From yangkuan81 at gmail.com  Sun May  3 00:26:38 2009
From: yangkuan81 at gmail.com (Kuan Yang)
Date: Sun, 3 May 2009 00:26:38 -0400
Subject: [MOBY-l] Connection refused error?
Message-ID: <a68367020905022126m1ee99314sb33de708683bf31e@mail.gmail.com>

Hi all,

I am trying to get a list of services and query them each for information.
I used jMOBY for this purpose. I did get some results but I also got
Connection refused error. How should I deal with this type of errors?

I first defined the services that I want needs to consume a
"AGI_LocusCode" as input and then I findservice() by that datatype.
Then, for each service returned, I query for information. It should be
a very simple procedure.

here is the error message I got for some services

AxisFault
 faultCode: {http://schemas.xmlsoap.org/soap/envelope/}Server.userException
 faultSubcode:
 faultString: java.net.ConnectException: Connection refused
 faultActor:
 faultNode:
 faultDetail:

source code is attached.

Thanks very much

Kuan

From edward.kawas at gmail.com  Sun May  3 12:31:57 2009
From: edward.kawas at gmail.com (Eddie Kawas)
Date: Sun, 3 May 2009 09:31:57 -0700
Subject: [MOBY-l] Connection refused error?
In-Reply-To: <a68367020905022126m1ee99314sb33de708683bf31e@mail.gmail.com>
References: <a68367020905022126m1ee99314sb33de708683bf31e@mail.gmail.com>
Message-ID: <b4bcf7b10905030931v6cf847brdd17fd9c4f0049dc@mail.gmail.com>

Hi Kuan,

Unfortunately, not all services that are found are live. Some have been
abandoned and may no longer work.

What service are you calling (authority/service name)?

Thanks,

Eddie

On Sat, May 2, 2009 at 9:26 PM, Kuan Yang <yangkuan81 at gmail.com> wrote:

> Hi all,
>
> I am trying to get a list of services and query them each for information.
> I used jMOBY for this purpose. I did get some results but I also got
> Connection refused error. How should I deal with this type of errors?
>
> I first defined the services that I want needs to consume a
> "AGI_LocusCode" as input and then I findservice() by that datatype.
> Then, for each service returned, I query for information. It should be
> a very simple procedure.
>
> here is the error message I got for some services
>
> AxisFault
>  faultCode: {
> http://schemas.xmlsoap.org/soap/envelope/}Server.userException<http://schemas.xmlsoap.org/soap/envelope/%7DServer.userException>
>  faultSubcode:
>  faultString: java.net.ConnectException: Connection refused
>  faultActor:
>  faultNode:
>  faultDetail:
>
> source code is attached.
>
> Thanks very much
>
> Kuan
>
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l
>
>

From mgerlich at ipb-halle.de  Mon May  4 06:13:33 2009
From: mgerlich at ipb-halle.de (Michael Gerlich)
Date: Mon, 04 May 2009 12:13:33 +0200
Subject: [MOBY-l] Testing Registry
Message-ID: <49FEBFCD.7050105@ipb-halle.de>

Hi all,

does anyone encounter the following error when trying to register a new 
service via Dashboard into testing registry?


===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: DBI 
connect('moby_central:bioinfo.icapture.ubc.ca:3306','moby',...) failed: 
Can't connect to MySQL server on 'bioinfo.icapture.ubc.ca' (111) at 
/usr/lib/perl5/site_perl/5.8.5/MOBY/Adaptor/moby/queryapi/mysql.pm line 93

Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server
Fault actor:  null
When calling:
    http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========



Regards,
Michael

-- 

Michael Gerlich
Group Bioinformatics & Mass Spectrometry
Leibniz Institute of Plant Biochemistry
06120 Halle, Germany


From edward.kawas at gmail.com  Mon May  4 10:54:03 2009
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 4 May 2009 07:54:03 -0700
Subject: [MOBY-l] Testing Registry
In-Reply-To: <49FEBFCD.7050105@ipb-halle.de>
References: <49FEBFCD.7050105@ipb-halle.de>
Message-ID: <49ff019a.16538c0a.7f4e.16f6@mx.google.com>

Hi Michael,

You should be able to register services correctly now on the test registry!

Thanks for the heads up.

Eddie

-----Original Message-----
From: moby-l-bounces at lists.open-bio.org
[mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Michael Gerlich
Sent: May-04-09 3:14 AM
To: moby-l at biomoby.org
Subject: [MOBY-l] Testing Registry

Hi all,

does anyone encounter the following error when trying to register a new 
service via Dashboard into testing registry?


