From chapmanb at 50mail.com  Fri Apr  2 09:06:43 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 2 Apr 2010 09:06:43 -0400
Subject: [MOBY-dev] BOSC and OpenBio solution challenge reminder -- April
	15th
Message-ID: <20100402130643.GI36623@sobchak.mgh.harvard.edu>

Hello all;
A friendly reminder that the deadline for the Bioinformatics Open
Source Conference (BOSC) is coming up on April 15th:

http://www.open-bio.org/wiki/BOSC_2010

This is a great opportunity to discuss code and biology with fellow
developers.

One session which I'd like to emphasize is the OpenBio Solution
Challenge, a section of talks that describes how to solve practical
problems in bioinformatics using a variety of approaches:

http://www.open-bio.org/wiki/SolutionChallenge

Any toolkit developers who are interested in giving a talk are
encouraged to submit an abstract for the challenge. We have some initial
project ideas on the page and welcome your feedback for other useful
workflows that would emphasize the advantages of using open source
toolkits to solve biological problems. Please copy messages to the
OpenBio mailing list as a central point for discussion and
questions:

http://lists.open-bio.org/mailman/listinfo/open-bio-l

Looking forward to seeing everyone in July,
Brad

BOSC contact and dates:
Date: July 9-10, 2010
Location: Boston, Massachusetts, USA
BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010
Abstract submission via Open Conference System site:  http://events.open-bio.org/BOSC2010/openconf.php
E-mail: bosc at open-bio.org
Bosc-announce list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates
April 15: Abstract deadline
May 5:  Notification of accepted abstracts
May 28: Early Registration Discount Cut-off date
July 8-9:  Codefest 2010
July 9-10: BOSC 2010
August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics

From r.biczok at Dkfz-Heidelberg.de  Wed Apr 14 11:20:45 2010
From: r.biczok at Dkfz-Heidelberg.de (Biczok Rudolf)
Date: Wed, 14 Apr 2010 17:20:45 +0200
Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>

Hello BioMoby Com,

I'm working  with the  MOSES::MOBY Perl package and have a question about the
moses-install.pl script.

Is  it possible to generate the whole directory "Perl-MoSeS" in another directory
rather than /home/<uname>?

Best wishes,
Rudolf Biczok & Anika J?cker


Rudolf Biczok
Bioinformatics HUSAR
Mobile Phone : +49 171 6289148
Phone:               +49 (0) 6221 42 2342

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
D-69120 Heidelberg
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From edward.kawas at gmail.com  Wed Apr 14 11:24:05 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 14 Apr 2010 08:24:05 -0700
Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>
References: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>
Message-ID: <004e01cadbe6$85acdd20$91069760$@gmail.com>

You should be able to move the directory as long as you set the environment
variable BIOMOBY_CFG_DIR to be the location of that directory.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Biczok Rudolf
> Sent: Wednesday, April 14, 2010 8:21 AM
> To: 'moby-dev at lists.open-bio.org'
> Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
> 
> Hello BioMoby Com,
> 
> I'm working  with the  MOSES::MOBY Perl package and have a question about
> the moses-install.pl script.
> 
> Is  it possible to generate the whole directory "Perl-MoSeS" in another
> directory rather than /home/<uname>?
> 
> Best wishes,
> Rudolf Biczok & Anika J?cker
> 
> 
> Rudolf Biczok
> Bioinformatics HUSAR
> Mobile Phone : +49 171 6289148
> Phone:               +49 (0) 6221 42 2342
> 
> Deutsches Krebsforschungszentrum
> Im Neuenheimer Feld 280
> D-69120 Heidelberg
> [cid:image001.gif at 01CADBF6.D18088E0]
> 




From r.biczok at dkfz-heidelberg.de  Wed Apr 28 05:12:08 2010
From: r.biczok at dkfz-heidelberg.de (Biczok Rudolf)
Date: Wed, 28 Apr 2010 11:12:08 +0200
Subject: [MOBY-dev] get datatype information at runtime
Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>

Hello MOBY com,

I'm working with the Perl-Moses package and I want to implement some
functionality which converts us internal perl objects automatically into
BioMOBY objects.

