From darin.london at duke.edu  Mon Jul  3 08:41:33 2006
From: darin.london at duke.edu (Darin London)
Date: Mon, 03 Jul 2006 08:41:33 -0400
Subject: [MOBY-l] Call For Birds of a Feather Suggestions
Message-ID: <44A9107D.2050304@duke.edu>

The BOSC organizing comittee is currently seeking suggestions for Birds
of a Feather meeting ideas. Birds of a Feather meetings are one of the
more popular activities at BOSC, occurring at the end of each days
session. These are free-form meetings organized by the attendees
themselves to discuss one or a few topics of interest in greater detail.
BOF?s have been formed to allow developers and users of individual OBF
software to meet each other face-to-face to discuss the project, or to
discuss completely new ideas, and even start new software development
projects. These meetings offer a unique opportunity for individuals to
explore more about the activities of the various Open Source Projects,
and, in some cases, even take an active role influencing the future of
Open Source Software development. If you would like to create a BOF,
just sign up for a wiki account, login, and edit the <a
href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
2006 Birds of a Feather page</a>.

From harttig at mail.dife.de  Mon Jul 10 09:43:58 2006
From: harttig at mail.dife.de (Ulrich Harttig)
Date: Mon, 10 Jul 2006 15:43:58 +0200
Subject: [MOBY-l] biomoby Perl API - error in t/dbConnect
Message-ID: <44B2599E.6030809@dife.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello all,

trying to upgrade to the current development version of biomoby, I came across
the following error when testing the Perl API

 t/dbConnect...................NOK 1
 #   Failed test 'use MOBY::lsid::authority::dbConnect;'
 #   in t/dbConnect.t at line 18.
 #     Tried to use 'MOBY::lsid::authority::dbConnect'.
 #     Error:  Can't locate MOBY/lsid/authority/dbConnect.pm in @INC (@INC contains:

since the Perl LSID code is now deprecated and has been removed from the
repository the test, maybe this test could also be removed ?

best regards
Ulrich

- --
Ulrich Harttig, Ph.D.
German Institute of Human Nutrition Potsdam-Rehbruecke
Dept. of Epidemiology
Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.1 (GNU/Linux)

iD8DBQFEslmeeYdmlKJoHzkRAmd0AJ934ovycVUggLlHLYC+GEkKLKjRawCgnix9
sxmrzdPceNoIzaDjvJUOSG0=
=prhR
-----END PGP SIGNATURE-----

From markw at illuminae.com  Mon Jul 24 11:49:49 2006
From: markw at illuminae.com (mark wilkinson)
Date: Mon, 24 Jul 2006 15:49:49 +0000 GMT
Subject: [MOBY-l] Fw: [MYGRID-MAN] Re: The Death of Life Science IDentifiers?
Message-ID: <312875668-1153756276-cardhu_blackberry.rim.net-7580-@engine03-cell01>


Heads-up everyone who has a vested interest in this issue (like many Mobyers!!)

M



--
Mark Wilkinson
...on the road!


-----Original Message-----
From: Paul Fisher <Paul.Fisher at postgrad.manchester.ac.uk>
Date: Mon, 24 Jul 2006 16:38:20 
To:Carole Goble <carole at cs.man.ac.uk>
Cc:Duncan Hull <duncan.hull at cs.man.ac.uk>, Jun Zhao <zhaoj at cs.man.ac.uk>,       Daniele Turi <dturi at cs.manchester.ac.uk>, Tom Oinn <tmo at ebi.ac.uk>,       Mark Wilkinson <markw at illuminae.com>, June Finch <jfinch at cs.man.ac.uk>,       "mygrid-man at lists.man.ac.uk" <mygrid-man at lists.man.ac.uk>
Subject: Re: [MYGRID-MAN] Re: The Death of Life Science IDentifiers?

One of the main problems with current biology/bioinformatics is the lack of
standardisation. If you take something away now instead of embracing it and
following it through (speaking to the people wanting to remove it now) is you
go back a step instead of forwards.

What are the alternatives?

Paul.

Quoting Carole Goble <carole at cs.man.ac.uk>:

> Duncan
>
> thanks for the heads up.
>
> This is important. I will need someone to assemble the arguments that 
> have been made and the consequences for us in particular.
>
> Who can do this? We haven't paid attention and this could be the price
>
> Carole
>
>> Hello
>>
>> Susie Stephens wrote:
>>
>>> Don't forget the URI discussion on July 31!
>>
>> In case you didn't already know, the next BioRDF telecon will be a 
>> "do-or-die" decision for LSIDs, according to Susie Stephens.
>>
>> It sounds like the W3C might put some final nails in the LSID 
>> coffin, unless somebody makes a very strong counter argument.
>>
>> Of course, this doesn't stop people using them, but they might not 
>> survive very long without W3C approval.
>>
>> So if you care either way about LSIDs, you might want to take part 
>> on Monday July 31st, details below.
>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2006-07-31_Conference_Call ...and please don't shoot me, I'm just the 
>> messenger!
>>
>> Duncan
>>
>
>
> _______________________________________________
> myGrid-man mailing list
> myGrid-man at mygrid.info
> http://mygrid.info/mailman/listinfo/mygrid-man
>




