[Gmod-ajax] Jbrowse to blast interface

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[Gmod-ajax] Jbrowse to blast interface

thomasg

Dear Chris and other Jbrowse users,

 

On the GMOD ajax list Monica Munoz-Torres posted the following screenshot  of a webservice for blasting features from jbrowse. Is the configuration of these features publicly available somewhere? I’d be really interested. Also, I’m posting this on the GMOD-ajax list again a I think more people would be interested in this feature.

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

+31(317) 702 709

+31(6) 472 421 09


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Re: Jbrowse to blast interface

Monica Munoz-Torres
Hi Thomas, 

Adding a few notes with an update -- I can't remember how long ago since I posted that screenshot. :) 
  • Alexie Papanicolaou wrote this extension; it has been implemented in some of the Apollo instances at the i5k Workspace@NAL. I don't know if this code lives publicly anywhere yet, but I've copied Alexie here -- in addition to ChrisC. --- in case Alexie can communicate directly with you in the mean time.
  • The Worskpace@NAL team has also implemented a DJANGO version of BLAST.  This is a way in (you create a new track with the results of the BLAST query), and it does not round-trip in and out of Apollo/JBrowse. The code lives here https://github.com/hotdogee/django-blast
  • Eric Yao, lead developer of JBrowse, is currently working on a BLAST round-trip feature. It isn't quite finished but progress is far along and I believe he'll be ready to give updates to the community soon. I won't steal anymore of his thunder. :)  
cheers, 
~moni. 


On Sun, May 15, 2016 at 6:31 AM, Thomas van Gurp <[hidden email]> wrote:

Dear Chris and other Jbrowse users,

 

On the GMOD ajax list Monica Munoz-Torres posted the following screenshot  of a webservice for blasting features from jbrowse. Is the configuration of these features publicly available somewhere? I’d be really interested. Also, I’m posting this on the GMOD-ajax list again a I think more people would be interested in this feature.

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

<a href="tel:%2B31%28317%29%20702%20709" value="+31317702709" target="_blank">+31(317) 702 709

+31(6) 472 421 09


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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--
Mentorship Matters!
--
Monica Munoz-Torres, PhD.
Berkeley Bioinformatics Open-source Projects (BBOP)
Environmental Genomics and Systems Biology Division
Lawrence Berkeley National Laboratory

Mailing Address:
Lawrence Berkeley National Laboratory
1 Cyclotron Road Mailstop 977
Berkeley, CA 94720

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bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: Jbrowse to blast interface

Childers, Christopher
In reply to this post by thomasg
Hi Thomas,

Alexie did provide the code for this web service, and I'm happy to share it with you. The only caveat is that we host this tool, but it is not currently supported, either by Alexie (the creator, or us).  For our project we opted to design an updated web framework for BLAST searches.  This works agains the organisms in the i5k Workspace@NAL, and does not currently include call-outs for NCBI or other datasets not hosted with our project.  


You are welcome to check out our code here (it is written in Python under the Django framework):
The original project is still hosted on Han Lin's Github repository:

We've subsequently forked the project, and have been working to add support other services which you can view here:

Please write back if you have any questions.

Respectfully,
Chris

From: Thomas van Gurp <[hidden email]>
Date: Sunday, May 15, 2016 at 9:31 AM
To: Christopher Childers <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Jbrowse to blast interface

Dear Chris and other Jbrowse users,

 

On the GMOD ajax list Monica Munoz-Torres posted the following screenshot  of a webservice for blasting features from jbrowse. Is the configuration of these features publicly available somewhere? I’d be really interested. Also, I’m posting this on the GMOD-ajax list again a I think more people would be interested in this feature.

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

+31(317) 702 709

+31(6) 472 421 09





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.
------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: Jbrowse to blast interface

thomasg

Dear Chris,

 

Thanks for your reply.  I’m not yet decided on the web-interface I’d like to use for blast, at this moment I’m working with sequenceserver. What jbrowse json configuration did you implement to send the feature sequence (fasta) to your blast platform?

 

@jbrowse devs: For linking jbrowse with third party apps it would help to have an overview of the object which can be used for a given feature. http://gmod.org/wiki/JBrowse_Configuration_Guide#Customizing_Right-click_Context_Menus lacks on overview of the available feature object types which can be used for constructing links to third party websites. Right now, most of them use name, start or end. How to get the feature sequence?

I’ve tried:

+feature.get('fasta')

+feature.get('seq')

"url": "function(track,feature) { return 'http://www.example.com?refseq='+track.refSeq.name +'&featurename='+feature.get('start')+'&start='+feature.get('start')+'&end='+feature.get('end'); }"

 

So what options do I have for feature.get and where are they listed?

