mitch

On 01/26/2011 11:46 PM, Bernd Jagla wrote:
> Hi Ambarish,
>
> I have met the developers some two years ago and they are very nice 
> and helpful people. I am in the same boat as you are still waiting for 
> some responses. I am assuming they are on a conference or something 
> without much connection to the internet. I still have hope that 
> JBrowse is the better solution... Time will tell..
> Don't give up just now...
>
> Best,
>
> Bernd
>
> On 1/25/2011 3:41 AM, ambarish biswas wrote:
>> is this mailing list still works
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
>> Finally, a world-class log management solution at an even better price-free!
>> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
>> February 28th, so secure your free ArcSight Logger TODAY!
>> http://p.sf.net/sfu/arcsight-sfd2d
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] is this mailing list still works

[Bernd J. <ber...@pa...>]

Hi Ambarish,

I have met the developers some two years ago and they are very nice and 
helpful people. I am in the same boat as you are still waiting for some 
responses. I am assuming they are on a conference or something without 
much connection to the internet. I still have hope that JBrowse is the 
better solution... Time will tell..
Don't give up just now...

Best,

Bernd

On 1/25/2011 3:41 AM, ambarish biswas wrote:
> is this mailing list still works
>
>
>
> ------------------------------------------------------------------------------
> Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)!
> Finally, a world-class log management solution at an even better price-free!
> Download using promo code Free_Logger_4_Dev2Dev. Offer expires
> February 28th, so secure your free ArcSight Logger TODAY!
> http://p.sf.net/sfu/arcsight-sfd2d
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] JSON data format documentation

[Philippe L. <phi...@ob...>]

Hi,

Is there some documentation on the JSON format for track data and refseqs?
There's some documentation on the JSON config file, but I'd like to learn
about the JSON formats for data.

I'd like to generate track data at runtime. I already have everything in a
custom database, so I'd like to use this data to generate the required JSON.

Thanks,
Philippe

[Gmod-ajax] genes at the end of the Browser are not ploted

[常啸 <xc...@si...>]

Hi all,

I have created a E.coli genome browser by Jbrowse. The length of the
ecoli genome is 4,639,675bp.
It seems everything is fine except the last small part of the browser
from 4,630,783 to the end.
Genes located at this area are not displayed.
Can someone give me some advise to cope with this problem?

Thanks,
Xiao

[Gmod-ajax] help getting started...

[Bernd J. <ber...@pa...>]

Hi,

since I couldn't the flatfile-to-json.pl work with large bam file 
(apparently a known issue) and my problems with git, I now downloaded 
without git the jsongen-refactor branch. I wasn't able to find the 
lasyfeatures that are advertised in the tutorial either...
With branch I now get "Can't use an undefined value as a HASH reference 
at ...JsonGenerator.pm line 164." I had a quick look at the source but 
couldn't see anything that I could possibly do to understand where this 
error message is coming from..

With some smaller test data I noticed that there are sometime problems 
with wig graphs that are not loaded completely and don't scale 
correctly. Are you aware of issues with wig files and line plots???

Otherwise, I would really to use jbrowse as I think it has some really 
cool features, but I also need a working solution VERY soon...
Can you give me some advice in this respect as well?

Thanks a lot for your kind help and support,

Best,

Bernd

[Gmod-ajax] is this mailing list still works

[ambarish b. <amb...@gm...>]

is this mailing list still works

[Gmod-ajax] loading problem with GFF files

[Bernd J. <ber...@pa...>]

Hi again...

I am starting to work with JBrowse .... therefore I have many problems 
and questions ... ;)

I sent an e-mail yesterday but the attachments were too big... so here 
the short version...

I am working on a mac 10.5.8

and get the following error message:

sh-3.2# bin/biodb-to-json.pl --conf data/config/HBN9.config.json

working on refseq HNB8
working on track Genes
got 1 features for Genes
encountered object 'Bio::DB::GFF::Featname=ARRAY(0x6eab14)', but neither 
allow_blessed nor convert_blessed settings are enabled at 
/usr/local/apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 113.

I believe this problem is related to the ID property in the last column 
as without this there is no problem.
Should I remove all the IDs

Also, do you have another example (in addition to the one on the web) 
that already displays the features CDS, gene, start/stop codon with the 
parent property in a nice way? Can I have it???

