gmod-ajax — JBrowse list

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

Hi Mitch, 

thanks for the reply.
My reference sequence is lemna minor, I have it in gbk, fasta or gff format. 

Anja

Date: Wed, 29 Sep 2010 11:29:02 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
    E-Mail-Text
  
  
    Hi,

    

    prepare-refseqs.pl is trying to get a reference sequence
    (chromosome, contig, scaffold, or whatever you have) out of the
    database.  But it's not getting back what it expected to get.

    

    I randomly chose "1" as the name of the reference sequence in the
    example I sent you; I don't know how your reference sequences are
    named.  Are they chromosomes, or scaffolds, or something else?  And
    how are they named?  Is there a reference sequence called "1"?

    

    The intended usage of prepare-refseqs.pl is for you to put a list of
    reference sequence names on the command line, as the values of the
    "--refs" argument.  For example,  if you have 3 scaffolds named
    scaf1, scaf2, and scaf3, your prepare-refseqs.pl command would look
    like this:

    

    bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

    

    In order for that to work, those sequences should already have been
    loaded into your database.

    

    Hope this helps,

    Mitch

    

    On 09/29/2010 07:51 AM, Anja Friedrich wrote:
    
      
      

      

      From: fri...@ho...

      To: gmo...@li...

      Subject: error by runing prepare-refseqs.pl

      Date: Wed, 29 Sep 2010 16:32:22 +0200

      

      
      
      Hi all, 

      

      I tried to run:

      

      >bin/prepare-refseqs.pl --conf taro.json --refs 1

      

      but I get:

      

      Can't call method "name" on an undefined value at
      bin/prepare-refseqs.pl line 72.

      

      Any idea?

      

      Cheers, 

      Anja
      
------------------------------------------------------------------------------
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Re: [Gmod-ajax] error by runing prepare-refseqs.pl

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

  Hi,

prepare-refseqs.pl is trying to get a reference sequence (chromosome, 
contig, scaffold, or whatever you have) out of the database.  But it's 
not getting back what it expected to get.

I randomly chose "1" as the name of the reference sequence in the 
example I sent you; I don't know how your reference sequences are 
named.  Are they chromosomes, or scaffolds, or something else?  And how 
are they named?  Is there a reference sequence called "1"?

The intended usage of prepare-refseqs.pl is for you to put a list of 
reference sequence names on the command line, as the values of the 
"--refs" argument.  For example,  if you have 3 scaffolds named scaf1, 
scaf2, and scaf3, your prepare-refseqs.pl command would look like this:

bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

In order for that to work, those sequences should already have been 
loaded into your database.

Hope this helps,
Mitch

On 09/29/2010 07:51 AM, Anja Friedrich wrote:
>
>
> ------------------------------------------------------------------------
> From: fri...@ho...
> To: gmo...@li...
> Subject: error by runing prepare-refseqs.pl
> Date: Wed, 29 Sep 2010 16:32:22 +0200
>
> Hi all,
>
> I tried to run:
>
> >bin/prepare-refseqs.pl --conf taro.json --refs 1
>
> but I get:
>
> Can't call method "name" on an undefined value at 
> bin/prepare-refseqs.pl line 72.
>
> Any idea?
>
> Cheers,
> Anja
>
>
> ------------------------------------------------------------------------------
> 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

[Gmod-ajax] error by runing prepare-refseqs.pl

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

From: fri...@ho...
To: gmo...@li...
Subject: error by runing prepare-refseqs.pl
Date: Wed, 29 Sep 2010 16:32:22 +0200








Hi all, 

I tried to run:

    

    >bin/prepare-refseqs.pl --conf taro.json --refs 1


    but I get:

Can't call method "name" on an undefined value at bin/prepare-refseqs.pl line 72.

Any idea?

Cheers, 
Anja 		 	   		  

Re: [Gmod-ajax] auto-complete problem

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

  Since some data sources (chado, SeqFeature::Store) have IDs which 
aren't meaningful to users, JBrowse currently doesn't do searches on the 
ID field.  In the future, we probably should, but for right now you can 
add an Alias tag to your GFF3, something like:

NC_007488       GenBank gene    109368  110333  .       -       1       
ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942

And if you have more than one, you can make Alias be a comma-separated list:

NC_007488       GenBank gene    109368  110333  .       -       1       
ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942;Alias=RSP_3942,foo,bar

Regards,
Mitch


On 09/26/2010 01:53 AM, David Breimann wrote:
> Hello,
>
> I have a GFF3 file with lines like:
> NC_007488       GenBank gene    109368  110333  .       -       
> 1       ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
> NC_007488       GenBank gene    108526  109371  .       -       
> 1       ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943
>
> I added it using --type=gene --autocomplete=all, then generated names.
> However, I can only look for genes using their names (e.g. yurN) and 
> not their IDs or locus_tags.
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
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[Gmod-ajax] auto-complete problem

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

Hello,

I have a GFF3 file with lines like:
NC_007488       GenBank gene    109368  110333  .       -       1
ID=RSP_3942;Dbxref=GeneID:3712061;Name=yurN;locus_tag=RSP_3942
NC_007488       GenBank gene    108526  109371  .       -       1
ID=RSP_3943;Dbxref=GeneID:3712060;Name=yurM;locus_tag=RSP_3943

I added it using --type=gene --autocomplete=all, then generated names.
However, I can only look for genes using their names (e.g. yurN) and not
their IDs or locus_tags.

