From markw at illuminae.com  Tue Oct 18 16:49:13 2005
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue Oct 18 17:20:20 2005
Subject: [MOBY-l] Migrating MOBY Central to the new object API - MONDAY OCT
	24th
Message-ID: <1129668553.6798.17.camel@bioinfo.icapture.ubc.ca>

Hi all, 

Eddie and I have been discussing the object ontology migration now that
we are not allowing inheritance from primitives.  No matter what we do
this will break some services, and though I was originally hoping to
soften the blow by having a deprecation period, the amount of pain this
causes (i.e. everyone having to edit and re-register their services
TWICE!) is just inhumane :-)

So... I am sure that some of you will cheer this decision, and others
will loathe it... we're going to simply migrate the object ontology (in
the public MOBY Central here at iCAPTURE) with **no deprecation period
at all**.  

The object names will remain exactly as they are, but will (in some
cases) now have different definitions.  As such, for those of you
running services that are affected by this change, you will only need to
update your service code, but NOT need to de/re-register your service.

We plan to do this Monday October 24th, so you have a few days to update
your services now to reduce the down-time.  The way to go about updating
your services is as follows:  Any XML node that currently has content,
but is not a nominal primitive, will now be modified such that it
CONTAINS a node that is a primitive, and that primitive will have data
content.  It's articleName is "content" in every case.  

e.g.  

  <FASTA namespace='' id=''><![CDATA[
     >name
     ACGTGTAGTGCTAGTC
   ]]></FASTA>

will become

   <FASTA  namespace='' id=''>
	<String namespace='' id='' articleName='content'><![CDATA[
		>name
                ACGTGTGCTGATGAC
	]]></String>
   </FASTA>


And similarly for Integers, Floats, DateTime, etc.  The definition of
DateTime will also change, such that it is a primitive, rather than
inheriting from String, as it currently does.

Eddie has a migration script that will update your mySQL databases
automatically.  He will make this available on his website (details to
follow).


Any objections?  (don't all yell at once ;-) )

Cheers!

Mark



-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274

From mlangill at sfu.ca  Tue Oct 18 17:20:29 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Tue Oct 18 18:54:30 2005
Subject: [MOBY-l] Re: [Taverna-users] problems with moby services
In-Reply-To: <43556643.4090503@sfu.ca>
References: <43556643.4090503@sfu.ca>
Message-ID: <4355671D.60100@sfu.ca>


Of course I forgot to attach my workflow. So here it is.

Morgan


Morgan Langille wrote:

> This morning I decided try out some of biomoby's new functionality in 
> taverna (http://www.ebi.ac.uk/~tmo/mygrid/releases/latest/mobyguide/) 
> <http://www.ebi.ac.uk/%7Etmo/mygrid/releases/latest/mobyguide/>.
> I followed the guide and I was able to get everything to work (except 
> for adding a service from within Moby Service Details pop up window). 
> I then added services that the moby object "DNAsequence" was used as 
> input for (very cool!). However, when I run the workflow with any 
> service that takes a DNAsequence it gives errors (2 services give 
> "denied access to method", 1 service gives "(500) Internal Error 
> Service"). Is the problem related to the services I am trying or is 
> this a problem with the moby object? Also, I was wondering why a 
> DNAsequence object is used in the guide instead of a GenericSequence 
> object, which the runFasta service uses (although I tested this and it 
> works with both!)?
>
> Slighty confused,
>
> Morgan
>
>
> ------------------------------------------------------------------------
>

From mlangill at sfu.ca  Tue Oct 18 17:16:51 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Tue Oct 18 18:54:30 2005
Subject: [MOBY-l] problems with moby services
Message-ID: <43556643.4090503@sfu.ca>

This morning I decided try out some of biomoby's new functionality in 
taverna (http://www.ebi.ac.uk/~tmo/mygrid/releases/latest/mobyguide/) 
<http://www.ebi.ac.uk/%7Etmo/mygrid/releases/latest/mobyguide/>.
I followed the guide and I was able to get everything to work (except 
for adding a service from within Moby Service Details pop up window). I 
then added services that the moby object "DNAsequence" was used as input 
for (very cool!). However, when I run the workflow with any service that 
takes a DNAsequence it gives errors (2 services give "denied access to 
method", 1 service gives "(500) Internal Error Service"). Is the problem 
related to the services I am trying or is this a problem with the moby 
object? Also, I was wondering why a DNAsequence object is used in the 
guide instead of a GenericSequence object, which the runFasta service 
uses (although I tested this and it works with both!)?

