[Gmod-gbrowse] NIH RFA for software development

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[Gmod-gbrowse] NIH RFA for software development

Lincoln Stein-2
Hi GMOD developers,

Here is information on an NIH program that provides support for biological
software development. There are two application deadlines per year, and the
next deadline is in May. I strongly recommend that you consider applying for
support! I will be happy to provide strong letters of support from GMOD.

Lincoln

Title:  Continued Development and Maintenance of Software

Executive Summary:  Biomedical research laboratories increasingly undertake
a software development project to solve a problem of interest to that
laboratory. These software packages sometimes become useful to a much
broader community of users that can include translational and clinical
researchers. The goal of this program announcement is to support the
continued development, maintenance, testing and evaluation of existing
software...

http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [hidden email]


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Re: [Gmod-schema] NIH RFA for software development

Suzanna Lewis
We will be putting in a proposal for Apollo complementing the
work proposed on the DAS2 proposal.

-S

On Dec 12, 2005, at 2:20 PM, Lincoln Stein wrote:

> Hi GMOD developers,
>
> Here is information on an NIH program that provides support for
> biological
> software development. There are two application deadlines per year,
> and the
> next deadline is in May. I strongly recommend that you consider
> applying for
> support! I will be happy to provide strong letters of support from
> GMOD.
>
> Lincoln
>
> Title:  Continued Development and Maintenance of Software
>
> Executive Summary:  Biomedical research laboratories increasingly
> undertake
> a software development project to solve a problem of interest to that
> laboratory. These software packages sometimes become useful to a much
> broader community of users that can include translational and clinical
> researchers. The goal of this program announcement is to support the
> continued development, maintenance, testing and evaluation of existing
> software...
>
> http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT [hidden email]
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



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Re: [Gmod-schema] NIH RFA for software development

Suzanna Lewis
In reply to this post by Lincoln Stein-2
This is just a thought that occurred to me, and I'd like to hear
opinions.

I'm thinking maybe we (Chris, me, other interested parties)  should go
in for some level of Chado support and/or development of new/current
modules?

-S

On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:

> Hi GMOD developers,
>
> Here is information on an NIH program that provides support for
> biological
> software development. There are two application deadlines per year,
> and the
> next deadline is in May. I strongly recommend that you consider
> applying for
> support! I will be happy to provide strong letters of support from
> GMOD.
>
> Lincoln
>
> Title:  Continued Development and Maintenance of Software
>
> Executive Summary:  Biomedical research laboratories increasingly
> undertake
> a software development project to solve a problem of interest to that
> laboratory. These software packages sometimes become useful to a much
> broader community of users that can include translational and clinical
> researchers. The goal of this program announcement is to support the
> continued development, maintenance, testing and evaluation of existing
> software...
>
> http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT [hidden email]
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



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RE: Re: [Gmod-schema] NIH RFA for software development

Shimoyama, Mary
[GMOD-devel] Re: [Gmod-schema] NIH RFA for software development
Hi Suzanna - I think this is an excellent idea.  More and more genomes are being sequenced and more and more groups will be using Chado as well as Apollo.  I believe that changes to existing modulels and the addition of new modules will become of interest to many groups.  I think we need to keep in mind that most of the genomes will not be taken to a finished condition and there will be a greater need for robust tools to help these groups annotate, store and provide access to their data.
 
Mary Shimoyama
Data Development Manager
Rat Genome Database


From: [hidden email] on behalf of Suzanna Lewis
Sent: Sat 12/17/2005 12:51 PM
To: [hidden email]
Cc: [hidden email]; [hidden email]; [hidden email]
Subject: [GMOD-devel] Re: [Gmod-schema] NIH RFA for software development

This is just a thought that occurred to me, and I'd like to hear
opinions.

I'm thinking maybe we (Chris, me, other interested parties)  should go
in for some level of Chado support and/or development of new/current
modules?

-S

On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:


> Hi GMOD developers,
>
> Here is information on an NIH program that provides support for
> biological
> software development. There are two application deadlines per year,
> and the
> next deadline is in May. I strongly recommend that you consider
> applying for
> support! I will be happy to provide strong letters of support from
> GMOD.
>
> Lincoln
>
> Title:  Continued Development and Maintenance of Software
>
> Executive Summary:  Biomedical research laboratories increasingly
> undertake
> a software development project to solve a problem of interest to that
> laboratory. These software packages sometimes become useful to a much
> broader community of users that can include translational and clinical
> researchers. The goal of this program announcement is to support the
> continued development, maintenance, testing and evaluation of existing
> software...
>
> http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT [hidden email]
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



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Re: Re: [Gmod-schema] NIH RFA for software development

Lincoln Stein-2
In reply to this post by Suzanna Lewis
That's a good idea. I'd like to hear from Harvard on this.