Re: [Gmod-ajax] displaying NTR in JBrowse

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

##gff-version   3
##sequence-region 1 1 2000
1	NTRFinder	nested_tandem_repeat	790	1032	.	+	.	ID=NTR-a
1	NTRFinder	motif1_small_b	790	800	.	+	.	ID=NTR-a1;Parent=NTR-a;Name=motif1_small_b
1	NTRFinder	motif1_small_a	812	822	.	+	.	ID=NTR-a2;Parent=NTR-a;Name=motif1_small_a
1	NTRFinder	motif1_small_a	823	833	.	+	.	ID=NTR-a3;Parent=NTR-a;Name=motif1_small_a
1	NTRFinder	motif1_tall_a	834	881	.	+	.	ID=NTR-a4;Parent=NTR-a;Name=motif1_tall_a	
1	NTRFinder	motif1_small_a	882	892	.	+	.	ID=NTR-a5;Parent=NTR-a;Name=motif1_small_a
1	NTRFinder	motif1_small_b	893	903	.	+	.	ID=NTR-a6;Parent=NTR-a;Name=motif1_small_b
1	NTRFinder	motif1_small_a	904	914	.	+	.	ID=NTR-a7;Parent=NTR-a;Name=motif1_small_a
1	NTRFinder	motif1_tall_b	915	962	.	+	.	ID=NTR-a8;Parent=NTR-a;Name=motif1_tall_b
1	NTRFinder	motif1_small_c	963	973	.	+	.	ID=NTR-a9;Parent=NTR-a;Name=motif1_small_c
1	NTRFinder	motif1_small_b	974	1021	.	+	.	ID=NTR-a10;Parent=NTR-a;Name=motif1_small_b
1	NTRFinder	motif1_small_a	1022	1032	.	+	.	ID=NTR-a11;Parent=NTR-a;Name=motif1_small_a

Re: [Gmod-ajax] Question on basic database paradigm

[Paul S. <pau...@gm...>]

On Thu, Sep 16, 2010 at 8:12 PM, Ian Holmes <ih...@be...> wrote:

>
> Do you have some such application in mind, or are you just curious about
> the implementation decisions behind JBrowse..?
>
>
I'm not sure that it's exactly what you are looking for, but dynamically
generated tracks might be one way to implement transformations on wiggle
tracks. E.g., log-transform, clip at 50, scale height to current window. I'm
thinking of the sorts of things that one can do with user-defined functions
in Artemis. Admittedly, generating the images on the fly might take too long
on the server to maintain responsiveness.

[Gmod-ajax] jbrowse in iPad?

[Harry Y. <hy...@vb...>]

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

Re: [Gmod-ajax] Question on basic database paradigm

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

Hi Scott,

The reason there are lots of JSON files and lots of GETs, rather than 
just a few, is that the SNP track has deliberately been split up on the 
server - so that the client doesn't have to download all human SNPs 
whenever the user asks to view a small region.

You're right that in principle this could be implemented as a webservice 
instead. Is there a particular reason you want/need to do this? Most of 
what GBrowse does dynamically (rendering the image panel) is done by 
JBrowse in the web browser, by the JavaScript client software. So there 
is no need for the server to be dynamic (at least for the use cases 
JBrowse currently supports).

I can certainly imagine scenarios where you might want to generate 
JBrowse JSON files dynamically - e.g. for a track that represents the 
transient results of an analysis, or if the data store is itself dynamic 
and changing, or if you wanted to offer a JBrowse view onto a large 
existing datastore (e.g. NCBI Genome) but didn't want to generate tracks 
until they were specifically requested for the first time by a user, etc.

Do you have some such application in mind, or are you just curious about 
the implementation decisions behind JBrowse..?

FWIW - some sort of dynamic webservice-driven JBrowse-JSON-generating 
code will probably emerge from GMOD Labs at *some* point - so I am 
genuinely interested in how you'd imagine using this.

Best wishes..
Ian


Saccone, Scott wrote:
> Hello, I have implemented and worked with GBrowse in the past and was 
> considering working with JBrowse. I’m confused about how the data is 
> sent from the server to the JBrowse client. In the human demo page I see 
> lots of GET calls to .json files and I see that at 
> http://jbrowse.org/ucsc/hg19/data/tracks/chr2/SNPs-130/ you have stored 
> many .json files. Is it true that the only way to get the data from the 
> server to the client is by creating many, presumably reasonably sized, 
> .json files on the server? Or is there a way to use, say, PHP and MySQL, 
> to automate the transmission of JSON data? For example, instead what 
> looks to me like an Ajax call to
> 
> GET 
> http://jbrowse.org/ucsc/hg19/data/tracks/chr1/Ge...riants-CEU-mother-2892//lazyfeatures-180819.json 
> <http://jbrowse.org/ucsc/hg19/data/tracks/chr1/Ge...riants-CEU-mother-2892/lazyfeatures-180819.json>, 
> could JBrowse be configured to do the same thing with PHP where “ucsc”, 
> “hg19”, etc, are all arguments?
> 
>  
> 
> Thanks,
> 
>  
> 
> Scott
> 
>  
> 
> *Scott Saccone, Ph.D.*
> 
> Department of Psychiatry, Box 8134
> Washington University School of Medicine
> 660 South Euclid Avenue
> Saint Louis, Missouri 63110-1093
> Voice: (314) 286-2581
> FAX: (314) 286-2577
> Email: ssa...@wu... <mailto:ssa...@wu...>
> 
>  
> 
> 
> ------------------------------------------------------------------------
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If 
> you are not the intended recipient, be advised that any unauthorized 
> use, disclosure, copying or the taking of any action in reliance on the 
> contents of this information is strictly prohibited. If you have 
> received this email in error, please immediately notify the sender via 
> telephone or return mail.
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> 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
> 
> 
> ------------------------------------------------------------------------
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Re: [Gmod-ajax] wig2png compile error