Slighty confused,

Morgan

From silvia77 at dist.unige.it  Tue Oct 18 04:06:13 2005
From: silvia77 at dist.unige.it (scaglione)
Date: Tue Oct 18 18:54:53 2005
Subject: [MOBY-l] Error in BIOMOBY
Message-ID: <1129622773.4354acf5262c5@webmail.unige.it>


hello,
this morning I'cannot reach the biomoby central since an error appears (see 
attachment). In particular, I've worked in taverna and I tried to "Add new 
Biomoby scavenger" .
What does it mean?
Is it a problem related to the central BIOmoby?
thanks
silvia 

-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505
----- Fine messaggio inoltrato -----


-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505
----- Fine messaggio inoltrato -----


-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505
From edward.kawas at gmail.com  Tue Oct 18 18:41:58 2005
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue Oct 18 22:22:28 2005
Subject: [MOBY-l] RE: problems with moby services
In-Reply-To: <43556643.4090503@sfu.ca>
Message-ID: <000601c5d435$27cdef90$2566a8c0@notebook>

Hi Morgan,

Those errors are due to the service provider. It may be that
the service is no longer running or that the server that
houses the service is temporarily offline.

Also, there is no problem in running a service that takes a
GenericSequence with a DNASequence due to the object
hierarchy in Moby. A DNASequence is just a more specialized
form of GenericSequence (probably not the best way to put
it) and everything that GenericSequence is, DNASequence is
also.

Eddie


> I followed the guide and I was able to get everything to
> work (except
> for adding a service from within Moby Service Details pop
> up window). I
> then added services that the moby object "DNAsequence" was
> used as input
> for (very cool!). However, when I run the workflow with
> any service that
> takes a DNAsequence it gives errors (2 services give
> "denied access to
> method", 1 service gives "(500) Internal Error Service").
> Is the problem
> related to the services I am trying or is this a problem
> with the moby
> object? Also, I was wondering why a DNAsequence object is
> used in the
> guide instead of a GenericSequence object, which the
> runFasta service
> uses (although I tested this and it works with both!)?
> 
> Slighty confused,
> 
> Morgan


From m.rouard at cgiar.org  Fri Oct 21 14:09:22 2005
From: m.rouard at cgiar.org (Rouard, Mathieu (INIBAP - Montpellier))
Date: Fri Oct 21 16:51:37 2005
Subject: [MOBY-l] Tags for secondary articles
Message-ID: <31AB896A0E7ED211BFBE0008C7283D13DE706C@inibapnt1.inibap.org>

Hello,

I am looking for some guidelines about the xml tags allowed in secondary
articles.
Until now, I have found those tags in the documentation

datatype 
default
max 
min 
enum

Is there a tag allowing to describe the paramater? 
I think it would be helpful when the parameter name (or the value expected)
is unclear for the end user of the service.

I have another concern about the service deregistration. I would like to
update some information about some of my services.
Since the deregistration method is deprecated, I believe that the only
solution is to remove the RDF file and wait for the agent, right?
If so, how long does it take? Is there a way to call it in order to speed up
the process? 

Thanks for your help.

