Tripal Phylogeny Module Discussion

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Tripal Phylogeny Module Discussion

Stephen Ficklin-2
Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

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Re: Tripal Phylogeny Module Discussion

adf_ncgr
Hi Stephen-
thanks for getting this ball rolling again. I just looked at the poll
and am going
to provisionally suggest that you limit the choices to the week of
4/18-4/22; I have
some conflicting responsibilities the preceding week that may be a bit
of a distraction, and
if you go ahead and limit the poll choices it may save other people some
time in responding.
For now, I'll just fill out times for the 4/18-4/22 week, and if it
proves difficult to come
up with a good time that week we can revisit.

I should note that our work so far has been mostly focused on "gene
family" trees rather than
species trees. If anyone wants to peek at the module in its current
working state in the
context of our site to help them decide on their level of interest, the
search view is here:
http://legumeinfo.org/search/phylotree

or they can go directly to a representative gene tree here:
http://legumeinfo.org/chado_phylotree/phytozome_10_2.59083055

There's also a built-in "quick tour" accessible through the help button
that points out some
of the less obvious interactive features.

we're very much looking forward to getting some input from this
community on what might be of
general interest...

Andrew


On 3/29/16 10:37 PM, Stephen Ficklin wrote:

> Hi All,
>
> In our Tripal Developer's Meeting this month we discussed the Tripal
> Phylogeny module which has been created by Andrew Farmer's group at
> NCGR.  The goal is to make this module publicly available but some
> feedback is needed from the larger group to identify how to generalize
> the module sufficiently so that it can be used by a broad user base.  I
> promised I would send out a Doodle poll to organize a meeting for that
> discussion.
>
> If you are interested in displaying phylogenetic trees on your Tripal
> site please consider joining this discussion to provide feedback.  A
> Doodle poll has been setup to select an optimal time for those who would
> like to participate:
>
> http://doodle.com/poll/pugdmbhpb7cerb9h
>
> Thanks,
> Stephen
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
> _______________________________________________
> Gmod-tripal mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-tripal

--
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche


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Re: Tripal Phylogeny Module Discussion

Stephen Ficklin-2
For those interested in attending the Tripal Phylogeny Module
discussion, it looks as though the best time will be Wednesday April
20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or
two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:

>> Hi All,
>>
>> In our Tripal Developer's Meeting this month we discussed the Tripal
>> Phylogeny module which has been created by Andrew Farmer's group at
>> NCGR.  The goal is to make this module publicly available but some
>> feedback is needed from the larger group to identify how to generalize
>> the module sufficiently so that it can be used by a broad user base.  I
>> promised I would send out a Doodle poll to organize a meeting for that
>> discussion.
>>
>> If you are interested in displaying phylogenetic trees on your Tripal
>> site please consider joining this discussion to provide feedback.  A
>> Doodle poll has been setup to select an optimal time for those who would
>> like to participate:
>>
>> http://doodle.com/poll/pugdmbhpb7cerb9h
>>
>> Thanks,
>> Stephen
>>
>> ------------------------------------------------------------------------------
>> Transform Data into Opportunity.
>> Accelerate data analysis in your applications with
>> Intel Data Analytics Acceleration Library.
>> Click to learn more.
>> http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
>> _______________________________________________
>> Gmod-tripal mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal


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Re: Tripal Phylogeny Module Discussion

Stephen Ficklin-2

Hi All,

Below are connection details for our meeting this Wednesday regarding the Tripal Phylogeny module. Anyone interested in using this module is welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Phylogeny Module Discussion

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/630740901

You can also dial in using your phone.
United States : +1 (408) 650-3123

Access Code: 630-740-901

Stephen

On 4/12/2016 10:18 AM, Stephen Ficklin wrote:
For those interested in attending the Tripal Phylogeny Module discussion, it looks as though the best time will be Wednesday April 20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:
Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

------------------------------------------------------------------------------
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Intel Data Analytics Acceleration Library.
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_______________________________________________
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Re: Tripal Phylogeny Module Discussion

adf_ncgr
Thanks Stephen-
just following up for the benefit of anyone who may be unsure if they should attend tomorrow's meeting or not,
the basic agenda I have in mind for the call is:

Use case driven tour of phylogeny module. Focus on utility for finding possible areas for
    investigation of issues around gene annotation/assembly vs truly interesting biological phenomena;
    illustrate gene-family connectivity to other modules/tools implemented on legumeinfo.org (genome context viewer,
    multiple sequence alignment display, protein domain module)
Our current protocols for building families, MSAs, trees; protocols for data loading; use of standard chado
    tables + tripal materialized views; could be opportunity for some discussion on the differences between this
    full-phylogeny approach to gene family representation vs the flatter representation possible through the
    up-and-coming chado group module.
Discussion of areas of divergence between phylogeny module branches (legumeinfo
     implementation and proposed core implementation) and attempted resolution of what interested
     parties would like to have included in the core (could also include some discussion of ideas for where
     to go next with development of new features)
If there's time, some discussion of what it will take to make the phylogeny module compliant with Tripal 3.    

apologies for not getting this out to you all sooner (especially those in much earlier time zones!), but looking
forward to receiving feedback.