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

Actually, scratch that - it looks like what's actually happening is 
you've got an old version of libpng. The missing function 
"png_set_longjmp_fn" was introduced in libpng 1.4.0

Autoconf can probably check this, but it currently doesn't. I've added a 
bug ticket:
http://jbrowse.lighthouseapp.com/projects/23792-jbrowse/tickets/63

In the meantime, the best thing for you to do is to install a newer 
version of libpng (>1.4)

Best wishes,
Ian

Ian Holmes wrote:
> Hi Xiao,
> 
> Looks like gcc is not finding libpng - this is what the configure script 
> is for. Try typing './configure' before 'make'.
> 
> Best wishes
> Ian
> 
> 常啸 wrote:
>> hi,
>> I meet an error when compile wig2png after typing "make".
>>
>> g++ -g -O2 -include src/config.h  -lpng  -o bin/wig2png src/wig2png.cc src/opts_list.cc
>> /tmp/cc1x8bbj.o: In function `write_png_file(char const*, int, int, unsigned char**, png_color_struct*, int, int)':
>> /var/www/html/jbrowse-jbrowse-9a1542d/src/wig2png.cc:59: undefined reference to `png_set_longjmp_fn'
>> collect2: ld returned 1 exit status
>>
>> Can anyone tell me what's the problem?
>>
>> Thanks,
>> Xiao
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> 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
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] wig2png compile error

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

Hi Xiao,

Looks like gcc is not finding libpng - this is what the configure script 
is for. Try typing './configure' before 'make'.

Best wishes
Ian

常啸 wrote:
> hi,
> I meet an error when compile wig2png after typing "make".
> 
> g++ -g -O2 -include src/config.h  -lpng  -o bin/wig2png src/wig2png.cc src/opts_list.cc
> /tmp/cc1x8bbj.o: In function `write_png_file(char const*, int, int, unsigned char**, png_color_struct*, int, int)':
> /var/www/html/jbrowse-jbrowse-9a1542d/src/wig2png.cc:59: undefined reference to `png_set_longjmp_fn'
> collect2: ld returned 1 exit status
> 
> Can anyone tell me what's the problem?
> 
> Thanks,
> Xiao
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
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> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

[Gmod-ajax] wig2png compile error

[常啸 <xc...@si...>]

hi,
I meet an error when compile wig2png after typing "make".

g++ -g -O2 -include src/config.h  -lpng  -o bin/wig2png src/wig2png.cc src/opts_list.cc
/tmp/cc1x8bbj.o: In function `write_png_file(char const*, int, int, unsigned char**, png_color_struct*, int, int)':
/var/www/html/jbrowse-jbrowse-9a1542d/src/wig2png.cc:59: undefined reference to `png_set_longjmp_fn'
collect2: ld returned 1 exit status

Can anyone tell me what's the problem?

Thanks,
Xiao

[Gmod-ajax] Question on basic database paradigm

[Saccone, S. <ssa...@wu...>]

Hello, I have implemented and worked with GBrowse in the past and was considering working with JBrowse. I'm confused about how the data is sent from the server to the JBrowse client. In the human demo page I see lots of GET calls to .json files and I see that at http://jbrowse.org/ucsc/hg19/data/tracks/chr2/SNPs-130/ you have stored many .json files. Is it true that the only way to get the data from the server to the client is by creating many, presumably reasonably sized, .json files on the server? Or is there a way to use, say, PHP and MySQL, to automate the transmission of JSON data? For example, instead what looks to me like an Ajax call to
GET http://jbrowse.org/ucsc/hg19/data/tracks/chr1/Ge...riants-CEU-mother-2892//lazyfeatures-180819.json<http://jbrowse.org/ucsc/hg19/data/tracks/chr1/Ge...riants-CEU-mother-2892/lazyfeatures-180819.json>, could JBrowse be configured to do the same thing with PHP where "ucsc", "hg19", etc, are all arguments?

Thanks,

Scott

Scott Saccone, Ph.D.
Department of Psychiatry, Box 8134
Washington University School of Medicine
660 South Euclid Avenue
Saint Louis, Missouri 63110-1093
Voice: (314) 286-2581
FAX: (314) 286-2577
Email: ssa...@wu...<mailto:ssa...@wu...>


________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[Gmod-ajax] A suggestion

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

First, congratulations for the 1.1 release.

Second, I wish to suggest a feature I am missing. Currently I use the "link"
option very often to email my colleagues interesting regions I would like to
discuss with them. However, sometimes this is not enough. It would be great
if I could choose a feature (e.g. gene), then send a link and the selected
feature will be highlighted / blink.

Best,
Dave

[Gmod-ajax] JBrowse 1.1 released

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

The announcement:
http://jbrowse.org/?p=56

You can download it here:
http://jbrowse.org/releases/jbrowse-1.1.zip

Release notes:
version 1.1, September 2010.