Cheers,
Mathieu

--
Mathieu Rouard
IPGRI-INIBAP < www.inibap.org >
Parc Scientifique Agropolis II                
34397 Montpellier - Cedex 5 - France
Tel: +33 (0)467 61 13 02          
Fax: +33 (0)467 61 03 34



From senger at ebi.ac.uk  Sun Oct 23 13:57:14 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Sun Oct 23 14:11:52 2005
Subject: [MOBY-l] Tags for secondary articles
In-Reply-To: <31AB896A0E7ED211BFBE0008C7283D13DE706C@inibapnt1.inibap.org>
Message-ID: <Pine.OSF.4.21.0510231851350.984338-100000@ice.ebi.ac.uk>

> I have another concern about the service deregistration. I would like
> to update some information about some of my services. Since the
> deregistration method is deprecated
>
   [Mark, do you see what I meant that the "deprecation" remark caused
confusion?]
   Mathieu, my understanding (and hope!) is that the deregistration is
*not* deprecated. It just can be used only in some circumstances:
   - Which are none for data types, namespaces and service types,
   - and for service instances, it can be used only if a service instance
was registered without (or with an empty) 'signatureRDF'.

> solution is to remove the RDF file and wait for the agent, right? If
> so, how long does it take?
>
   Not long, just about a year or so. We all are still waiting for the
first agent's visit :-) (of course, unless I missed him; or is it her?)

   Cheers,
   Martin

-- 
Martin Senger
   email: martin.senger@gmail.com
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)

From maria.mirto at unile.it  Tue Oct 25 11:55:07 2005
From: maria.mirto at unile.it (Maria Mirto)
Date: Sat Nov  5 10:11:43 2005
Subject: [MOBY-l] CFP: Special Issue FGCS on Life Science Grids for
 Biomedicine and Bioinformatics
Message-ID: <3458.193.204.74.230.1130255707.squirrel@webmail2.unile.it>

*************************************************************************
* Call for papers for the Special issue                                 *
*                                                                       *
* Life Science Grids for Biomedicine and Bioinformatics                 *
*                                                                       *
* Future Generation Computer System                                     *
* Elsevier                                                              *
* http://www.elsevier.com/inca/publications/misc/lifesciencegrid05.doc  *
*                                                                       *
*************************************************************************


IMPORTANT DATES
Submission for manuscripts:                December 15, 2005
Acceptance notification:                January 28, 2006
Due date of revised manuscripts:         February 28, 2006
Approximate date of publication:         Spring, 2006



Purpose of the Special Issue
----------------------------

Omics technologies (genomics - DNA, transcriptomics - RNA, proteomics -
protein, metabolomics - metabolite and phenomics ?V phenotype, etc.) and
medical informatics have changed the arena of life sciences research
forever. They allow generation of data at a large-scale, which started
with the whole-genome followed by micro-array gene-expression analysis,
mass spectrometry of proteins and metabolites, biomedical imaging
processing and health care.
Omics technologies require substantial paradigm shifts for the way life
sciences research is carried out. Biological experiments are relatively
expensive, which forces scientists to focus on advanced design for
experimentation as part of a whole-chain research approach. Furthermore,
the data generally contains information outside the scope of the original
experiment. Hence, to maximize scope of experiments, biological data needs
to be reusable, shareable and suitable for in-silico experiments. All of
this poses high demands on annotation of data and standardization of data
formats. Furthermore, the conversion of data into information and
knowledge to support scientists answering biological questions, requires
advanced analysis methods and tools that enable mining and integrating
these complex datasets. The bottlenecks for life sciences have shifted
from data generation to data storage, pre-processing, analysis, and
interpretation. The current challenge is to remove these bottlenecks by a
combination of life sciences and information technology (IT).

The effective and efficient management and use of stored data, and in
particular the transformation of these data into information and
knowledge, is thus a key requirement for success in Life Sciences, as
already has been recognized in many others sectors such as industry,
science, government.

Life Science Grids are based on the integration of emerging technologies
such as Grids, Bioinformatics, Web/Grid Services, Workflow, Semantic Web,
to support applications and research in different fields of Life Sciences,
such as Health Care, Biomedicine, Computational Chemistry. They promise to
provide reliable and secure computing infrastructures facilitating the
seamless use of distributed datasets, bioinformatics tools and systems,
data mining applications, and knowledge, building a so-called Grid Problem
Solving Environment (G-PSE), for solving complex problems in Biomedicine
and Health Care.