===ERROR===
Fault details:
[stackTrace: null]
[hostname: null]
Fault string: DBI 
connect('moby_central:bioinfo.icapture.ubc.ca:3306','moby',...) failed: 
Can't connect to MySQL server on 'bioinfo.icapture.ubc.ca' (111) at 
/usr/lib/perl5/site_perl/5.8.5/MOBY/Adaptor/moby/queryapi/mysql.pm line 93

Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Server
Fault actor:  null
When calling:
    http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl
===========



Regards,
Michael

-- 

Michael Gerlich
Group Bioinformatics & Mass Spectrometry
Leibniz Institute of Plant Biochemistry
06120 Halle, Germany

_______________________________________________
moby-l mailing list
moby-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-l


From paolo.romano at istge.it  Wed May 27 12:16:04 2009
From: paolo.romano at istge.it (Paolo Romano)
Date: Wed, 27 May 2009 18:16:04 +0200
Subject: [MOBY-l] NETTAB 2009: Last Call for Participation
Message-ID: <200905271631.n4RGV37A036630@ibm43p.biotech.ist.unige.it>


Last Call for Participation

NETTAB 2009 Workshop on
"Technologies, Tools and Applications for 
Collaborative and Social Bioinformatics Research and Development"
with a Special Session on:
"Methods and Tools for RNA Structure and Functional Analysis"

June 10-13, 2009
Department of Computer Science, University of Catania, Italy

http://www.nettab.org/2009/


KEYNOTE TALKS

RNA WikiProject: Community annotation of RNA families
Alex Bateman, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

Who are you? Managing collaborative digital 
identities in bioinformatics with myExperiment
Duncan Hull, School of Chemistry, University of Manchester, Manchester, UK.

Semantically Integrated eCommunities in 
Biomedicine: Next-Generation Models of Biomedical Communication
Tim Clark, Director of Informatics, MassGeneral 
Institute for Neurodegenerative Disease Neurology 
Research Department, Massachusetts General Hospital, Boston, USA.

Bacterial Phylogeny and Taxonomy in the High-Throughput Sequencing World
Gabriel Valiente, Technical University of 
Catalonia, Department of Software, Barcelona, Spain.

Non coding RNAs (title to be confirmed)
Doron Betel, MSKCC - Computational Biology Center, New York, USA .


SELECTED ORAL COMMUNICATIONS

The DC-THERA Directory: A Knowledge Management 
System to Support Collaboration on Dendritic Cell and Immunology Research
Michaela Guendel, Ciro Scognamiglio, Marco Brandizi and Andrea Splendiani

Bioinformatics Experimentation in a New 
Agent-Based Infrastructure OpenKnowledge
Dietlind Gerloff, Xueping Quan, Adrian de 
Pinninck, Paolo Besana, Siu-wai Leung, Marco Schorlemmer and David Robertson

Abstraction based cooperation for the design of bioinformatics workflows
Fr?d?ric Cadier and Philippe Picouet

Biomedical applications in the EELA-2 Project
Leandro N Ciuffo and Rafael Mayo

Make Histri: collaborative curation of exchange 
histories of bacterial and archaeal type strains
Bert Verslyppe, Paul De Vos, Bernard De Baets and Peter Dawyndt

SBMM Assistant: Social Pathway Annotation
Ismael Navas-Delgado, Alejandro del 
Real-Chicharro, Francisca S?nchez-Jim?nez and Jose F Aldana Montes

GePh-CARD: an information exchange application 
for an Hub & Spoke Network for Skeletal Dysplasias
Marina Mordenti and Luca Sangiorgi

ProDaMa-C: a collaborative web application to 
generate specialized protein structure datasets
Giuliano Armano and Andrea Manconi

RNA tertiary structure prediction with ModeRNA
Magdalena Musielak, Kristian Rother, Tomasz Puton and Janusz M. Bujnicki

Improved heuristic for pairwise RNA secondary structure prediction
Olivier Perriquet and Pedro Barahona

Analysing the microRNA-17-92/Myc/E2F/RB Compound 
Toggle Switch by Theorem Proving
Giampaolo Bella and Pietro Li?

Mapping miRNA genes on human fragile sites and translocation breakpoints
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Alfredo Pulvirenti and Francesco Russo

MicroRNA.gr: A suite of web based tools for elucidating microRNA function
Giorgio L. Papadopoulos, Panagiotis Alexiou, 
Manolis Maragkakis, Martin Reczko and Artemis G. Hatzigeorgiou

miRScape: A Cytoscape Plugin to Annotate Biological Networks with microRNAs
Alfredo Ferro, rosalba giugno, Alessandro Lagan?, 
Misael Mongiov?, Giuseppe Pigola, Alfredo 
Pulvirenti, Gary Bader and Dennis Shasha


POSTERS

A web site supporting collaborative activities 
within the Italian Network for Oncology Bioinformatics
Silvia Giuliani, Elda Rossi, Stefania Parodi and Paolo Romano

Prediction of human targets for viral encoded microRNAs
Alessandro Lagan?, Stefano Forte, Rosalba Giugno, 
Alfredo Pulvirenti and Alfredo Ferro

Genome-wide microRNA target gene identification 
and annotation using multiple prediction algorithms
Dario Corrada, Luciano Milanesi and Daniele Catalucci

Design of highly specific synthetic miRNAs
Alessandro Lagan?, Stefano Forte, Angela Papa, 
Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha and Alfredo Ferro



NETTAB '09 - Ninth International Workshop on 
Network Tools and Applications in Biology
10-13 June 2009, Catania, Italy
http://www.nettab.org/2009/

Paolo Romano (paolo.romano at istge.it)
Bioinformatics
National Cancer Research Institute (IST)