But I don't really know how to get information about a BioMOBY datatype
at the runtime, because every generate Package handles these attributes
in an abstract why:

my %_allowed =
    (
         id         => undef,
         namespace  => undef,
         provision  => {type => 'MOSES::MOBY::Data::ProvisionInformation'},
         xrefs      => {type => 'MOSES::MOBY::Data::Xref', is_array => 1},
         primitive  => {type => MOSES::MOBY::Base->BOOLEAN},
     );

.. which means I can't access these information from a other package.

So is there any mechanism that allows me to get these suff without calling the MOBY-Central
(just an static method)?

Best wishes,
Rudolf


Rudolf Biczok
Bioinformatics HUSAR
Mobile Phone : +49 171 6289148
Phone:               +49 (0) 6221 42 2342

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
D-69120 Heidelberg
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From edward.kawas at gmail.com  Wed Apr 28 09:39:01 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 28 Apr 2010 06:39:01 -0700
Subject: [MOBY-dev] get datatype information at runtime
In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>
References: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>
Message-ID: <002a01cae6d8$2a504af0$7ef0e0d0$@gmail.com>

Hi Rudolf,

Probably the easiest way to get this information without calling mobycentral
is to go to the cache. Usually datatypes in Perl MoSeS are generated as
needed from the cache, so you could get the most up to date information from
there.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Biczok Rudolf
> Sent: Wednesday, April 28, 2010 2:12 AM
> To: 'moby-dev at lists.open-bio.org'
> Subject: [MOBY-dev] get datatype information at runtime
> 
> Hello MOBY com,
> 
> I'm working with the Perl-Moses package and I want to implement some
> functionality which converts us internal perl objects automatically into
> BioMOBY objects.
> 
> But I don't really know how to get information about a BioMOBY datatype at
> the runtime, because every generate Package handles these attributes in an
> abstract why:
> 
> my %_allowed =
>     (
>          id         => undef,
>          namespace  => undef,
>          provision  => {type =>
'MOSES::MOBY::Data::ProvisionInformation'},
>          xrefs      => {type => 'MOSES::MOBY::Data::Xref', is_array => 1},
>          primitive  => {type => MOSES::MOBY::Base->BOOLEAN},
>      );
> 
> .. which means I can't access these information from a other package.
> 
> So is there any mechanism that allows me to get these suff without calling
> the MOBY-Central (just an static method)?
> 
> Best wishes,
> Rudolf
> 
> 
> Rudolf Biczok
> Bioinformatics HUSAR
> Mobile Phone : +49 171 6289148
> Phone:               +49 (0) 6221 42 2342
> 
> Deutsches Krebsforschungszentrum
> Im Neuenheimer Feld 280
> D-69120 Heidelberg
> [cid:image001.gif at 01CAE6BE.9F358520]
> 



From gllambi at fing.edu.uy  Fri Apr 30 11:15:45 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Fri, 30 Apr 2010 12:15:45 -0300
Subject: [MOBY-dev] Error while running tutorial sample
Message-ID: <20100430121545.12875dsk43mmu8g8@www.fing.edu.uy>

Hi Moby Team!

I'm doing some test with Taverna BioMoby plug-in and found it really  
interesting and usefull! I started with your tutorial but when I  
wanted to run the experiment I got an error using the  
getDragonAllelesByKeyword service from the
antirrhinum.net authority. The input I used is the same of the  
tutorial. I build an Object with keyword=petal and  
namespace=Global_Keyword.

Here's the error:

org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: Can't call method "find" on an undefined value at  
/opt/coolstack/apache2/moby_services//Services/DragonServices.pm line  
140, <DATA> line 192.

Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server
Fault actor:  null
When calling:
	http://moby.ucalgary.ca/moby_services/Services.cgi
===========

org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
org.biomoby.client.CentralImpl.call(CentralImpl.java:1560)
net.sf.taverna.t2.activities.biomoby.ExecuteMobyService.executeMobyService(ExecuteMobyService.java:35)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.executeService(BiomobyActivity.java:1307)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.access$400(BiomobyActivity.java:60)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity$1.run(BiomobyActivity.java:694)
java.lang.Thread.run(Thread.java:619)


Is there something wrong with the service or am I missing something?

Thanks in advance!
Guzman

----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY


From gllambi at fing.edu.uy  Fri Apr 30 11:28:00 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Fri, 30 Apr 2010 12:28:00 -0300
Subject: [MOBY-dev] Format Example
Message-ID: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>

Hi!

First of all, sorry in advance if this is a very stupid question, but  
I'm new with BioMoby.

I've been searching in myexperiment website for a format example  
workflow using bioMoby, but I couldn't find anyone. I'm looking for an  
example where you have things in Fasta, GFF, Genbank or any other  
format and take advantage of the bioMoby friendly format features to  
make format unaware.

Does anybody knows a workflow example of this? or maybe I understood  
wrong the objetives of BioMoby

Best Regards
Guzman

----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY


From edward.kawas at gmail.com  Fri Apr 30 14:19:23 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 30 Apr 2010 11:19:23 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
Message-ID: <003f01cae891$aa594700$ff0bd500$@gmail.com>

Hi Guzman,

There are a few tutorials for using moby with Taverna. There is this one
(http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
ndex.html), and while it refers to an older version of taverna, it should be
relevant.

Also, there is a power point presentation hosted @
http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
Taverna_Tutorial.ppt 

If these resources don't help, or if you have more questions, please do not
hesitate to ask them here!

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> Sent: Friday, April 30, 2010 8:28 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Format Example
> 
> Hi!
> 
> First of all, sorry in advance if this is a very stupid question, but I'm
new with
> BioMoby.
> 
> I've been searching in myexperiment website for a format example
> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
> example where you have things in Fasta, GFF, Genbank or any other format
> and take advantage of the bioMoby friendly format features to make format
> unaware.
> 
> Does anybody knows a workflow example of this? or maybe I understood
> wrong the objetives of BioMoby
> 
> Best Regards
> Guzman
> 
> ----------------------------------------
> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
> URUGUAY
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Fri Apr 30 15:23:39 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 30 Apr 2010 12:23:39 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <003f01cae891$aa594700$ff0bd500$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
	<003f01cae891$aa594700$ff0bd500$@gmail.com>
Message-ID: <op.vbzphpamnbznux@dd0710001l.icapture.ubc.ca>

Eddie, let's direct people to the Taverna tutorials that we use for the  
Advanced Computational Genomics Course, since those are always kept  
up-to-date (at least, on a 6 month interval :-) ).  In addition, those  
tutorials will soon also contain the SADI plugin tutorial for Taverna, so  
then people can learn how to use both interoperability frameworks - old  
and new!

Mark




On Fri, 30 Apr 2010 11:19:23 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:

> Hi Guzman,
>
> There are a few tutorials for using moby with Taverna. There is this one
> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
> ndex.html), and while it refers to an older version of taverna, it  
> should be
> relevant.
>
> Also, there is a power point presentation hosted @
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
> Taverna_Tutorial.ppt
>
> If these resources don't help, or if you have more questions, please do  
> not
> hesitate to ask them here!
>
> Eddie
>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
>> Sent: Friday, April 30, 2010 8:28 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] Format Example
>>
>> Hi!
>>
>> First of all, sorry in advance if this is a very stupid question, but  
>> I'm
> new with
>> BioMoby.
>>
>> I've been searching in myexperiment website for a format example
>> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
>> example where you have things in Fasta, GFF, Genbank or any other format
>> and take advantage of the bioMoby friendly format features to make  
>> format
>> unaware.
>>
>> Does anybody knows a workflow example of this? or maybe I understood
>> wrong the objetives of BioMoby
>>
>> Best Regards
>> Guzman
>>
>> ----------------------------------------
>> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
>> URUGUAY
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From alanrw at cs.man.ac.uk  Fri Apr 30 16:17:40 2010
From: alanrw at cs.man.ac.uk (Alan R Williams)
Date: Fri, 30 Apr 2010 21:17:40 +0100
Subject: [MOBY-dev] Format Example
Message-ID: <E1O7wea-0002hB-00@phoebus>

Mark,

The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
plugin.  It should show up under the standard plugins menu.

