From senger at ebi.ac.uk  Wed Mar  1 01:51:07 2006
From: senger at ebi.ac.uk (Martin Senger)
Date: Wed, 1 Mar 2006 06:51:07 +0000 (GMT)
Subject: [MOBY-l] java error
In-Reply-To: <44049F0D.9060000@purdue.edu>
Message-ID: <Pine.OSF.4.21.0603010638110.1464314-100000@mozart.ebi.ac.uk>

Hi,
> I don't see /org folder in mine..
>
   The otg is under src - and you have it there - but it is not anymore
important because I think the problem cause is found...

> Is it because I downloaded the tarball from the biomoby.org website
> instead of using CVS?
>
   That's it! Some tar programs limit the length of the file names. It
seems that the tar used by biomoby.org is one of them (yes, it is, I have
just checked it). So you are not getting correct file names. I will report
it to the CVS maintainer, but your solution is clear - use please a
regular CVS:
 
> how do I set up my CVS if I want to get the files from CVS?
> 
   Are you on Unix or windows? On Unix you should have already a 'cvs'
command line client available (if not, use your package manager - it can
install it for you easily - its name depends on the Linux distribution you
are using; which one it is?). On Windows, I recommend to use TortoiseCVS
(or WinCVS).
   On Unix, do as described
here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CVS.html.

   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 nsutanto at purdue.edu  Wed Mar  1 15:34:17 2006
From: nsutanto at purdue.edu (Nicholas Sutanto)
Date: Wed,  1 Mar 2006 15:34:17 -0500
Subject: [MOBY-l] java error
In-Reply-To: <Pine.OSF.4.21.0603010638110.1464314-100000@mozart.ebi.ac.uk>
References: <Pine.OSF.4.21.0603010638110.1464314-100000@mozart.ebi.ac.uk>
Message-ID: <1141245257.4406054998037@webmail.purdue.edu>

Hi Martin,

Thanks a lot for your help.. It works now.. :)

Best Regards,
Nicholas Sutanto.


Quoting Martin Senger <senger at ebi.ac.uk>:

> Hi,
> > I don't see /org folder in mine..
> >
>    The otg is under src - and you have it there - but it is not anymore
> important because I think the problem cause is found...
> 
> > Is it because I downloaded the tarball from the biomoby.org website
> > instead of using CVS?
> >
>    That's it! Some tar programs limit the length of the file names. It
> seems that the tar used by biomoby.org is one of them (yes, it is, I have
> just checked it). So you are not getting correct file names. I will report
> it to the CVS maintainer, but your solution is clear - use please a
> regular CVS:
>  
> > how do I set up my CVS if I want to get the files from CVS?
> > 
>    Are you on Unix or windows? On Unix you should have already a 'cvs'
> command line client available (if not, use your package manager - it can
> install it for you easily - its name depends on the Linux distribution you
> are using; which one it is?). On Windows, I recommend to use TortoiseCVS
> (or WinCVS).
>    On Unix, do as described
> here: http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/CVS.html.
> 
>    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 admin at unleashedinformatics.com  Thu Mar  2 18:14:35 2006
From: admin at unleashedinformatics.com (Unleashed Informatics Administration)
Date: Thu, 02 Mar 2006 18:14:35 -0500
Subject: [MOBY-l] SeqHound User Support
Message-ID: <44077C5B.1080201@unleashedinformatics.com>

As announced on 2 March 2006, SeqHound has been replaced by "DogBox
Online".

 From 3 April 2006, users of the SeqHound API will be required to
provide their e-mail address when beginning a block of SeqHound (now
DogBox Online) calls.

Users who fail to provide a valid address will not have access to the
API, and will not have access to user support.

The following FAQ has been posted to the DogBox Online website.

FAQ:

Q. What is DogBox Online?

DogBox Online is a powerful integrated data service for the life science
community, and represents the new name for the SeqHound service offered
by The Blueprint Initiative. The new service is located at:

http://dogboxonline.unleashedinformatics.com

Q. What happened to SeqHound?

The SeqHound service is being phased out. Please change to DogBox Online.

Q. How will DogBox Online differ?

DogBox Online includes several new
features previously available only to DogBox customers.

Q. Will my use of the SeqHound API be affected?

Yes. On 3 April 2006, Unleashed Informatics will require SeqHound users
to submit a valid e-mail address as part of the initial SHoundInit call.
  If you were not using a SHoundInit call or similar in your code,
ensure that you now begin your scripts with this call.

Q. Can you give me an example?

Using the Perl API, you need to begin your series of SeqHound queries
like so:

> use SeqHound;
> SHoundInit('Program Name');

Replace the 'Program Name' text with your valid e-mail address:

> use SeqHound;
> SHoundInit('joe.bloggs at blogme.com');

To avoid disappointment, we recommend you change your scripts now to
employ the new URL, http://dogboxonline.unleashedinformatics.com.

Q. What happens if I don't provide a valid email address?

Your use of the API will be blocked until you do so.

Q. Why is this change happening?

1. To obtain feedback from users regarding API use and improvement.

2. To notify users of future developments and new features.

Q. Where do I sign up?

https://secure.unleashedinformatics.com/index.php?pg=support.register

Thank you for your co-operation.



From admin at unleashedinformatics.com  Thu Mar  2 18:08:14 2006
From: admin at unleashedinformatics.com (Unleashed Informatics Administration)
Date: Thu, 02 Mar 2006 18:08:14 -0500
Subject: [MOBY-l] Unleashed Informatics Supports DogBox Online Community
Message-ID: <44077ADE.9030000@unleashedinformatics.com>

In December 2005, Unleashed Informatics acquired commercial rights to 
Blueprint Initiative intellectual property from Mount Sinai Hospital.

Spun-off from The Blueprint Initiative public research program at 
Toronto?s Mount Sinai Hospital, Unleashed Informatics provides 
integrated hardware and software products designed to harness the power 
of increasingly complex scientific data.

On 22 February, Unleashed Informatics released DogBox Online as an open 
access product to the life science community.

DogBox Online is an integrated, online data retrieval service and 
represents the new, re-named SeqHound service previously offered by the 
Blueprint Initiative.

The new service is located at 
http://dogboxonline.unleashedinformatics.com, and requires a free 
Unleashed Informatics account for unrestricted access.

The DogBox Online registration process will help Unleashed Informatics 
better understand the resource user base, and ultimately help us improve 
our open access offerings in line with the needs of the life sciences 
community.

Importantly, the collection of such user feedback is essential for the 
preparation of planned public good research grant applications aimed at 
funding the ongoing provision of open source and freely available 
bioinformatics resources.

Unleashed Informatics is making a concerted effort to develop, maintain 
and improve open access resources for global researchers. The release 
this past week of the freely accessible DogBox Online reaffirms the 
company?s commitment to open access resources.

Specific support documentation for new DogBox Online service can be 
found in the Help section.

From Marc.Logghe at DEVGEN.com  Mon Mar  6 05:30:14 2006
From: Marc.Logghe at DEVGEN.com (Marc Logghe)
Date: Mon, 6 Mar 2006 11:30:14 +0100
Subject: [MOBY-l] Demo moby scufl workflow
Message-ID: <0C528E3670D8CE4B8E013F6749231AA6746B8D@ANTARESIA.be.devgen.com>

Hi all,
Has anybody a working demo moby workflow for taverna to share ? I see
plenty of moby services available but I don't succeed in making a flow
:-(
You have for instance the moby object NCBI_Blast_Database. When that
object is added to the model I see plenty of inputs to be filled but I
don't have any clue what is expected or what the service is actually
doing. If you allow me to compare, the metadata coming with soaplab
services seem much more informative to me.
Anybody willing to reveal the mystery of a moby service ?
Thanks,
Marc


From Marc.Logghe at DEVGEN.com  Mon Mar  6 07:40:06 2006
From: Marc.Logghe at DEVGEN.com (Marc Logghe)
Date: Mon, 6 Mar 2006 13:40:06 +0100
Subject: [MOBY-l] RE : [Taverna-users] Demo moby scufl workflow
Message-ID: <0C528E3670D8CE4B8E013F6749231AA6746B8F@ANTARESIA.be.devgen.com>

> You should have a look to the workflows provided by the 
> PlaNet network.
> http://mips.gsf.de/projects/plants/PlaNetPortal/taverna_workflows.html

Ahh, with input examples ! Great, thanks.

> 
> >I see plenty of inputs to be filled but I don't have any 
> clue what is 
> >expected or what the service is actually doing.
> That is the problem when the service is not documented well enough.
> Have you read the description of the service using this 
> datatype as input?
> I looked at the service list but I did not see any service 
> using NCBI_Blast_Database.

I have found this one in the list of Moby objects when taverna.defaultbiomoby = http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl is set in the mygrid.properties file.

Thanks again for the link.
Regards,
Marc

> 
> Mathieu
> 
> 
> -------- Message d'origine--------
> De: taverna-users-admin at lists.sourceforge.net de la part de 
> Marc Logghe
> Date: lun. 06/03/2006 11:30
> ?: taverna-users at lists.sourceforge.net; moby-l at biomoby.org 
> Objet : [Taverna-users] Demo moby scufl workflow
>  
> Hi all,
> Has anybody a working demo moby workflow for taverna to share 
> ? I see plenty of moby services available but I don't succeed 
> in making a flow :-( You have for instance the moby object 
> NCBI_Blast_Database. When that object is added to the model I 
> see plenty of inputs to be filled but I don't have any clue 
> what is expected or what the service is actually doing. If 
> you allow me to compare, the metadata coming with soaplab 
> services seem much more informative to me.
> Anybody willing to reveal the mystery of a moby service ?
> Thanks,
> Marc
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by xPML, a groundbreaking 
> scripting language that extends applications into web and 
> mobile media. Attend the live webcast and join the prime 
> developer group breaking into this new coding territory!
> http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642
> _______________________________________________
> Taverna-users mailing list
> Taverna-users at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/taverna-users
> 
> 


From m.rouard at cgiar.org  Mon Mar  6 06:40:44 2006
From: m.rouard at cgiar.org (Rouard, Mathieu (INIBAP))
Date: Mon, 6 Mar 2006 12:40:44 +0100
Subject: [MOBY-l] RE : [Taverna-users] Demo moby scufl workflow
References: <0C528E3670D8CE4B8E013F6749231AA6746B8D@ANTARESIA.be.devgen.com>
Message-ID: <F5A641F773C34D449A50970A6CA3B11A10F127@HQ62VS.IPGRI.CGIARAD.ORG>

Hi Marc,

You should have a look to the workflows provided by the PlaNet network.
http://mips.gsf.de/projects/plants/PlaNetPortal/taverna_workflows.html

>I see plenty of inputs to be filled but I
>don't have any clue what is expected or what the service is actually
>doing.
That is the problem when the service is not documented well enough.
Have you read the description of the service using this datatype as input?
I looked at the service list but I did not see any service using NCBI_Blast_Database.

Mathieu


-------- Message d'origine--------
De: taverna-users-admin at lists.sourceforge.net de la part de Marc Logghe
Date: lun. 06/03/2006 11:30
?: taverna-users at lists.sourceforge.net; moby-l at biomoby.org
Objet : [Taverna-users] Demo moby scufl workflow
 
Hi all,
Has anybody a working demo moby workflow for taverna to share ? I see
plenty of moby services available but I don't succeed in making a flow
:-(
You have for instance the moby object NCBI_Blast_Database. When that
object is added to the model I see plenty of inputs to be filled but I
don't have any clue what is expected or what the service is actually
doing. If you allow me to compare, the metadata coming with soaplab
services seem much more informative to me.
Anybody willing to reveal the mystery of a moby service ?
Thanks,
Marc


-------------------------------------------------------
This SF.Net email is sponsored by xPML, a groundbreaking scripting language
that extends applications into web and mobile media. Attend the live webcast
and join the prime developer group breaking into this new coding territory!
http://sel.as-us.falkag.net/sel?cmd=k&kid0944&bid$1720&dat1642
_______________________________________________
Taverna-users mailing list
Taverna-users at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/taverna-users



From xsz7001 at genomecenter.columbia.edu  Tue Mar  7 12:06:25 2006
From: xsz7001 at genomecenter.columbia.edu (Sean Zhou)
Date: Tue, 7 Mar 2006 12:06:25 -0500
Subject: [MOBY-l] Question about Object Ontology
Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AED38C95@cgcmail.cgc.cpmc.columbia.edu>

Hi there,

 

I am a new comer for BioMOBY. I have two questions related to Object Ontology
in BioMOBY. 

1) Where can I download Object Ontology?

2) What tool shall I use to view it?

 

Thank you very much for the help.

 

Best,

 

Sean



From markw at illuminae.com  Tue Mar  7 12:26:06 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 07 Mar 2006 09:26:06 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AED38C95@cgcmail.cgc.cpmc.columbia.edu>
References: <6CA15ADD82E5724F88CB53D50E61C9AED38C95@cgcmail.cgc.cpmc.columbia.edu>
Message-ID: <1141752366.30213.52.camel@bioinfo.icapture.ubc.ca>

=================
The Official way:

The "retrieveResourceURLs" API call of MOBY Central (implemented in both
the Perl and the Java clients, I believe) will give you the URL's from
which you can download the various MOBY ontologies.
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-
S_API/XMLPayloads.html#retrieveResourceURLs
===================

===================
"Fast" (but not supported) way:

At the moment, the Object ontology is at:
http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
====================


The ontologies are returned in RDF, and can be viewed in any RDF-capable
viewer.  There are some tools in the MOBY CVS that are specifically
designed to browse/edit the ontologies - e.g. Martin Senger's MOBY
Dashboard.  Which tool you chose depends on what you need to use the
ontologies for, I guess...

Hope that helps!

M



On Tue, 2006-03-07 at 12:06 -0500, Sean Zhou wrote:
> Hi there,
> 
>  
> 
> I am a new comer for BioMOBY. I have two questions related to Object Ontology
> in BioMOBY. 
> 
> 1) Where can I download Object Ontology?
> 
> 2) What tool shall I use to view it?
> 
>  
> 
> Thank you very much for the help.
> 
>  
> 
> Best,
> 
>  
> 
> Sean
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From edward.kawas at gmail.com  Tue Mar  7 11:40:18 2006
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 7 Mar 2006 08:40:18 -0800
Subject: [MOBY-l] The agent
Message-ID: <000401c64205$d2735000$6500a8c0@notebook>

Hi,

I am just curious as to why no-one has tested the agent on the 'test'
registry? Did my last email go un-noticed?

Thanks,

Eddie


From xsz7001 at genomecenter.columbia.edu  Tue Mar  7 15:13:54 2006
From: xsz7001 at genomecenter.columbia.edu (Sean Zhou)
Date: Tue, 7 Mar 2006 15:13:54 -0500
Subject: [MOBY-l] [moby]  Question about Object Ontology
Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>

Dear Mark,

Thanks a lot for answering my question. At this stage I don't want to write a
script to retrieve the ontologies through API. So, the "Fast" way you
suggested is more suitable for my current interest. But unfortunately, the
url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
provided didn't give me the object ontology file that I wished to download. 

I've also tried the CVS-> moby-live
(http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
by). But not sure which one I should dig into. The object ontology is
definitely I want. Also, I wonder whether there is a service-ontology too.

I found on the BioMOBY homepage that Mr. Yan Wong has developed an Object
Ontology browser for Windows
(http://biomoby.open-bio.org/index.php/moby-clients/ontology_clients ). But
the username and password didn't work. This problem actually has been
mentioned in the previous discussion (
http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
solved.

Anyway, I would really appreciate if you or some other experts of BioMOBY can
help me with these questions.

Thanks a lot.

Sean

-----Original Message-----
From: Mark Wilkinson [mailto:markw at illuminae.com] 
Sent: Tuesday, March 07, 2006 12:26 PM
To: Sean Zhou
Cc: moby-l at biomoby.org
Subject: Re: [moby] [MOBY-l] Question about Object Ontology

=================
The Official way:

The "retrieveResourceURLs" API call of MOBY Central (implemented in both
the Perl and the Java clients, I believe) will give you the URL's from
which you can download the various MOBY ontologies.
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-
S_API/XMLPayloads.html#retrieveResourceURLs
===================

===================
"Fast" (but not supported) way:

At the moment, the Object ontology is at:
http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
====================


The ontologies are returned in RDF, and can be viewed in any RDF-capable
viewer.  There are some tools in the MOBY CVS that are specifically
designed to browse/edit the ontologies - e.g. Martin Senger's MOBY
Dashboard.  Which tool you chose depends on what you need to use the
ontologies for, I guess...

Hope that helps!

M



On Tue, 2006-03-07 at 12:06 -0500, Sean Zhou wrote:
> Hi there,
> 
>  
> 
> I am a new comer for BioMOBY. I have two questions related to Object
Ontology
> in BioMOBY. 
> 
> 1) Where can I download Object Ontology?
> 
> 2) What tool shall I use to view it?
> 
>  
> 
> Thank you very much for the help.
> 
>  
> 
> Best,
> 
>  
> 
> Sean
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future



From edward.kawas at gmail.com  Tue Mar  7 15:19:27 2006
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 7 Mar 2006 12:19:27 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>
Message-ID: <001101c64224$711d0160$6500a8c0@notebook>

For the object ontology, try:
http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects without a
trailing forward slash.

If all you want to do is browse the ontologies, then checkout the code from
the cvs (http://biomoby.open-bio.org/index.php/for-developers/get_code), and
run Dashboard
(http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html)
.

Eddie 

> -----Original Message-----
> From: moby-l-bounces at biomoby.org 
> [mailto:moby-l-bounces at biomoby.org] On Behalf Of Sean Zhou
> Sent: Tuesday, March 07, 2006 12:14 PM
> To: markw at illuminae.com
> Cc: moby-l at biomoby.org
> Subject: Re: [MOBY-l] [moby] Question about Object Ontology
> 
> Dear Mark,
> 
> Thanks a lot for answering my question. At this stage I don't 
> want to write a script to retrieve the ontologies through 
> API. So, the "Fast" way you suggested is more suitable for my 
> current interest. But unfortunately, the url 
> (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/)
>  you provided didn't give me the object ontology file that I 
> wished to download. 
> 
> I've also tried the CVS-> moby-live
> (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live
> /?cvsroot=biomo
> by). But not sure which one I should dig into. The object 
> ontology is definitely I want. Also, I wonder whether there 
> is a service-ontology too.
> 
> I found on the BioMOBY homepage that Mr. Yan Wong has 
> developed an Object Ontology browser for Windows 
> (http://biomoby.open-bio.org/index.php/moby-clients/ontology_c
> lients ). But the username and password didn't work. This 
> problem actually has been mentioned in the previous 
> discussion ( 
> http://biomoby.org/pipermail/moby-l/2005-July/002612.html). 
> But it is not solved.
> 
> Anyway, I would really appreciate if you or some other 
> experts of BioMOBY can help me with these questions.
> 
> Thanks a lot.
> 
> Sean
> 
> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com]
> Sent: Tuesday, March 07, 2006 12:26 PM
> To: Sean Zhou
> Cc: moby-l at biomoby.org
> Subject: Re: [moby] [MOBY-l] Question about Object Ontology
> 
> =================
> The Official way:
> 
> The "retrieveResourceURLs" API call of MOBY Central 
> (implemented in both the Perl and the Java clients, I 
> believe) will give you the URL's from which you can download 
> the various MOBY ontologies.
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-
> S_API/XMLPayloads.html#retrieveResourceURLs
> ===================
> 
> ===================
> "Fast" (but not supported) way:
> 
> At the moment, the Object ontology is at:
> http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
> ====================
> 
> 
> The ontologies are returned in RDF, and can be viewed in any 
> RDF-capable viewer.  There are some tools in the MOBY CVS 
> that are specifically designed to browse/edit the ontologies 
> - e.g. Martin Senger's MOBY Dashboard.  Which tool you chose 
> depends on what you need to use the ontologies for, I guess...
> 
> Hope that helps!
> 
> M
> 
> 
> 
> On Tue, 2006-03-07 at 12:06 -0500, Sean Zhou wrote:
> > Hi there,
> > 
> >  
> > 
> > I am a new comer for BioMOBY. I have two questions related to Object
> Ontology
> > in BioMOBY. 
> > 
> > 1) Where can I download Object Ontology?
> > 
> > 2) What tool shall I use to view it?
> > 
> >  
> > 
> > Thank you very much for the help.
> > 
> >  
> > 
> > Best,
> > 
> >  
> > 
> > Sean
> > 
> > 
> > _______________________________________________
> > moby-l mailing list
> > moby-l at biomoby.org
> > http://biomoby.org/mailman/listinfo/moby-l
> -- 
> 
> --
> 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
> 
> "For most of this century we have viewed communications as a conduit, 
>        a pipe between physical locations on the planet. 
> What's happened now is that the conduit has become so big and 
> interesting 
>       that communication has become more than a conduit, 
>        it has become a destination in its own right..."
> 
>                 Paul Saffo - Director, Institute for the Future
> 
> 
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l


From markw at illuminae.com  Tue Mar  7 15:21:24 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 07 Mar 2006 12:21:24 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>
References: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>
Message-ID: <1141762884.15204.11.camel@bioinfo.icapture.ubc.ca>

On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:

> But unfortunately, the
> url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
> provided didn't give me the object ontology file that I wished to download. 

Ummm.... there's only one Object ontology, so if that isn't the one you
wanted, then you're a bit stuck :-)


> I've also tried the CVS-> moby-live
> (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
> by). But not sure which one I should dig into. The object ontology is
> definitely I want. 

The ontologies are not in the CVS - the only ways to get them are
through the URL that I gave you, or through the API.




> Also, I wonder whether there is a service-ontology too.

http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/


> the username and password didn't work. This problem actually has been
> mentioned in the previous discussion (
> http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
> solved.

I'll have to let Yan answer that one... 

Why is the ontology from that URL not what you wanted?  What are you
hoping for?

M


-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From markw at illuminae.com  Tue Mar  7 18:05:28 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Tue, 07 Mar 2006 15:05:28 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <1141762884.15204.11.camel@bioinfo.icapture.ubc.ca>
References: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>
	<1141762884.15204.11.camel@bioinfo.icapture.ubc.ca>
Message-ID: <1141772728.18136.3.camel@bioinfo.icapture.ubc.ca>

Eddie is right - you need to remove the trailing "/" on those URL's to
get the ontologies

Sorry about that!

M



On Tue, 2006-03-07 at 12:21 -0800, Mark Wilkinson wrote:
> On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:
> 
> > But unfortunately, the
> > url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
> > provided didn't give me the object ontology file that I wished to download. 
> 
> Ummm.... there's only one Object ontology, so if that isn't the one you
> wanted, then you're a bit stuck :-)
> 
> 
> > I've also tried the CVS-> moby-live
> > (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
> > by). But not sure which one I should dig into. The object ontology is
> > definitely I want. 
> 
> The ontologies are not in the CVS - the only ways to get them are
> through the URL that I gave you, or through the API.
> 
> 
> 
> 
> > Also, I wonder whether there is a service-ontology too.
> 
> http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
> 
> 
> > the username and password didn't work. This problem actually has been
> > mentioned in the previous discussion (
> > http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
> > solved.
> 
> I'll have to let Yan answer that one... 
> 
> Why is the ontology from that URL not what you wanted?  What are you
> hoping for?
> 
> M
> 
> 
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From xsz7001 at genomecenter.columbia.edu  Wed Mar  8 11:29:44 2006
From: xsz7001 at genomecenter.columbia.edu (Sean Zhou)
Date: Wed, 8 Mar 2006 11:29:44 -0500
Subject: [MOBY-l] [moby]  Question about Object Ontology
Message-ID: <6CA15ADD82E5724F88CB53D50E61C9AED38D50@cgcmail.cgc.cpmc.columbia.edu>

Dear Mark and Eddie,

Thank you very much for the help. It worked. Just summarize what I have done
to get it.
1) Downloaded Object Ontology from
http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects
2) Used SmartCVS to get moby-live
3) Built Dashboard following the instruction of 
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html
4) Note: Building Dashboard did take quite a while as mentioned in the
instruction.

Thanks again for all the help.

Best,

Sean

-----Original Message-----
From: Mark Wilkinson [mailto:markw at illuminae.com] 
Sent: Tuesday, March 07, 2006 6:05 PM
To: Sean Zhou
Cc: moby-l at biomoby.org
Subject: Re: [MOBY-l] [moby] Question about Object Ontology

Eddie is right - you need to remove the trailing "/" on those URL's to
get the ontologies

Sorry about that!

M



On Tue, 2006-03-07 at 12:21 -0800, Mark Wilkinson wrote:
> On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:
> 
> > But unfortunately, the
> > url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
> > provided didn't give me the object ontology file that I wished to
download. 
> 
> Ummm.... there's only one Object ontology, so if that isn't the one you
> wanted, then you're a bit stuck :-)
> 
> 
> > I've also tried the CVS-> moby-live
> >
(http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
> > by). But not sure which one I should dig into. The object ontology is
> > definitely I want. 
> 
> The ontologies are not in the CVS - the only ways to get them are
> through the URL that I gave you, or through the API.
> 
> 
> 
> 
> > Also, I wonder whether there is a service-ontology too.
> 
> http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
> 
> 
> > the username and password didn't work. This problem actually has been
> > mentioned in the previous discussion (
> > http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
> > solved.
> 
> I'll have to let Yan answer that one... 
> 
> Why is the ontology from that URL not what you wanted?  What are you
> hoping for?
> 
> M
> 
> 
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future



From markw at illuminae.com  Wed Mar  8 11:30:55 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 08 Mar 2006 08:30:55 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <6CA15ADD82E5724F88CB53D50E61C9AED38D50@cgcmail.cgc.cpmc.columbia.edu>
References: <6CA15ADD82E5724F88CB53D50E61C9AED38D50@cgcmail.cgc.cpmc.columbia.edu>
Message-ID: <1141835455.16213.19.camel@bioinfo.icapture.ubc.ca>

That's great news!

