[Gmod-help] Sequence browser and version clarification

[Scott Cain]

Hi Olen,

I'll answer in line below so that I hopefully won't miss anything.

Scott


On Tue, Feb 15, 2011 at 8:05 AM, Olen Vance Sluder Jr <olen at acm.org> wrote:
> I am an IT consultant working with the Texas Biomedical Research
> Institute <http://txbiomed.org/> (formerly, the Southwest Foundation
> for Biomedical Research) in San Antonio, Texas. I will be installing a
> number of tools for them from the GMOD suite. I come from a primarily
> enterprise IT background, so bioinformatics is a new problem domain
> for me.
>
> I have been working through the wealth of information on the GMOD
> wiki, but seek some clarification concerning the various sequence
> browsers. I see that there are two branches to GBrowse, 1.x and 2.x,
> and JBrowser is listed as a "successor" to GBrowse. Also, the
> researchers I am working with require use of annotation and
> comparative tools, so Apollo, GBrowse_syn, etc. are needed.
>
> At present, I am leaning towards the following toolset based on the
> case studies given in the overview on the wiki:
>
> OS: CentOS
> Web server: Apache
> Database: PostgreSQL
> Database schema: Chado
> Sequence annotator: Apollo
> Sequence browser: GBrowser
> Synteny browser: GBrowse_syn

Since you're in IT already, I won't give you a warning about CentOS,
but I will at least mention that SELinux sometimes gives people a hard
time.  People frequently find it easier to work with other distros
like Debian or Ubuntu.

>
> My questions:
>
> 1) What is the status of GBrowse_syn support with GBrowse 2.x?

GBrowse_syn does work with GBrowse2, though with "legacy" libraries
that are brought over from GBrowse 1.x.  There is work on going to
make GBrowse_syn work natively with GBrowse2, but I don't know when
that work will be ready for release.

> 2) Is there a roadmap for a transition from GBrowse to JBrowse?

No.  We see JBrowse as the future for genome browsing, but it is
currently not nearly as feature complete as GBrowse2.  They can work
from the same data sources (that is, there are JBrowse loading scripts
that will talk to any database that GBrowse talks to), so the
transition would be relatively painless.  There are some sites that
run both.
>
> Any guidance would be greatly appreciated.
>
> I am making arrangements to attend the March meeting in North Carolina
> and I have applied for a slot in the subsequent "spring training"
> session. I look forward to meeting other members of the GMOD
> community.

I look forward to seeing you there.

Scott

>
> Regards,
> Olen
>



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