Alan


From markw at illuminae.com  Fri Apr 30 17:18:30 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 30 Apr 2010 14:18:30 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <E1O7wea-0002hB-00@phoebus>
References: <E1O7wea-0002hB-00@phoebus>
Message-ID: <op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>

Confirmed!  Thank you!

Mark



On Fri, 30 Apr 2010 13:17:40 -0700, Alan R Williams <alanrw at cs.man.ac.uk>  
wrote:

> Mark,
>
> The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
> plugin.  It should show up under the standard plugins menu.
>
> Alan
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From chapmanb at 50mail.com  Fri Apr  2 13:06:43 2010
From: chapmanb at 50mail.com (Brad Chapman)
Date: Fri, 2 Apr 2010 09:06:43 -0400
Subject: [MOBY-dev] BOSC and OpenBio solution challenge reminder -- April
	15th
Message-ID: <20100402130643.GI36623@sobchak.mgh.harvard.edu>

Hello all;
A friendly reminder that the deadline for the Bioinformatics Open
Source Conference (BOSC) is coming up on April 15th:

http://www.open-bio.org/wiki/BOSC_2010

This is a great opportunity to discuss code and biology with fellow
developers.

One session which I'd like to emphasize is the OpenBio Solution
Challenge, a section of talks that describes how to solve practical
problems in bioinformatics using a variety of approaches:

http://www.open-bio.org/wiki/SolutionChallenge

Any toolkit developers who are interested in giving a talk are
encouraged to submit an abstract for the challenge. We have some initial
project ideas on the page and welcome your feedback for other useful
workflows that would emphasize the advantages of using open source
toolkits to solve biological problems. Please copy messages to the
OpenBio mailing list as a central point for discussion and
questions:

http://lists.open-bio.org/mailman/listinfo/open-bio-l

Looking forward to seeing everyone in July,
Brad

BOSC contact and dates:
Date: July 9-10, 2010
Location: Boston, Massachusetts, USA
BOSC 2010 web site: http://www.open-bio.org/wiki/BOSC_2010
Abstract submission via Open Conference System site:  http://events.open-bio.org/BOSC2010/openconf.php
E-mail: bosc at open-bio.org
Bosc-announce list:  http://lists.open-bio.org/mailman/listinfo/bosc-announce

Important Dates
April 15: Abstract deadline
May 5:  Notification of accepted abstracts
May 28: Early Registration Discount Cut-off date
July 8-9:  Codefest 2010
July 9-10: BOSC 2010
August 15:  Manuscript deadline for BOSC 2010 Proceedings published in BMC Bioinformatics


From r.biczok at Dkfz-Heidelberg.de  Wed Apr 14 15:20:45 2010
From: r.biczok at Dkfz-Heidelberg.de (Biczok Rudolf)
Date: Wed, 14 Apr 2010 17:20:45 +0200
Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>

Hello BioMoby Com,

I'm working  with the  MOSES::MOBY Perl package and have a question about the
moses-install.pl script.

Is  it possible to generate the whole directory "Perl-MoSeS" in another directory
rather than /home/<uname>?