The scope of this special issue is to focus on challenge, applications and
services in modern Life Science Grid computing environments.
Topics of interest include, but are not limited to the following:

        - Grid solutions for Life Science applications
        - Grid infrastructures for bio data analysis
        - Parallel bio data-intensive applications
        - Grid infrastructures, middleware and tools for Life Science Grids
        - Web Services for Life Science Grids
        - Workflow for Life Science Grids
        - Semantic Grid for Life Science applications
        - Bio data analysis and management
        - Databases and the grid in biomedical field
        - Data grids for biomedicine and bioinformatics
        - Data mining of truly large and high-dimensional bio data sets
        - Security in bio data grids
        - Biology, Biochemistry and Biomedicine for Grid Environments
              - Drug Design
              - Protein Folding
              - Systems Biology
              - Genome informatics and phylogeny


Guest Editors
-------------

Giovanni Aloisio
University of Lecce, Italy
giovanni.aloisio@unile.it

Vincent Breton
CNRS/IN2P3, LPC Clermont-Ferrand, France
breton@clermont.in2p3.fr

Maria Mirto
University of Lecce, Italy
maria.mirto@unile.it

Almerico Murli
University of Naples, Italy
almerico.murli@dma.unina.it

Tony Solomonides
University of West of England, UK
Tony.Solomonides@uwe.ac.uk


Important Dates
---------------

Paper submission deadline       December 15, 2005
Notification of acceptance      January 28, 2006
Camera-ready papers             February 28, 2006
Desired publication             End of 2006



-- 
============================================================

Maria Mirto

PhD student, Center for Advanced Computational Technologies
via per Monteroni, 73100 Lecce (Le), ITALY

S.P.A.C.I. srl
ph:  +39 0832 297304
fax: +39 0832 297279
============================================================

From markw at illuminae.com  Tue Oct 18 16:49:13 2005
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 18 Oct 2005 13:49:13 -0700
Subject: [MOBY-l] Migrating MOBY Central to the new object API - MONDAY OCT
	24th
Message-ID: <1129668553.6798.17.camel@bioinfo.icapture.ubc.ca>

Hi all, 

Eddie and I have been discussing the object ontology migration now that
we are not allowing inheritance from primitives.  No matter what we do
this will break some services, and though I was originally hoping to
soften the blow by having a deprecation period, the amount of pain this
causes (i.e. everyone having to edit and re-register their services
TWICE!) is just inhumane :-)

So... I am sure that some of you will cheer this decision, and others
will loathe it... we're going to simply migrate the object ontology (in
the public MOBY Central here at iCAPTURE) with **no deprecation period
at all**.  

The object names will remain exactly as they are, but will (in some
cases) now have different definitions.  As such, for those of you
running services that are affected by this change, you will only need to
update your service code, but NOT need to de/re-register your service.

We plan to do this Monday October 24th, so you have a few days to update
your services now to reduce the down-time.  The way to go about updating
your services is as follows:  Any XML node that currently has content,
but is not a nominal primitive, will now be modified such that it
CONTAINS a node that is a primitive, and that primitive will have data
content.  It's articleName is "content" in every case.  

e.g.  

  <FASTA namespace='' id=''><![CDATA[
     >name
     ACGTGTAGTGCTAGTC
   ]]></FASTA>

will become

   <FASTA  namespace='' id=''>
	<String namespace='' id='' articleName='content'><![CDATA[
		>name
                ACGTGTGCTGATGAC
	]]></String>
   </FASTA>


And similarly for Integers, Floats, DateTime, etc.  The definition of
DateTime will also change, such that it is a primitive, rather than
inheriting from String, as it currently does.

Eddie has a migration script that will update your mySQL databases
automatically.  He will make this available on his website (details to
follow).


Any objections?  (don't all yell at once ;-) )

Cheers!

Mark



-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274



From mlangill at sfu.ca  Tue Oct 18 17:20:29 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Tue, 18 Oct 2005 14:20:29 -0700
Subject: [MOBY-l] Re: [Taverna-users] problems with moby services
In-Reply-To: <43556643.4090503@sfu.ca>
References: <43556643.4090503@sfu.ca>
Message-ID: <4355671D.60100@sfu.ca>


Of course I forgot to attach my workflow. So here it is.