I'm sorry for being the cause of your initial problems :-/

M



On Wed, 2006-03-08 at 11:29 -0500, Sean Zhou wrote:
> Dear Mark and Eddie,
> 
> Thank you very much for the help. It worked. Just summarize what I have done
> to get it.
> 1) Downloaded Object Ontology from
> http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects
> 2) Used SmartCVS to get moby-live
> 3) Built Dashboard following the instruction of 
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/Dashboard.html
> 4) Note: Building Dashboard did take quite a while as mentioned in the
> instruction.
> 
> Thanks again for all the help.
> 
> Best,
> 
> Sean
> 
> -----Original Message-----
> From: Mark Wilkinson [mailto:markw at illuminae.com] 
> Sent: Tuesday, March 07, 2006 6:05 PM
> To: Sean Zhou
> Cc: moby-l at biomoby.org
> Subject: Re: [MOBY-l] [moby] Question about Object Ontology
> 
> Eddie is right - you need to remove the trailing "/" on those URL's to
> get the ontologies
> 
> Sorry about that!
> 
> M
> 
> 
> 
> On Tue, 2006-03-07 at 12:21 -0800, Mark Wilkinson wrote:
> > On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:
> > 
> > > But unfortunately, the
> > > url (http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
> > > provided didn't give me the object ontology file that I wished to
> download. 
> > 
> > Ummm.... there's only one Object ontology, so if that isn't the one you
> > wanted, then you're a bit stuck :-)
> > 
> > 
> > > I've also tried the CVS-> moby-live
> > >
> (http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
> > > by). But not sure which one I should dig into. The object ontology is
> > > definitely I want. 
> > 
> > The ontologies are not in the CVS - the only ways to get them are
> > through the URL that I gave you, or through the API.
> > 
> > 
> > 
> > 
> > > Also, I wonder whether there is a service-ontology too.
> > 
> > http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
> > 
> > 
> > > the username and password didn't work. This problem actually has been
> > > mentioned in the previous discussion (
> > > http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
> > > solved.
> > 
> > I'll have to let Yan answer that one... 
> > 
> > Why is the ontology from that URL not what you wanted?  What are you
> > hoping for?
> > 
> > M
> > 
> > 
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From gss at ncgr.org  Wed Mar  8 11:46:15 2006
From: gss at ncgr.org (Gary Schiltz)
Date: Wed, 08 Mar 2006 09:46:15 -0700
Subject: [MOBY-l] BioMOBY mentioned in this Infoworld article
In-Reply-To: <op.s5jd7mcmnbznux@wayyye>
References: <op.s5jd7mcmnbznux@wayyye>
Message-ID: <440F0A57.3050503@ncgr.org>

Always great to see us getting some press! Incidentally, the mention of 
BioMOBY is in regards to the Legume Information Network (LIN) project 
that Andrew Farmer discussed in a post to the moby-dev list in February 
(http://biomoby.org/pipermail/moby-dev/2006-February/003139.html). LIN 
uses Semantic MOBY to discover and integrate a set of Semantic MOBY 
resources (aka "Services").

// Gary

Mark Wilkinson wrote:
> A brief mention, but... :-)
>
> http://www.infoworld.nl/idgns/bericht.phtml?id=002570DE00740E180025711D0082365C
>
> M
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
>
>
>   

From admin at unleashedinformatics.com  Thu Mar  2 18:05:35 2006
From: admin at unleashedinformatics.com (Unleashed Informatics Administration)
Date: Thu, 02 Mar 2006 18:05:35 -0500
Subject: [MOBY-l] SeqHound User Support
Message-ID: <44077A3F.2030304@unleashedinformatics.com>

As announced on 2 March 2006, SeqHound has been replaced by "DogBox
Online".

 From 3 April 2006, users of the SeqHound API will be required to
provide their e-mail address when beginning a block of SeqHound (now 
DogBox Online) calls.

Users who fail to provide a valid address will not have access to the 
API, and will not have access to user support.

The following FAQ has been posted to the DogBox Online website.

FAQ:

Q. What is DogBox Online?

DogBox Online is a powerful integrated data service for the life science
community, and represents the new name for the SeqHound service offered
by The Blueprint Initiative. The new service is located at:

http://dogboxonline.unleashedinformatics.com

Q. What happened to SeqHound?

The SeqHound service is being phased out. Please change to DogBox Online.

Q. How will DogBox Online differ?

DogBox Online includes several new
features previously available only to DogBox customers.

Q. Will my use of the SeqHound API be affected?

Yes. On 3 April 2006, Unleashed Informatics will require SeqHound users 
to submit a valid e-mail address as part of the initial SHoundInit call. 
  If you were not using a SHoundInit call or similar in your code, 
ensure that you now begin your scripts with this call.

Q. Can you give me an example?

Using the Perl API, you need to begin your series of SeqHound queries 
like so:

 > use SeqHound;
 > SHoundInit('Program Name');

Replace the 'Program Name' text with your valid e-mail address:

 > use SeqHound;
 > SHoundInit('joe.bloggs at blogme.com');

To avoid disappointment, we recommend you change your scripts now to 
employ the new URL, http://dogboxonline.unleashedinformatics.com.

Q. What happens if I don't provide a valid email address?

Your use of the API will be blocked until you do so.

Q. Why is this change happening?

1. To obtain feedback from users regarding API use and improvement.

2. To notify users of future developments and new features.

Q. Where do I sign up?

https://secure.unleashedinformatics.com/index.php?pg=support.register

Thank you for your co-operation.

From gss at ncgr.org  Tue Mar  7 18:03:08 2006
From: gss at ncgr.org (Gary Schiltz)
Date: Tue, 07 Mar 2006 16:03:08 -0700
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <1141762884.15204.11.camel@bioinfo.icapture.ubc.ca>
References: <6CA15ADD82E5724F88CB53D50E61C9AED38CCA@cgcmail.cgc.cpmc.columbia.edu>
	<1141762884.15204.11.camel@bioinfo.icapture.ubc.ca>
Message-ID: <440E112C.3000702@ncgr.org>


   Hey Mark,
   Did you actually go to the link that Sean mentioned just now? When I do, I
   get an HTML document that looks suspect, i.e. a 404 NOT FOUND, but which
   doesn't actually get rendered by Firefox (but does get rendered by IE as a
   NOT FOUND with a text box scrolling clever witticisms)... go ahead and click
   on either of:
   [1]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
   [2]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
   // Gary
   Mark Wilkinson wrote:

On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:



But unfortunately, the
url ([3]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/) you
provided didn't give me the object ontology file that I wished to download.


Ummm.... there's only one Object ontology, so if that isn't the one you
wanted, then you're a bit stuck :-)




I've also tried the CVS-> moby-live
([4]http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biom
o
by). But not sure which one I should dig into. The object ontology is
definitely I want.


The ontologies are not in the CVS - the only ways to get them are
through the URL that I gave you, or through the API.