Lincoln

On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:

> This is just a thought that occurred to me, and I'd like to hear
> opinions.
>
> I'm thinking maybe we (Chris, me, other interested parties)  should go
> in for some level of Chado support and/or development of new/current
> modules?
>
> -S
>
> On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
> > Hi GMOD developers,
> >
> > Here is information on an NIH program that provides support for
> > biological
> > software development. There are two application deadlines per year,
> > and the
> > next deadline is in May. I strongly recommend that you consider
> > applying for
> > support! I will be happy to provide strong letters of support from
> > GMOD.
> >
> > Lincoln
> >
> > Title:  Continued Development and Maintenance of Software
> >
> > Executive Summary:  Biomedical research laboratories increasingly
> > undertake
> > a software development project to solve a problem of interest to that
> > laboratory. These software packages sometimes become useful to a much
> > broader community of users that can include translational and clinical
> > researchers. The goal of this program announcement is to support the
> > continued development, maintenance, testing and evaluation of existing
> > software...
> >
> > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
> >
> > --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > FOR URGENT MESSAGES & SCHEDULING,
> > PLEASE CONTACT MY ASSISTANT,
> > SANDRA MICHELSEN, AT [hidden email]
> >
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> > files
> > for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > _______________________________________________
> > Gmod-schema mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> files for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

--
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING,
PLEASE CONTACT MY ASSISTANT,
SANDRA MICHELSEN, AT [hidden email]


-------------------------------------------------------
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Re: Re: [Gmod-schema] NIH RFA for software development

Peili Zhang
In reply to this post by Lincoln Stein-2

i'm interested in helping develop an interaction module (i.e. a module dedicated
to interaction data) for chado. the interaction module will be extending the
current pairwise feature_relationship to store any complex
interactions/networks, imo.

peili

> From: Lincoln Stein <[hidden email]>
> To: [hidden email]
> Subject: Re: [GMOD-devel] Re: [Gmod-schema] NIH RFA for software development
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>
> That's a good idea. I'd like to hear from Harvard on this.
>
> Lincoln
>
> On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:
> > This is just a thought that occurred to me, and I'd like to hear
> > opinions.
> >
> > I'm thinking maybe we (Chris, me, other interested parties)  should go
> > in for some level of Chado support and/or development of new/current
> > modules?
> >
> > -S
> >
> > On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
> > > Hi GMOD developers,
> > >
> > > Here is information on an NIH program that provides support for
> > > biological
> > > software development. There are two application deadlines per year,
> > > and the
> > > next deadline is in May. I strongly recommend that you consider
> > > applying for
> > > support! I will be happy to provide strong letters of support from
> > > GMOD.
> > >
> > > Lincoln
> > >
> > > Title:  Continued Development and Maintenance of Software
> > >
> > > Executive Summary:  Biomedical research laboratories increasingly
> > > undertake
> > > a software development project to solve a problem of interest to that
> > > laboratory. These software packages sometimes become useful to a much
> > > broader community of users that can include translational and clinical
> > > researchers. The goal of this program announcement is to support the
> > > continued development, maintenance, testing and evaluation of existing
> > > software...
> > >
> > > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
> > >
> > > --
> > > Lincoln D. Stein
> > > Cold Spring Harbor Laboratory
> > > 1 Bungtown Road
> > > Cold Spring Harbor, NY 11724
> > > FOR URGENT MESSAGES & SCHEDULING,
> > > PLEASE CONTACT MY ASSISTANT,
> > > SANDRA MICHELSEN, AT [hidden email]
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> > > files
> > > for problems?  Stop!  Download the new AJAX search engine that makes
> > > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> > > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> > > _______________________________________________
> > > Gmod-schema mailing list
> > > [hidden email]
> > > https://lists.sourceforge.net/lists/listinfo/gmod-schema
> >
> > -------------------------------------------------------
> > This SF.net email is sponsored by: Splunk Inc. Do you grep through log
> > files for problems?  Stop!  Download the new AJAX search engine that makes
> > searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
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> > _______________________________________________
> > Gmod-devel mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT [hidden email]
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
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> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel



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Re: Re: [Gmod-schema] NIH RFA for software development

David Emmert
In reply to this post by Lincoln Stein-2
Hi,

I mentioned Suzi's proposal to Bill this morning.  He asked what
multi-year chado development project(s) want/need to be done.  Its a
good question!  Suzi, what specific areas for chado development did you
have in mind?