Best wishes,
Rudolf Biczok & Anika J?cker


Rudolf Biczok
Bioinformatics HUSAR
Mobile Phone : +49 171 6289148
Phone:               +49 (0) 6221 42 2342

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
D-69120 Heidelberg
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From edward.kawas at gmail.com  Wed Apr 14 15:24:05 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 14 Apr 2010 08:24:05 -0700
Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>
References: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A76A@DKFZEX01.ad.dkfz-heidelberg.de>
Message-ID: <004e01cadbe6$85acdd20$91069760$@gmail.com>

You should be able to move the directory as long as you set the environment
variable BIOMOBY_CFG_DIR to be the location of that directory.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Biczok Rudolf
> Sent: Wednesday, April 14, 2010 8:21 AM
> To: 'moby-dev at lists.open-bio.org'
> Subject: [MOBY-dev] Perl-MoSeS direcotry not in home
> 
> Hello BioMoby Com,
> 
> I'm working  with the  MOSES::MOBY Perl package and have a question about
> the moses-install.pl script.
> 
> Is  it possible to generate the whole directory "Perl-MoSeS" in another
> directory rather than /home/<uname>?
> 
> Best wishes,
> Rudolf Biczok & Anika J?cker
> 
> 
> Rudolf Biczok
> Bioinformatics HUSAR
> Mobile Phone : +49 171 6289148
> Phone:               +49 (0) 6221 42 2342
> 
> Deutsches Krebsforschungszentrum
> Im Neuenheimer Feld 280
> D-69120 Heidelberg
> [cid:image001.gif at 01CADBF6.D18088E0]
> 





From r.biczok at dkfz-heidelberg.de  Wed Apr 28 09:12:08 2010
From: r.biczok at dkfz-heidelberg.de (Biczok Rudolf)
Date: Wed, 28 Apr 2010 11:12:08 +0200
Subject: [MOBY-dev] get datatype information at runtime
Message-ID: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>

Hello MOBY com,

I'm working with the Perl-Moses package and I want to implement some
functionality which converts us internal perl objects automatically into
BioMOBY objects.

But I don't really know how to get information about a BioMOBY datatype
at the runtime, because every generate Package handles these attributes
in an abstract why:

my %_allowed =
    (
         id         => undef,
         namespace  => undef,
         provision  => {type => 'MOSES::MOBY::Data::ProvisionInformation'},
         xrefs      => {type => 'MOSES::MOBY::Data::Xref', is_array => 1},
         primitive  => {type => MOSES::MOBY::Base->BOOLEAN},
     );

.. which means I can't access these information from a other package.

So is there any mechanism that allows me to get these suff without calling the MOBY-Central
(just an static method)?

Best wishes,
Rudolf


Rudolf Biczok
Bioinformatics HUSAR
Mobile Phone : +49 171 6289148
Phone:               +49 (0) 6221 42 2342

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
D-69120 Heidelberg
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From edward.kawas at gmail.com  Wed Apr 28 13:39:01 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 28 Apr 2010 06:39:01 -0700
Subject: [MOBY-dev] get datatype information at runtime
In-Reply-To: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>
References: <4F91222C659D5B4E8C89CE4D710BB08E3D1E82A9C4@DKFZEX01.ad.dkfz-heidelberg.de>
Message-ID: <002a01cae6d8$2a504af0$7ef0e0d0$@gmail.com>

Hi Rudolf,

Probably the easiest way to get this information without calling mobycentral
is to go to the cache. Usually datatypes in Perl MoSeS are generated as
needed from the cache, so you could get the most up to date information from
there.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Biczok Rudolf
> Sent: Wednesday, April 28, 2010 2:12 AM
> To: 'moby-dev at lists.open-bio.org'
> Subject: [MOBY-dev] get datatype information at runtime
> 
> Hello MOBY com,
> 
> I'm working with the Perl-Moses package and I want to implement some
> functionality which converts us internal perl objects automatically into
> BioMOBY objects.
> 
> But I don't really know how to get information about a BioMOBY datatype at
> the runtime, because every generate Package handles these attributes in an
> abstract why:
> 
> my %_allowed =
>     (
>          id         => undef,
>          namespace  => undef,
>          provision  => {type =>
'MOSES::MOBY::Data::ProvisionInformation'},
>          xrefs      => {type => 'MOSES::MOBY::Data::Xref', is_array => 1},
>          primitive  => {type => MOSES::MOBY::Base->BOOLEAN},
>      );
> 
> .. which means I can't access these information from a other package.
> 
> So is there any mechanism that allows me to get these suff without calling
> the MOBY-Central (just an static method)?
> 
> Best wishes,
> Rudolf
> 
> 
> Rudolf Biczok
> Bioinformatics HUSAR
> Mobile Phone : +49 171 6289148
> Phone:               +49 (0) 6221 42 2342
> 
> Deutsches Krebsforschungszentrum
> Im Neuenheimer Feld 280
> D-69120 Heidelberg
> [cid:image001.gif at 01CAE6BE.9F358520]
> 