Andrew



On 4/18/16 10:44 AM, Stephen Ficklin wrote:

Hi All,

Below are connection details for our meeting this Wednesday regarding the Tripal Phylogeny module. Anyone interested in using this module is welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Phylogeny Module Discussion

Please join my meeting from your computer, tablet or smartphone.
https://global.gotomeeting.com/join/630740901

You can also dial in using your phone.
United States : +1 (408) 650-3123

Access Code: 630-740-901

Stephen

On 4/12/2016 10:18 AM, Stephen Ficklin wrote:
For those interested in attending the Tripal Phylogeny Module discussion, it looks as though the best time will be Wednesday April 20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:
Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

------------------------------------------------------------------------------
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Intel Data Analytics Acceleration Library.
Click to learn more.
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_______________________________________________
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[hidden email]
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-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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Re: [Gmod-tripal-devel] Tripal Phylogeny Module Discussion

Guignon, Valentin (Bioversity-France)
In reply to this post by Stephen Ficklin-2

Hi there!

 

Just a quick question as I could not attempt to the phylogeny module meeting the other day: is there any meeting notes we can access to see what has been said?

 

   Val

 

 

From: Stephen Ficklin [mailto:[hidden email]]
Sent: lundi 18 avril 2016 18:44
To: [hidden email]; gmod tripal devel <[hidden email]>
Subject: Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion

 

Hi All,

Below are connection details for our meeting this Wednesday regarding the Tripal Phylogeny module. Anyone interested in using this module is welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Phylogeny Module Discussion

 

Please join my meeting from your computer, tablet or smartphone.

https://global.gotomeeting.com/join/630740901

You can also dial in using your phone.

United States : +1 (408) 650-3123


Access Code: 630-740-901

Stephen

 

On 4/12/2016 10:18 AM, Stephen Ficklin wrote:

For those interested in attending the Tripal Phylogeny Module discussion, it looks as though the best time will be Wednesday April 20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:

Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

------------------------------------------------------------------------------
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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785471&iu=/4140
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 

 


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Re: [Gmod-tripal-devel] Tripal Phylogeny Module Discussion

adf_ncgr
Hi Valentin-
sorry you couldn't make it to the meeting. The _very_ rough document I put together to help structure the
discussion is here:
https://docs.google.com/document/d/15AZPn6-itD50QnD7EsOHFedLZOEh4U28ndsAr5sUbew/edit

Stephen and I have been carrying on a few threads of follow-on discussion from the meeting in comments there,
feel free to add to it if you have any further questions or thoughts.

Overall, it seems that there aren't any other sites with immediate plans to add phylogenetic data to their
tripal instances, so questions about what to do in a generic, reusable version of the module don't seem to
be a big priority for us to resolve now, but if you do have interest in pursuing it for your site in the near term
we'd be happy to work with you.

One other result of the discussion had to do with representation of taxonomic information; Stephen had
added a loader for taxonomic data into the version of the phylogeny module that he was helping us to
make more generic, but I think we agreed during the meeting that it made more sense to move this into
the organism module (see document comments for some further discussion). People with multi-species
sites who aren't yet trying to handle phylogenies per se will probably find this more suited to their needs
than wrapping it in with the phylogeny module.

Hope that helps

Andrew


On 4/22/16 2:26 AM, Guignon, Valentin (Bioversity-France) wrote:

Hi there!

 

Just a quick question as I could not attempt to the phylogeny module meeting the other day: is there any meeting notes we can access to see what has been said?

 

   Val

 

 

From: Stephen Ficklin [[hidden email]]
Sent: lundi 18 avril 2016 18:44
To: [hidden email]; gmod tripal devel [hidden email]
Subject: Re: [Gmod-tripal-devel] [Gmod-tripal] Tripal Phylogeny Module Discussion

 

Hi All,

Below are connection details for our meeting this Wednesday regarding the Tripal Phylogeny module. Anyone interested in using this module is welcome to attend and provide feedback.

Times are at:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Phylogeny Module Discussion

 

Please join my meeting from your computer, tablet or smartphone.

https://global.gotomeeting.com/join/630740901

You can also dial in using your phone.

United States : +1 (408) 650-3123


Access Code: 630-740-901

Stephen

 

On 4/12/2016 10:18 AM, Stephen Ficklin wrote:

For those interested in attending the Tripal Phylogeny Module discussion, it looks as though the best time will be Wednesday April 20th at the following time:

UTC: 15:00 (3pm)
European Central:  17:00 (5pm)
Eastern US:  11am
Central US: 10am
Regina Canada: 9am
Pacific US: 8am

Please mark your calendars. I will send out connection details a day or two before the meeting.

Stephen

On 3/29/16 10:37 PM, Stephen Ficklin wrote:

Hi All,

In our Tripal Developer's Meeting this month we discussed the Tripal
Phylogeny module which has been created by Andrew Farmer's group at
NCGR.  The goal is to make this module publicly available but some
feedback is needed from the larger group to identify how to generalize
the module sufficiently so that it can be used by a broad user base.  I
promised I would send out a Doodle poll to organize a meeting for that
discussion.

If you are interested in displaying phylogenetic trees on your Tripal
site please consider joining this discussion to provide feedback.  A
Doodle poll has been setup to select an optimal time for those who would
like to participate:

http://doodle.com/poll/pugdmbhpb7cerb9h

Thanks,
Stephen

------------------------------------------------------------------------------
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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
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_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal

 

 



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-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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