These notes document JBrowse developments in the period from July 2009
(online publication of the first JBrowse paper in Genome Research, the
de facto "version 1.0") up to September 2010 (the first in a planned
series of quarterly releases).


New features in this release:

- Scalability. JBrowse can now handle very large data tracks,
   including human EST/SNP tracks, or tracks of next-gen sequence
   reads. Large datasets are broken into smaller chunks, so there is no
   loading delay for big tracks.

- Extensibility. A Perl module (ImageTrackRenderer.pm) for creating
   user-drawn image tracks is now available, based on the CPAN GD.pm
   module. An example program is provided, draw-basepair-track.pl, that
   uses this module to draw arcs over a sequence representing the
   base-pairing interactions of RNA secondary structure.

- Bug fixes. Numerous display glitches have been fixed, including
   issues with wide-screen monitors and long mostly-offscreen features.

Known issues/limitations with this release:

- No JSON-level backward compatibility. If you are upgrading from an
   older version of JBrowse, you will have to regenerate all the JSON
   files on your server. This means wiping your jbrowse/data directory
   and re-running all server scripts (flatfile-to-json, biodb-to-json,
   wig-to-json, etc.) to regenerate your data from the original
   FASTA/GFF/BED/WIG files.

- Next-gen sequence display is currently restricted to the
   co-ordinates of the outermost region to which a single read is
   mapped. There is no support (yet) for displaying pairing between
   reads, sequences of reads, alignment of read to reference sequence
   (e.g. splicing), or mismatches between read and reference.

- Processing SAM/BAM next-gen sequence files takes a lot of memory
   (about 500 megabytes per million features).

- Numerical (as opposed to comparative) readout of the data in Wiggle
   tracks, e.g. via a y-axis label or mouseover popup, is still
   unsupported.

[Gmod-ajax] GMOD Europe 2010: Less than a week to go

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

Hello all,

GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts on
Monday, 13 September, less than a week from now.  This event runs for
4 days and includes:
* September 2010 GMOD Meeting - has openings
* GMOD Satellite Meetings - has openings
* InterMine Workshop - has openings
* BioMart Workshop - full (but you can get on the short waiting list)

If you haven't already registered, please do so as soon as possible.
This will assure you a seat and help us plan meeting logistics.  See
http://gmod.org/wiki/GMOD_Europe_2010 for details and a registration
link.

This is the last broadcast reminder I'll send out.  Please let me know
if you have any questions.

Thanks,

Dave C.

--
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/GMOD_Europe_2010
http://hinv.jp/biocuration2010/
http://gmod.org/wiki/Help_Desk_Feedback

Re: [Gmod-ajax] print/save as image

[Thomas D. <tho...@gm...>]

Hi David,

I'm not sure what platform you're on, but if you've got a browser which
supports printing as PDF, I've had good results in a fairly similar
situation by setting the paper size ("Page Setup" dialog or similar) to
something large, then print as a PDF and use other tools (e.g. Apple
Preview, if you have access to a Mac) to convert to the desired bitmap
format.

                  Thomas.

On Mon, Aug 30, 2010 at 2:14 PM, David Breimann <dav...@gm...>wrote:

> Hello,
>
> Do you have any idea how can I print a region with all its data?
> I have multiple tracks so they don't fit all in a single window (I have to
> scroll down).
> There are several browser plugins that allow capturing long web pages into
> a single image file by automatically scrolling them all the way down,
> however they do not work with JBrowse (I guess it's because it's not using
> the "normal" browser scroll). So, do you have any suggestion on how to
> export/print from JBrowse without manually merging multiple print screens?
>
> Thanks,
> dave
>
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
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>
>

[Gmod-ajax] print/save as image

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

Hello,

Do you have any idea how can I print a region with all its data?
I have multiple tracks so they don't fit all in a single window (I have to
scroll down).
There are several browser plugins that allow capturing long web pages into a
single image file by automatically scrolling them all the way down, however
they do not work with JBrowse (I guess it's because it's not using the
"normal" browser scroll). So, do you have any suggestion on how to
export/print from JBrowse without manually merging multiple print screens?

Thanks,
dave

Re: [Gmod-ajax] how to modify the bar graph's setting?

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

I will certainly keep tracking JBrowse since I really like it. I hope it
will soon catch up with GBrowse and other popular browsers so I could
migrate and use it as a first choice.

On Wed, Aug 25, 2010 at 11:57 PM, Ian Holmes <ih...@be...> wrote:

> David,
>
> We are in the process of initiating formal, version-numbered releases of
> JBrowse on a quarterly basis. This should bring our release schedule in line
> with the projected development timelines that we provide to NIH.
> Consequently, it should allow us to publish more specific forecasts about
> the timing of new feature implementations.
>
> The first quarterly release will be in early September, and will focus on
> display of high-volume Next Generation Sequencing (NGS) data, along with a
> large number of bugfixes.
>
> One of the features you requested, the y-axis scale indicator for
> quantitative tracks, narrowly missed our list of targets for the September
> release. Instead it will be in the following (December) release. It remains
> a high priority, and will likely be one of the first things we implement
> after the September release.
>
> So, if you are prepared to continue following this mailing list and
> fetching the latest code from github, you could probably get y-axis scales
> by early this fall. I can announce this particular feature on this mailing
> list when it is ready, if that will help.
>
> In summary, our new release system will, I think, address both the
> high-level issues that you raise (concerning the development schedule) and
> the specific feature that you cited (reading off y-information from
> quantitative tracks). I hope that this will persuade you to persist with
> JBrowse a little longer. We remain keen to help you to get the most out of
> it.
>
> Best wishes,
> Ian
>
>
> David Breimann wrote:
>
>> Hi,
>>  I read this message at the online archive
>>
>> http://sourceforge.net/mailarchive/message.php?msg_name=4C6BEF8C.9070404%40berkeley.edu
>> and let me comment that I think a y-axis scale indicator as well as
>> display-value-on-mouse-hover is the number one need for me.
>> Unforutantly I had to quit using JBrowse a couple of weeks ago and
>> postpone my plan to make my database public, since all my numeric tracks are
>> useless without these features implemented. I am currently considering going
>> back to GBrowse or finding some other browser, since I have no idea when
>> these features will be available.
>>  Don't misunderstand me - I  love JBrowse and think it will be great, but
>> currently it's missing some essential features, and the uncertainty
>> regarding the future development schedule makes it difficult for me to plan
>> ahead and count on it.
>>  Keep up the great work,
>> Dave
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------------
>> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> Be part of this innovative community and reach millions of netbook users
>> worldwide. Take advantage of special opportunities to increase revenue and
>> speed time-to-market. Join now, and jumpstart your future.
>> http://p.sf.net/sfu/intel-atom-d2d
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>

Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff

[Suzanna L. <se...@lb...>]

For other applications having additional levels of nesting would be desired. The bracketing type of display as provide by Anja&Scott would still work nicely, particularly at low zoom levels. At higher zoom levels it would be nice to show more details of the inserted element embedded within this (see http://en.wikipedia.org/wiki/Transposon for one rough version, other things like promoters could be added as well).

-S

On Aug 26, 2010, at 5:13 PM, Mitch Skinner wrote:

> So, how deeply can these features be nested?  Anja's sketches so far (if I am understanding them correctly) only show two levels of nesting, but do they go deeper than that?  And is it important to visually distinguish every level?  At first when I heard the word "nested", I assumed you meant something like the attached sketch, which shows three levels of nesting.
> 
> The sketch idea is a great one, thanks Scott and Anja.
> 
> Mitch
> <ntr-3level.png>------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users 
> worldwide. Take advantage of special opportunities to increase revenue and 
> speed time-to-market. Join now, and jumpstart your future.
> http://p.sf.net/sfu/intel-atom-d2d_______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff

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

Hi Mitch,

sorry for the late answer, I had to talk to my supervisors first. They want me to display it as a level 2 

>The NTR's should be expressed as a level 2 motif, with different colours for the two motifs, there is not a hierarchy, the 
>patterns are of the form:
 
xxxxXxxxXxXxxxxXxxxxxxxxxXxxxxxxxxxxxxxXxxxxxxxXxxxxxxxXxxxx 
 
>etc, (with x the pattern of 11bp, and X with 48bp) with no higher level repetitivity.

Shouldn't be to hard to display it... Can I create the gff in the form that I have a line for the whole repeat region as a 
"overbar" and then 1 line for each motif? Would that work?

Cheers, Anja

> Date: Thu, 26 Aug 2010 17:13:15 -0700
> From: mit...@be...
> To: fri...@ho...
> CC: sc...@sc...; gmo...@li...
> Subject: Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff
> 
>   So, how deeply can these features be nested?  Anja's sketches so far 
> (if I am understanding them correctly) only show two levels of nesting, 
> but do they go deeper than that?  And is it important to visually 
> distinguish every level?  At first when I heard the word "nested", I 
> assumed you meant something like the attached sketch, which shows three 
> levels of nesting.
> 
> The sketch idea is a great one, thanks Scott and Anja.
> 
> Mitch
 		 	   		  

Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff

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

  So, how deeply can these features be nested?  Anja's sketches so far 
(if I am understanding them correctly) only show two levels of nesting, 
but do they go deeper than that?  And is it important to visually 
distinguish every level?  At first when I heard the word "nested", I 
assumed you meant something like the attached sketch, which shows three 
levels of nesting.

The sketch idea is a great one, thanks Scott and Anja.

Mitch

Re: [Gmod-ajax] [Gmod-schema] nested tandem repeats/gff

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

Hi Anja,

I exported your drawing as a pdf to make it more widely viewable
(though I imagine many people on this list have OpenOffice).  What you
drew is easy to display.  I was expecting that you wanted them all to
be on the same line with different icons representing the different
types of repeats, as opposed to each element being in a separate
track.

