Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Scott Cain
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Scott Cain
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
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Ontario Institute for Cancer Research

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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Asma Riyaz
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Scott Cain
Hi Asma,

That's what happens: when you run make clean, you delete all of the install related files other than what's in the tmp directory--that's why I said after you run make clean, you have to start over from perl Makefile.PL.

I'm concerned about the broken pipe though--what makes you think that it won't happen again?  Did it happen because the machine ran out of memory?

Finally, what software do you plan on using with Chado to implement your example of tagging a picture with a gene name?  There isn't anything native in the Chado distribution to do that.  Are you going to write your own code or use something like Tripal?  If you plan on using Tripal, I'd suggest that you use Tripal to install and populate Chado with data.

Scott


On Mon, Nov 24, 2014 at 3:37 PM, Asma Riyaz <[hidden email]> wrote:
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
------------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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: [Gmod-gbrowse] Re-load gene ontologies into Chado

Asma Riyaz
I am sshing into another server to do so, and I am thinking broken pipe error was generated when the ssh was terminated due to the long time it took. 
(Although it's pure guesswork). 




On Mon, Nov 24, 2014 at 3:43 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

That's what happens: when you run make clean, you delete all of the install related files other than what's in the tmp directory--that's why I said after you run make clean, you have to start over from perl Makefile.PL.

I'm concerned about the broken pipe though--what makes you think that it won't happen again?  Did it happen because the machine ran out of memory?

Finally, what software do you plan on using with Chado to implement your example of tagging a picture with a gene name?  There isn't anything native in the Chado distribution to do that.  Are you going to write your own code or use something like Tripal?  If you plan on using Tripal, I'd suggest that you use Tripal to install and populate Chado with data.

Scott


On Mon, Nov 24, 2014 at 3:37 PM, Asma Riyaz <[hidden email]> wrote:
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
------------------------------------------------------------------------------
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------------------------------------------------------------------------
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GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
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


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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Scott Cain
Oh, in that case, the unix command 'screen' is your friend; it will keep things running and look at the output even if your connection drops.  Take a look at:


for a quick tutorial on how to use it.

Scott


On Mon, Nov 24, 2014 at 3:51 PM, Asma Riyaz <[hidden email]> wrote:
I am sshing into another server to do so, and I am thinking broken pipe error was generated when the ssh was terminated due to the long time it took. 
(Although it's pure guesswork). 




On Mon, Nov 24, 2014 at 3:43 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

That's what happens: when you run make clean, you delete all of the install related files other than what's in the tmp directory--that's why I said after you run make clean, you have to start over from perl Makefile.PL.

I'm concerned about the broken pipe though--what makes you think that it won't happen again?  Did it happen because the machine ran out of memory?

Finally, what software do you plan on using with Chado to implement your example of tagging a picture with a gene name?  There isn't anything native in the Chado distribution to do that.  Are you going to write your own code or use something like Tripal?  If you plan on using Tripal, I'd suggest that you use Tripal to install and populate Chado with data.

Scott


On Mon, Nov 24, 2014 at 3:37 PM, Asma Riyaz <[hidden email]> wrote:
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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: [Gmod-gbrowse] Re-load gene ontologies into Chado

Mara Kim-3
Warning, bit of a shameless plug here.  If you want a nice way to ensure all your SSH sessions are managed by screen, check out my project, autoscreen (https://github.com/autochthe/autoscreen), which automatically encapsulates all of your SSH login sessions in a GNU screen session.

On Mon, Nov 24, 2014 at 3:02 PM, Scott Cain <[hidden email]> wrote:
Oh, in that case, the unix command 'screen' is your friend; it will keep things running and look at the output even if your connection drops.  Take a look at:


for a quick tutorial on how to use it.

Scott


On Mon, Nov 24, 2014 at 3:51 PM, Asma Riyaz <[hidden email]> wrote:
I am sshing into another server to do so, and I am thinking broken pipe error was generated when the ssh was terminated due to the long time it took. 
(Although it's pure guesswork). 




On Mon, Nov 24, 2014 at 3:43 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

That's what happens: when you run make clean, you delete all of the install related files other than what's in the tmp directory--that's why I said after you run make clean, you have to start over from perl Makefile.PL.

I'm concerned about the broken pipe though--what makes you think that it won't happen again?  Did it happen because the machine ran out of memory?

Finally, what software do you plan on using with Chado to implement your example of tagging a picture with a gene name?  There isn't anything native in the Chado distribution to do that.  Are you going to write your own code or use something like Tripal?  If you plan on using Tripal, I'd suggest that you use Tripal to install and populate Chado with data.

Scott


On Mon, Nov 24, 2014 at 3:37 PM, Asma Riyaz <[hidden email]> wrote:
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
------------------------------------------------------------------------------
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Get technology previously reserved for billion-dollar corporations, FREE
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_______________________________________________
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--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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

------------------------------------------------------------------------------
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with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Mara Kim

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

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Re: [Gmod-gbrowse] Re-load gene ontologies into Chado

Scott Cain
Nice!  I forgot about that; thanks for the reminder.


On Mon, Nov 24, 2014 at 4:06 PM, Mara Kim <[hidden email]> wrote:
Warning, bit of a shameless plug here.  If you want a nice way to ensure all your SSH sessions are managed by screen, check out my project, autoscreen (https://github.com/autochthe/autoscreen), which automatically encapsulates all of your SSH login sessions in a GNU screen session.

On Mon, Nov 24, 2014 at 3:02 PM, Scott Cain <[hidden email]> wrote:
Oh, in that case, the unix command 'screen' is your friend; it will keep things running and look at the output even if your connection drops.  Take a look at:


for a quick tutorial on how to use it.

Scott


On Mon, Nov 24, 2014 at 3:51 PM, Asma Riyaz <[hidden email]> wrote:
I am sshing into another server to do so, and I am thinking broken pipe error was generated when the ssh was terminated due to the long time it took. 
(Although it's pure guesswork). 




On Mon, Nov 24, 2014 at 3:43 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

That's what happens: when you run make clean, you delete all of the install related files other than what's in the tmp directory--that's why I said after you run make clean, you have to start over from perl Makefile.PL.

I'm concerned about the broken pipe though--what makes you think that it won't happen again?  Did it happen because the machine ran out of memory?

Finally, what software do you plan on using with Chado to implement your example of tagging a picture with a gene name?  There isn't anything native in the Chado distribution to do that.  Are you going to write your own code or use something like Tripal?  If you plan on using Tripal, I'd suggest that you use Tripal to install and populate Chado with data.

Scott


On Mon, Nov 24, 2014 at 3:37 PM, Asma Riyaz <[hidden email]> wrote:
No, I am running GBrowse out of MySQL and not Chado. I wasn't aware of different mailing lists at the time of posting. 

Having said that I am trying to access certain features of Beetles from Chado, to tag a picture with say a gene name. While installing Chado, make ontologies-> gene ontology took a long time and resulted in a Broken pipe error. I am trying to use the make clean command you stated but resulted in a :

make: *** No rule to make target `clean'.  Stop.



On Mon, Nov 24, 2014 at 3:22 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Do you mind if we back up a little bit?  Since you started out posting on the GBrowse mailing list, I'm guessing that you primarily want a genome browser.  Are you sure you need Chado?  It is quite heavy weight just for a genome browser and is probably the slowest option for powering GBrowse.  

As to your question, assuming you installed Chado with the Makefile option (not with Tripal that is), if you want to start from scratch, all you have to do is remove the directory called "tmp" in the chado directory.  When you run "make clean" it removes all of the files that are created when "perl Makefile.PL" is run, including the Makefile itself, so that no make commands will work.  To get them to work again, you have to start from "perl Makefile.PL".

Scott


On Mon, Nov 24, 2014 at 2:42 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

I cc'ed this to the schema mailing list which is where we discuss chado related stuff; I'll reply to that and trim the gbrowse list off. 

Scott


Sent from my iPhone

On Nov 24, 2014, at 12:48 PM, Asma Riyaz <[hidden email]> wrote:

Hi,

I need to re-load the ontologies into Chado as I don't think the 1st installed all of it. According https://github.com/scottcain/chado_test/blob/master/chado/INSTALL.Chado, I will need to delete the temporary files but I don't know where to locate these. Could someone point me in the right direction for this?

Thank you 
Asma
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--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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




--
------------------------------------------------------------------------
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

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--
Mara Kim

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



--
------------------------------------------------------------------------
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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