From gllambi at fing.edu.uy  Fri Apr 30 15:15:45 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Fri, 30 Apr 2010 12:15:45 -0300
Subject: [MOBY-dev] Error while running tutorial sample
Message-ID: <20100430121545.12875dsk43mmu8g8@www.fing.edu.uy>

Hi Moby Team!

I'm doing some test with Taverna BioMoby plug-in and found it really  
interesting and usefull! I started with your tutorial but when I  
wanted to run the experiment I got an error using the  
getDragonAllelesByKeyword service from the
antirrhinum.net authority. The input I used is the same of the  
tutorial. I build an Object with keyword=petal and  
namespace=Global_Keyword.

Here's the error:

org.biomoby.shared.MobyException: ===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: Can't call method "find" on an undefined value at  
/opt/coolstack/apache2/moby_services//Services/DragonServices.pm line  
140, <DATA> line 192.

Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server
Fault actor:  null
When calling:
	http://moby.ucalgary.ca/moby_services/Services.cgi
===========

org.biomoby.client.CentralImpl.doCall(CentralImpl.java:251)
org.biomoby.client.CentralImpl.call(CentralImpl.java:1560)
net.sf.taverna.t2.activities.biomoby.ExecuteMobyService.executeMobyService(ExecuteMobyService.java:35)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.executeService(BiomobyActivity.java:1307)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity.access$400(BiomobyActivity.java:60)
net.sf.taverna.t2.activities.biomoby.BiomobyActivity$1.run(BiomobyActivity.java:694)
java.lang.Thread.run(Thread.java:619)


Is there something wrong with the service or am I missing something?

Thanks in advance!
Guzman

----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY



From gllambi at fing.edu.uy  Fri Apr 30 15:28:00 2010
From: gllambi at fing.edu.uy (Guzman Llambias - INCO)
Date: Fri, 30 Apr 2010 12:28:00 -0300
Subject: [MOBY-dev] Format Example
Message-ID: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>

Hi!

First of all, sorry in advance if this is a very stupid question, but  
I'm new with BioMoby.

I've been searching in myexperiment website for a format example  
workflow using bioMoby, but I couldn't find anyone. I'm looking for an  
example where you have things in Fasta, GFF, Genbank or any other  
format and take advantage of the bioMoby friendly format features to  
make format unaware.

Does anybody knows a workflow example of this? or maybe I understood  
wrong the objetives of BioMoby

Best Regards
Guzman

----------------------------------------
Enviado usando el Servicio de Correo Web
Facultad de Ingenieria - UR - URUGUAY



From edward.kawas at gmail.com  Fri Apr 30 18:19:23 2010
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 30 Apr 2010 11:19:23 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
Message-ID: <003f01cae891$aa594700$ff0bd500$@gmail.com>

Hi Guzman,

There are a few tutorials for using moby with Taverna. There is this one
(http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
ndex.html), and while it refers to an older version of taverna, it should be
relevant.

Also, there is a power point presentation hosted @
http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
Taverna_Tutorial.ppt 

If these resources don't help, or if you have more questions, please do not
hesitate to ask them here!