Thanks a lot for your kind support,

Best,

Bernd

Re: [Gmod-ajax] out of memory error

[Bernd J. <ber...@pa...>]

Hi Ian,
Thanks for your help!!!
could you please remind me on how to use git?

I am following the instructions on http://gmod.org/wiki/JBrowse_Tutorial
The following two lines produce error messages:

$ git branch --track lazyfeatures origin/lazyfeatures
$ git checkout lazyfeatures

fatal: Not a valid object name: 'origin/lazyfeatures'.

and I don't know how to update using git..

I believe there are some instructions missing (I just created a 
directory called origin...)

I also don't know what these lazyfeatures are and why I need them...

Then I believe I am not on the latest git branch but the release 
branch... How would I get access to the development branch?

Well sorry for these many questions, but I already have loaded the fasta 
file and some annotations and it looks very promising...

Kind regards and congratulations on your nice work,

Bernd


On 1/19/2011 6:21 PM, Ian Holmes wrote:
> Hi Bernd, yes this is a known issue, should be fixed on the latest git branch or in the next release (which is imminent)
>
> -Ian (by phone)
>
> On Jan 19, 2011, at 7:27 AM, Bernd Jagla<ber...@pa...>  wrote:
>
>> Hi,
>>
>> I am running into an out of memory error when reading/converting bam
>> files...
>>
>> Any suggestions?
>>
>> zoppel:jbrowse bernd$ bin/flatfile-to-json.pl --bam
>> data/annotation/HNB8/101217/L1.HPB8.bowtie.sam.bam --cssclass exon
>> --tracklabel L1 --key "Lane 1 data"
>>
>> working on seq HNB8
>> perl(6233) malloc: *** mmap(size=16777216) failed (error code=12)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> Out of memory!
>>
>>
>> I have another machine with more memory, but I am not sure if I can
>> install everything on that one as I am not the sys admin.
>> and if I would have installed it could I use it to create whatever is
>> being created and then copy that to the web server?
>>
>> Thanks,
>>
>> Bernd
>>
>>
>> ------------------------------------------------------------------------------
>> Protect Your Site and Customers from Malware Attacks
>> Learn about various malware tactics and how to avoid them. Understand
>> malware threats, the impact they can have on your business, and how you
>> can protect your company and customers by using code signing.
>> http://p.sf.net/sfu/oracle-sfdevnl
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] out of memory error

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

Hi Bernd, yes this is a known issue, should be fixed on the latest git branch or in the next release (which is imminent)

-Ian (by phone)

On Jan 19, 2011, at 7:27 AM, Bernd Jagla <ber...@pa...> wrote:

> Hi,
> 
> I am running into an out of memory error when reading/converting bam 
> files...
> 
> Any suggestions?
> 
> zoppel:jbrowse bernd$ bin/flatfile-to-json.pl --bam 
> data/annotation/HNB8/101217/L1.HPB8.bowtie.sam.bam --cssclass exon 
> --tracklabel L1 --key "Lane 1 data"
> 
> working on seq HNB8
> perl(6233) malloc: *** mmap(size=16777216) failed (error code=12)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> Out of memory!
> 
> 
> I have another machine with more memory, but I am not sure if I can 
> install everything on that one as I am not the sys admin.
> and if I would have installed it could I use it to create whatever is 
> being created and then copy that to the web server?
> 
> Thanks,
> 
> Bernd
> 
> 
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand 
> malware threats, the impact they can have on your business, and how you 
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] out of memory error

[Bernd J. <ber...@pa...>]

Hi,

I am running into an out of memory error when reading/converting bam 
files...

Any suggestions?

zoppel:jbrowse bernd$ bin/flatfile-to-json.pl --bam 
data/annotation/HNB8/101217/L1.HPB8.bowtie.sam.bam --cssclass exon 
--tracklabel L1 --key "Lane 1 data"

working on seq HNB8
perl(6233) malloc: *** mmap(size=16777216) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
Out of memory!


I have another machine with more memory, but I am not sure if I can 
install everything on that one as I am not the sys admin.
and if I would have installed it could I use it to create whatever is 
being created and then copy that to the web server?

Thanks,

Bernd

Re: [Gmod-ajax] bigwig files

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

Dear Bernd, 

The bedGraph files can be processed by wig-to-json just like wiggle tracks.  I'm not sure about bigWig files. 

Brent


On Jan 19, 2011, at 7:02 AM, Bernd Jagla wrote:

> Hi,
> I am wondering if jbrowse/wig-to-json can also read bigWig files or even 
> BedGraph files...
> How would I read in those files?
> 
> thanks,
> 
> Bernd
> 
> 
> ------------------------------------------------------------------------------
> Protect Your Site and Customers from Malware Attacks
> Learn about various malware tactics and how to avoid them. Understand 
> malware threats, the impact they can have on your business, and how you 
> can protect your company and customers by using code signing.
> http://p.sf.net/sfu/oracle-sfdevnl
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] help: GFF import

[Bernd J. <ber...@pa...>]

Hi,

I am new to JBrowse...

I have succesfully loaded my first reference sequence and now would like 
to load some GFF annotation.

But when I try to upload the GFF file I get the following error message:


 > bin/biodb-to-json.pl --conf data/config/HBN9.config.json

working on refseq HNB8
working on track CDS
got 1711 features for CDS
encountered object 'Bio::DB::GFF::Featname=ARRAY(0x717d80)', but neither 
allow_blessed nor convert_blessed settings are enabled at 
/usr/local/apache/htdocs/jbrowse/bin/../lib/JsonGenerator.pm line 113.

Unfortunately this message doesn't help me understand the problem.
could you please clarify what I am doing wrong?

Thanks
Bernd

Attachements: 1 config file
2 GFF file

[Gmod-ajax] bigwig files

[Bernd J. <ber...@pa...>]

Hi,
I am wondering if jbrowse/wig-to-json can also read bigWig files or even 
BedGraph files...
How would I read in those files?

thanks,

Bernd

[Gmod-ajax] GMOD at PAG 2011, Jan 15-19

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

Hello all,

GMOD will have a stronger presence then ever at the Plant and Animal Genome
Conference (PAG 2011) <http://gmod.org/wiki/PAG_2011>, being held January
15-19 in San Diego. This includes, for the first time, *an all day GMOD
Workshop <http://www.intl-pag.org/19/19-gmod.html>* on Wednesday, January
19th, featuring extended talks on

   - MAKER <http://gmod.org/wiki/MAKER>: An easy to use genome annotation
   pipeline <http://www.intl-pag.org/19/19-gmod.html#MAKER>
   - Galaxy <http://gmod.org/wiki/Galaxy>: Analyze, Visualize,
Communicate<http://www.intl-pag.org/19/19-gmod.html#Galaxy>
   - JBrowse <http://gmod.org/wiki/JBrowse>: A Next Generation Genome
   Browser <http://www.intl-pag.org/19/19-gmod.html#JBrowse>
   - Tripal <http://gmod.org/wiki/Tripal>: A Construction Toolkit for Online
   Genomic Databases <http://www.intl-pag.org/19/19-gmod.html#Tripal>
   - GMODviews <http://gmod.org/wiki/GMODviews>: A web-based knowledge-base
   and user-configurable interface for GMOD databases and tools, including
   Tripal, GBrowse, and Chado
DBs<http://www.intl-pag.org/19/19-gmod.html#GMODviews>
   - GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>: The Generic Synteny
   Browser <http://www.intl-pag.org/19/19-gmod.html#GBrowse_syn>

PAG 2011 <http://gmod.org/wiki/PAG_2011> will also feature workshops and
tutorials covering

   - BioMart <http://gmod.org/wiki/BioMart>: Ensembl and Ensembl
Genomes<http://www.intl-pag.org/19/abstracts/W29_PAGXIX_188.html>
   - GBrowse <http://gmod.org/wiki/GBrowse>: The Generic Genome Browser: A
   Hands on Workshop for Installing, Configuring and Using Your Own
GBrowse<http://www.intl-pag.org/19/19-gbrowse.html>
   - CMap <http://gmod.org/wiki/CMap>: Using Gramene: A Genomics and
   Genetics Resource for Rice and other
Grasses<http://www.intl-pag.org/19/19-gramene.html>

Plus *at least 25 more
talks<http://gmod.org/wiki/PAG_2011#Projects_Using_GMOD_Components>and
posters <http://gmod.org/wiki/PAG_2011#Posters>* about or using Pathway
Tools <http://www.intl-pag.org/19/abstracts/C02_PAGXIX_903.html>,
GBrowse<http://www.intl-pag.org/19/abstracts/P08b_PAGXIX_828.html>,
Galaxy <http://gmod.org/wiki/Galaxy>, CMap <http://gmod.org/wiki/Cmap>,
Apollo <http://gmod.org/wiki/Apollo>, Chado <http://gmod.org/wiki/Chado>,
GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>,
JBrowse<http://gmod.org/wiki/JBrowse>,
BioMart <http://gmod.org/wiki/BioMart>, MAKER <http://gmod.org/wiki/MAKER>,
Tripal <http://gmod.org/wiki/Tripal>, and the GMOD Evo
Hackathon<http://www.intl-pag.org/19/abstracts/P08a_PAGXIX_814.html>.
 See http://gmod.org/wiki/PAG_2011 for a more complete list.

Many GMOD users<http://gmod.org/wiki/PAG_2011#Projects_Using_GMOD_Components>and
GMOD developers, including Stephen
Ficklin <http://gmod.org/wiki/User:Sficklin>
(Tripal<http://gmod.org/wiki/Tripal>),
Carson Holt <http://gmod.org/wiki/User:Carsonholt>
(MAKER<http://gmod.org/wiki/MAKER>),
Barry Moore <http://gmod.org/wiki/User:Bmoore>
(SOBA<http://gmod.org/wiki/SOBA>,
MAKER <http://gmod.org/wiki/MAKER>), Dan
Blankenberg<http://gmod.org/wiki/User:DanB>(
Galaxy <http://gmod.org/wiki/Galaxy>), Mitch
Skinner<http://gmod.org/wiki/User:MitchSkinner>(
JBrowse <http://gmod.org/wiki/JBrowse>), Ken Youens-Clark
(CMap<http://gmod.org/wiki/CMap>),
Mike Caudy <http://gmod.org/wiki/User:Mcaudy>
(GMODviews<http://gmod.org/wiki/GMODviews>),
Rob Buels <http://gmod.org/wiki/User:RobertBuels>
(Bio::Chado::Schema<http://gmod.org/wiki/Bio::Chado::Schema>,
GBrowse_syn <http://gmod.org/wiki/GBrowse_syn>), and Scott
Cain<http://gmod.org/wiki/User:Scott>(
Chado <http://gmod.org/wiki/Chado>, GBrowse <http://gmod.org/wiki/GBrowse>,
...) will be attending PAG this year. Please seek each other out.

Dave Clements <http://gmod.org/wiki/User:Clements>
Galaxy Project <http://gmod.org/wiki/Galaxy>

PS: In addition, three of the GMOD developers (Dan, Mitch, Scott) are
also available
to visit organizations in the San Diego
area<http://gmod.org/wiki/GMOD_News#GMOD_Roadshow_in_San_Diego>during
the meeting.
-- 
http://gmod.org/wiki/GMOD_Americas_2011
http://gmod.org/wiki/GMOD_News
http://usegalaxy.org/

[Gmod-ajax] GMOD Roadshow In San Diego this month

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

Hello all,

I sent this to gmod-announce yesterday, but forgot to send it to the JBrowse
list.

If your organization is in the San Diego area then Mitch Skinner (well known
on this list) is available during the Plant and Animal Genome meeting this
month to visit your organization to discuss/present JBrowse.

And Dan Blankenberg of Galaxy, and Scott Cain of GMOD are also available to
discuss Galaxy and the rest of GMOD, respectively.

If you are interested, please contact Mitch, Dan, and Scott (all CC'd here)
directly.

There will also be a full-day GMOD workshop at PAG, but that's the topic of
another email.

Thanks,

Dave C.


---------- Forwarded message ----------
From: Dave Clements <cle...@gm...>
Date: Wed, Jan 5, 2011 at 9:59 AM
Subject: [Gmod-announce] GMOD Roadshow In San Diego this month
To: GMOD Announcements List <gmo...@li...>
Cc: Dan Blankenberg <da...@bx...>, Mitch Skinner <
mit...@be...>


Hello all,

GMOD will have a large number of representatives at Plant and Animal Genome
(PAG) <http://gmod.org/wiki/PAG_2011> in San Diego this month. Three of
them,

   - Dan Blankenberg <http://gmod.org/wiki/User:DanB> of the
Galaxy<http://gmod.org/wiki/Galaxy>project,
   - Mitch Skinner <http://gmod.org/wiki/User:MitchSkinner>, lead
JBrowse<http://gmod.org/wiki/JBrowse>developer, and
   - Scott Cain <http://gmod.org/wiki/User:Scott>, GMOD Project Coordinator

are available to visit organizations in the San Diego area during the
conference.

If you would like to arrange a visit with *Dan, Mitch*, and/or *Scott* to
discuss *Galaxy <http://gmod.org/wiki/Galaxy>,
JBrowse<http://gmod.org/wiki/JBrowse>
*, or any other *GMOD Components <http://gmod.org/wiki/GMOD_Components>*,
please contact Dan <da...@bx...>, Mitch <mit...@be...> and
Scott <sc...@sc...> directly.

Thanks,
Dave Clements

-- 
http://galaxyproject.org

_______________________________________________
Gmod-announce mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-announce




-- 
http://gmod.org/wiki/GMOD_Americas_2011
http://gmod.org/wiki/GMOD_News
http://usegalaxy.org

[Gmod-ajax] GMOD Spring Training Application Deadline January 7

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

Hello all,

The application deadline for the 2011 GMOD Spring Training
(http://gmod.org/wiki/2011_GMOD_Spring_Training) is the end of this
coming Friday, January 7.  Admission is competitive, so please apply
by Friday to avoid being automatically placed on the waiting list.
Details are below.

Thanks, and happy new year!

Dave C
-------

Applications are now being accepted for the 2011 GMOD Spring Training
course (http://gmod.org/wiki/2011_GMOD_Spring_Training), 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.

These components will be covered:
   * Apollo - genome annotation editor
   * Chado - biological database schema
   * Galaxy - analysis and data integration framework
   * 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.

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

[Gmod-ajax] Article on Quora

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

Thought experiment: a genome-oriented questions-answers site?

http://www.bothsidesofthetable.com/2010/08/23/the-power-of-quora-why-benchmark-was-right-to-pay-up/

[Gmod-ajax] jbrowse track density

[Wolfsberg, T. (NIH/N. [E] <ty...@nh...>]

Hi,

We're new to Jbrowse, and we're wondering if there is a way to set the track feature density for individual tracks.

The problem is shown in this screenshot-at this level of zoom, we would like to see the individual exons on the Cufflinks track just as we see the exons on the EVM track.

[cid:3375866015_144004317]


if you zoom in, the exons are indeed there:

[cid:3375866015_144015638]
Is there a way to configure the Cufflinks track (or any other track with dense features) so you see the individual exons and the track labels?

thanks
tyra


--
Tyra Wolfsberg, Ph.D.
Associate Investigator
Associate Director, Bioinformatics and Scientific Programming Core
NIH/NHGRI/GTB
Building 50, Room 5228B
50 South Drive
Bethesda, MD  20892

(301) 435-5990 phone
(301) 480-1109 fax
ty...@nh...

Re: [Gmod-ajax] jbrowse in iPad?

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

Cool Ian. I may have some developer hours I could throw at this in the
new year too.  Let me know if you want to chat after the holidays
about the approach you want to be used for this feature.

Brian

Sent from iPad

On Dec 18, 2010, at 1:27 PM, Ian Holmes <ih...@be...> wrote:

> Thanks Brian!
>
> Custom tracks have always been on our wishlist since Day 1 but for various reasons have repeatedly been postponed. At one point we prototyped using TWiki - this code is still in the repo but not very mature. However, I suspect the quickest way to do this now would be via Galaxy. Do we have any Galaxy experts in the house..... Otherwise I may take a crack at it in the New Year.
>
> -Ian (by phone)
>
> On Dec 18, 2010, at 9:15 AM, "Brian O'Connor" <bri...@gm...> wrote:
>
>> Hey,
>>
>> Ian, great to hear you guys are working on this (and the release is
>> coming up too!).  I showed a version I hacked to get the touch to work
>> to a bunch of people over the last few weeks and everyone is really
>> impressed with this browser.  There's something about the iPad touch
>> interface + this browser that makes people smile!  So I'm glad to hear
>> the touch feature is being added to the official release.  If anyone
>> is interested in hacking this to work right now here's what I had to
>> add to the index.html.  This worked for me on a checkout from a couple
>> weeks ago...
>>
>> function init()
>> {
>>   document.addEventListener("touchstart", touchHandle, true);
>>   document.addEventListener("touchmove", touchHandle, true);
>>   document.addEventListener("touchend", touchHandle, true);
>>   document.addEventListener("touchcancel", touchHandle, true);
>>
>>   load();
>>   console.log("In init");
>> }
>>
>> init();
>>
>> But looking at the current demo HTML it looks like you just include
>> the touch.js file now...
>>
>> On a different topic, what is the plan for adding custom tracks to the
>> browser?  Right now I can add via importing a GFF file but are there
>> plans to provide a mechanism for end users to upload their custom
>> tracks?  I'm building a query engine (http://seqware.sf.net) and it
>> integrates with genome browsers by providing back a URL to load a
>> custom track with.  This has been a really convenient way to display
>> the results of queries in a genome browser like UCSC or IGV.  Is this
>> sort of functionality planned for JBrowse?
>>
>> --Brian
>>
>> On Sat, Dec 18, 2010 at 12:53 AM, Ian Holmes <ih...@be...> wrote:
>>> Hi Harry, thanks for your interest in JBrowse. You can now get to the
>>> touchscreen demo if you point your iPad here:
>>>
>>> http://jbrowse.org/ucsc/hg19/touch.html
>>>
>>> A few more details here:
>>> http://jbrowse.org/?page_id=11
>>>
>>> It should be present in the next release (which is imminent)
>>>
>>> All the best, Ian
>>>
>>> (cc'd Brenton, Ann & Brian, all of whom asked about this. NB the pinch-zoom
>>> is not yet implemented, though could probably be added fairly easily)
>>>
>>>
>>> On 9/16/10 7:25 AM, Harry Yoo wrote:
>>>>
>>>> Congratulations for the 1.1 release.
>>>>
>>>> I integrated the new version into our system and tested. It works
>>>> great!. But when I tested with iPad, it did not work and was not able to
>>>> find any place that works for iPad. Neither two demos at
>>>> http://jbrowse.org/?page_id=22 does not work as showed in the youtube
>>>> video.
>>>>
>>>> Where can I find a demo that I can work with my iPad?
>>>>
>>>> I also found a touchBrowse.js from the git branch, it seems like I need
>>>> to do some activation in addition to adding the js lib into the page. Is
>>>> that correct?
>>>>
>>>> Can you show how to make it work with iPad?
>>>>
>>>>
>>>> Thanks,
>>>> Harry Yoo
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Start uncovering the many advantages of virtual appliances
>>>> and start using them to simplify application deployment and
>>>> accelerate your shift to cloud computing.
>>>> http://p.sf.net/sfu/novell-sfdev2dev
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> Gmo...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>

Re: [Gmod-ajax] jbrowse in iPad?

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

Thanks Brian!

Custom tracks have always been on our wishlist since Day 1 but for various reasons have repeatedly been postponed. At one point we prototyped using TWiki - this code is still in the repo but not very mature. However, I suspect the quickest way to do this now would be via Galaxy. Do we have any Galaxy experts in the house..... Otherwise I may take a crack at it in the New Year.

-Ian (by phone)

On Dec 18, 2010, at 9:15 AM, "Brian O'Connor" <bri...@gm...> wrote:

> Hey,
> 
> Ian, great to hear you guys are working on this (and the release is
> coming up too!).  I showed a version I hacked to get the touch to work
> to a bunch of people over the last few weeks and everyone is really
> impressed with this browser.  There's something about the iPad touch
> interface + this browser that makes people smile!  So I'm glad to hear
> the touch feature is being added to the official release.  If anyone
> is interested in hacking this to work right now here's what I had to
> add to the index.html.  This worked for me on a checkout from a couple
> weeks ago...
> 
> function init()
> {
>    document.addEventListener("touchstart", touchHandle, true);
>    document.addEventListener("touchmove", touchHandle, true);
>    document.addEventListener("touchend", touchHandle, true);
>    document.addEventListener("touchcancel", touchHandle, true);
> 
>    load();
>    console.log("In init");
> }
> 
> init();
> 
> But looking at the current demo HTML it looks like you just include
> the touch.js file now...
> 
> On a different topic, what is the plan for adding custom tracks to the
> browser?  Right now I can add via importing a GFF file but are there
> plans to provide a mechanism for end users to upload their custom
> tracks?  I'm building a query engine (http://seqware.sf.net) and it
> integrates with genome browsers by providing back a URL to load a
> custom track with.  This has been a really convenient way to display
> the results of queries in a genome browser like UCSC or IGV.  Is this
> sort of functionality planned for JBrowse?
> 
> --Brian
> 
> On Sat, Dec 18, 2010 at 12:53 AM, Ian Holmes <ih...@be...> wrote:
>> Hi Harry, thanks for your interest in JBrowse. You can now get to the
>> touchscreen demo if you point your iPad here:
>> 
>> http://jbrowse.org/ucsc/hg19/touch.html
>> 
>> A few more details here:
>> http://jbrowse.org/?page_id=11
>> 
>> It should be present in the next release (which is imminent)
>> 
>> All the best, Ian
>> 
>> (cc'd Brenton, Ann & Brian, all of whom asked about this. NB the pinch-zoom
>> is not yet implemented, though could probably be added fairly easily)
>> 
>> 
>> On 9/16/10 7:25 AM, Harry Yoo wrote:
>>> 
>>> Congratulations for the 1.1 release.
>>> 
>>> I integrated the new version into our system and tested. It works
>>> great!. But when I tested with iPad, it did not work and was not able to
>>> find any place that works for iPad. Neither two demos at
>>> http://jbrowse.org/?page_id=22 does not work as showed in the youtube
>>> video.
>>> 
>>> Where can I find a demo that I can work with my iPad?
>>> 
>>> I also found a touchBrowse.js from the git branch, it seems like I need
>>> to do some activation in addition to adding the js lib into the page. Is
>>> that correct?
>>> 
>>> Can you show how to make it work with iPad?
>>> 
>>> 
>>> Thanks,
>>> Harry Yoo
>>> 
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Start uncovering the many advantages of virtual appliances
>>> and start using them to simplify application deployment and
>>> accelerate your shift to cloud computing.
>>> http://p.sf.net/sfu/novell-sfdev2dev
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>> 

Re: [Gmod-ajax] jbrowse in iPad?

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

Hey,

Ian, great to hear you guys are working on this (and the release is
coming up too!).  I showed a version I hacked to get the touch to work
to a bunch of people over the last few weeks and everyone is really
impressed with this browser.  There's something about the iPad touch
interface + this browser that makes people smile!  So I'm glad to hear
the touch feature is being added to the official release.  If anyone
is interested in hacking this to work right now here's what I had to
add to the index.html.  This worked for me on a checkout from a couple
weeks ago...

function init()
{
    document.addEventListener("touchstart", touchHandle, true);
    document.addEventListener("touchmove", touchHandle, true);
    document.addEventListener("touchend", touchHandle, true);
    document.addEventListener("touchcancel", touchHandle, true);

    load();
    console.log("In init");
}

init();

But looking at the current demo HTML it looks like you just include
the touch.js file now...

On a different topic, what is the plan for adding custom tracks to the
browser?  Right now I can add via importing a GFF file but are there
plans to provide a mechanism for end users to upload their custom
tracks?  I'm building a query engine (http://seqware.sf.net) and it
integrates with genome browsers by providing back a URL to load a
custom track with.  This has been a really convenient way to display
the results of queries in a genome browser like UCSC or IGV.  Is this
sort of functionality planned for JBrowse?

--Brian

On Sat, Dec 18, 2010 at 12:53 AM, Ian Holmes <ih...@be...> wrote:
> Hi Harry, thanks for your interest in JBrowse. You can now get to the
> touchscreen demo if you point your iPad here:
>
> http://jbrowse.org/ucsc/hg19/touch.html
>
> A few more details here:
> http://jbrowse.org/?page_id=11
>
> It should be present in the next release (which is imminent)
>
> All the best, Ian
>
> (cc'd Brenton, Ann & Brian, all of whom asked about this. NB the pinch-zoom
> is not yet implemented, though could probably be added fairly easily)
>
>
> On 9/16/10 7:25 AM, Harry Yoo wrote:
>>
>> Congratulations for the 1.1 release.
>>
>> I integrated the new version into our system and tested. It works
>> great!. But when I tested with iPad, it did not work and was not able to
>> find any place that works for iPad. Neither two demos at
>> http://jbrowse.org/?page_id=22 does not work as showed in the youtube
>> video.
>>
>> Where can I find a demo that I can work with my iPad?
>>
>> I also found a touchBrowse.js from the git branch, it seems like I need
>> to do some activation in addition to adding the js lib into the page. Is
>> that correct?
>>
>> Can you show how to make it work with iPad?
>>
>>
>> Thanks,
>> Harry Yoo
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Start uncovering the many advantages of virtual appliances
>> and start using them to simplify application deployment and
>> accelerate your shift to cloud computing.
>> http://p.sf.net/sfu/novell-sfdev2dev
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

Re: [Gmod-ajax] jbrowse in iPad?