Morgan


Morgan Langille wrote:

> This morning I decided try out some of biomoby's new functionality in 
> taverna (http://www.ebi.ac.uk/~tmo/mygrid/releases/latest/mobyguide/) 
> <http://www.ebi.ac.uk/%7Etmo/mygrid/releases/latest/mobyguide/>.
> I followed the guide and I was able to get everything to work (except 
> for adding a service from within Moby Service Details pop up window). 
> I then added services that the moby object "DNAsequence" was used as 
> input for (very cool!). However, when I run the workflow with any 
> service that takes a DNAsequence it gives errors (2 services give 
> "denied access to method", 1 service gives "(500) Internal Error 
> Service"). Is the problem related to the services I am trying or is 
> this a problem with the moby object? Also, I was wondering why a 
> DNAsequence object is used in the guide instead of a GenericSequence 
> object, which the runFasta service uses (although I tested this and it 
> works with both!)?
>
> Slighty confused,
>
> Morgan
>
>
> ------------------------------------------------------------------------
>


From mlangill at sfu.ca  Tue Oct 18 17:16:51 2005
From: mlangill at sfu.ca (Morgan Langille)
Date: Tue, 18 Oct 2005 14:16:51 -0700
Subject: [MOBY-l] problems with moby services
Message-ID: <43556643.4090503@sfu.ca>

This morning I decided try out some of biomoby's new functionality in 
taverna (http://www.ebi.ac.uk/~tmo/mygrid/releases/latest/mobyguide/) 
<http://www.ebi.ac.uk/%7Etmo/mygrid/releases/latest/mobyguide/>.
I followed the guide and I was able to get everything to work (except 
for adding a service from within Moby Service Details pop up window). I 
then added services that the moby object "DNAsequence" was used as input 
for (very cool!). However, when I run the workflow with any service that 
takes a DNAsequence it gives errors (2 services give "denied access to 
method", 1 service gives "(500) Internal Error Service"). Is the problem 
related to the services I am trying or is this a problem with the moby 
object? Also, I was wondering why a DNAsequence object is used in the 
guide instead of a GenericSequence object, which the runFasta service 
uses (although I tested this and it works with both!)?

Slighty confused,

Morgan


From silvia77 at dist.unige.it  Tue Oct 18 04:06:13 2005
From: silvia77 at dist.unige.it (scaglione)
Date: Tue, 18 Oct 2005 10:06:13 +0200
Subject: [MOBY-l] Error in BIOMOBY
Message-ID: <1129622773.4354acf5262c5@webmail.unige.it>


hello,
this morning I'cannot reach the biomoby central since an error appears (see 
attachment). In particular, I've worked in taverna and I tried to "Add new 
Biomoby scavenger" .
What does it mean?
Is it a problem related to the central BIOmoby?
thanks
silvia 

-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505
----- Fine messaggio inoltrato -----


-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505
----- Fine messaggio inoltrato -----


-- 
PhD. Silvia Scaglione
DIST University of Genoa
Viale Causa,13
16145 Genoa
phone +39 010 353 2789
phone CBA +39 010 5737 505
fax +39 010 5737 505

From edward.kawas at gmail.com  Tue Oct 18 18:41:58 2005
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 18 Oct 2005 15:41:58 -0700
Subject: [MOBY-l] RE: problems with moby services
In-Reply-To: <43556643.4090503@sfu.ca>
Message-ID: <000601c5d435$27cdef90$2566a8c0@notebook>

Hi Morgan,

Those errors are due to the service provider. It may be that
the service is no longer running or that the server that
houses the service is temporarily offline.

Also, there is no problem in running a service that takes a
GenericSequence with a DNASequence due to the object
hierarchy in Moby. A DNASequence is just a more specialized
form of GenericSequence (probably not the best way to put
it) and everything that GenericSequence is, DNASequence is
also.