Scott


On Thu, Aug 26, 2010 at 2:45 PM, Anja Friedrich
<fri...@ho...> wrote:
> Hi Scott,
>
> I attached a little sketch (just for 1 region). I hope you can open it...
> Ithink it should be possible to display it like this in JBrowse...
> I saw that I forgott to answer your other questions. Sorry for that. Taro
> (Colocasia esculenta) is the name plant I got the squwnce from. The feature
> is called Nested Tandem Repeat (NTR).
>
> Anja
>
>> Date: Thu, 26 Aug 2010 14:33:48 -0400
>> Subject: Re: [Gmod-schema] nested tandem repeats/gff
>> From: sc...@sc...
>> To: fri...@ho...; gmo...@li...
>> CC: gmo...@li...
>>
>> Hi Anja,
>>
>> I'm cc'ing this to the JBrowse list they can chime in to.
>>
>> The wonderful thing about JBrowse is that it is quite flexible in what
>> it can display; that is also a downside, though, as it might require
>> you to create the underlying graphics if native support isn't there.
>> Since I don't really understand what you would want the image to look
>> like, would it be possible for you to create a sketch of what you want
>> to see? That would make it a lot easier to say whether what you want
>> to do is possible, easy or hard.
>>
>> Scott
>>
>>
>> On Thu, Aug 26, 2010 at 2:21 PM, Anja Friedrich
>> <fri...@ho...> wrote:
>> > Hi Scott,
>> >
>> > thanks for your explanation. I will go through it.
>> > As I told J my request to add nested_tandem_repeat to SO was accepted.
>> > My
>> > problem is that I have 3 different repeat regions with 2 motifs. I want
>> > to
>> > display the regions and the motifs in JBrowse. I was wondering how I
>> > have to
>> > create the single lines. One line for the region and 1 for each motif?
>> > For
>> > all 3 repeat regions of course... Would that work?
>> >
>> > Cheers,
>> > Anja
>> >
>> >
>> >> Date: Thu, 26 Aug 2010 14:10:58 -0400
>> >> Subject: Re: [Gmod-schema] nested tandem repeats/gff
>> >> From: sc...@sc...
>> >> To: jm...@vc...
>> >> CC: fri...@ho...; gmo...@li...
>> >>
>> >> Hi Anja,
>> >>
>> >> I'm going to put comments below in response to both you and J.
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Thu, Aug 26, 2010 at 11:54 AM, J.M.P. Alves <jm...@vc...> wrote:
>> >> > Hallo,
>> >> >
>> >> > A few possibilities I see, although I am not positive they are the
>> >> > actual problem:
>> >> >
>> >> >  > 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >> >
>> >> > Are "nested_repeat" and "repeat_fragment" part of the sequence
>> >> > ontology
>> >> > vocabulary? I think you can use anything you want on the second
>> >> > column
>> >> > there ("program"), but the 3rd one is restricted.
>> >>
>> >> In my instance of Chado (a few weeks old at the most), SO has both
>> >> terms, so that isn't likely the problem, but it's a good idea to
>> >> check. A query like this would tell you if it's present:
>> >>
>> >> select cvterm.* from cvterm join cv using (cv_id)
>> >> where cv.name='sequence' and cvterm.name='nested_repeat';
>> >>
>> >> >
>> >> > NTR is the name of the sequence (as in the FASTA file), right?
>> >>
>> >> Right, if a feature named NTR isn't already in the database, you will
>> >> have problems. From the error message you are getting, I'm guessing
>> >> it's already there (or it would have complained about that), but
>> >> perhaps I misremembering the order of error messaging. I would
>> >> suggest getting rid of the sequence-region directive, as unless you
>> >> have a fairly recent checkout of bioperl-live it will cause problems,
>> >> and in any event, will never be supported for defining a feature (and
>> >> this one isn't properly formed anyway--there's no start value and "bp"
>> >> isn't part of the spec). Instead, add a full gff line:
>> >>
>> >> NTR . contig 1 5428 . . . ID=NTR;Name=NTR
>> >>
>> >> Looking at your sample GFF again, it looks to me like you want these
>> >> feature to reside on a feature called "taro", is that right? Or is
>> >> there a feature called NTR? If the contig/chromosome/whatever is
>> >> called taro, then you should replace the text in the first column of
>> >> the gff with "taro" and create a GFF line for it, like I did for NTR
>> >> above.
>> >>
>> >> >
>> >> > Another possible problem:
>> >> >
>> >> >  > 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >> >
>> >> > I don't know if this is the case, but I thought every line had to
>> >> > have
>> >> > an ID attribute, e.g.:
>> >> >
>> >> > NTR program repeat_fragment 1505 1553 . + . ID=rf1;Parent=ID1
>> >>
>> >> Not so: ID tags are only needed in two cases:
>> >>
>> >> 1. To identify a feature so it can be referred to later to show
>> >> parentage (as Anja did in the sample GFF) and
>> >>
>> >> 2. To identify a reference sequence so it can be referred to in column
>> >> one (this is NOT part of the GFF3 spec, but life will work a lot
>> >> better with Chado if reference sequences look like
>> >> "ID=chr1;Name=chr1..."
>> >>
>> >> Scott
>> >>
>> >> >
>> >> > I hope some of these ideas help.
>> >> >
>> >> > J
>> >> >
>> >> > Anja Friedrich wrote:
>> >> >> Hi all,
>> >> >>
>> >> >> not sure if my earlier mail reached, because I was texting from a
>> >> >> different e-mail.
>> >> >>
>> >> >> I tried to load nested tandem repeats into chado. As this fature
>> >> >> doesnt
>> >> >> exist yet for gff3 I tried to get around:
>> >> >>
>> >> >> 0  ##gff-version   3
>> >> >> 1  ##sequence-region   taro 5428 bp
>> >> >> 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >> >> 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >> >> 4 NTR program repeat_fragement 473 483 . + . Parent=ID1
>> >> >>
>> >> >> But I get this error message:
>> >> >>
>> >> >> anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism Taro
>> >> >>  --gfffile
>> >> >> taro.gffCommand line argument used for root
>> >> >> Preparing data for inserting into the chado database
>> >> >> (This may take a while ...)
>> >> >>
>> >> >> --------------------- WARNING ---------------------
>> >> >> MSG: Calling end without a defined start position
>> >> >> ---------------------------------------------------
>> >> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 808, <GEN0> line 1.
>> >> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 809, <GEN0> line 1.
>> >> >>
>> >> >> ------------- EXCEPTION: Bio::Root::Exception -------------
>> >> >> MSG: no cvterm for
>> >> >> STACK: Error::throw
>> >> >> STACK: Bio::Root::Root::throw
>> >> >> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
>> >> >> STACK: Bio::GMOD::DB::Adapter::get_type
>> >> >> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4579
>> >> >> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:838
>> >> >> -----------------------------------------------------------
>> >> >>
>> >> >> Someone an idea? Cant I add the feature like this?
>> >> >>
>> >> >> Cheers,
>> >> >> Anja
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------------
>> >> >> Sell apps to millions through the Intel(R) Atom(Tm) Developer
>> >> >> Program
>> >> >> Be part of this innovative community and reach millions of netbook
>> >> >> users
>> >> >> worldwide. Take advantage of special opportunities to increase
>> >> >> revenue
>> >> >> and
>> >> >> speed time-to-market. Join now, and jumpstart your future.
>> >> >> http://p.sf.net/sfu/intel-atom-d2d
>> >> >>
>> >> >>
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >>
>> >> >> _______________________________________________
>> >> >> Gmod-schema mailing list
>> >> >> Gmo...@li...
>> >> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >> > --
>> >> > -------------------------------
>> >> > João Marcelo Pereira Alves (J)
>> >> > Post-doctoral fellow
>> >> > MCV / VCU - Richmond, VA
>> >> > http://bioinfo.lpb.mic.vcu.edu
>> >> > f. 1-804-828-3897
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> >> > Be part of this innovative community and reach millions of netbook
>> >> > users
>> >> > worldwide. Take advantage of special opportunities to increase
>> >> > revenue
>> >> > and
>> >> > speed time-to-market. Join now, and jumpstart your future.
>> >> > http://p.sf.net/sfu/intel-atom-d2d
>> >> > _______________________________________________
>> >> > Gmod-schema mailing list
>> >> > Gmo...@li...
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
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] [Gmod-schema] nested tandem repeats/gff