Best,

-Dave

On Mon, 19 Dec 2005 13:03, Lincoln Stein wrote:

> That's a good idea. I'd like to hear from Harvard on this.
>
> Lincoln
>
> On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:
>>  This is just a thought that occurred to me, and I'd like to hear
>>  opinions.
>>
>>  I'm thinking maybe we (Chris, me, other interested parties)  should go
>>  in for some level of Chado support and/or development of new/current
>>  modules?
>>
>>  -S
>>
>>  On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
>>  > Hi GMOD developers,
>>  >
>>  > Here is information on an NIH program that provides support for
>>  > biological
>>  > software development. There are two application deadlines per year,
>>  > and the
>>  > next deadline is in May. I strongly recommend that you consider
>>  > applying for
>>  > support! I will be happy to provide strong letters of support from
>>  > GMOD.
>>  >
>>  > Lincoln
>>  >
>>  > Title:  Continued Development and Maintenance of Software
>>  >
>>  > Executive Summary:  Biomedical research laboratories increasingly
>>  > undertake
>>  > a software development project to solve a problem of interest to
>> that
>>  > laboratory. These software packages sometimes become useful to a
>> much
>>  > broader community of users that can include translational and
>> clinical
>>  > researchers. The goal of this program announcement is to support the
>>  > continued development, maintenance, testing and evaluation of
>> existing
>>  > software...
>>  >
>>  > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>>  >
>>  > --
>>  > Lincoln D. Stein
>>  > Cold Spring Harbor Laboratory
>>  > 1 Bungtown Road
>>  > Cold Spring Harbor, NY 11724
>>  > FOR URGENT MESSAGES & SCHEDULING,
>>  > PLEASE CONTACT MY ASSISTANT,
>>  > SANDRA MICHELSEN, AT [hidden email]
>>  >
>>  >
>>  > -------------------------------------------------------
>>  > This SF.net email is sponsored by: Splunk Inc. Do you grep through
>> log
>>  > files
>>  > for problems?  Stop!  Download the new AJAX search engine that makes
>>  > searching your log files as easy as surfing the  web.  DOWNLOAD
>> SPLUNK!
>>  > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>>  > _______________________________________________
>>  > Gmod-schema mailing list
>>  > [hidden email]
>>  > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>  -------------------------------------------------------
>>  This SF.net email is sponsored by: Splunk Inc. Do you grep through log
>>  files for problems?  Stop!  Download the new AJAX search engine that
>> makes
>>  searching your log files as easy as surfing the  web.  DOWNLOAD
>> SPLUNK!
>>  http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>>  _______________________________________________
>>  Gmod-devel mailing list
>>  [hidden email]
>>  https://lists.sourceforge.net/lists/listinfo/gmod-devel
>
> --
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT [hidden email]
>
>
> -------------------------------------------------------
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Re: Re: [Gmod-schema] NIH RFA for software development

Chris Mungall
Off the top of my head:

  - New modules
       systems biology/pathways/interactions (Peili and I have made
independent starts here)
       additional modules for relating model organism data to human
disease

  - More work and testing of existing non-core modules: phylogeny,
phenotype, expression ..

  - Standardized software architecture
       either XORT or multi-language O/R layer, or both. more
coordination of efforts
       more integration with other GMOD tools, plus bioperl, biojava,
caBIG, etc

  - Compatibility layers
       BioSQL, GO-DB, GUS, Ensembl, EnsMart, CMap, MAGE....
       either at the relational layer or the middleware layer
       (I favour the former - the godb view/bridge layer proves that
this works; could do with more work on optimisation though)

  - More domain logic implemented at DBMS level (possibly a
controversial one..)
       The range of pgsql functions for chado is already quite wide -
ports to other DBMSs required

  - Optimisation

  - Documentation and outreach


On Dec 19, 2005, at 12:44 PM, David Emmert wrote:

> Hi,
>
> I mentioned Suzi's proposal to Bill this morning.  He asked what
> multi-year chado development project(s) want/need to be done.  Its a
> good question!  Suzi, what specific areas for chado development did
> you have in mind?
>
> Best,
>
> -Dave
>
> On Mon, 19 Dec 2005 13:03, Lincoln Stein wrote:
>> That's a good idea. I'd like to hear from Harvard on this.
>>
>> Lincoln
>>
>> On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:
>>>  This is just a thought that occurred to me, and I'd like to hear
>>>  opinions.
>>>
>>>  I'm thinking maybe we (Chris, me, other interested parties)  should
>>> go
>>>  in for some level of Chado support and/or development of new/current
>>>  modules?
>>>
>>>  -S
>>>
>>>  On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
>>>  > Hi GMOD developers,
>>>  >
>>>  > Here is information on an NIH program that provides support for
>>>  > biological
>>>  > software development. There are two application deadlines per
>>> year,
>>>  > and the
>>>  > next deadline is in May. I strongly recommend that you consider
>>>  > applying for
>>>  > support! I will be happy to provide strong letters of support from
>>>  > GMOD.
>>>  >
>>>  > Lincoln
>>>  >
>>>  > Title:  Continued Development and Maintenance of Software
>>>  >
>>>  > Executive Summary:  Biomedical research laboratories increasingly
>>>  > undertake
>>>  > a software development project to solve a problem of interest to
>>> that
>>>  > laboratory. These software packages sometimes become useful to a
>>> much
>>>  > broader community of users that can include translational and
>>> clinical
>>>  > researchers. The goal of this program announcement is to support
>>> the
>>>  > continued development, maintenance, testing and evaluation of
>>> existing
>>>  > software...
>>>  >
>>>  > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>>>  >
>>>  > --
>>>  > Lincoln D. Stein
>>>  > Cold Spring Harbor Laboratory
>>>  > 1 Bungtown Road
>>>  > Cold Spring Harbor, NY 11724
>>>  > FOR URGENT MESSAGES & SCHEDULING,
>>>  > PLEASE CONTACT MY ASSISTANT,
>>>  > SANDRA MICHELSEN, AT [hidden email]
>>>  >
>>>  >
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>>
>> --
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> FOR URGENT MESSAGES & SCHEDULING,
>> PLEASE CONTACT MY ASSISTANT,
>> SANDRA MICHELSEN, AT [hidden email]
>>
>>
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Re: Re: [Gmod-schema] NIH RFA for software development

Peili Zhang
In reply to this post by Lincoln Stein-2

>
>   - New modules
>        systems biology/pathways/interactions (Peili and I have made
> independent starts here)

i've only done some research/thinking for an interaction module in chado, no
concrete module design yet. i'd love to contribute to the design effort if it
gets underway.

cheers,
peili



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Re: Re: [Gmod-schema] NIH RFA for software development

Suzanna Lewis
In reply to this post by Chris Mungall
Hi Dave,

I think Chris has nailed it. There may be other new modules as well to
consider,
but it is clear that there is a lot of biology that doesn't yet have a
home within the
current Chado. In addition; since the RFA includes making things
generic,
maintenance, and support;  there is quite a bit of work to be done in
the areas
of testing, compatibility, standardization, documentation, ease of
installation,
and customization.

I really hope you will consider it. We'd love to have you on this
project.

-S

On Dec 19, 2005, at 2:22 PM, chris mungall wrote:

> Off the top of my head:
>
>  - New modules
>       systems biology/pathways/interactions (Peili and I have made
> independent starts here)
>       additional modules for relating model organism data to human
> disease
>
>  - More work and testing of existing non-core modules: phylogeny,
> phenotype, expression ..
>
>  - Standardized software architecture
>       either XORT or multi-language O/R layer, or both. more
> coordination of efforts
>       more integration with other GMOD tools, plus bioperl, biojava,
> caBIG, etc
>
>  - Compatibility layers
>       BioSQL, GO-DB, GUS, Ensembl, EnsMart, CMap, MAGE....
>       either at the relational layer or the middleware layer
>       (I favour the former - the godb view/bridge layer proves that
> this works; could do with more work on optimisation though)
>
>  - More domain logic implemented at DBMS level (possibly a
> controversial one..)
>       The range of pgsql functions for chado is already quite wide -
> ports to other DBMSs required
>
>  - Optimisation
>
>  - Documentation and outreach
>
>
> On Dec 19, 2005, at 12:44 PM, David Emmert wrote:
>
>> Hi,
>>
>> I mentioned Suzi's proposal to Bill this morning.  He asked what
>> multi-year chado development project(s) want/need to be done.  Its a
>> good question!  Suzi, what specific areas for chado development did
>> you have in mind?
>>
>> Best,
>>
>> -Dave
>>
>> On Mon, 19 Dec 2005 13:03, Lincoln Stein wrote:
>>> That's a good idea. I'd like to hear from Harvard on this.
>>>
>>> Lincoln
>>>
>>> On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:
>>>>  This is just a thought that occurred to me, and I'd like to hear
>>>>  opinions.
>>>>
>>>>  I'm thinking maybe we (Chris, me, other interested parties)  
>>>> should go
>>>>  in for some level of Chado support and/or development of
>>>> new/current
>>>>  modules?
>>>>
>>>>  -S
>>>>
>>>>  On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
>>>>  > Hi GMOD developers,
>>>>  >
>>>>  > Here is information on an NIH program that provides support for
>>>>  > biological
>>>>  > software development. There are two application deadlines per
>>>> year,
>>>>  > and the
>>>>  > next deadline is in May. I strongly recommend that you consider
>>>>  > applying for
>>>>  > support! I will be happy to provide strong letters of support
>>>> from
>>>>  > GMOD.
>>>>  >
>>>>  > Lincoln
>>>>  >
>>>>  > Title:  Continued Development and Maintenance of Software
>>>>  >
>>>>  > Executive Summary:  Biomedical research laboratories increasingly
>>>>  > undertake
>>>>  > a software development project to solve a problem of interest to
>>>> that
>>>>  > laboratory. These software packages sometimes become useful to a
>>>> much
>>>>  > broader community of users that can include translational and
>>>> clinical
>>>>  > researchers. The goal of this program announcement is to support
>>>> the
>>>>  > continued development, maintenance, testing and evaluation of
>>>> existing
>>>>  > software...
>>>>  >
>>>>  > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>>>>  >
>>>>  > --
>>>>  > Lincoln D. Stein
>>>>  > Cold Spring Harbor Laboratory
>>>>  > 1 Bungtown Road
>>>>  > Cold Spring Harbor, NY 11724
>>>>  > FOR URGENT MESSAGES & SCHEDULING,
>>>>  > PLEASE CONTACT MY ASSISTANT,
>>>>  > SANDRA MICHELSEN, AT [hidden email]
>>>>  >
>>>>  >
>>>>  > -------------------------------------------------------
>>>>  > This SF.net email is sponsored by: Splunk Inc. Do you grep
>>>> through log
>>>>  > files
>>>>  > for problems?  Stop!  Download the new AJAX search engine that
>>>> makes
>>>>  > searching your log files as easy as surfing the  web.  DOWNLOAD
>>>> SPLUNK!
>>>>  > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>>>>  > _______________________________________________
>>>>  > Gmod-schema mailing list
>>>>  > [hidden email]
>>>>  > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>>  -------------------------------------------------------
>>>>  This SF.net email is sponsored by: Splunk Inc. Do you grep through
>>>> log
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>>>>  searching your log files as easy as surfing the  web.  DOWNLOAD
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>>>>  _______________________________________________
>>>>  Gmod-devel mailing list
>>>>  [hidden email]
>>>>  https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>>
>>> --
>>> Lincoln D. Stein
>>> Cold Spring Harbor Laboratory
>>> 1 Bungtown Road
>>> Cold Spring Harbor, NY 11724
>>> FOR URGENT MESSAGES & SCHEDULING,
>>> PLEASE CONTACT MY ASSISTANT,
>>> SANDRA MICHELSEN, AT [hidden email]
>>>
>>>
>>> -------------------------------------------------------
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>>> _______________________________________________
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>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel
>>
>>
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>
>
>
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RE: Re: [Gmod-schema] NIH RFA for software development

Shimoyama, Mary
In reply to this post by Chris Mungall
Re: [GMOD-devel] Re: [Gmod-schema] NIH RFA for software development
I believe that in the next several years the demands for proposed and new modules will increase. In particular many groups would be interested in the pathway/interaction modules, relating model organism data to human disease, phenotypes and expression. Modules related to phylogeny and strains would also be great.  Compatibility layers mentioned below would allow integration of more tools and data. Integration of data analysis and visualization tools would also be great - many would like to access the data in subsets and analyze for over representation of functions, pathway involvement, expression and other types of data. 


