[Fwd: Re: [Gmod-help] Displaying wiggle tracks]

[Jeff Bowes]

Hi Scott, Dave

About your suggestion to Kevin that we move to GBrowse 2.0.:

1) Is there a best practice for the user it should be installed under, 
do you usually give GBrowse its own user?,  This was not clear in the 
install Wiki.

2)  I'm a little leery about using Beta software in production.  How 
solid is Gbrowse 2.0 ?

3) Who is using it in production now?

4) When is the expected release date for  gbrowse 2.0

5) If we install Gbrowse 2.0 beta what would be the process for 
installing fixes and the updating to the final release version. (Will it 
be pain-free?!)

Currently we run Gbrowse using the Chado adpator.  At the time we did 
this I only new of us and dictybase that were doing this. Like, dicty to 
make this work we had to rewrite a number of queries to speed it up.  
This makes it a pain to keep up with upgrades.  Additionally, the 
methylation data Kevin mentioned would require 46 million feature 
entries- I'm not sure the Chado adaptor can handle this.  So I am 
thinking we should move to having Gbrowse have its own data store and 
batch updates from chado.So my questions are:

1) Do you agree that we should move away from the Chado adaptor

2) What is the fastest back end data store choice  for Gbrowse

3) Is the process for keeping it up to data to just do batch GFF3 
exports from chado and import them into GBrowse?

4) For whatever data store you recommend,  is it possible to make 
incremental updates to it or do updates have to pretty much work as blow 
away and replace it.

5) Any other advice about this?

Thanks very much,

Jeff







  



Kevin Snyder wrote:
>
>
> ------------------------------------------------------------------------
>
> Subject:
> Re: [Gmod-help] Displaying wiggle tracks
> From:
> Scott Cain <scott at scottcain.net>
> Date:
> Thu, 10 Sep 2009 13:02:45 -0400
> To:
> scott at scottcain.net
>
> To:
> scott at scottcain.net
> CC:
> Kevin Snyder <ksnyder at ucalgary.ca>, help at gmod.org
>
>
> Hi Kevin,
>
> Since you're likely doing an upgrade anyway, you might want to look at 
> GBrowse2 (not officially released yet, but available on CPAN), as it 
> will have many performance boosts over what you are currently using.
>
> Scott
>
> On Sep 10, 2009, at 12:31 PM, Scott Cain wrote:
>
>> Hi Kevin,
>>
>> You won't be able to display wiggle plots without a never version of 
>> Bio::Graphics (which is no longer part of BioPerl) and a newer 
>> version of BioPerl (1.6 or better).
>>
>> Scott
>>
>> On Sep 10, 2009, at 12:22 PM, Kevin Snyder wrote:
>>
>>> Hello,
>>>
>>> We are using a rather old version of gbrowse at the moment (1.64) 
>>> along with Perl 5.8.8 and BioPerl 1.5.1.  We have been give a large 
>>> set of data in wiggle BED format.  Will this version properly 
>>> display the  data in wiggle format
>>> or do we need to upgrade?
>>>
>>> Kevin Snyder
>>> Xenbase
>>
>> -----------------------------------------------------------------------
>> 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
>
>
>
>
>

-- 
Jeff Bowes M.Sc.
Technical Director, Xenbase
Department of Biological Sciences
University of Calgary
Calgary, Alberta T2N 1N4
CANADA
Tel: (403) 220-2824 
Fax: (403) 284-4707