Topics for discussion at tomorrow's dinner meeting (and/or later)

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Topics for discussion at tomorrow's dinner meeting (and/or later)

Michael Caudy

Topics for discussion at tomorrow's dinner meeting (and/or later)


Hi everyone,


There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.


* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 


* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

including full integration with Views and Views-related functionality, such as CCK and Panels.  

* Porting Tripal to Drupal 7, now that D7 is out.


* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features


It probably makes sense for the Features development to wait until after the D7 port is completed


Mike

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:
I'll see you all at the fountain. Thanks!
Meg


Sent from my iPhone

On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

I look forward to see you all tomorrow.

MIke


On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email][hidden email]> wrote:
> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email][hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email][hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email][hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email][hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email][hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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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Fwd: Topics for discussion at tomorrow's dinner meeting (and/or later)

Michael Caudy
Hi Lacey,

I just got the message you sent to the Tripal group about Views integration. That sounds really great.

I was just sending a related message called "Topics for discussion at tomorrow's dinner meeting (and/or later)".

This also is partly about Views integration with Tripal, as you will see in the message below. I don't think there will necessarily be a duplication of effort, but we should be careful to keep each other updated about what we are doing.

As a first approximation, it sounds as though your work will cover much / all of Views integration for Tripal 2. Drupal 7 has just been released, and a port of Tripal to D7 could involve rewriting part of Tripal so that CCK, Views, etc, are there automatically, rather than added on separately. For example, integration of Tripal with "Drupal Features" (discussed in my message, below) will probably work out easiest after the D7 port, and integration of Tripal with CCK and Views. (As you may know, most of CCK is now in Drupal Core - where it is now called the "Fields API" - so everything in D7 has to work with these APIs, which are all designed to work with each other.)

Thanks for all of your work on Tripal.

Best regards,

Mike

Michael Caudy



---------- Forwarded message ----------
From: Michael Caudy <[hidden email]>
Date: Mon, Jan 17, 2011 at 11:11 PM
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)
To: Meg Staton <[hidden email]>
Cc: Scott Cain <[hidden email]>, Stephen Ficklin <[hidden email]>, "[hidden email]" <[hidden email]>, Ilhyung Cho <[hidden email]>, "[hidden email]" <[hidden email]>, Sook Jung <[hidden email]>


Topics for discussion at tomorrow's dinner meeting (and/or later)


Hi everyone,


There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.


* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 


* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

including full integration with Views and Views-related functionality, such as CCK and Panels.  

* Porting Tripal to Drupal 7, now that D7 is out.


* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features


It probably makes sense for the Features development to wait until after the D7 port is completed


Mike

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:
I'll see you all at the fountain. Thanks!
Meg


Sent from my iPhone

On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

I look forward to see you all tomorrow.

MIke


On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email][hidden email]> wrote:
Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email][hidden email]> wrote:
> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email][hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email][hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email][hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email][hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email][hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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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malware threats, the impact they can have on your business, and how you
can protect your company and customers by using code signing.
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_______________________________________________
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Re: Topics for discussion at tomorrow's dinner meeting (and/or later)

Stephen Ficklin-2
In reply to this post by Michael Caudy

Hi All,

 

My flight has been delayed due to bad weather in the northeast today.  I see Michael’s has been as well.   So, unfortunately, I will not make it to San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m sorry.  I was looking forward to the meeting and dinner :-(

 

But here are some thoughts related to the discussion whether it happens without me or not.

 

The improvements to Tripal that we are able to do right now are prioritized by the objectives of our current funded projects.   I think we should make a prioritized list of future development tasks for Tripal, however I think it’s important to remember that we may not be able to implement those ideas unless our various PI’s agree or see that our ideas fit within the scope of the current projects.   I would like to see  one day funding for dedicated staff (at least one person) to develop infrastructure, develop documentation, respond to user requests.  My impression is that this of course will be tied to a larger scientific investigation for which Tripal development will play an important role. 

 

Michael, if you have time and resources to do some work with CCK, Panels, Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could create a separate branch in the GMOD SVN repository for a Drupal 7 version that you could work out of.  I’m not so sure we can completely remove the need for PHP Drupal modules as we currently have them.   Currently they are more portable.  But, perhaps I don’t understand enough about CCK and Drupal 7 to know how that can be changed.  I’m happy to be educated :-)

 

As Lacey mentioned in a previous email she has just about handled the Views, and we now have a way to install Chado local to the Drupal database so we have the major hurdle for integration with Drupal Views handled.

 

My goal is that we release a new version of Tripal by early March that will have many of Lacey’s improvements as well as some others that I have worked in. 

 

One other thought I would like to add is that we recognize the three different levels of users that I think Tripal should support:  1. The wet-lab scientist who has few IT resources, but who wants a functional, searchable online resources for his/her data that is easy to setup and manage.   2.  The larger lab with good bioinformatics support that will want to fully customize visualizations  of their data, will want a flexible platform that is well supported with a responsive community.    3.   The Chado-expert who understands the schema, understands the data and wants to look at it in novel ways  which perhaps are not available through the resources/tools/visualizations of the primary database, but who doesn’t want to do a lot of PHP coding either (Mike, If I understand your goals, I think you would fall into case #3,  right?).   Have I captured these three groups correctly?  Am I missing any?

 

Thanks!  Happy PAG’ing.

Stephen

 

 

 

From: Michael Caudy [mailto:[hidden email]]
Sent: Monday, January 17, 2011 11:12 PM
To: Meg Staton
Cc: Scott Cain; Stephen Ficklin; [hidden email]; Ilhyung Cho; [hidden email]; Sook Jung
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Hi everyone,

 

There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.

 

* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 

 

* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

                including full integration with Views and Views-related functionality, such as CCK and Panels.  

               

* Porting Tripal to Drupal 7, now that D7 is out.

 

* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features

 

It probably makes sense for the Features development to wait until after the D7 port is completed

 

Mike

 

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:

I'll see you all at the fountain. Thanks!

Meg



Sent from my iPhone


On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

 

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

 

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

 

I look forward to see you all tomorrow.