From darin.london at duke.edu  Mon Jul  3 12:41:33 2006
From: darin.london at duke.edu (Darin London)
Date: Mon, 03 Jul 2006 08:41:33 -0400
Subject: [MOBY-l] Call For Birds of a Feather Suggestions
Message-ID: <44A9107D.2050304@duke.edu>

The BOSC organizing comittee is currently seeking suggestions for Birds
of a Feather meeting ideas. Birds of a Feather meetings are one of the
more popular activities at BOSC, occurring at the end of each days
session. These are free-form meetings organized by the attendees
themselves to discuss one or a few topics of interest in greater detail.
BOF?s have been formed to allow developers and users of individual OBF
software to meet each other face-to-face to discuss the project, or to
discuss completely new ideas, and even start new software development
projects. These meetings offer a unique opportunity for individuals to
explore more about the activities of the various Open Source Projects,
and, in some cases, even take an active role influencing the future of
Open Source Software development. If you would like to create a BOF,
just sign up for a wiki account, login, and edit the <a
href="http://www.open-bio.org/wiki/BOSC_2006/Birds-of-a-Feather">BOSC
2006 Birds of a Feather page</a>.


From harttig at mail.dife.de  Mon Jul 10 13:43:58 2006
From: harttig at mail.dife.de (Ulrich Harttig)
Date: Mon, 10 Jul 2006 15:43:58 +0200
Subject: [MOBY-l] biomoby Perl API - error in t/dbConnect
Message-ID: <44B2599E.6030809@dife.de>

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Hello all,

trying to upgrade to the current development version of biomoby, I came across
the following error when testing the Perl API

 t/dbConnect...................NOK 1
 #   Failed test 'use MOBY::lsid::authority::dbConnect;'
 #   in t/dbConnect.t at line 18.
 #     Tried to use 'MOBY::lsid::authority::dbConnect'.
 #     Error:  Can't locate MOBY/lsid/authority/dbConnect.pm in @INC (@INC contains:

since the Perl LSID code is now deprecated and has been removed from the
repository the test, maybe this test could also be removed ?

best regards
Ulrich

- --
Ulrich Harttig, Ph.D.
German Institute of Human Nutrition Potsdam-Rehbruecke
Dept. of Epidemiology
Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
phone: +49 (0)33200 88-729, fax: +49 (0)33200 88-721
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.1 (GNU/Linux)

iD8DBQFEslmeeYdmlKJoHzkRAmd0AJ934ovycVUggLlHLYC+GEkKLKjRawCgnix9
sxmrzdPceNoIzaDjvJUOSG0=
=prhR
-----END PGP SIGNATURE-----


From markw at illuminae.com  Mon Jul 24 15:49:49 2006
From: markw at illuminae.com (mark wilkinson)
Date: Mon, 24 Jul 2006 15:49:49 +0000 GMT
Subject: [MOBY-l] Fw: [MYGRID-MAN] Re: The Death of Life Science IDentifiers?
Message-ID: <312875668-1153756276-cardhu_blackberry.rim.net-7580-@engine03-cell01>


Heads-up everyone who has a vested interest in this issue (like many Mobyers!!)

M



--
Mark Wilkinson
...on the road!


-----Original Message-----
From: Paul Fisher <Paul.Fisher at postgrad.manchester.ac.uk>
Date: Mon, 24 Jul 2006 16:38:20 
To:Carole Goble <carole at cs.man.ac.uk>
Cc:Duncan Hull <duncan.hull at cs.man.ac.uk>, Jun Zhao <zhaoj at cs.man.ac.uk>,       Daniele Turi <dturi at cs.manchester.ac.uk>, Tom Oinn <tmo at ebi.ac.uk>,       Mark Wilkinson <markw at illuminae.com>, June Finch <jfinch at cs.man.ac.uk>,       "mygrid-man at lists.man.ac.uk" <mygrid-man at lists.man.ac.uk>
Subject: Re: [MYGRID-MAN] Re: The Death of Life Science IDentifiers?

One of the main problems with current biology/bioinformatics is the lack of
standardisation. If you take something away now instead of embracing it and
following it through (speaking to the people wanting to remove it now) is you
go back a step instead of forwards.

What are the alternatives?

Paul.

Quoting Carole Goble <carole at cs.man.ac.uk>:

> Duncan
>
> thanks for the heads up.
>
> This is important. I will need someone to assemble the arguments that 
> have been made and the consequences for us in particular.
>
> Who can do this? We haven't paid attention and this could be the price
>
> Carole
>
>> Hello
>>
>> Susie Stephens wrote:
>>
>>> Don't forget the URI discussion on July 31!
>>
>> In case you didn't already know, the next BioRDF telecon will be a 
>> "do-or-die" decision for LSIDs, according to Susie Stephens.
>>
>> It sounds like the W3C might put some final nails in the LSID 
>> coffin, unless somebody makes a very strong counter argument.
>>
>> Of course, this doesn't stop people using them, but they might not 
>> survive very long without W3C approval.
>>
>> So if you care either way about LSIDs, you might want to take part 
>> on Monday July 31st, details below.
>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2006-07-31_Conference_Call ...and please don't shoot me, I'm just the 
>> messenger!
>>
>> Duncan
>>
>
>
> _______________________________________________
> myGrid-man mailing list
> myGrid-man at mygrid.info
> http://mygrid.info/mailman/listinfo/mygrid-man
>