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

Hi Anja,

I'm cc'ing this to the JBrowse list they can chime in to.

The wonderful thing about JBrowse is that it is quite flexible in what
it can display; that is also a downside, though, as it might require
you to create the underlying graphics if native support isn't there.
Since I don't really understand what you would want the image to look
like, would it be possible for you to create a sketch of what you want
to see?  That would make it a lot easier to say whether what you want
to do is possible, easy or hard.

Scott


On Thu, Aug 26, 2010 at 2:21 PM, Anja Friedrich
<fri...@ho...> wrote:
> Hi Scott,
>
> thanks for your explanation. I will go through it.
> As I told J my request to add nested_tandem_repeat to SO was accepted. My
> problem is that I have 3 different repeat regions with 2 motifs. I want to
> display the regions and the motifs in JBrowse. I was wondering how I have to
> create the single lines. One line for the region and 1 for each motif? For
> all 3 repeat regions of course... Would that work?
>
> Cheers,
> Anja
>
>
>> Date: Thu, 26 Aug 2010 14:10:58 -0400
>> Subject: Re: [Gmod-schema] nested tandem repeats/gff
>> From: sc...@sc...
>> To: jm...@vc...
>> CC: fri...@ho...; gmo...@li...
>>
>> Hi Anja,
>>
>> I'm going to put comments below in response to both you and J.
>>
>> Scott
>>
>>
>> On Thu, Aug 26, 2010 at 11:54 AM, J.M.P. Alves <jm...@vc...> wrote:
>> > Hallo,
>> >
>> > A few possibilities I see, although I am not positive they are the
>> > actual problem:
>> >
>> >  > 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >
>> > Are "nested_repeat" and "repeat_fragment" part of the sequence ontology
>> > vocabulary? I think you can use anything you want on the second column
>> > there ("program"), but the 3rd one is restricted.
>>
>> In my instance of Chado (a few weeks old at the most), SO has both
>> terms, so that isn't likely the problem, but it's a good idea to
>> check. A query like this would tell you if it's present:
>>
>> select cvterm.* from cvterm join cv using (cv_id)
>> where cv.name='sequence' and cvterm.name='nested_repeat';
>>
>> >
>> > NTR is the name of the sequence (as in the FASTA file), right?
>>
>> Right, if a feature named NTR isn't already in the database, you will
>> have problems. From the error message you are getting, I'm guessing
>> it's already there (or it would have complained about that), but
>> perhaps I misremembering the order of error messaging. I would
>> suggest getting rid of the sequence-region directive, as unless you
>> have a fairly recent checkout of bioperl-live it will cause problems,
>> and in any event, will never be supported for defining a feature (and
>> this one isn't properly formed anyway--there's no start value and "bp"
>> isn't part of the spec). Instead, add a full gff line:
>>
>> NTR . contig 1 5428 . . . ID=NTR;Name=NTR
>>
>> Looking at your sample GFF again, it looks to me like you want these
>> feature to reside on a feature called "taro", is that right? Or is
>> there a feature called NTR? If the contig/chromosome/whatever is
>> called taro, then you should replace the text in the first column of
>> the gff with "taro" and create a GFF line for it, like I did for NTR
>> above.
>>
>> >
>> > Another possible problem:
>> >
>> >  > 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >
>> > I don't know if this is the case, but I thought every line had to have
>> > an ID attribute, e.g.:
>> >
>> > NTR program repeat_fragment 1505 1553 . + . ID=rf1;Parent=ID1
>>
>> Not so: ID tags are only needed in two cases:
>>
>> 1. To identify a feature so it can be referred to later to show
>> parentage (as Anja did in the sample GFF) and
>>
>> 2. To identify a reference sequence so it can be referred to in column
>> one (this is NOT part of the GFF3 spec, but life will work a lot
>> better with Chado if reference sequences look like
>> "ID=chr1;Name=chr1..."
>>
>> Scott
>>
>> >
>> > I hope some of these ideas help.
>> >
>> > J
>> >
>> > Anja Friedrich wrote:
>> >> Hi all,
>> >>
>> >> not sure if my earlier mail reached, because I was texting from a
>> >> different e-mail.
>> >>
>> >> I tried to load nested tandem repeats into chado. As this fature doesnt
>> >> exist yet for gff3 I tried to get around:
>> >>
>> >> 0  ##gff-version   3
>> >> 1  ##sequence-region   taro 5428 bp
>> >> 2 NTR program nested_repeat 831 1720 . . . ID=ID1;Name=ID1
>> >> 3 NTR program repeat_fragment 1505 1553 . + . Parent=ID1
>> >> 4 NTR program repeat_fragement 473 483 . + . Parent=ID1
>> >>
>> >> But I get this error message:
>> >>
>> >> anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism Taro  --gfffile
>> >> taro.gffCommand line argument used for root
>> >> Preparing data for inserting into the chado database
>> >> (This may take a while ...)
>> >>
>> >> --------------------- WARNING ---------------------
>> >> MSG: Calling end without a defined start position
>> >> ---------------------------------------------------
>> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 808, <GEN0> line 1.
>> >> Use of uninitialized value $featuretype in pattern match (m//) at
>> >> /usr/local/bin/gmod_bulk_load_gff3.pl line 809, <GEN0> line 1.
>> >>
>> >> ------------- EXCEPTION: Bio::Root::Exception -------------
>> >> MSG: no cvterm for
>> >> STACK: Error::throw
>> >> STACK: Bio::Root::Root::throw
>> >> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
>> >> STACK: Bio::GMOD::DB::Adapter::get_type
>> >> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4579
>> >> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:838
>> >> -----------------------------------------------------------
>> >>
>> >> Someone an idea? Cant I add the feature like this?
>> >>
>> >> Cheers,
>> >> Anja
>> >>
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------
>> >>
>> >>
>> >> ------------------------------------------------------------------------------
>> >> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> >> Be part of this innovative community and reach millions of netbook
>> >> users
>> >> worldwide. Take advantage of special opportunities to increase revenue
>> >> and
>> >> speed time-to-market. Join now, and jumpstart your future.
>> >> http://p.sf.net/sfu/intel-atom-d2d
>> >>
>> >>
>> >>
>> >> ------------------------------------------------------------------------
>> >>
>> >> _______________________________________________
>> >> Gmod-schema mailing list
>> >> Gmo...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> > --
>> > -------------------------------
>> > João Marcelo Pereira Alves (J)
>> > Post-doctoral fellow
>> > MCV / VCU - Richmond, VA
>> > http://bioinfo.lpb.mic.vcu.edu
>> > f. 1-804-828-3897
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
>> > Be part of this innovative community and reach millions of netbook users
>> > worldwide. Take advantage of special opportunities to increase revenue
>> > and
>> > speed time-to-market. Join now, and jumpstart your future.
>> > http://p.sf.net/sfu/intel-atom-d2d
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > Gmo...@li...
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



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

[Gmod-ajax] GMOD Europe 2010 Update

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

Hello all,

GMOD Europe 2010 (http://gmod.org/wiki/GMOD_Europe_2010) starts in
less than two weeks. If you are planning on attending and haven't yet
registered, then please do so in the next few days. The BioMart
Workshop has only a few slots left, and the registration fee for the
GMOD Meeting goes from £50 to £65 on 6 September. We are encouraging
people to submit topic suggestions for the GMOD Meeting and the GMOD
Satellite Meetings.

We are also pleased to announce that Jason Swedlow of the University
of Dundee will be the guest speaker at the GMOD Meeting. Jason will
speak on "The Open Microscopy Environment: Open Informatics for
Biological Imaging," a particularly timely topic as many researchers
move into image intensive areas such as phenotypes and gene
expression, and as high-throughput imaging platforms become available.

There is still space available at all 4 events, and registration for
the GMOD Satellite Meetings, InterMine Workshop and BioMart Workshop
is free.

Scott Cain and Dave Clements

Links:
http://gmod.org/wiki/GMOD_Europe_2010
http://gmod.org/wiki/September_2010_GMOD_Meeting
http://gmod.org/wiki/Satellite_Meetings_-_GMOD_Europe_2010
http://gmod.org/wiki/InterMine_Workshop_-_GMOD_Europe_2010
http://gmod.org/wiki/BioMart_Workshop_-_GMOD_Europe_2010