[Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

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[Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

Kucheran, Lacey Sanderson
Hi Everyone!

I'm happy to introduce two new Tripal Extension modules that have just been released:

Tripal Daemon
The Tripal Daemon module provides a demonized Tripal job management system. It is controlled through simple drush commands (drush trpjob-daemon start/status/show-log/stop) and once running will periodically check for waiting Tripal jobs and run them when they are found. It's built on PHP-Daemon to ensure a robust deamon with lock files, built-in signal handling and logging.

Tripal BLAST UI
The Tripal BLAST UI module provides an interface allowing users of your website to execute their BLASTs using NCBI BLAST+ on your server. It supports blastn, blastx, blastp and tblastx with each program having it's own user-friendly form. BLASTs are submitted as Tripal jobs and results have their own bookmark-able page. Results can be downloaded in HTML, TSV and XML and are presented to the user in an expandable table that summarizes the results while making alignment and detailed information easily available. This module even has some advanced features including configurable example sequences, optional database upload for your users and per BLAST database external references to provide link-outs from BLAST results. This module is already live on KnowPulse and PeanutBase if you want to take it for a test-drive :)

Developers
Tripal Daemon: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan). 
Tripal BLAST: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan), Amir Zadeh (University of Saskatchewan) and Deepak Venkata (PeanutBase) with valuable input from Ethy & Steven Cannon, as well as, the rest of the crew behind PeanutBase.

I hope these modules will be useful to the community and, as always, Feedback is Welcome :)

Have a Good Weekend!
~Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan


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Re: [Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

Mara Kim
Hi Lacey,

Does the BLAST UI store the results in the database?  If not, is there a way to integrate this module to store results into the database?

On Fri, Sep 12, 2014 at 1:03 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Everyone!

I'm happy to introduce two new Tripal Extension modules that have just been released:

Tripal Daemon
The Tripal Daemon module provides a demonized Tripal job management system. It is controlled through simple drush commands (drush trpjob-daemon start/status/show-log/stop) and once running will periodically check for waiting Tripal jobs and run them when they are found. It's built on PHP-Daemon to ensure a robust deamon with lock files, built-in signal handling and logging.

Tripal BLAST UI
The Tripal BLAST UI module provides an interface allowing users of your website to execute their BLASTs using NCBI BLAST+ on your server. It supports blastn, blastx, blastp and tblastx with each program having it's own user-friendly form. BLASTs are submitted as Tripal jobs and results have their own bookmark-able page. Results can be downloaded in HTML, TSV and XML and are presented to the user in an expandable table that summarizes the results while making alignment and detailed information easily available. This module even has some advanced features including configurable example sequences, optional database upload for your users and per BLAST database external references to provide link-outs from BLAST results. This module is already live on KnowPulse and PeanutBase if you want to take it for a test-drive :)

Developers
Tripal Daemon: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan). 
Tripal BLAST: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan), Amir Zadeh (University of Saskatchewan) and Deepak Venkata (PeanutBase) with valuable input from Ethy & Steven Cannon, as well as, the rest of the crew behind PeanutBase.

I hope these modules will be useful to the community and, as always, Feedback is Welcome :)

Have a Good Weekend!
~Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-4975" value="+13069664975" target="_blank">(306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




--
M

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Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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Re: [Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

Mara Kim-2
In reply to this post by Kucheran, Lacey Sanderson
Hi Lacey,

Does the BLAST UI store the results in the database?  If not, is there a way to integrate this module to store results into the database?

On Fri, Sep 12, 2014 at 1:03 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Everyone!

I'm happy to introduce two new Tripal Extension modules that have just been released:

Tripal Daemon
The Tripal Daemon module provides a demonized Tripal job management system. It is controlled through simple drush commands (drush trpjob-daemon start/status/show-log/stop) and once running will periodically check for waiting Tripal jobs and run them when they are found. It's built on PHP-Daemon to ensure a robust deamon with lock files, built-in signal handling and logging.

Tripal BLAST UI
The Tripal BLAST UI module provides an interface allowing users of your website to execute their BLASTs using NCBI BLAST+ on your server. It supports blastn, blastx, blastp and tblastx with each program having it's own user-friendly form. BLASTs are submitted as Tripal jobs and results have their own bookmark-able page. Results can be downloaded in HTML, TSV and XML and are presented to the user in an expandable table that summarizes the results while making alignment and detailed information easily available. This module even has some advanced features including configurable example sequences, optional database upload for your users and per BLAST database external references to provide link-outs from BLAST results. This module is already live on KnowPulse and PeanutBase if you want to take it for a test-drive :)

Developers
Tripal Daemon: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan). 
Tripal BLAST: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan), Amir Zadeh (University of Saskatchewan) and Deepak Venkata (PeanutBase) with valuable input from Ethy & Steven Cannon, as well as, the rest of the crew behind PeanutBase.

I hope these modules will be useful to the community and, as always, Feedback is Welcome :)

Have a Good Weekend!
~Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-4975" value="+13069664975" target="_blank">(306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
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Re: [Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

Kucheran, Lacey Sanderson
Hi Mara,

It does not yet store the results in chado. However, the Tripal BLAST Analysis module which already exists will load an XML file into chado and associate each result with the corresponding feature including showing information on the feature page. For example, go to http://www.citrusgenomedb.org/node/461311 and clock on "TAIR10 Homologs". Since the BLAST UI will produce XML for download, you should be able to take results from BLAST UI and load them into chado/Tripal pretty seamlessly using Tripal BLAST Analysis.