 

MIke

 

On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email]> wrote:

Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email]> wrote:


> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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: Topics for discussion at tomorrow's dinner meeting (and/or later)

Scott Cain
I accidentally only sent this to Stephen; let's try that again:

Well, that's a drag. Since neither Mike nor Stephen will make dinner, I suggest that we try to talk over <a href="x-apple-data-detectors://1" x-apple-data-detectors="true" style="color: blue; text-decoration: underline; ">lunch tomorrow. I realize that will leave Meg out (sorry!), but it seems like the best adjustment. Thoughts?

Sent from my iPad

On 2011-01-18, at 7:13 AM, "Stephen Ficklin" <[hidden email]> wrote:

Hi All,

 

My flight has been delayed due to bad weather in the northeast today.  I see Michael’s has been as well.   So, unfortunately, I will not make it to San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m sorry.  I was looking forward to the meeting and dinner :-(

 

But here are some thoughts related to the discussion whether it happens without me or not.

 

The improvements to Tripal that we are able to do right now are prioritized by the objectives of our current funded projects.   I think we should make a prioritized list of future development tasks for Tripal, however I think it’s important to remember that we may not be able to implement those ideas unless our various PI’s agree or see that our ideas fit within the scope of the current projects.   I would like to see  one day funding for dedicated staff (at least one person) to develop infrastructure, develop documentation, respond to user requests.  My impression is that this of course will be tied to a larger scientific investigation for which Tripal development will play an important role. 

 

Michael, if you have time and resources to do some work with CCK, Panels, Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could create a separate branch in the GMOD SVN repository for a Drupal 7 version that you could work out of.  I’m not so sure we can completely remove the need for PHP Drupal modules as we currently have them.   Currently they are more portable.  But, perhaps I don’t understand enough about CCK and Drupal 7 to know how that can be changed.  I’m happy to be educated :-)

 

As Lacey mentioned in a previous email she has just about handled the Views, and we now have a way to install Chado local to the Drupal database so we have the major hurdle for integration with Drupal Views handled.

 

My goal is that we release a new version of Tripal by early March that will have many of Lacey’s improvements as well as some others that I have worked in. 

 

One other thought I would like to add is that we recognize the three different levels of users that I think Tripal should support:  1. The wet-lab scientist who has few IT resources, but who wants a functional, searchable online resources for his/her data that is easy to setup and manage.   2.  The larger lab with good bioinformatics support that will want to fully customize visualizations  of their data, will want a flexible platform that is well supported with a responsive community.    3.   The Chado-expert who understands the schema, understands the data and wants to look at it in novel ways  which perhaps are not available through the resources/tools/visualizations of the primary database, but who doesn’t want to do a lot of PHP coding either (Mike, If I understand your goals, I think you would fall into case #3,  right?).   Have I captured these three groups correctly?  Am I missing any?

 

Thanks!  Happy PAG’ing.

Stephen

 

 

 

From: Michael Caudy [mailto:[hidden email]]
Sent: Monday, January 17, 2011 11:12 PM
To: Meg Staton
Cc: Scott Cain; Stephen Ficklin; [hidden email]; Ilhyung Cho; [hidden email]; Sook Jung
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Hi everyone,

 

There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.

 

* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 

 

* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

                including full integration with Views and Views-related functionality, such as CCK and Panels.  

               

* Porting Tripal to Drupal 7, now that D7 is out.

 

* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features

 

It probably makes sense for the Features development to wait until after the D7 port is completed

 

Mike

 

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:

I'll see you all at the fountain. Thanks!

Meg



Sent from my iPhone


On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

 

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

 

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

 

I look forward to see you all tomorrow.

 

MIke

 

On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email]> wrote:

Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email]> wrote:


> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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: Topics for discussion at tomorrow's dinner meeting (and/or later)

Michael Caudy
Hi Scott,

Thanks for your message. Lunch tomorrow would be fine with me.  I am sorry if that leaves Meg out, though.

Also, I will be available for dinner after tomorrow's sessions. Can some of us go out for dinner, as well?

Mike

On Tue, Jan 18, 2011 at 3:08 PM, Scott Cain <[hidden email]> wrote:
I accidentally only sent this to Stephen; let's try that again:

Well, that's a drag. Since neither Mike nor Stephen will make dinner, I suggest that we try to talk over lunch tomorrow. I realize that will leave Meg out (sorry!), but it seems like the best adjustment. Thoughts?

Sent from my iPad

On 2011-01-18, at 7:13 AM, "Stephen Ficklin" <[hidden email]> wrote:

Hi All,

 

My flight has been delayed due to bad weather in the northeast today.  I see Michael’s has been as well.   So, unfortunately, I will not make it to San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m sorry.  I was looking forward to the meeting and dinner :-(

 

But here are some thoughts related to the discussion whether it happens without me or not.

 

The improvements to Tripal that we are able to do right now are prioritized by the objectives of our current funded projects.   I think we should make a prioritized list of future development tasks for Tripal, however I think it’s important to remember that we may not be able to implement those ideas unless our various PI’s agree or see that our ideas fit within the scope of the current projects.   I would like to see  one day funding for dedicated staff (at least one person) to develop infrastructure, develop documentation, respond to user requests.  My impression is that this of course will be tied to a larger scientific investigation for which Tripal development will play an important role. 

 

Michael, if you have time and resources to do some work with CCK, Panels, Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could create a separate branch in the GMOD SVN repository for a Drupal 7 version that you could work out of.  I’m not so sure we can completely remove the need for PHP Drupal modules as we currently have them.   Currently they are more portable.  But, perhaps I don’t understand enough about CCK and Drupal 7 to know how that can be changed.  I’m happy to be educated :-)

 

As Lacey mentioned in a previous email she has just about handled the Views, and we now have a way to install Chado local to the Drupal database so we have the major hurdle for integration with Drupal Views handled.

 

My goal is that we release a new version of Tripal by early March that will have many of Lacey’s improvements as well as some others that I have worked in. 

 

One other thought I would like to add is that we recognize the three different levels of users that I think Tripal should support:  1. The wet-lab scientist who has few IT resources, but who wants a functional, searchable online resources for his/her data that is easy to setup and manage.   2.  The larger lab with good bioinformatics support that will want to fully customize visualizations  of their data, will want a flexible platform that is well supported with a responsive community.    3.   The Chado-expert who understands the schema, understands the data and wants to look at it in novel ways  which perhaps are not available through the resources/tools/visualizations of the primary database, but who doesn’t want to do a lot of PHP coding either (Mike, If I understand your goals, I think you would fall into case #3,  right?).   Have I captured these three groups correctly?  Am I missing any?

 

Thanks!  Happy PAG’ing.

Stephen

 

 

 

From: Michael Caudy [mailto:[hidden email]]
Sent: Monday, January 17, 2011 11:12 PM
To: Meg Staton
Cc: Scott Cain; Stephen Ficklin; [hidden email]; Ilhyung Cho; [hidden email]; Sook Jung
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Hi everyone,

 

There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.

 

* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 

 

* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

                including full integration with Views and Views-related functionality, such as CCK and Panels.  

               

* Porting Tripal to Drupal 7, now that D7 is out.

 

* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features

 

It probably makes sense for the Features development to wait until after the D7 port is completed

 

Mike

 

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email][hidden email]> wrote:

I'll see you all at the fountain. Thanks!

Meg



Sent from my iPhone


On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email][hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

 

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

 

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

 

I look forward to see you all tomorrow.

 

MIke

 

On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email][hidden email]> wrote:

Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email][hidden email]> wrote:
> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email][hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email][hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email][hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email][hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email][hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email][hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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: Topics for discussion at tomorrow's dinner meeting (and/or later)

Meg Staton
In reply to this post by Stephen Ficklin-2
I will be starting a new project this month using Tripal, and I am planning to install Drupal 7 and work on porting the old modules.  Hopefully, I'll can port the new version slated for March as well since the site development will still be relatively immature.  We've got a big investment in Tripal, and the changes in Drupal 7 are very exciting.  We definitely want to leverage those.

Meg
 
--
Margaret E. Staton, PhD
Clemson University Genomics Institute
[hidden email]
864-656-4643



From: Stephen Ficklin <[hidden email]>
To: Michael Caudy <[hidden email]>; Meg Staton <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Ilhyung Cho <[hidden email]>; [hidden email]; Sook Jung <[hidden email]>; "Main, Doreen" <[hidden email]>; Lacey-Anne Sanderson <[hidden email]>
Sent: Tue, January 18, 2011 10:13:47 AM
Subject: RE: Topics for discussion at tomorrow's dinner meeting (and/or later)

Hi All,

 

My flight has been delayed due to bad weather in the northeast today.  I see Michael’s has been as well.   So, unfortunately, I will not make it to San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m sorry.  I was looking forward to the meeting and dinner :-(

 

But here are some thoughts related to the discussion whether it happens without me or not.

 

The improvements to Tripal that we are able to do right now are prioritized by the objectives of our current funded projects.   I think we should make a prioritized list of future development tasks for Tripal, however I think it’s important to remember that we may not be able to implement those ideas unless our various PI’s agree or see that our ideas fit within the scope of the current projects.   I would like to see  one day funding for dedicated staff (at least one person) to develop infrastructure, develop documentation, respond to user requests.  My impression is that this of course will be tied to a larger scientific investigation for which Tripal development will play an important role. 

 

Michael, if you have time and resources to do some work with CCK, Panels, Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could create a separate branch in the GMOD SVN repository for a Drupal 7 version that you could work out of.  I’m not so sure we can completely remove the need for PHP Drupal modules as we currently have them.   Currently they are more portable.  But, perhaps I don’t understand enough about CCK and Drupal 7 to know how that can be changed.  I’m happy to be educated :-)

 

As Lacey mentioned in a previous email she has just about handled the Views, and we now have a way to install Chado local to the Drupal database so we have the major hurdle for integration with Drupal Views handled.

 

My goal is that we release a new version of Tripal by early March that will have many of Lacey’s improvements as well as some others that I have worked in. 

 

One other thought I would like to add is that we recognize the three different levels of users that I think Tripal should support:  1. The wet-lab scientist who has few IT resources, but who wants a functional, searchable online resources for his/her data that is easy to setup and manage.   2.  The larger lab with good bioinformatics support that will want to fully customize visualizations  of their data, will want a flexible platform that is well supported with a responsive community.    3.   The Chado-expert who understands the schema, understands the data and wants to look at it in novel ways  which perhaps are not available through the resources/tools/visualizations of the primary database, but who doesn’t want to do a lot of PHP coding either (Mike, If I understand your goals, I think you would fall into case #3,  right?).   Have I captured these three groups correctly?  Am I missing any?

 

Thanks!  Happy PAG’ing.

Stephen

 

 

 

From: Michael Caudy [mailto:[hidden email]]
Sent: Monday, January 17, 2011 11:12 PM
To: Meg Staton
Cc: Scott Cain; Stephen Ficklin; [hidden email]; Ilhyung Cho; [hidden email]; Sook Jung
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Hi everyone,

 

There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.

 

* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 

 

* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

                including full integration with Views and Views-related functionality, such as CCK and Panels.  

               

* Porting Tripal to Drupal 7, now that D7 is out.

 

* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features

 

It probably makes sense for the Features development to wait until after the D7 port is completed

 

Mike

 

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:

I'll see you all at the fountain. Thanks!

Meg



Sent from my iPhone


On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

 

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

 

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

 

I look forward to see you all tomorrow.

 

MIke

 

On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email]> wrote:

Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email]> wrote:


> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com

>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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: Topics for discussion at tomorrow's dinner meeting (and/or later)

Michael Caudy

Hi Stephen,


It was great to meet and talk with you again at the GMOD session at the end of the PAG2011 meeting last week. I think we had very useful discussions at lunch and dinner, which also included Scott Cain for most of the time. Scott and I also reviewed these discussions on the GMOD call last Monday, but I want to summarize them for everyone working on the project. If you want to make any additions or corrections to this, please let me know.


The following "bullets" are the main points that we discussed about how best to proceed, which are each discussed further below:

   *  porting Tripal to Drupal 7

   *  improved integration of Tripal with the CCK, Views and Panels functionality that is available in Drupal 6, 

   *  integration Views 3 and the new APIs that are now in D7, since Views 2 will not be ported to D7.

   *  use of the new Drupal "Features" system to create exportable content types without writing PHP modules.


As I told you last week, I am very interested in helping with these aspects of the Tripal project, as much as I am able.


*   Integration of Tripal with Drupal Views in Drupal 6 and Drupal 7: As we have discussed several times over the past few months, the decision write modules for new content types in Tripal was a very creative approach to solving the problem of how to achieve persistence of special genomics content types within new installations of Tripal in Drupal 6.  However, writing modules, rather than using CCK to create new content types, had the downside of breaking Tripal integration with many other Drupal functionalities, including Views. In addition, it also likely breaks integration with Panels, Image handling, and many other Drupal features, which generally build on having CCK content types, since CCK content types were actually added to Drupal core in D6. 


Lacey Sanderson's recent work to write code that allows Views integration with Tripal in Drupal 6 looks very promising. However, as we have discussed, it will be important to avoid having to write (or rewrite) such code for the Drupal 7 version of Tripal.  Otherwise, other users will not be able to create their own Views for Tripal data, without also writing custom PHP code, which very few of them can do. 


*   Porting Tripal to Drupal 7: As we discussed, when Tripal is ported to Drupal 7, it will be important to revise it so that it includes full integration with both CCK content types and CCK fields, which in D7 are now called 'entities' and 'fields', and are now both in core.  There is a corresponding, new API for these called the "Field API", which is documented on drupal.org at this link:

     http://api.drupal.org/api/drupal/modules--field--field.module/group/field/7


There also are a whole new set of hooks for integrating contrib modules with Drupal, including several new node hooks that replace the single "hook_node_api" in Drupal 6, and also several new, more general hooks for "entities". These are documented at:

     http://api.drupal.org/api/drupal/includes--module.inc/group/hooks/7


It is important to have a clear understanding of "entities" (which include 'nodes", "comments, any new content types, etc), and how to integrate Tripal with the new Field API, in order to get full integration of Tripal with other Drupal components, such as Views and Panels.  Otherwise, it will likely be necessary to write a lot of custom code again, in order to get Views integration in D7, just as it was in D6.


There are a number of good books on Drupal 7 development - and how best to use the APIs - including the following: 


     Pro_Drupal_7_Development_Third_Edition 

     Drupal-7-Module-Development


In particular, the second book gives a good description of how the new "entity" content types relate to the old "node" and "comments" content types.  Both books also provide good descririptions of the Drupal response "lifecycle", and how the various hooks works at different stages in response to system events during that process.  This is a very complex process, and it is important to know how diffferent hooks provide functions, such as validation, for various node, file, and comments, at different stages in the process.


If you need any more information about these topics, I can help you with this.


*   Views 3 integration: As you know, I have been pursuing the Views integration / D7 port by a stepwise approach in I am first integrating Tripal in D6 using the new Views 3 dev module that has been available for D6. This should make it easier to port Tripal to D7, where only Views 3 will available.


*   Integration of Tripal with Drupal "Features" In Drupal 7:  As we also discussed, another benefit of closer integration of Tripal with the Drupal APIs is that it will allow the use the new Drupal "Features" functionality to create content type persistence, rather than to create new content types through modules that do not integrate with CCK. Over the last two years, the "Features" system has been widely adopted for implementing such persistence, and appears to be a very powerful and robust system for doing so.


*   Careful coordination / planning of work: shortly after the meeting, Meg sent the following message:


"I will be starting a new project this month using Tripal, and I am planning to install Drupal 7 and work on porting the old modules.  Hopefully, I'll can port the new version slated for March as well since the site development will still be relatively immature.  We've got a big investment in Tripal, and the changes in Drupal 7 are very exciting.  We definitely want to leverage those."


Unfortunately, since Stephen and I were delayed due to the weather, the planned meeting for Tuesday was postponed until Wedenesday, and Meg could not attend the Wednesday meetings. As a result, she missed the discussions we had, which are summarized above.


To my understanding, Stephen, and Scott and I agreed that:


* the port to D7 would try to use Drupal Features to create Tripal content types, not "porting the old modules", as this will only recreate the problem with CCK, Views, etc, integrations, which we were a problem for Tripal in D6, and which we are now trying to avoid.


*   I agree completely that D7 has many advantages which are very exciting, and should be leveraged by Tripal when it is ported to D7. However, it will be necessary to fully integrate Tripal with the new Entity / Field APIs that are in D7, or that new functionality will largely be broken, and much custom code for creating Views, etc., will again have to be written.


If after reading my above summary notes, Meg has questions about the plan for the D7 port - or whether to use "Features" - she should let us know ASAP, before she starts "porting the old modules" to D7.


I will be happy to try to work with her on learning the new APIs and how to build Features. 


Also, in general, based on my past experience with Drupal and other web frameworks, I think it is too early to plan to build new client sites on D7 until all of the needed contrib modules have been included and tested.  I generally wait until about the "x.4" release (7.4 in this case) before trying to build real production sites, as too many things are not yet working together properly.


*   Tripal Conference Calls: Scott agreed that we need to have a conference call soon, to avoid duplication of effort, and/or to avoid moving ahead in different directions.


Again, I am very interested in working on these aspects of the Tripal project, as much as I am able.


I look forward to talking with you, and Meg, and Lacey on future Tripal conference calls, which I understand Scott will be setting up soon.


Best regards,


Mike



On Fri, Jan 21, 2011 at 6:29 PM, Meg Staton <[hidden email]> wrote:
I will be starting a new project this month using Tripal, and I am planning to install Drupal 7 and work on porting the old modules.  Hopefully, I'll can port the new version slated for March as well since the site development will still be relatively immature.  We've got a big investment in Tripal, and the changes in Drupal 7 are very exciting.  We definitely want to leverage those.

Meg
 
--
Margaret E. Staton, PhD
Clemson University Genomics Institute
[hidden email]
864-656-4643



From: Stephen Ficklin <[hidden email]>
To: Michael Caudy <[hidden email]>; Meg Staton <[hidden email]>
Cc: Scott Cain <[hidden email]>; [hidden email]; Ilhyung Cho <[hidden email]>; [hidden email]; Sook Jung <[hidden email]>; "Main, Doreen" <[hidden email]>; Lacey-Anne Sanderson <[hidden email]>
Sent: Tue, January 18, 2011 10:13:47 AM
Subject: RE: Topics for discussion at tomorrow's dinner meeting (and/or later)

Hi All,

 

My flight has been delayed due to bad weather in the northeast today.  I see Michael’s has been as well.   So, unfortunately, I will not make it to San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m sorry.  I was looking forward to the meeting and dinner :-(

 

But here are some thoughts related to the discussion whether it happens without me or not.

 

The improvements to Tripal that we are able to do right now are prioritized by the objectives of our current funded projects.   I think we should make a prioritized list of future development tasks for Tripal, however I think it’s important to remember that we may not be able to implement those ideas unless our various PI’s agree or see that our ideas fit within the scope of the current projects.   I would like to see  one day funding for dedicated staff (at least one person) to develop infrastructure, develop documentation, respond to user requests.  My impression is that this of course will be tied to a larger scientific investigation for which Tripal development will play an important role. 

 

Michael, if you have time and resources to do some work with CCK, Panels, Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could create a separate branch in the GMOD SVN repository for a Drupal 7 version that you could work out of.  I’m not so sure we can completely remove the need for PHP Drupal modules as we currently have them.   Currently they are more portable.  But, perhaps I don’t understand enough about CCK and Drupal 7 to know how that can be changed.  I’m happy to be educated :-)

 

As Lacey mentioned in a previous email she has just about handled the Views, and we now have a way to install Chado local to the Drupal database so we have the major hurdle for integration with Drupal Views handled.

 

My goal is that we release a new version of Tripal by early March that will have many of Lacey’s improvements as well as some others that I have worked in. 

 

One other thought I would like to add is that we recognize the three different levels of users that I think Tripal should support:  1. The wet-lab scientist who has few IT resources, but who wants a functional, searchable online resources for his/her data that is easy to setup and manage.   2.  The larger lab with good bioinformatics support that will want to fully customize visualizations  of their data, will want a flexible platform that is well supported with a responsive community.    3.   The Chado-expert who understands the schema, understands the data and wants to look at it in novel ways  which perhaps are not available through the resources/tools/visualizations of the primary database, but who doesn’t want to do a lot of PHP coding either (Mike, If I understand your goals, I think you would fall into case #3,  right?).   Have I captured these three groups correctly?  Am I missing any?

 

Thanks!  Happy PAG’ing.

Stephen

 

 

 

From: Michael Caudy [mailto:[hidden email]]
Sent: Monday, January 17, 2011 11:12 PM
To: Meg Staton
Cc: Scott Cain; Stephen Ficklin; [hidden email]; Ilhyung Cho; [hidden email]; Sook Jung
Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Topics for discussion at tomorrow's dinner meeting (and/or later)

 

Hi everyone,

 

There have been a number of recent phone conversations between me and Stephen and/or Scott about a number of important issues for future Tripal / Drupal / GMODviews development. I would like to go over those briefly at dinner tomorrow, so that everyone is informed about them.

 

* Scott suggested having regular Tripal conference calls soon that include all Tripal-related developers, so that the next stages of the development plan can be discussed, and different parts assigned to different developers. 

 

* I am definitely interested and willing to work further on the integration of Tripal with some of the newer, more advanced Drupal functionality:

                including full integration with Views and Views-related functionality, such as CCK and Panels.  

               

* Porting Tripal to Drupal 7, now that D7 is out.

 

* I also am definitely interested creating "Features" based on Tripal, so that content types don't have to be defined by custom content modules, which is now the case.  Note: I am referring here to "Drupal Features", not "Chado Features", where "Features" are a new development in Drupal in which specific content types and/or configurations are made "exportable" and persistant, so that they can be included in base installations, rather than manually-configured each time a new installation is made.

    see http://drupal.org/project/features

 

It probably makes sense for the Features development to wait until after the D7 port is completed

 

Mike

 

On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:

I'll see you all at the fountain. Thanks!

Meg



Sent from my iPhone


On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:

Hi Scott and Stephen and everyone at PAG,

 

I was just about to send an e-mail message about the plan for a Tripal-related dinner on Tuesday, when I got these messages from Scott and Stephen,

 

Scott's suggestions for where to eat sound fine to me. We should try to find some place where we can hear each other talk, however.

 

I look forward to see you all tomorrow.

 

MIke

 

On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email]> wrote:

Hi Stephan and all,

Sorry I forgot to email about this earlier. I meant to do it on Monday
last week.

Perhaps we should shoot for 6:30, since the meeting schedule goes
until 6:00. We could meet at the fountain outside the convention hall.
 For where to go from there, I can suggest a few things.  Very close
is california pizza kitchen and pf changs (at the mall).  A little
father away is a good sushi restaurant at the crowne plaza hotel, and
farther away (just barely walking distance, up a big hill) is
Hillcrest, where there are several good restaurants.  Does anyone have
a preference?

Thanks,
Scott

On Monday, January 17, 2011, Stephen Ficklin <[hidden email]> wrote:
> Hi Scott,
>
> Is there still interest on your side to have a Tripal meeting Tuesday night
> at PAG?  If so, would 6pm work for you?  I'm at a loss for where though...
> Would you mind making a suggestion?
>
> Thanks,
> Stephen
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Tuesday, January 04, 2011 4:04 PM
> To: Stephen Ficklin
> Cc: [hidden email]
> Subject: Re: [Gmod-tripal] Who's attending PAG?
>
> Hi Stephen and Meg,
>
> Depending on Stephen's schedule, would you be interested in sitting
> down to chat about future development for Tripal on Tuesday evening
> (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
> would be of course welcome too.
>
> Scott
>
>
> On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email]> wrote:
>> Hi Scott,
>>
>> I'm scheduled to be there Tuesday evening and Wednesday.
>>
>> Stephen
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]]
>> Sent: Wednesday, December 08, 2010 2:28 PM
>> To: [hidden email]
>> Subject: [Gmod-tripal] Who's attending PAG?
>>
>> Hi all,
>>
>> I was wondering who associated with Tripal is attending PAG in
>> January.  I was thinking that it might be nice to have everyone sit
>> down at a table at some point during the meeting to chat about coming
>> plans and needs for Tripal.
>>
>> Scott
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
> dot
>> net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>>
> ----------------------------------------------------------------------------
>> --
>> This SF Dev2Dev email is sponsored by:
>>
>> WikiLeaks The End of the Free Internet
>> http://p.sf.net/sfu/therealnews-com
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     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: Topics for discussion at tomorrow's dinner meeting (and/or later)

Scott Cain
Mike,

Thanks for reminding me: I put together a doodle poll for next week to
have a one hour (max!) call to discuss development directions for
Tripal:

  http://www.doodle.com/i2rm3raxcx9gueat

Please take the poll if you'd like to participate.  Everybody is welcome.

Scott


On Thu, Jan 27, 2011 at 8:59 PM, Michael Caudy <[hidden email]> wrote:

> Hi Stephen,
>
> It was great to meet and talk with you again at the GMOD session at the end
> of the PAG2011 meeting last week. I think we had very useful discussions at
> lunch and dinner, which also included Scott Cain for most of the time. Scott
> and I also reviewed these discussions on the GMOD call last Monday, but I
> want to summarize them for everyone working on the project. If you want to
> make any additions or corrections to this, please let me know.
>
> The following "bullets" are the main points that we discussed about how best
> to proceed, which are each discussed further below:
>
>    *  porting Tripal to Drupal 7
>
>    *  improved integration of Tripal with the CCK, Views and Panels
> functionality that is available in Drupal 6,
>
>    *  integration Views 3 and the new APIs that are now in D7, since Views 2
> will not be ported to D7.
>
>    *  use of the new Drupal "Features" system to create exportable content
> types without writing PHP modules.
>
> As I told you last week, I am very interested in helping with these aspects
> of the Tripal project, as much as I am able.
>
> *   Integration of Tripal with Drupal Views in Drupal 6 and Drupal 7: As we
> have discussed several times over the past few months, the decision write
> modules for new content types in Tripal was a very creative approach to
> solving the problem of how to achieve persistence of special genomics
> content types within new installations of Tripal in Drupal 6.  However,
> writing modules, rather than using CCK to create new content types, had the
> downside of breaking Tripal integration with many other Drupal
> functionalities, including Views. In addition, it also likely breaks
> integration with Panels, Image handling, and many other Drupal features,
> which generally build on having CCK content types, since CCK content types
> were actually added to Drupal core in D6.
>
> Lacey Sanderson's recent work to write code that allows Views integration
> with Tripal in Drupal 6 looks very promising. However, as we have discussed,
> it will be important to avoid having to write (or rewrite) such code for the
> Drupal 7 version of Tripal.  Otherwise, other users will not be able to
> create their own Views for Tripal data, without also writing custom PHP
> code, which very few of them can do.
>
> *   Porting Tripal to Drupal 7: As we discussed, when Tripal is ported to
> Drupal 7, it will be important to revise it so that it includes full
> integration with both CCK content types and CCK fields, which in D7 are now
> called 'entities' and 'fields', and are now both in core.  There is a
> corresponding, new API for these called the "Field API", which is documented
> on drupal.org at this link:
>
>
> http://api.drupal.org/api/drupal/modules--field--field.module/group/field/7
>
> There also are a whole new set of hooks for integrating contrib modules with
> Drupal, including several new node hooks that replace the single
> "hook_node_api" in Drupal 6, and also several new, more general hooks for
> "entities". These are documented at:
>
>      http://api.drupal.org/api/drupal/includes--module.inc/group/hooks/7
>
> It is important to have a clear understanding of "entities" (which include
> 'nodes", "comments, any new content types, etc), and how to integrate Tripal
> with the new Field API, in order to get full integration of Tripal with
> other Drupal components, such as Views and Panels.  Otherwise, it will
> likely be necessary to write a lot of custom code again, in order to get
> Views integration in D7, just as it was in D6.
>
> There are a number of good books on Drupal 7 development - and how best to
> use the APIs - including the following:
>
>      Pro_Drupal_7_Development_Third_Edition
>
>      Drupal-7-Module-Development
>
> In particular, the second book gives a good description of how the new
> "entity" content types relate to the old "node" and "comments" content
> types.  Both books also provide good descririptions of the Drupal response
> "lifecycle", and how the various hooks works at different stages in response
> to system events during that process.  This is a very complex process, and
> it is important to know how diffferent hooks provide functions, such as
> validation, for various node, file, and comments, at different stages in the
> process.
>
> If you need any more information about these topics, I can help you with
> this.
>
> *   Views 3 integration: As you know, I have been pursuing the Views
> integration / D7 port by a stepwise approach in I am first integrating
> Tripal in D6 using the new Views 3 dev module that has been available for
> D6. This should make it easier to port Tripal to D7, where only Views 3 will
> available.
>
> *   Integration of Tripal with Drupal "Features" In Drupal 7:  As we also
> discussed, another benefit of closer integration of Tripal with the Drupal
> APIs is that it will allow the use the new Drupal "Features" functionality
> to create content type persistence, rather than to create new content types
> through modules that do not integrate with CCK. Over the last two years, the
> "Features" system has been widely adopted for implementing such persistence,
> and appears to be a very powerful and robust system for doing so.
>
> *   Careful coordination / planning of work: shortly after the meeting, Meg
> sent the following message:
>
> "I will be starting a new project this month using Tripal, and I am planning
> to install Drupal 7 and work on porting the old modules.  Hopefully, I'll
> can port the new version slated for March as well since the site development
> will still be relatively immature.  We've got a big investment in Tripal,
> and the changes in Drupal 7 are very exciting.  We definitely want to
> leverage those."
>
> Unfortunately, since Stephen and I were delayed due to the weather, the
> planned meeting for Tuesday was postponed until Wedenesday, and Meg could
> not attend the Wednesday meetings. As a result, she missed the discussions
> we had, which are summarized above.
>
> To my understanding, Stephen, and Scott and I agreed that:
>
> * the port to D7 would try to use Drupal Features to create Tripal content
> types, not "porting the old modules", as this will only recreate the problem
> with CCK, Views, etc, integrations, which we were a problem for Tripal in
> D6, and which we are now trying to avoid.
>
> *   I agree completely that D7 has many advantages which are very exciting,
> and should be leveraged by Tripal when it is ported to D7. However, it will
> be necessary to fully integrate Tripal with the new Entity / Field APIs that
> are in D7, or that new functionality will largely be broken, and much custom
> code for creating Views, etc., will again have to be written.
>
> If after reading my above summary notes, Meg has questions about the plan
> for the D7 port - or whether to use "Features" - she should let us know
> ASAP, before she starts "porting the old modules" to D7.
>
> I will be happy to try to work with her on learning the new APIs and how to
> build Features.
>
> Also, in general, based on my past experience with Drupal and other web
> frameworks, I think it is too early to plan to build new client sites on D7
> until all of the needed contrib modules have been included and tested.  I
> generally wait until about the "x.4" release (7.4 in this case) before
> trying to build real production sites, as too many things are not yet
> working together properly.
>
> *   Tripal Conference Calls: Scott agreed that we need to have a conference
> call soon, to avoid duplication of effort, and/or to avoid moving ahead in
> different directions.
>
> Again, I am very interested in working on these aspects of the Tripal
> project, as much as I am able.
>
> I look forward to talking with you, and Meg, and Lacey on future Tripal
> conference calls, which I understand Scott will be setting up soon.
>
> Best regards,
>
> Mike
>
> On Fri, Jan 21, 2011 at 6:29 PM, Meg Staton <[hidden email]> wrote:
>>
>> I will be starting a new project this month using Tripal, and I am
>> planning to install Drupal 7 and work on porting the old modules.
>>  Hopefully, I'll can port the new version slated for March as well since the
>> site development will still be relatively immature.  We've got a big
>> investment in Tripal, and the changes in Drupal 7 are very exciting.  We
>> definitely want to leverage those.
>> Meg
>>
>> --
>> Margaret E. Staton, PhD
>> Clemson University Genomics Institute
>> [hidden email]
>> 864-656-4643
>>
>> ________________________________
>> From: Stephen Ficklin <[hidden email]>
>> To: Michael Caudy <[hidden email]>; Meg Staton <[hidden email]>
>> Cc: Scott Cain <[hidden email]>; [hidden email];
>> Ilhyung Cho <[hidden email]>; [hidden email]; Sook Jung
>> <[hidden email]>; "Main, Doreen" <[hidden email]>; Lacey-Anne
>> Sanderson <[hidden email]>
>> Sent: Tue, January 18, 2011 10:13:47 AM
>> Subject: RE: Topics for discussion at tomorrow's dinner meeting (and/or
>> later)
>>
>> Hi All,
>>
>>
>>
>> My flight has been delayed due to bad weather in the northeast today.  I
>> see Michael’s has been as well.   So, unfortunately, I will not make it to
>> San Diego until around 9pm tonight, and probably to the hotel by 10pm.   I’m
>> sorry.  I was looking forward to the meeting and dinner :-(
>>
>>
>>
>> But here are some thoughts related to the discussion whether it happens
>> without me or not.
>>
>>
>>
>> The improvements to Tripal that we are able to do right now are
>> prioritized by the objectives of our current funded projects.   I think we
>> should make a prioritized list of future development tasks for Tripal,
>> however I think it’s important to remember that we may not be able to
>> implement those ideas unless our various PI’s agree or see that our ideas
>> fit within the scope of the current projects.   I would like to see  one day
>> funding for dedicated staff (at least one person) to develop infrastructure,
>> develop documentation, respond to user requests.  My impression is that this
>> of course will be tied to a larger scientific investigation for which Tripal
>> development will play an important role.
>>
>>
>>
>> Michael, if you have time and resources to do some work with CCK, Panels,
>> Drupal 7, Drupal features, etc. I think that’s wonderful.  Perhaps we could
>> create a separate branch in the GMOD SVN repository for a Drupal 7 version
>> that you could work out of.  I’m not so sure we can completely remove the
>> need for PHP Drupal modules as we currently have them.   Currently they are
>> more portable.  But, perhaps I don’t understand enough about CCK and Drupal
>> 7 to know how that can be changed.  I’m happy to be educated :-)
>>
>>
>>
>> As Lacey mentioned in a previous email she has just about handled the
>> Views, and we now have a way to install Chado local to the Drupal database
>> so we have the major hurdle for integration with Drupal Views handled.
>>
>>
>>
>> My goal is that we release a new version of Tripal by early March that
>> will have many of Lacey’s improvements as well as some others that I have
>> worked in.
>>
>>
>>
>> One other thought I would like to add is that we recognize the three
>> different levels of users that I think Tripal should support:  1. The
>> wet-lab scientist who has few IT resources, but who wants a functional,
>> searchable online resources for his/her data that is easy to setup and
>> manage.   2.  The larger lab with good bioinformatics support that will want
>> to fully customize visualizations  of their data, will want a flexible
>> platform that is well supported with a responsive community.    3.   The
>> Chado-expert who understands the schema, understands the data and wants to
>> look at it in novel ways  which perhaps are not available through the
>> resources/tools/visualizations of the primary database, but who doesn’t want
>> to do a lot of PHP coding either (Mike, If I understand your goals, I think
>> you would fall into case #3,  right?).   Have I captured these three groups
>> correctly?  Am I missing any?
>>
>>
>>
>> Thanks!  Happy PAG’ing.
>>
>> Stephen
>>
>>
>>
>>
>>
>>
>>
>> From: Michael Caudy [mailto:[hidden email]]
>> Sent: Monday, January 17, 2011 11:12 PM
>> To: Meg Staton
>> Cc: Scott Cain; Stephen Ficklin; [hidden email];
>> Ilhyung Cho; [hidden email]; Sook Jung
>> Subject: Topics for discussion at tomorrow's dinner meeting (and/or later)
>>
>>
>>
>> Topics for discussion at tomorrow's dinner meeting (and/or later)
>>
>>
>>
>> Hi everyone,
>>
>>
>>
>> There have been a number of recent phone conversations between me and
>> Stephen and/or Scott about a number of important issues for future Tripal /
>> Drupal / GMODviews development. I would like to go over those briefly at
>> dinner tomorrow, so that everyone is informed about them.
>>
>>
>>
>> * Scott suggested having regular Tripal conference calls soon that include
>> all Tripal-related developers, so that the next stages of the development
>> plan can be discussed, and different parts assigned to different
>> developers.
>>
>>
>>
>> * I am definitely interested and willing to work further on the
>> integration of Tripal with some of the newer, more advanced Drupal
>> functionality:
>>
>>                 including full integration with Views and Views-related
>> functionality, such as CCK and Panels.
>>
>>
>>
>> * Porting Tripal to Drupal 7, now that D7 is out.
>>
>>
>>
>> * I also am definitely interested creating "Features" based on Tripal, so
>> that content types don't have to be defined by custom content modules, which
>> is now the case.  Note: I am referring here to "Drupal Features", not "Chado
>> Features", where "Features" are a new development in Drupal in which
>> specific content types and/or configurations are made "exportable" and
>> persistant, so that they can be included in base installations, rather than
>> manually-configured each time a new installation is made.
>>
>>     see http://drupal.org/project/features
>>
>>
>>
>> It probably makes sense for the Features development to wait until after
>> the D7 port is completed
>>
>>
>>
>> Mike
>>
>>
>>
>> On Mon, Jan 17, 2011 at 6:53 PM, Meg Staton <[hidden email]> wrote:
>>
>> I'll see you all at the fountain. Thanks!
>>
>> Meg
>>
>> Sent from my iPhone
>>
>> On Jan 17, 2011, at 5:15 PM, Michael Caudy <[hidden email]> wrote:
>>
>> Hi Scott and Stephen and everyone at PAG,
>>
>>
>>
>> I was just about to send an e-mail message about the plan for a
>> Tripal-related dinner on Tuesday, when I got these messages from Scott and
>> Stephen,
>>
>>
>>
>> Scott's suggestions for where to eat sound fine to me. We should try to
>> find some place where we can hear each other talk, however.
>>
>>
>>
>> I look forward to see you all tomorrow.
>>
>>
>>
>> MIke
>>
>>
>>
>> On Mon, Jan 17, 2011 at 5:07 PM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Stephan and all,
>>
>> Sorry I forgot to email about this earlier. I meant to do it on Monday
>> last week.
>>
>> Perhaps we should shoot for 6:30, since the meeting schedule goes
>> until 6:00. We could meet at the fountain outside the convention hall.
>>  For where to go from there, I can suggest a few things.  Very close
>> is california pizza kitchen and pf changs (at the mall).  A little
>> father away is a good sushi restaurant at the crowne plaza hotel, and
>> farther away (just barely walking distance, up a big hill) is
>> Hillcrest, where there are several good restaurants.  Does anyone have
>> a preference?
>>
>> Thanks,
>> Scott
>>
>> On Monday, January 17, 2011, Stephen Ficklin <[hidden email]> wrote:
>> > Hi Scott,
>> >
>> > Is there still interest on your side to have a Tripal meeting Tuesday
>> > night
>> > at PAG?  If so, would 6pm work for you?  I'm at a loss for where
>> > though...
>> > Would you mind making a suggestion?
>> >
>> > Thanks,
>> > Stephen
>> >
>> > -----Original Message-----
>> > From: Scott Cain [mailto:[hidden email]]
>> > Sent: Tuesday, January 04, 2011 4:04 PM
>> > To: Stephen Ficklin
>> > Cc: [hidden email]
>> > Subject: Re: [Gmod-tripal] Who's attending PAG?
>> >
>> > Hi Stephen and Meg,
>> >
>> > Depending on Stephen's schedule, would you be interested in sitting
>> > down to chat about future development for Tripal on Tuesday evening
>> > (Jan 18)?  I'll be there, as will Mike Caudy.  Anybody else interested
>> > would be of course welcome too.
>> >
>> > Scott
>> >
>> >
>> > On Wed, Dec 8, 2010 at 2:31 PM, Stephen Ficklin <[hidden email]>
>> > wrote:
>> >> Hi Scott,
>> >>
>> >> I'm scheduled to be there Tuesday evening and Wednesday.
>> >>
>> >> Stephen
>> >>
>> >> -----Original Message-----
>> >> From: Scott Cain [mailto:[hidden email]]
>> >> Sent: Wednesday, December 08, 2010 2:28 PM
>> >> To: [hidden email]
>> >> Subject: [Gmod-tripal] Who's attending PAG?
>> >>
>> >> Hi all,
>> >>
>> >> I was wondering who associated with Tripal is attending PAG in
>> >> January.  I was thinking that it might be nice to have everyone sit
>> >> down at a table at some point during the meeting to chat about coming
>> >> plans and needs for Tripal.
>> >>
>> >> Scott
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> >> net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >>
>> >>
>> >
>> > ----------------------------------------------------------------------------
>> >> --
>> >> This SF Dev2Dev email is sponsored by:
>> >>
>> >> WikiLeaks The End of the Free Internet
>> >> http://p.sf.net/sfu/therealnews-com
>> >> _______________________________________________
>> >> Gmod-tripal mailing list
>> >> [hidden email]
>> >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     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
>>
>>
>>
>>
>
>



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