Also, I wonder whether there is a service-ontology too.


[5]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/




the username and password didn't work. This problem actually has been
mentioned in the previous discussion (
[6]http://biomoby.org/pipermail/moby-l/2005-July/002612.html). But it is not
solved.


I'll have to let Yan answer that one...

Why is the ontology from that URL not what you wanted?  What are you
hoping for?

M

References

   1. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
   2. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
   3. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
   4. http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/?cvsroot=biomo
   5. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
   6. http://biomoby.org/pipermail/moby-l/2005-July/002612.html

From edward.kawas at gmail.com  Tue Mar 14 10:04:10 2006
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 14 Mar 2006 07:04:10 -0800
Subject: [MOBY-l] [moby]  Question about Object Ontology
In-Reply-To: <440E112C.3000702@ncgr.org>
Message-ID: <001701c64778$8da02c50$6500a8c0@notebook>

If you remove the trailing forward slash, the links are good.

Eddie
 

> -----Original Message-----
> From: moby-l-bounces at lists.open-bio.org 
> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Gary Schiltz
> Sent: Tuesday, March 07, 2006 3:03 PM
> To: moby-l at biomoby.org
> Subject: Re: [MOBY-l] [moby] Question about Object Ontology
> 
> 
>    Hey Mark,
>    Did you actually go to the link that Sean mentioned just 
> now? When I do, I
>    get an HTML document that looks suspect, i.e. a 404 NOT 
> FOUND, but which
>    doesn't actually get rendered by Firefox (but does get 
> rendered by IE as a
>    NOT FOUND with a text box scrolling clever witticisms)... 
> go ahead and click
>    on either of:
>    [1]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
>    [2]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
>    // Gary
>    Mark Wilkinson wrote:
> 
> On Tue, 2006-03-07 at 15:13 -0500, Sean Zhou wrote:
> 
> 
> 
> But unfortunately, the
> url 
> ([3]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Object
> s/) you provided didn't give me the object ontology file that 
> I wished to download.
> 
> 
> Ummm.... there's only one Object ontology, so if that isn't 
> the one you wanted, then you're a bit stuck :-)
> 
> 
> 
> 
> I've also tried the CVS-> moby-live
> ([4]http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-l
> ive/?cvsroot=biom
> o
> by). But not sure which one I should dig into. The object 
> ontology is definitely I want.
> 
> 
> The ontologies are not in the CVS - the only ways to get them 
> are through the URL that I gave you, or through the API.
> 
> 
> 
> 
> 
> 
> Also, I wonder whether there is a service-ontology too.
> 
> 
> [5]http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
> 
> 
> 
> 
> the username and password didn't work. This problem actually 
> has been mentioned in the previous discussion ( 
> [6]http://biomoby.org/pipermail/moby-l/2005-July/002612.html).
>  But it is not solved.
> 
> 
> I'll have to let Yan answer that one...
> 
> Why is the ontology from that URL not what you wanted?  What 
> are you hoping for?
> 
> M
> 
> References
> 
>    1. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
>    2. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
>    3. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Objects/
>    4. 
> http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/moby-live/
> ?cvsroot=biomo
>    5. http://mobycentral.icapture.ubc.ca/RESOURCES/MOBY-S/Services/
>    6. http://biomoby.org/pipermail/moby-l/2005-July/002612.html
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l


From markw at illuminae.com  Thu Mar 23 12:43:23 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 23 Mar 2006 09:43:23 -0800
Subject: [MOBY-l] MOBY RSS feeds should now always have content
Message-ID: <1143135803.31146.24.camel@bioinfo.icapture.ubc.ca>

Hi all, 

As per Simon's request, I've changed the code of the MOBY RSS feeds such
that the last 30 services and objects registered should always be in the
feed.  I want to watch it run on the cron a few times to make sure that
it is getting the timestamps right (i.e. so that your RSS reader will
recognize the difference between old and new entries), but I *think* it
is OK.

Please let me know if you notice odd behaviours.

Sorry for the delay, Simon - between applying for money and getting the
RSS feed right, the former took precedence ;-)

Cheers all!

M

-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From markw at illuminae.com  Thu Mar 23 13:25:37 2006
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 23 Mar 2006 10:25:37 -0800
Subject: [MOBY-l] [moby] RE: MOBY RSS feeds should now always
	have	content
In-Reply-To: <1448A38A42714048B9C53E473E13CCF0401E12@davis.hmgc.mcw.edu>
References: <1143135803.31146.24.camel@bioinfo.icapture.ubc.ca>
	<1448A38A42714048B9C53E473E13CCF0401E12@davis.hmgc.mcw.edu>
Message-ID: <1143138337.31497.12.camel@bioinfo.icapture.ubc.ca>

Hey!!!  Congratulations!

Let us know when she builds her first service ;-)

M



On Thu, 2006-03-23 at 12:22 -0600, Twigger, Simon wrote:
> Hi Mark,
> 
> No problem, between worrying about MOBY RSS feeds and my wife giving birth to a 9lb 2oz baby daugher, Mia, yesterday, I hadnt been worrying about it too much. :)
> 
> S.
> 
> 
> -----Original Message-----
> From: moby-l-bounces at lists.open-bio.org on behalf of Mark Wilkinson
> Sent: Thu 3/23/2006 11:43 AM
> To: mobyl
> Subject: [MOBY-l] MOBY RSS feeds should now always have content
>  
> Hi all, 
> 
> As per Simon's request, I've changed the code of the MOBY RSS feeds such
> that the last 30 services and objects registered should always be in the
> feed.  I want to watch it run on the cron a few times to make sure that
> it is getting the timestamps right (i.e. so that your RSS reader will
> recognize the difference between old and new entries), but I *think* it
> is OK.
> 
> Please let me know if you notice odd behaviours.
> 
> Sorry for the delay, Simon - between applying for money and getting the
> RSS feed right, the former took precedence ;-)
> 
> Cheers all!
> 
> M
> 
-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future


From simont at mcw.edu  Thu Mar 23 13:22:25 2006
From: simont at mcw.edu (Twigger, Simon)
Date: Thu, 23 Mar 2006 12:22:25 -0600
Subject: [MOBY-l] MOBY RSS feeds should now always have content
References: <1143135803.31146.24.camel@bioinfo.icapture.ubc.ca>
Message-ID: <1448A38A42714048B9C53E473E13CCF0401E12@davis.hmgc.mcw.edu>

Hi Mark,

No problem, between worrying about MOBY RSS feeds and my wife giving birth to a 9lb 2oz baby daugher, Mia, yesterday, I hadnt been worrying about it too much. :)

S.


-----Original Message-----
From: moby-l-bounces at lists.open-bio.org on behalf of Mark Wilkinson
Sent: Thu 3/23/2006 11:43 AM
To: mobyl
Subject: [MOBY-l] MOBY RSS feeds should now always have content
 
Hi all, 

As per Simon's request, I've changed the code of the MOBY RSS feeds such
that the last 30 services and objects registered should always be in the
feed.  I want to watch it run on the cron a few times to make sure that
it is getting the timestamps right (i.e. so that your RSS reader will
recognize the difference between old and new entries), but I *think* it
is OK.

Please let me know if you notice odd behaviours.

Sorry for the delay, Simon - between applying for money and getting the
RSS feed right, the former took precedence ;-)

Cheers all!

M

-- 

--
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

"For most of this century we have viewed communications as a conduit, 
       a pipe between physical locations on the planet. 
What's happened now is that the conduit has become so big and interesting 
      that communication has become more than a conduit, 
       it has become a destination in its own right..."

                Paul Saffo - Director, Institute for the Future

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



From usadel at mpimp-golm.mpg.de  Fri Mar 24 04:50:58 2006
From: usadel at mpimp-golm.mpg.de (=?ISO-8859-1?Q?Bj=F6rn_Usadel?=)
Date: Fri, 24 Mar 2006 10:50:58 +0100
Subject: [MOBY-l] missing RFC1863 support in perl CommonSubs
Message-ID: <4423C102.3000704@mpimp-golm.mpg.de>

Dear list,

I just learned how to use Biomoby and stumbled over the problem that it 
is not possible to integrate
moby Exceptions (as specified in RFC1863) into the header using the perl 
method "responseHeader"  from CommonSubs (latest cvs). Since everything 
there which is passed in the parameter notes gets HTMLified and wrapped 
into notes as well as service notes.

Is anybody working on fixing that?
Otherwise I could try developing a  version here with the additional 
paramter exception (and post it on this list?)


Cheers,
Bj?rn



From dag at sonsorol.org  Sat Mar 25 18:50:57 2006
From: dag at sonsorol.org (Chris Dagdigian)
Date: Sat, 25 Mar 2006 18:50:57 -0500
Subject: [MOBY-l] Important news for developers on open-bio machines
Message-ID: <1BB8AE37-91CA-45C7-AA81-A12826D5F422@sonsorol.org>


Hi, apologies for the massive cross-post. I'll keep it short!

This message is a last-ditch attempt to contact people with developer  
accounts on pub.open-bio.org who may have not received the individual  
mails we've been sending via the obf-developers at lists.open-bio.org  
mailing list. We suspect that there are a number of devs out there  
for whom we don't have up to date email addresses.

All open-bio services have been migrated to new hardware and a new  
datacenter. Part of this migration process involved moving all  
developer accounts and all source-code repositories to a new server.  
The developer migration was completed a few minutes ago. An  
unavoidable side effect of the move is that all developers are now  
locked out of their accounts until they contact us for a password reset.

If you are a developer and this news comes as a surprise to you, it  
means we don't have your contact info. Your best way to get up to  
speed on the history and technical details behind the migration is to  
point your browser here:

http://lists.open-bio.org/mailman/private/obf-developers/2006-March/ 
thread.html

... and read the various messages we've posted this month. Included  
in the first message is the information on how to request an account  
reset.


Regards,
Chris Dagdigian
open-bio.org



From darin.london at duke.edu  Tue Mar 28 09:42:45 2006
From: darin.london at duke.edu (Darin London)
Date: Tue, 28 Mar 2006 09:42:45 -0500
Subject: [MOBY-l] Announcing BOSC 2006
Message-ID: <44294B65.4050207@duke.edu>

MEETING ANNOUNCEMENT & CALL FOR SPEAKERS

The 7th annual Bioinformatics Open Source Conference (BOSC 2006) is
organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
Aug 4,5th in Fortaleza, Brasil, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 14th
International Conference
on Intelligent Systems for Molecular Biology.  Please consult The Official
BOSC 2006 Website at

http://www.open-bio.org/wiki/BOSC_2006

for details and information. 

In addition, a BOSC weblog has been setup to make it easier to
desiminate all BOSC
related announcements:

http://wiki.open-bio.org/boscblog/

And if you have an ICAL compatible Calendar, there is an EventDB calendar
set up with all BOSC related deadlines.

http://eventful.com/groups/G0-001-000014747-0

More information about ISMB can be found at the Official
ISMB 2006 Website:

http://ismb2006.cbi.cnptia.embrapa.br/


Thank You, and we look forward to seeing you all,
The BOSC Organizing Committee.