Eddie

> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
> Sent: Friday, April 30, 2010 8:28 AM
> To: moby-dev at lists.open-bio.org
> Subject: [MOBY-dev] Format Example
> 
> Hi!
> 
> First of all, sorry in advance if this is a very stupid question, but I'm
new with
> BioMoby.
> 
> I've been searching in myexperiment website for a format example
> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
> example where you have things in Fasta, GFF, Genbank or any other format
> and take advantage of the bioMoby friendly format features to make format
> unaware.
> 
> Does anybody knows a workflow example of this? or maybe I understood
> wrong the objetives of BioMoby
> 
> Best Regards
> Guzman
> 
> ----------------------------------------
> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
> URUGUAY
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Fri Apr 30 19:23:39 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 30 Apr 2010 12:23:39 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <003f01cae891$aa594700$ff0bd500$@gmail.com>
References: <20100430122800.96492nbipnd58y04@www.fing.edu.uy>
	<003f01cae891$aa594700$ff0bd500$@gmail.com>
Message-ID: <op.vbzphpamnbznux@dd0710001l.icapture.ubc.ca>

Eddie, let's direct people to the Taverna tutorials that we use for the  
Advanced Computational Genomics Course, since those are always kept  
up-to-date (at least, on a 6 month interval :-) ).  In addition, those  
tutorials will soon also contain the SADI plugin tutorial for Taverna, so  
then people can learn how to use both interoperability frameworks - old  
and new!

Mark




On Fri, 30 Apr 2010 11:19:23 -0700, Edward Kawas <edward.kawas at gmail.com>  
wrote:

> Hi Guzman,
>
> There are a few tutorials for using moby with Taverna. There is this one
> (http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/taverna/guide/i
> ndex.html), and while it refers to an older version of taverna, it  
> should be
> relevant.
>
> Also, there is a power point presentation hosted @
> http://www.bioinformatics.nl/events/webservices/slides//BioMOBY/BioMoby_and_
> Taverna_Tutorial.ppt
>
> If these resources don't help, or if you have more questions, please do  
> not
> hesitate to ask them here!
>
> Eddie
>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-
>> bounces at lists.open-bio.org] On Behalf Of Guzman Llambias - INCO
>> Sent: Friday, April 30, 2010 8:28 AM
>> To: moby-dev at lists.open-bio.org
>> Subject: [MOBY-dev] Format Example
>>
>> Hi!
>>
>> First of all, sorry in advance if this is a very stupid question, but  
>> I'm
> new with
>> BioMoby.
>>
>> I've been searching in myexperiment website for a format example
>> workflow using bioMoby, but I couldn't find anyone. I'm looking for an
>> example where you have things in Fasta, GFF, Genbank or any other format
>> and take advantage of the bioMoby friendly format features to make  
>> format
>> unaware.
>>
>> Does anybody knows a workflow example of this? or maybe I understood
>> wrong the objetives of BioMoby
>>
>> Best Regards
>> Guzman
>>
>> ----------------------------------------
>> Enviado usando el Servicio de Correo Web Facultad de Ingenieria - UR -
>> URUGUAY
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From alanrw at cs.man.ac.uk  Fri Apr 30 20:17:40 2010
From: alanrw at cs.man.ac.uk (Alan R Williams)
Date: Fri, 30 Apr 2010 21:17:40 +0100
Subject: [MOBY-dev] Format Example
Message-ID: <E1O7wea-0002hB-00@phoebus>

Mark,

The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
plugin.  It should show up under the standard plugins menu.

Alan



From markw at illuminae.com  Fri Apr 30 21:18:30 2010
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 30 Apr 2010 14:18:30 -0700
Subject: [MOBY-dev] Format Example
In-Reply-To: <E1O7wea-0002hB-00@phoebus>
References: <E1O7wea-0002hB-00@phoebus>
Message-ID: <op.vbzus4znnbznux@dd0710001l.icapture.ubc.ca>

Confirmed!  Thank you!

Mark



On Fri, 30 Apr 2010 13:17:40 -0700, Alan R Williams <alanrw at cs.man.ac.uk>  
wrote:

> Mark,
>
> The SADI plugin has just gone live in Taverna 2.1.2 as a prototype
> plugin.  It should show up under the standard plugins menu.
>
> Alan
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada