Re: [apollo] Fwd: Webapollo->Chado->JBrowse

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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

Scott Cain
I'm pretty sure there isn't a way currently for JBrowse to talk directly to Chado.  The logical thing to do (and I've thought about doing but haven't even started) is writing a simple REST server that sits on top of Chado to serve up data that JBrowse wants.  Of course, Rob can chime in too.

Scott



On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]> wrote:
Hi Marc,


- Is it good practice to keep multiple WebApollo projects saved to the
same Chado DB? When setting up gmod/chado, it didn't seem like having
multiple DBs was very practical, but I could be wrong.


Chado shouldn't have any issues with hosting multiple organisms.  The WebApollo adapter makes sure to write annotations specific to the organism, so it shouldn't be a problem.  In my opinion one of the benefits of having one instance per organism is that it might make it a bit easier to manage multiple organisms since each data source is specific to that organism.  That being said, that also means you also have more instances to manage, which can get a bit hairy if you have a lot of organisms.
 
- I understand there is a config file that I need to write for JBrowse
to connect to Chado, but the documentation seems a bit sparse.
Specifically, is there a way to specify a species/organism_id from which
track data should be loaded (since the feature table holds data from
multiple species)?


Rob would be the best person to answer the question of Chado track loading in JBrowse.  For WebApollo, we have a system to read data directly of Chado, but it's still in alpha state and not quite ready for public use.

Cheers,
Ed



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

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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

Jamie Estill
A REST service for Chado would be awesome. Could that get started as a Google Summer of Code project this summer?

-- Jamie


On Thu, Feb 13, 2014 at 1:50 PM, Scott Cain <[hidden email]> wrote:
I'm pretty sure there isn't a way currently for JBrowse to talk directly to Chado.  The logical thing to do (and I've thought about doing but haven't even started) is writing a simple REST server that sits on top of Chado to serve up data that JBrowse wants.  Of course, Rob can chime in too.

Scott



On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]> wrote:
Hi Marc,


- Is it good practice to keep multiple WebApollo projects saved to the
same Chado DB? When setting up gmod/chado, it didn't seem like having
multiple DBs was very practical, but I could be wrong.


Chado shouldn't have any issues with hosting multiple organisms.  The WebApollo adapter makes sure to write annotations specific to the organism, so it shouldn't be a problem.  In my opinion one of the benefits of having one instance per organism is that it might make it a bit easier to manage multiple organisms since each data source is specific to that organism.  That being said, that also means you also have more instances to manage, which can get a bit hairy if you have a lot of organisms.
 
- I understand there is a config file that I need to write for JBrowse
to connect to Chado, but the documentation seems a bit sparse.
Specifically, is there a way to specify a species/organism_id from which
track data should be loaded (since the feature table holds data from
multiple species)?


Rob would be the best person to answer the question of Chado track loading in JBrowse.  For WebApollo, we have a system to read data directly of Chado, but it's still in alpha state and not quite ready for public use.

Cheers,
Ed



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
-- Jamie

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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

Eric Rasche
In reply to this post by Scott Cain

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Hash: SHA1

For us, chado doesn't have any issue with multiple organism. We have
>300 bacteriophage genomes in some, though it's not accessed by
WebApollo (yet).

We'd love to see a chado REST API which could hook up to chado and
handle display of multiple organisms in a single database. (Bonus points
if it could safely be wrapped in HTTP Auth as some of our databases are
user-specific)

Marc, if you already have one instance and are wanting to create more
chado databases, you might be interested in precompiled schemas which
you can just load into new Postgres databases. See:
http://gmod.org/wiki/Precompiled_Chado_Databases
They come precompiled with all five ontologies available in a default
chado installation. Just load into a new postgres database and you're
ready to go. (Disclaimer, I'm the one producing them weekly, and my org.
is the one hosting them)


Eric

On 02/13/2014 12:50 PM, Scott Cain wrote:

> I'm pretty sure there isn't a way currently for JBrowse to talk directly to
> Chado.  The logical thing to do (and I've thought about doing but haven't
> even started) is writing a simple REST server that sits on top of Chado to
> serve up data that JBrowse wants.  Of course, Rob can chime in too.
>
> Scott
>
>
>
> On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]> wrote:
>
>> Hi Marc,
>>
>>
>>> - Is it good practice to keep multiple WebApollo projects saved to the
>>> same Chado DB? When setting up gmod/chado, it didn't seem like having
>>> multiple DBs was very practical, but I could be wrong.
>>>
>>>
>> Chado shouldn't have any issues with hosting multiple organisms.  The
>> WebApollo adapter makes sure to write annotations specific to the
organism,
>> so it shouldn't be a problem.  In my opinion one of the benefits of
having

>> one instance per organism is that it might make it a bit easier to manage
>> multiple organisms since each data source is specific to that organism.
>>  That being said, that also means you also have more instances to manage,
>> which can get a bit hairy if you have a lot of organisms.
>>
>>
>>> - I understand there is a config file that I need to write for JBrowse
>>> to connect to Chado, but the documentation seems a bit sparse.
>>> Specifically, is there a way to specify a species/organism_id from which
>>> track data should be loaded (since the feature table holds data from
>>> multiple species)?
>>>
>>>
>> Rob would be the best person to answer the question of Chado track
loading
>> in JBrowse.  For WebApollo, we have a system to read data directly of
>> Chado, but it's still in alpha state and not quite ready for public use.
>>
>> Cheers,
>> Ed
>>
>
>
>


- --
Eric Rasche Programmer II Center for Phage Technology Texas A&M
University College Station, TX 77843 404-692-2048 [hidden email]
[hidden email]
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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

Robert Buels-2
In reply to this post by Scott Cain
Yes, that is exactly the logical thing to do.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/13/2014 01:50 PM, Scott Cain wrote:

> I'm pretty sure there isn't a way currently for JBrowse to talk directly
> to Chado.  The logical thing to do (and I've thought about doing but
> haven't even started) is writing a simple REST server that sits on top
> of Chado to serve up data that JBrowse wants.  Of course, Rob can chime
> in too.
>
> Scott
>
>
>
> On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Marc,
>
>
>         - Is it good practice to keep multiple WebApollo projects saved
>         to the
>         same Chado DB? When setting up gmod/chado, it didn't seem like
>         having
>         multiple DBs was very practical, but I could be wrong.
>
>
>     Chado shouldn't have any issues with hosting multiple organisms.
>       The WebApollo adapter makes sure to write annotations specific to
>     the organism, so it shouldn't be a problem.  In my opinion one of
>     the benefits of having one instance per organism is that it might
>     make it a bit easier to manage multiple organisms since each data
>     source is specific to that organism.  That being said, that also
>     means you also have more instances to manage, which can get a bit
>     hairy if you have a lot of organisms.
>
>         - I understand there is a config file that I need to write for
>         JBrowse
>         to connect to Chado, but the documentation seems a bit sparse.
>         Specifically, is there a way to specify a species/organism_id
>         from which
>         track data should be loaded (since the feature table holds data from
>         multiple species)?
>
>
>     Rob would be the best person to answer the question of Chado track
>     loading in JBrowse.  For WebApollo, we have a system to read data
>     directly of Chado, but it's still in alpha state and not quite ready
>     for public use.
>
>     Cheers,
>     Ed
>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research

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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

girlwithglasses
In reply to this post by Jamie Estill
If someone is willing to act as a mentor and can write up a little description of this proposal, please do!


Feel free to email me the details if you'd prefer me to post it.

We're putting in our GSoC application late today... :)



On Thu, Feb 13, 2014 at 11:12 AM, Jamie Estill <[hidden email]> wrote:
A REST service for Chado would be awesome. Could that get started as a Google Summer of Code project this summer?