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

+31(317) 702 709

+31(6) 472 421 09

 

Van: "Childers, Christopher" <[hidden email]>
Datum: maandag 16 mei 2016 14:45
Aan: Thomas van Gurp <[hidden email]>
CC: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Onderwerp: Re: Jbrowse to blast interface

 

Hi Thomas,

 

Alexie did provide the code for this web service, and I'm happy to share it with you. The only caveat is that we host this tool, but it is not currently supported, either by Alexie (the creator, or us).  For our project we opted to design an updated web framework for BLAST searches.  This works agains the organisms in the i5k Workspace@NAL, and does not currently include call-outs for NCBI or other datasets not hosted with our project.  

 

 

You are welcome to check out our code here (it is written in Python under the Django framework):

The original project is still hosted on Han Lin's Github repository:

 

We've subsequently forked the project, and have been working to add support other services which you can view here:

 

Please write back if you have any questions.

 

Respectfully,

Chris

 

From: Thomas van Gurp <[hidden email]>
Date: Sunday, May 15, 2016 at 9:31 AM
To: Christopher Childers <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Jbrowse to blast interface

 

Dear Chris and other Jbrowse users,

 

On the GMOD ajax list Monica Munoz-Torres posted the following screenshot  of a webservice for blasting features from jbrowse. Is the configuration of these features publicly available somewhere? I’d be really interested. Also, I’m posting this on the GMOD-ajax list again a I think more people would be interested in this feature.

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

+31(317) 702 709

+31(6) 472 421 09





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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Re: Jbrowse to blast interface

Eric Yao
Yes indeed, I'm working on a blast integration for JBrowse, utilizing Galaxy tools.  This will introduce JBrowse server component based on Sails.js.

To grab the regseq region, it not entirely straight forward at this time, but you can take a look at /views/track/_featureDetailsMixin.js and FASTA.js.
It's not a synchronous operation.

Eric

On Mon, May 16, 2016 at 7:34 AM, Thomas van Gurp <[hidden email]> wrote:

Dear Chris,

 

Thanks for your reply.  I’m not yet decided on the web-interface I’d like to use for blast, at this moment I’m working with sequenceserver. What jbrowse json configuration did you implement to send the feature sequence (fasta) to your blast platform?

 

@jbrowse devs: For linking jbrowse with third party apps it would help to have an overview of the object which can be used for a given feature. http://gmod.org/wiki/JBrowse_Configuration_Guide#Customizing_Right-click_Context_Menus lacks on overview of the available feature object types which can be used for constructing links to third party websites. Right now, most of them use name, start or end. How to get the feature sequence?

I’ve tried:

+feature.get('fasta')

+feature.get('seq')

"url": "function(track,feature) { return 'http://www.example.com?refseq='+track.refSeq.name +'&featurename='+feature.get('start')+'&start='+feature.get('start')+'&end='+feature.get('end'); }"

 

So what options do I have for feature.get and where are they listed?

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

<a href="tel:%2B31%28317%29%20702%20709" value="+31317702709" target="_blank">+31(317) 702 709

+31(6) 472 421 09

 

Van: "Childers, Christopher" <[hidden email]>
Datum: maandag 16 mei 2016 14:45
Aan: Thomas van Gurp <[hidden email]>
CC: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Onderwerp: Re: Jbrowse to blast interface

 

Hi Thomas,

 

Alexie did provide the code for this web service, and I'm happy to share it with you. The only caveat is that we host this tool, but it is not currently supported, either by Alexie (the creator, or us).  For our project we opted to design an updated web framework for BLAST searches.  This works agains the organisms in the i5k Workspace@NAL, and does not currently include call-outs for NCBI or other datasets not hosted with our project.  

 

 

You are welcome to check out our code here (it is written in Python under the Django framework):

The original project is still hosted on Han Lin's Github repository:

 

We've subsequently forked the project, and have been working to add support other services which you can view here:

 

Please write back if you have any questions.

 

Respectfully,

Chris

 

From: Thomas van Gurp <[hidden email]>
Date: Sunday, May 15, 2016 at 9:31 AM
To: Christopher Childers <[hidden email]>
Cc: "[hidden email]" <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Jbrowse to blast interface

 

Dear Chris and other Jbrowse users,

 

On the GMOD ajax list Monica Munoz-Torres posted the following screenshot  of a webservice for blasting features from jbrowse. Is the configuration of these features publicly available somewhere? I’d be really interested. Also, I’m posting this on the GMOD-ajax list again a I think more people would be interested in this feature.

 

With kind regards,

 

Thomas van Gurp

Owner | Bioinformatician

Deena Bioinformatics

<a href="tel:%2B31%28317%29%20702%20709" value="+31317702709" target="_blank">+31(317) 702 709

+31(6) 472 421 09





This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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