pre-loading existing gene models

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pre-loading existing gene models

Hoover, Jeffrey

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute

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Re: pre-loading existing gene models

Ed Lee
Hi Jeff,

You can't do any kind of bulk loading of models in the current release of WebApollo.  This feature will be added in the next release.

Cheers,
Ed


On Wed, Apr 3, 2013 at 8:00 AM, Hoover, Jeffrey <[hidden email]> wrote:

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute


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RE: pre-loading existing gene models

Hoover, Jeffrey

Ed,

 

Would it be feasible to write a standalone java program that initiates an Annotation Editor and then model by model builds and adds the gene features (and their sub-features)?

 

I see java classes for creating a session, creating an editor, and building and adding the gene (etc.) objects in the various GMOD source code downloads.

 

Jeff

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Ed Lee
Sent: Wednesday, April 03, 2013 3:53 PM
To: [hidden email]
Subject: Re: [apollo] pre-loading existing gene models

 

Hi Jeff,

 

You can't do any kind of bulk loading of models in the current release of WebApollo.  This feature will be added in the next release.

 

Cheers,

Ed

 

On Wed, Apr 3, 2013 at 8:00 AM, Hoover, Jeffrey <[hidden email]> wrote:

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute

 


No virus found in this message.
Checked by AVG - www.avg.com
Version: 2013.0.3267 / Virus Database: 3162/6222 - Release Date: 04/03/13

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Re: pre-loading existing gene models

Ed Lee
Hi Jeff,

You wouldn't want to access AnnotationEditor directly, but rather AnnotationEditorService, as the web service is what uses the BerkeleyDB backend.  Plus the service does a lot of extra stuff, such as history management.  The next release will come bundled with a script that will take a GFF3 file and bulk load the annotations in the appropriate manner.

Cheers,
Ed


On Wed, Apr 3, 2013 at 1:13 PM, Hoover, Jeffrey <[hidden email]> wrote:

Ed,

 

Would it be feasible to write a standalone java program that initiates an Annotation Editor and then model by model builds and adds the gene features (and their sub-features)?

 

I see java classes for creating a session, creating an editor, and building and adding the gene (etc.) objects in the various GMOD source code downloads.

 

Jeff

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Ed Lee
Sent: Wednesday, April 03, 2013 3:53 PM
To: [hidden email]
Subject: Re: [apollo] pre-loading existing gene models

 

Hi Jeff,

 

You can't do any kind of bulk loading of models in the current release of WebApollo.  This feature will be added in the next release.

 

Cheers,

Ed

 

On Wed, Apr 3, 2013 at 8:00 AM, Hoover, Jeffrey <[hidden email]> wrote:

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute

 


No virus found in this message.
Checked by AVG - www.avg.com
Version: 2013.0.3267 / Virus Database: 3162/6222 - Release Date: 04/03/13


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Re: pre-loading existing gene models

Sheldon McKay
Hi Ed,

What is your target date for the next release?

Sheldon

Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
(516) 367-5185
www.dnalc.org


On Wed, Apr 3, 2013 at 6:36 PM, Ed Lee <[hidden email]> wrote:
Hi Jeff,

You wouldn't want to access AnnotationEditor directly, but rather AnnotationEditorService, as the web service is what uses the BerkeleyDB backend.  Plus the service does a lot of extra stuff, such as history management.  The next release will come bundled with a script that will take a GFF3 file and bulk load the annotations in the appropriate manner.

Cheers,
Ed


On Wed, Apr 3, 2013 at 1:13 PM, Hoover, Jeffrey <[hidden email]> wrote:

Ed,

 

Would it be feasible to write a standalone java program that initiates an Annotation Editor and then model by model builds and adds the gene features (and their sub-features)?

 

I see java classes for creating a session, creating an editor, and building and adding the gene (etc.) objects in the various GMOD source code downloads.

 

Jeff

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Ed Lee
Sent: Wednesday, April 03, 2013 3:53 PM
To: [hidden email]
Subject: Re: [apollo] pre-loading existing gene models

 

Hi Jeff,

 

You can't do any kind of bulk loading of models in the current release of WebApollo.  This feature will be added in the next release.

 

Cheers,

Ed

 

On Wed, Apr 3, 2013 at 8:00 AM, Hoover, Jeffrey <[hidden email]> wrote:

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute

 


No virus found in this message.
Checked by AVG - www.avg.com
Version: 2013.0.3267 / Virus Database: 3162/6222 - Release Date: 04/03/13



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Re: pre-loading existing gene models

Ed Lee
Hi Sheldon,

We're hoping for a new release soon, probably within the month.

Cheers,
Ed


On Wed, Apr 3, 2013 at 4:17 PM, Sheldon McKay <[hidden email]> wrote:
Hi Ed,

What is your target date for the next release?

Sheldon

Sheldon McKay, PhD
Computational Biologist
DNA Learning Center
Cold Spring Harbor Laboratory
1 Bungtown Rd
Cold Spring Harbor, NY 11724
<a href="tel:%28516%29%20367-5185" value="+15163675185" target="_blank">(516) 367-5185
www.dnalc.org


On Wed, Apr 3, 2013 at 6:36 PM, Ed Lee <[hidden email]> wrote:
Hi Jeff,

You wouldn't want to access AnnotationEditor directly, but rather AnnotationEditorService, as the web service is what uses the BerkeleyDB backend.  Plus the service does a lot of extra stuff, such as history management.  The next release will come bundled with a script that will take a GFF3 file and bulk load the annotations in the appropriate manner.

Cheers,
Ed


On Wed, Apr 3, 2013 at 1:13 PM, Hoover, Jeffrey <[hidden email]> wrote:

Ed,

 

Would it be feasible to write a standalone java program that initiates an Annotation Editor and then model by model builds and adds the gene features (and their sub-features)?

 

I see java classes for creating a session, creating an editor, and building and adding the gene (etc.) objects in the various GMOD source code downloads.

 

Jeff

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Ed Lee
Sent: Wednesday, April 03, 2013 3:53 PM
To: [hidden email]
Subject: Re: [apollo] pre-loading existing gene models

 

Hi Jeff,

 

You can't do any kind of bulk loading of models in the current release of WebApollo.  This feature will be added in the next release.

 

Cheers,

Ed

 

On Wed, Apr 3, 2013 at 8:00 AM, Hoover, Jeffrey <[hidden email]> wrote:

How do I pre-load my existing gene-models into the Berkeley DB so they will show up in the editing track?

 

Jeff Hoover

J. Craig Venter Institute

 


No virus found in this message.
Checked by AVG - www.avg.com
Version: 2013.0.3267 / Virus Database: 3162/6222 - Release Date: 04/03/13