Eddie


> I followed the guide and I was able to get everything to
> work (except
> for adding a service from within Moby Service Details pop
> up window). I
> then added services that the moby object "DNAsequence" was
> used as input
> for (very cool!). However, when I run the workflow with
> any service that
> takes a DNAsequence it gives errors (2 services give
> "denied access to
> method", 1 service gives "(500) Internal Error Service").
> Is the problem
> related to the services I am trying or is this a problem
> with the moby
> object? Also, I was wondering why a DNAsequence object is
> used in the
> guide instead of a GenericSequence object, which the
> runFasta service
> uses (although I tested this and it works with both!)?
> 
> Slighty confused,
> 
> Morgan




From m.rouard at cgiar.org  Fri Oct 21 14:09:22 2005
From: m.rouard at cgiar.org (Rouard, Mathieu (INIBAP - Montpellier))
Date: Fri, 21 Oct 2005 11:09:22 -0700
Subject: [MOBY-l] Tags for secondary articles
Message-ID: <31AB896A0E7ED211BFBE0008C7283D13DE706C@inibapnt1.inibap.org>

Hello,

I am looking for some guidelines about the xml tags allowed in secondary
articles.
Until now, I have found those tags in the documentation

datatype 
default
max 
min 
enum

Is there a tag allowing to describe the paramater? 
I think it would be helpful when the parameter name (or the value expected)
is unclear for the end user of the service.

I have another concern about the service deregistration. I would like to
update some information about some of my services.
Since the deregistration method is deprecated, I believe that the only
solution is to remove the RDF file and wait for the agent, right?
If so, how long does it take? Is there a way to call it in order to speed up
the process? 

Thanks for your help.

Cheers,
Mathieu

--
Mathieu Rouard
IPGRI-INIBAP < www.inibap.org >
Parc Scientifique Agropolis II                
34397 Montpellier - Cedex 5 - France
Tel: +33 (0)467 61 13 02          
Fax: +33 (0)467 61 03 34





From senger at ebi.ac.uk  Sun Oct 23 13:57:14 2005
From: senger at ebi.ac.uk (Martin Senger)
Date: Sun, 23 Oct 2005 18:57:14 +0100 (BST)
Subject: [MOBY-l] Tags for secondary articles
In-Reply-To: <31AB896A0E7ED211BFBE0008C7283D13DE706C@inibapnt1.inibap.org>
Message-ID: <Pine.OSF.4.21.0510231851350.984338-100000@ice.ebi.ac.uk>

> I have another concern about the service deregistration. I would like
> to update some information about some of my services. Since the
> deregistration method is deprecated
>
   [Mark, do you see what I meant that the "deprecation" remark caused
confusion?]
   Mathieu, my understanding (and hope!) is that the deregistration is
*not* deprecated. It just can be used only in some circumstances:
   - Which are none for data types, namespaces and service types,
   - and for service instances, it can be used only if a service instance
was registered without (or with an empty) 'signatureRDF'.

> solution is to remove the RDF file and wait for the agent, right? If
> so, how long does it take?
>
   Not long, just about a year or so. We all are still waiting for the
first agent's visit :-) (of course, unless I missed him; or is it her?)

   Cheers,
   Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger
consulting for:
   International Rice Research Institute
   Biometrics and Bioinformatics Unit
   DAPO BOX 7777, Metro Manila
   Philippines, phone: +63-2-580-5600 (ext.2324)



From maria.mirto at unile.it  Tue Oct 25 11:55:07 2005
From: maria.mirto at unile.it (Maria Mirto)
Date: Tue, 25 Oct 2005 17:55:07 +0200 (CEST)
Subject: [MOBY-l] CFP: Special Issue FGCS on Life Science Grids for
 Biomedicine and Bioinformatics
Message-ID: <3458.193.204.74.230.1130255707.squirrel@webmail2.unile.it>