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

Hi Harry, thanks for your interest in JBrowse. You can now get to the 
touchscreen demo if you point your iPad here:

http://jbrowse.org/ucsc/hg19/touch.html

A few more details here:
http://jbrowse.org/?page_id=11

It should be present in the next release (which is imminent)

All the best, Ian

(cc'd Brenton, Ann & Brian, all of whom asked about this. NB the 
pinch-zoom is not yet implemented, though could probably be added fairly 
easily)


On 9/16/10 7:25 AM, Harry Yoo wrote:
> Congratulations for the 1.1 release.
>
> I integrated the new version into our system and tested. It works
> great!. But when I tested with iPad, it did not work and was not able to
> find any place that works for iPad. Neither two demos at
> http://jbrowse.org/?page_id=22 does not work as showed in the youtube
> video.
>
> Where can I find a demo that I can work with my iPad?
>
> I also found a touchBrowse.js from the git branch, it seems like I need
> to do some activation in addition to adding the js lib into the page. Is
> that correct?
>
> Can you show how to make it work with iPad?
>
>
> Thanks,
> Harry Yoo
>
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] jbrowse/flatfile-to-json.pl not adding all tracks

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

I'm not aware of any reason why this would happen.  Could you send your 
GFF, so I can try to reproduce this?

Mitch

On 12/14/2010 08:15 PM, Dana Price wrote:
> I've got a gff generated via MAKER of a contig.  It's got 9 features 
> of type "gene", but when I run flatfile-to-json.pl 
> <http://flatfile-to-json.pl> to create a track out of these, it only 
> adds 5 of them.  I'm using the command:
> /var/www/jbrowse/bin/flatfile-to-json.pl <http://flatfile-to-json.pl> 
> --tracklabel "Genes" --key "Genes" --getType --getLabel --autocomplete 
> label --cssclass feature5 --type gene --gff ./ConsensusfromContig25517.gff
>
>
> Is there any particular reason it wouldn't add all features present?
>
> Thanks!
>
>
> -- 
> Dana Price
> Laboratory Researcher in Bioinformatics
> Rutgers, The State University
> Bhattacharya Lab
> http://dblab.rutgers.edu
> d....@ru... <mailto:d....@ru...>
>
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
> to the next level, and enter the era of Social Business.
> http://p.sf.net/sfu/lotusphere-d2d
>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] jbrowse/flatfile-to-json.pl not adding all tracks

[Dana P. <dan...@gm...>]

I've got a gff generated via MAKER of a contig.  It's got 9 features of type
"gene", but when I run flatfile-to-json.pl to create a track out of these,
it only adds 5 of them.  I'm using the command:
/var/www/jbrowse/bin/flatfile-to-json.pl --tracklabel "Genes" --key "Genes"
--getType --getLabel --autocomplete label --cssclass feature5 --type gene
--gff ./ConsensusfromContig25517.gff


Is there any particular reason it wouldn't add all features present?

Thanks!


-- 
Dana Price
Laboratory Researcher in Bioinformatics
Rutgers, The State University
Bhattacharya Lab
http://dblab.rutgers.edu
d....@ru...

[Gmod-ajax] New Mailing Lists: GMOD-PhenDiver, GMOD-CoGePhy

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

Hello all,

The feedback on the proposed lists was entirely positive.  So, GMOD now has
two new research-area based lists:

*CoGePhy* - Comparative Genomics, Phylogeny, and related topics discussion
list.
  Subscribe: https://lists.sourceforge.net/lists/listinfo/gmod-cogephy
  Archive:    http://gmod.827538.n3.nabble.com/CoGePhy-f2036734.html

*PhenDiver* - Phenotype, Natural Diversity, Population Genetics and related
topics discussion list.
  Subscribe:  https://lists.sourceforge.net/lists/listinfo/gmod-phendiver
  Archive:     http://gmod.827538.n3.nabble.com/PhenDiver-f2036309.html

If you are interested in these topics, please subscribe to the lists and
then post any comments or questions that you just didn't know where to post
before!

Thanks,

Dave C.


On Tue, Nov 30, 2010 at 2:30 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
>



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