Would this be enough for your purposes or do you want it to load the results into the database upon completion? This would be slightly more manual as you would have to setup a Tripal BLAST Analysis loading job manually for each set of BLAST UI results you want loaded… Though it wouldn't be that difficult to plug into the functionality to create the job automatically (I don't think, anyway).

There are plan in to better integrate these two modules and distribute them together in the future to make this connection more seamless but we don't have an ETA on that.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) 966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On Sep 17, 2014, at 1:54 PM, Mara Kim <[hidden email]> wrote:

Hi Lacey,

Does the BLAST UI store the results in the database?  If not, is there a way to integrate this module to store results into the database?

On Fri, Sep 12, 2014 at 1:03 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Everyone!

I'm happy to introduce two new Tripal Extension modules that have just been released:

Tripal Daemon
The Tripal Daemon module provides a demonized Tripal job management system. It is controlled through simple drush commands (drush trpjob-daemon start/status/show-log/stop) and once running will periodically check for waiting Tripal jobs and run them when they are found. It's built on PHP-Daemon to ensure a robust deamon with lock files, built-in signal handling and logging.

Tripal BLAST UI
The Tripal BLAST UI module provides an interface allowing users of your website to execute their BLASTs using NCBI BLAST+ on your server. It supports blastn, blastx, blastp and tblastx with each program having it's own user-friendly form. BLASTs are submitted as Tripal jobs and results have their own bookmark-able page. Results can be downloaded in HTML, TSV and XML and are presented to the user in an expandable table that summarizes the results while making alignment and detailed information easily available. This module even has some advanced features including configurable example sequences, optional database upload for your users and per BLAST database external references to provide link-outs from BLAST results. This module is already live on KnowPulse and PeanutBase if you want to take it for a test-drive :)

Developers
Tripal Daemon: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan). 
Tripal BLAST: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan), Amir Zadeh (University of Saskatchewan) and Deepak Venkata (PeanutBase) with valuable input from Ethy & Steven Cannon, as well as, the rest of the crew behind PeanutBase.

I hope these modules will be useful to the community and, as always, Feedback is Welcome :)

Have a Good Weekend!
~Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-4975" value="+13069664975" target="_blank">(306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
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Re: [Gmod-tripal-devel] Module Releases: Tripal Daemon & Tripal BLAST

Mara Kim-2
Hi Lacey,

Turns out that I don't really need the modules to be integrated.  Is there a way to programmatically add BLAST results using the Blast analysis module?  I have a system that performs the BLAST, and I would like to store the results in the database automatically.


On Wed, Sep 17, 2014 at 4:07 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Mara,

It does not yet store the results in chado. However, the Tripal BLAST Analysis module which already exists will load an XML file into chado and associate each result with the corresponding feature including showing information on the feature page. For example, go to http://www.citrusgenomedb.org/node/461311 and clock on "TAIR10 Homologs". Since the BLAST UI will produce XML for download, you should be able to take results from BLAST UI and load them into chado/Tripal pretty seamlessly using Tripal BLAST Analysis.

Would this be enough for your purposes or do you want it to load the results into the database upon completion? This would be slightly more manual as you would have to setup a Tripal BLAST Analysis loading job manually for each set of BLAST UI results you want loaded… Though it wouldn't be that difficult to plug into the functionality to create the job automatically (I don't think, anyway).

There are plan in to better integrate these two modules and distribute them together in the future to make this connection more seamless but we don't have an ETA on that.

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-3208" value="+13069663208" target="_blank">(306) 966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On Sep 17, 2014, at 1:54 PM, Mara Kim <[hidden email]> wrote:

Hi Lacey,

Does the BLAST UI store the results in the database?  If not, is there a way to integrate this module to store results into the database?

On Fri, Sep 12, 2014 at 1:03 PM, Lacey-Anne Sanderson <[hidden email]> wrote:
Hi Everyone!

I'm happy to introduce two new Tripal Extension modules that have just been released:

Tripal Daemon
The Tripal Daemon module provides a demonized Tripal job management system. It is controlled through simple drush commands (drush trpjob-daemon start/status/show-log/stop) and once running will periodically check for waiting Tripal jobs and run them when they are found. It's built on PHP-Daemon to ensure a robust deamon with lock files, built-in signal handling and logging.

Tripal BLAST UI
The Tripal BLAST UI module provides an interface allowing users of your website to execute their BLASTs using NCBI BLAST+ on your server. It supports blastn, blastx, blastp and tblastx with each program having it's own user-friendly form. BLASTs are submitted as Tripal jobs and results have their own bookmark-able page. Results can be downloaded in HTML, TSV and XML and are presented to the user in an expandable table that summarizes the results while making alignment and detailed information easily available. This module even has some advanced features including configurable example sequences, optional database upload for your users and per BLAST database external references to provide link-outs from BLAST results. This module is already live on KnowPulse and PeanutBase if you want to take it for a test-drive :)

Developers
Tripal Daemon: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan). 
Tripal BLAST: Lacey Sanderson (myself :), KnowPulse/University of Saskatchewan), Amir Zadeh (University of Saskatchewan) and Deepak Venkata (PeanutBase) with valuable input from Ethy & Steven Cannon, as well as, the rest of the crew behind PeanutBase.

I hope these modules will be useful to the community and, as always, Feedback is Welcome :)

Have a Good Weekend!
~Lacey


------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: <a href="tel:%28306%29%20966-4975" value="+13069664975" target="_blank">(306) 966-4975
Room 3C06 Agriculture
Department of Plant Sciences
University of Saskatchewan


------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-tripal-devel mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal-devel




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN




--
Mara Kim

Ph.D. Candidate
Computational Biology
Vanderbilt University
Nashville, TN

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