-- Jamie


On Thu, Feb 13, 2014 at 1:50 PM, Scott Cain <[hidden email]> wrote:
I'm pretty sure there isn't a way currently for JBrowse to talk directly to Chado.  The logical thing to do (and I've thought about doing but haven't even started) is writing a simple REST server that sits on top of Chado to serve up data that JBrowse wants.  Of course, Rob can chime in too.

Scott



On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]> wrote:
Hi Marc,


- Is it good practice to keep multiple WebApollo projects saved to the
same Chado DB? When setting up gmod/chado, it didn't seem like having
multiple DBs was very practical, but I could be wrong.


Chado shouldn't have any issues with hosting multiple organisms.  The WebApollo adapter makes sure to write annotations specific to the organism, so it shouldn't be a problem.  In my opinion one of the benefits of having one instance per organism is that it might make it a bit easier to manage multiple organisms since each data source is specific to that organism.  That being said, that also means you also have more instances to manage, which can get a bit hairy if you have a lot of organisms.
 
- I understand there is a config file that I need to write for JBrowse
to connect to Chado, but the documentation seems a bit sparse.
Specifically, is there a way to specify a species/organism_id from which
track data should be loaded (since the feature table holds data from
multiple species)?


Rob would be the best person to answer the question of Chado track loading in JBrowse.  For WebApollo, we have a system to read data directly of Chado, but it's still in alpha state and not quite ready for public use.

Cheers,
Ed



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
-- Jamie

---------------------------------------------------------------------------------
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http://jestill.myweb.uga.edu
---------------------------------------------------------------------------------

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GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject


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Re: [apollo] Fwd: Webapollo->Chado->JBrowse

Jillian Rowe
I'm not familiar with Chado, but I already have a REST service for the BioPerl BioDb written up. It should be similar, yes?

On 02/14/2014 01:02 AM, Amelia Ireland wrote:
If someone is willing to act as a mentor and can write up a little description of this proposal, please do!


Feel free to email me the details if you'd prefer me to post it.

We're putting in our GSoC application late today... :)



On Thu, Feb 13, 2014 at 11:12 AM, Jamie Estill <[hidden email]> wrote:
A REST service for Chado would be awesome. Could that get started as a Google Summer of Code project this summer?

-- Jamie


On Thu, Feb 13, 2014 at 1:50 PM, Scott Cain <[hidden email]> wrote:
I'm pretty sure there isn't a way currently for JBrowse to talk directly to Chado.  The logical thing to do (and I've thought about doing but haven't even started) is writing a simple REST server that sits on top of Chado to serve up data that JBrowse wants.  Of course, Rob can chime in too.

Scott



On Thu, Feb 13, 2014 at 10:05 AM, Ed Lee <[hidden email]> wrote:
Hi Marc,


- Is it good practice to keep multiple WebApollo projects saved to the
same Chado DB? When setting up gmod/chado, it didn't seem like having
multiple DBs was very practical, but I could be wrong.


Chado shouldn't have any issues with hosting multiple organisms.  The WebApollo adapter makes sure to write annotations specific to the organism, so it shouldn't be a problem.  In my opinion one of the benefits of having one instance per organism is that it might make it a bit easier to manage multiple organisms since each data source is specific to that organism.  That being said, that also means you also have more instances to manage, which can get a bit hairy if you have a lot of organisms.
 
- I understand there is a config file that I need to write for JBrowse
to connect to Chado, but the documentation seems a bit sparse.
Specifically, is there a way to specify a species/organism_id from which
track data should be loaded (since the feature table holds data from
multiple species)?


Rob would be the best person to answer the question of Chado track loading in JBrowse.  For WebApollo, we have a system to read data directly of Chado, but it's still in alpha state and not quite ready for public use.

Cheers,
Ed



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a moz-do-not-send="true" href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
-- Jamie

---------------------------------------------------------------------------------
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http://jestill.myweb.uga.edu
---------------------------------------------------------------------------------

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--
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GMOD Community Support
Generic Model Organism Database project
http://gmod.org || @gmodproject



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