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* Call for papers for the Special issue                                 *
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* Life Science Grids for Biomedicine and Bioinformatics                 *
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* Future Generation Computer System                                     *
* Elsevier                                                              *
* http://www.elsevier.com/inca/publications/misc/lifesciencegrid05.doc  *
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IMPORTANT DATES
Submission for manuscripts:                December 15, 2005
Acceptance notification:                January 28, 2006
Due date of revised manuscripts:         February 28, 2006
Approximate date of publication:         Spring, 2006



Purpose of the Special Issue
----------------------------

Omics technologies (genomics - DNA, transcriptomics - RNA, proteomics -
protein, metabolomics - metabolite and phenomics ?V phenotype, etc.) and
medical informatics have changed the arena of life sciences research
forever. They allow generation of data at a large-scale, which started
with the whole-genome followed by micro-array gene-expression analysis,
mass spectrometry of proteins and metabolites, biomedical imaging
processing and health care.
Omics technologies require substantial paradigm shifts for the way life
sciences research is carried out. Biological experiments are relatively
expensive, which forces scientists to focus on advanced design for
experimentation as part of a whole-chain research approach. Furthermore,
the data generally contains information outside the scope of the original
experiment. Hence, to maximize scope of experiments, biological data needs
to be reusable, shareable and suitable for in-silico experiments. All of
this poses high demands on annotation of data and standardization of data
formats. Furthermore, the conversion of data into information and
knowledge to support scientists answering biological questions, requires
advanced analysis methods and tools that enable mining and integrating
these complex datasets. The bottlenecks for life sciences have shifted
from data generation to data storage, pre-processing, analysis, and
interpretation. The current challenge is to remove these bottlenecks by a
combination of life sciences and information technology (IT).

The effective and efficient management and use of stored data, and in
particular the transformation of these data into information and
knowledge, is thus a key requirement for success in Life Sciences, as
already has been recognized in many others sectors such as industry,
science, government.

Life Science Grids are based on the integration of emerging technologies
such as Grids, Bioinformatics, Web/Grid Services, Workflow, Semantic Web,
to support applications and research in different fields of Life Sciences,
such as Health Care, Biomedicine, Computational Chemistry. They promise to
provide reliable and secure computing infrastructures facilitating the
seamless use of distributed datasets, bioinformatics tools and systems,
data mining applications, and knowledge, building a so-called Grid Problem
Solving Environment (G-PSE), for solving complex problems in Biomedicine
and Health Care.

The scope of this special issue is to focus on challenge, applications and
services in modern Life Science Grid computing environments.
Topics of interest include, but are not limited to the following:

        - Grid solutions for Life Science applications
        - Grid infrastructures for bio data analysis
        - Parallel bio data-intensive applications
        - Grid infrastructures, middleware and tools for Life Science Grids
        - Web Services for Life Science Grids
        - Workflow for Life Science Grids
        - Semantic Grid for Life Science applications
        - Bio data analysis and management
        - Databases and the grid in biomedical field
        - Data grids for biomedicine and bioinformatics
        - Data mining of truly large and high-dimensional bio data sets
        - Security in bio data grids
        - Biology, Biochemistry and Biomedicine for Grid Environments
              - Drug Design
              - Protein Folding
              - Systems Biology
              - Genome informatics and phylogeny


Guest Editors
-------------

Giovanni Aloisio
University of Lecce, Italy
giovanni.aloisio at unile.it

Vincent Breton
CNRS/IN2P3, LPC Clermont-Ferrand, France
breton at clermont.in2p3.fr

Maria Mirto
University of Lecce, Italy
maria.mirto at unile.it

Almerico Murli
University of Naples, Italy
almerico.murli at dma.unina.it

Tony Solomonides
University of West of England, UK
Tony.Solomonides at uwe.ac.uk


Important Dates
---------------

Paper submission deadline       December 15, 2005
Notification of acceptance      January 28, 2006
Camera-ready papers             February 28, 2006
Desired publication             End of 2006



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Maria Mirto

PhD student, Center for Advanced Computational Technologies
via per Monteroni, 73100 Lecce (Le), ITALY

S.P.A.C.I. srl
ph:  +39 0832 297304
fax: +39 0832 297279
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