From: [hidden email] on behalf of chris mungall
Sent: Mon 12/19/2005 4:22 PM
To: David Emmert
Cc: [hidden email]; [hidden email]; chris mungall; Bill Gelbart
Subject: Re: [GMOD-devel] Re: [Gmod-schema] NIH RFA for software development

Off the top of my head:

  - New modules
       systems biology/pathways/interactions (Peili and I have made
independent starts here)
       additional modules for relating model organism data to human
disease

  - More work and testing of existing non-core modules: phylogeny,
phenotype, expression ..

  - Standardized software architecture
       either XORT or multi-language O/R layer, or both. more
coordination of efforts
       more integration with other GMOD tools, plus bioperl, biojava,
caBIG, etc

  - Compatibility layers
       BioSQL, GO-DB, GUS, Ensembl, EnsMart, CMap, MAGE....
       either at the relational layer or the middleware layer
       (I favour the former - the godb view/bridge layer proves that
this works; could do with more work on optimisation though)

  - More domain logic implemented at DBMS level (possibly a
controversial one..)
       The range of pgsql functions for chado is already quite wide -
ports to other DBMSs required

  - Optimisation

  - Documentation and outreach


On Dec 19, 2005, at 12:44 PM, David Emmert wrote:


> Hi,
>
> I mentioned Suzi's proposal to Bill this morning.  He asked what
> multi-year chado development project(s) want/need to be done.  Its a
> good question!  Suzi, what specific areas for chado development did
> you have in mind?
>
> Best,
>
> -Dave
>
> On Mon, 19 Dec 2005 13:03, Lincoln Stein wrote:
>> That's a good idea. I'd like to hear from Harvard on this.
>>
>> Lincoln
>>
>> On Saturday 17 December 2005 01:51 pm, Suzanna Lewis wrote:
>>>  This is just a thought that occurred to me, and I'd like to hear
>>>  opinions.
>>>
>>>  I'm thinking maybe we (Chris, me, other interested parties)  should
>>> go
>>>  in for some level of Chado support and/or development of new/current
>>>  modules?
>>>
>>>  -S
>>>
>>>  On Dec 12, 2005, at 11:20 AM, Lincoln Stein wrote:
>>>  > Hi GMOD developers,
>>>  >
>>>  > Here is information on an NIH program that provides support for
>>>  > biological
>>>  > software development. There are two application deadlines per
>>> year,
>>>  > and the
>>>  > next deadline is in May. I strongly recommend that you consider
>>>  > applying for
>>>  > support! I will be happy to provide strong letters of support from
>>>  > GMOD.
>>>  >
>>>  > Lincoln
>>>  >
>>>  > Title:  Continued Development and Maintenance of Software
>>>  >
>>>  > Executive Summary:  Biomedical research laboratories increasingly
>>>  > undertake
>>>  > a software development project to solve a problem of interest to
>>> that
>>>  > laboratory. These software packages sometimes become useful to a
>>> much
>>>  > broader community of users that can include translational and
>>> clinical
>>>  > researchers. The goal of this program announcement is to support
>>> the
>>>  > continued development, maintenance, testing and evaluation of
>>> existing
>>>  > software...
>>>  >
>>>  > http://grants.nih.gov/grants/guide/pa-files/PAR-05-057.html
>>>  >
>>>  > --
>>>  > Lincoln D. Stein
>>>  > Cold Spring Harbor Laboratory
>>>  > 1 Bungtown Road
>>>  > Cold Spring Harbor, NY 11724
>>>  > FOR URGENT MESSAGES & SCHEDULING,
>>>  > PLEASE CONTACT MY ASSISTANT,
>>>  > SANDRA MICHELSEN, AT [hidden email]
>>>  >
>>>  >
>>>  > -------------------------------------------------------
>>>  > This SF.net email is sponsored by: Splunk Inc. Do you grep
>>> through log
>>>  > files
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>>>  > Gmod-schema mailing list
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>>>  > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
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>>
>> --
>> Lincoln D. Stein
>> Cold Spring Harbor Laboratory
>> 1 Bungtown Road
>> Cold Spring Harbor, NY 11724
>> FOR URGENT MESSAGES & SCHEDULING,
>> PLEASE CONTACT MY ASSISTANT,
>> SANDRA MICHELSEN, AT [hidden email]
>>
>>
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