From jits at cs.man.ac.uk  Wed Sep  2 06:01:57 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 02 Sep 2009 11:01:57 +0100
Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern
 module in the BioCatalogue
In-Reply-To: <d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>
References: <RT-Ticket-129246@broadinstitute.org>	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>
	<d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>
Message-ID: <4A9E4295.5070806@cs.man.ac.uk>

Hi Franck,

I'm fine with having a quick overview chat with them BUT I think we 
first need to clear some resources with Carole/Rodrigo/Steve before we 
commit to actually doing any work to support GenePattern. As things 
stand right now, we are overburdened and overcommitted with work and 
it's not a good idea to commit to anything else.

Otherwise, those dates are fine for me.

Cheers,
Jits


Franck Tanoh wrote:
> Hello guys,
>
> Are you available the week of 14/sept for a meeting with the 
> GenePattern team. This is an opportunity for us to see how we could 
> bring their services (modules) in the biocat.  The face 2 face is 14 
> and 15 so best date for me are 17 and 18.
> Some background about GenePattern can be found here:
> http://www.broadinstitute.org/cancer/software/genepattern/index.html
>
> cheers,
> Franck
>
>
>
> ---------- Forwarded message ----------
> From: *Michael Reich via RT* <gp-help at broadinstitute.org 
> <mailto:gp-help at broadinstitute.org>>
> Date: 2009/9/1
> Subject: [rt.broad #129246] GenePattern module in the BioCatalogue
> To: ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>
>
> Franck,
>
> Thanks for your message - we are familiar with BioCatalogue and will be
> glad to discuss how to post GenePattern modules there. We should
> probably have a technical discussion about how to classify the way to
> connect to the public GenePattern server via Web services - it is not
> straight WSDL-based.
>
> We are working on a grant deadline now - are you available the week of
> 9/14 to discuss?
>
> Best,
> Michael
>
> > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk> - Tue Sep 01 
> 08:18:35 2009]:
> >
> > Hello,
> >
> > The BioCatalogue team led by Prof. Carole Goble from the myGrid
> project and
> > Rodrigo Lopez from the European Bioinformatics Institute ( EBI) would
> really
> > like to investigate the possibility to bring GenePattern's modules and
> > annotations in the BioCatalogue (http://www.biocatalogue.org/).
> > The BioCatalogue project aims to create a curated catalogue of life
> science
> > Web Services. Through the BioCatalogue, the community can meet and 
> contact
> > the maintainers of life science services.
> > It is also a place where service provider can advertise and monitor the
> > usage of their services. The project is funded by the BBSRC 
> (Biotechnology
> > and Biological Sciences Research Council).
> > Since its launch in June, the BioCatalogue has more than 1000 services (
> > SOAP, REST, BioMoby, Soaplab).
> >
> > I strongly believe that the BioCatalogue can serve as a platform to
> > advertise GenePattern and its modules to the community.
> >
> > Could you point me to the person(s) to contact to start the 
> discussion and
> > possibly requirements gathering, please?
> >
> > Regards,
> >
> > Franck
> >
> > ..
> > Franck Tanoh
> > BioCatalogue team
> > University of Manchester
> > +441612750145
> >
> >
> >
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ericnzuo at ebi.ac.uk  Wed Sep  2 06:18:39 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 02 Sep 2009 11:18:39 +0100
Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern
 module in the BioCatalogue
In-Reply-To: <4A9E4295.5070806@cs.man.ac.uk>
References: <RT-Ticket-129246@broadinstitute.org>	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>	<d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>
	<4A9E4295.5070806@cs.man.ac.uk>
Message-ID: <4A9E467F.2060705@ebi.ac.uk>

Hi Franck,
I am also fine with those dates. Maybe we should try to have an idea 
with them what is actually involved without necessarily committing. It 
might be really 'simple' what they need or indeed we might already have it.

Eric


Jiten Bhagat wrote:
> Hi Franck,
>
> I'm fine with having a quick overview chat with them BUT I think we 
> first need to clear some resources with Carole/Rodrigo/Steve before we 
> commit to actually doing any work to support GenePattern. As things 
> stand right now, we are overburdened and overcommitted with work and 
> it's not a good idea to commit to anything else.
>
> Otherwise, those dates are fine for me.
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>> Hello guys,
>>
>> Are you available the week of 14/sept for a meeting with the 
>> GenePattern team. This is an opportunity for us to see how we could 
>> bring their services (modules) in the biocat.  The face 2 face is 14 
>> and 15 so best date for me are 17 and 18.
>> Some background about GenePattern can be found here:
>> http://www.broadinstitute.org/cancer/software/genepattern/index.html
>>
>> cheers,
>> Franck
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: *Michael Reich via RT* <gp-help at broadinstitute.org 
>> <mailto:gp-help at broadinstitute.org>>
>> Date: 2009/9/1
>> Subject: [rt.broad #129246] GenePattern module in the BioCatalogue
>> To: ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>>
>>
>> Franck,
>>
>> Thanks for your message - we are familiar with BioCatalogue and will be
>> glad to discuss how to post GenePattern modules there. We should
>> probably have a technical discussion about how to classify the way to
>> connect to the public GenePattern server via Web services - it is not
>> straight WSDL-based.
>>
>> We are working on a grant deadline now - are you available the week of
>> 9/14 to discuss?
>>
>> Best,
>> Michael
>>
>> > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk> - Tue Sep 01 
>> 08:18:35 2009]:
>> >
>> > Hello,
>> >
>> > The BioCatalogue team led by Prof. Carole Goble from the myGrid
>> project and
>> > Rodrigo Lopez from the European Bioinformatics Institute ( EBI) would
>> really
>> > like to investigate the possibility to bring GenePattern's modules and
>> > annotations in the BioCatalogue (http://www.biocatalogue.org/).
>> > The BioCatalogue project aims to create a curated catalogue of life
>> science
>> > Web Services. Through the BioCatalogue, the community can meet and 
>> contact
>> > the maintainers of life science services.
>> > It is also a place where service provider can advertise and monitor 
>> the
>> > usage of their services. The project is funded by the BBSRC 
>> (Biotechnology
>> > and Biological Sciences Research Council).
>> > Since its launch in June, the BioCatalogue has more than 1000 
>> services (
>> > SOAP, REST, BioMoby, Soaplab).
>> >
>> > I strongly believe that the BioCatalogue can serve as a platform to
>> > advertise GenePattern and its modules to the community.
>> >
>> > Could you point me to the person(s) to contact to start the 
>> discussion and
>> > possibly requirements gathering, please?
>> >
>> > Regards,
>> >
>> > Franck
>> >
>> > ..
>> > Franck Tanoh
>> > BioCatalogue team
>> > University of Manchester
>> > +441612750145
>> >
>> >
>> >
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity, and 
>> is the torch which illuminates the world." - Louis Pasteur
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>   
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ericnzuo at ebi.ac.uk  Wed Sep  2 06:21:53 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 02 Sep 2009 11:21:53 +0100
Subject: [BioCatalogue-developers] reminder
Message-ID: <4A9E4741.1010505@ebi.ac.uk>

Hi Guys,

I will be leaving earlier this afternoon as I will be going up to 
Cambridge for the festival of interactive technologies this evening.

Eric


From jits at cs.man.ac.uk  Wed Sep  2 06:39:47 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 02 Sep 2009 11:39:47 +0100
Subject: [BioCatalogue-developers] reminder
In-Reply-To: <4A9E4741.1010505@ebi.ac.uk>
References: <4A9E4741.1010505@ebi.ac.uk>
Message-ID: <4A9E4B73.50405@cs.man.ac.uk>

Okay, have fun Eric!


Eric Nzuobontane wrote:
> Hi Guys,
>
> I will be leaving earlier this afternoon as I will be going up to 
> Cambridge for the festival of interactive technologies this evening.
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Wed Sep  2 06:40:45 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 02 Sep 2009 11:40:45 +0100
Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern
 module in the BioCatalogue
In-Reply-To: <d0ee827d0909020328x3dc5d349oc04e13ad6baa68b1@mail.gmail.com>
References: <RT-Ticket-129246@broadinstitute.org>	
	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	
	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>	
	<d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>	
	<4A9E4295.5070806@cs.man.ac.uk>
	<d0ee827d0909020328x3dc5d349oc04e13ad6baa68b1@mail.gmail.com>
Message-ID: <4A9E4BAD.6030803@cs.man.ac.uk>

Hi Franck,

Okay, that's fair enough. Just pointing out that we should not commit to 
anything yet. We have a habit in our teams/projects to committing to 
collaborate with many "big names" without properly considering resources 
and without proper plans of action :-)

My concerns were raised from your quick email conversation with Michael 
Reich below, which already hints at a commitment on our part to support 
GenePattern (ie: that the decision has been made to support 
GenePattern). But like you say, we should treat this as a listening 
exercise first and foremost.

Cheers,
Jits


Franck Tanoh wrote:
> Hi Jits,
>
> The purpose of the meeting is for us to be familiar with GenePattern, 
> know what their requirements are and who to contact...
> Maybe we don't even need to right a code to have their services in the 
> BioCatalogue or they may right the code themselves...
> My point is, at this stage it is more a listening exercise than a 
> commitment to more work.  We're overburdened, that's absolutely true 
> BUT we should still listen, specially to these big names in the domain.
>
> Cheers,
> Franck
>
>
>
> 2009/9/2 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>
>     Hi Franck,
>
>     I'm fine with having a quick overview chat with them BUT I think
>     we first need to clear some resources with Carole/Rodrigo/Steve
>     before we commit to actually doing any work to support
>     GenePattern. As things stand right now, we are overburdened and
>     overcommitted with work and it's not a good idea to commit to
>     anything else.
>
>     Otherwise, those dates are fine for me.
>
>     Cheers,
>     Jits
>
>
>     Franck Tanoh wrote:
>
>         Hello guys,
>
>         Are you available the week of 14/sept for a meeting with the
>         GenePattern team. This is an opportunity for us to see how we
>         could bring their services (modules) in the biocat.  The face
>         2 face is 14 and 15 so best date for me are 17 and 18.
>         Some background about GenePattern can be found here:
>         http://www.broadinstitute.org/cancer/software/genepattern/index.html
>
>         cheers,
>         Franck
>
>
>
>         ---------- Forwarded message ----------
>         From: *Michael Reich via RT* <gp-help at broadinstitute.org
>         <mailto:gp-help at broadinstitute.org>
>         <mailto:gp-help at broadinstitute.org
>         <mailto:gp-help at broadinstitute.org>>>
>         Date: 2009/9/1
>         Subject: [rt.broad #129246] GenePattern module in the BioCatalogue
>         To: ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>         <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>>
>
>
>         Franck,
>
>         Thanks for your message - we are familiar with BioCatalogue
>         and will be
>         glad to discuss how to post GenePattern modules there. We should
>         probably have a technical discussion about how to classify the
>         way to
>         connect to the public GenePattern server via Web services - it
>         is not
>         straight WSDL-based.
>
>         We are working on a grant deadline now - are you available the
>         week of
>         9/14 to discuss?
>
>         Best,
>         Michael
>
>         > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>         <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>> -
>         Tue Sep 01 08:18:35 2009]:
>
>         >
>         > Hello,
>         >
>         > The BioCatalogue team led by Prof. Carole Goble from the myGrid
>         project and
>         > Rodrigo Lopez from the European Bioinformatics Institute (
>         EBI) would
>         really
>         > like to investigate the possibility to bring GenePattern's
>         modules and
>         > annotations in the BioCatalogue (http://www.biocatalogue.org/).
>         > The BioCatalogue project aims to create a curated catalogue
>         of life
>         science
>         > Web Services. Through the BioCatalogue, the community can
>         meet and contact
>         > the maintainers of life science services.
>         > It is also a place where service provider can advertise and
>         monitor the
>         > usage of their services. The project is funded by the BBSRC
>         (Biotechnology
>         > and Biological Sciences Research Council).
>         > Since its launch in June, the BioCatalogue has more than
>         1000 services (
>         > SOAP, REST, BioMoby, Soaplab).
>         >
>         > I strongly believe that the BioCatalogue can serve as a
>         platform to
>         > advertise GenePattern and its modules to the community.
>         >
>         > Could you point me to the person(s) to contact to start the
>         discussion and
>         > possibly requirements gathering, please?
>         >
>         > Regards,
>         >
>         > Franck
>         >
>         > ..
>         > Franck Tanoh
>         > BioCatalogue team
>         > University of Manchester
>         > +441612750145
>         >
>         >
>         >
>
>
>
>
>         -- 
>         "Science knows no country, because knowledge belongs to
>         humanity, and is the torch which illuminates the world." -
>         Louis Pasteur
>         ------------------------------------------------------------------------
>
>         _______________________________________________
>         BioCatalogue-developers mailing list
>         BioCatalogue-developers at rubyforge.org
>         <mailto:BioCatalogue-developers at rubyforge.org>
>         http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>          
>
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur


From ytanoh at cs.man.ac.uk  Wed Sep  2 06:45:29 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 2 Sep 2009 11:45:29 +0100
Subject: [BioCatalogue-developers] reminder
In-Reply-To: <4A9E4741.1010505@ebi.ac.uk>
References: <4A9E4741.1010505@ebi.ac.uk>
Message-ID: <AE3E6459-42EF-46C7-B324-F7AD68EE500B@cs.man.ac.uk>

Off with the biocat flags :-) ... cool

good luck

Franck


On 2 Sep 2009, at 11:21, Eric Nzuobontane wrote:

> Hi Guys,
>
> I will be leaving earlier this afternoon as I will be going up to  
> Cambridge for the festival of interactive technologies this evening.
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ytanoh at cs.man.ac.uk  Wed Sep  2 06:53:33 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 2 Sep 2009 11:53:33 +0100
Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern
	module in the BioCatalogue
In-Reply-To: <4A9E4BAD.6030803@cs.man.ac.uk>
References: <RT-Ticket-129246@broadinstitute.org>	
	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	
	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>	
	<d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>	
	<4A9E4295.5070806@cs.man.ac.uk>
	<d0ee827d0909020328x3dc5d349oc04e13ad6baa68b1@mail.gmail.com>
	<4A9E4BAD.6030803@cs.man.ac.uk>
Message-ID: <31EB60F5-E079-46E4-9D85-5DAA218A0F85@cs.man.ac.uk>

 >My concerns were raised from your quick email conversation with  
Michael Reich below,
my mistake then,  will try next time to handle a bit better  
Shakespeare's language  : -)

Franck

On 2 Sep 2009, at 11:40, Jiten Bhagat wrote:

> Hi Franck,
>
> Okay, that's fair enough. Just pointing out that we should not  
> commit to anything yet. We have a habit in our teams/projects to  
> committing to collaborate with many "big names" without properly  
> considering resources and without proper plans of action :-)
>
> My concerns were raised from your quick email conversation with  
> Michael Reich below, which already hints at a commitment on our part  
> to support GenePattern (ie: that the decision has been made to  
> support GenePattern). But like you say, we should treat this as a  
> listening exercise first and foremost.
>
> Cheers,
> Jits
>
>
> Franck Tanoh wrote:
>> Hi Jits,
>>
>> The purpose of the meeting is for us to be familiar with  
>> GenePattern, know what their requirements are and who to contact...
>> Maybe we don't even need to right a code to have their services in  
>> the BioCatalogue or they may right the code themselves...
>> My point is, at this stage it is more a listening exercise than a  
>> commitment to more work.  We're overburdened, that's absolutely  
>> true BUT we should still listen, specially to these big names in  
>> the domain.
>>
>> Cheers,
>> Franck
>>
>>
>>
>> 2009/9/2 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>>
>>    Hi Franck,
>>
>>    I'm fine with having a quick overview chat with them BUT I think
>>    we first need to clear some resources with Carole/Rodrigo/Steve
>>    before we commit to actually doing any work to support
>>    GenePattern. As things stand right now, we are overburdened and
>>    overcommitted with work and it's not a good idea to commit to
>>    anything else.
>>
>>    Otherwise, those dates are fine for me.
>>
>>    Cheers,
>>    Jits
>>
>>
>>    Franck Tanoh wrote:
>>
>>        Hello guys,
>>
>>        Are you available the week of 14/sept for a meeting with the
>>        GenePattern team. This is an opportunity for us to see how we
>>        could bring their services (modules) in the biocat.  The face
>>        2 face is 14 and 15 so best date for me are 17 and 18.
>>        Some background about GenePattern can be found here:
>>        http://www.broadinstitute.org/cancer/software/genepattern/index.html
>>
>>        cheers,
>>        Franck
>>
>>
>>
>>        ---------- Forwarded message ----------
>>        From: *Michael Reich via RT* <gp-help at broadinstitute.org
>>        <mailto:gp-help at broadinstitute.org>
>>        <mailto:gp-help at broadinstitute.org
>>        <mailto:gp-help at broadinstitute.org>>>
>>        Date: 2009/9/1
>>        Subject: [rt.broad #129246] GenePattern module in the  
>> BioCatalogue
>>        To: ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>>        <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>>
>>
>>
>>        Franck,
>>
>>        Thanks for your message - we are familiar with BioCatalogue
>>        and will be
>>        glad to discuss how to post GenePattern modules there. We  
>> should
>>        probably have a technical discussion about how to classify the
>>        way to
>>        connect to the public GenePattern server via Web services - it
>>        is not
>>        straight WSDL-based.
>>
>>        We are working on a grant deadline now - are you available the
>>        week of
>>        9/14 to discuss?
>>
>>        Best,
>>        Michael
>>
>>        > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>>        <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>> -
>>        Tue Sep 01 08:18:35 2009]:
>>
>>        >
>>        > Hello,
>>        >
>>        > The BioCatalogue team led by Prof. Carole Goble from the  
>> myGrid
>>        project and
>>        > Rodrigo Lopez from the European Bioinformatics Institute (
>>        EBI) would
>>        really
>>        > like to investigate the possibility to bring GenePattern's
>>        modules and
>>        > annotations in the BioCatalogue (http://www.biocatalogue.org/ 
>> ).
>>        > The BioCatalogue project aims to create a curated catalogue
>>        of life
>>        science
>>        > Web Services. Through the BioCatalogue, the community can
>>        meet and contact
>>        > the maintainers of life science services.
>>        > It is also a place where service provider can advertise and
>>        monitor the
>>        > usage of their services. The project is funded by the BBSRC
>>        (Biotechnology
>>        > and Biological Sciences Research Council).
>>        > Since its launch in June, the BioCatalogue has more than
>>        1000 services (
>>        > SOAP, REST, BioMoby, Soaplab).
>>        >
>>        > I strongly believe that the BioCatalogue can serve as a
>>        platform to
>>        > advertise GenePattern and its modules to the community.
>>        >
>>        > Could you point me to the person(s) to contact to start the
>>        discussion and
>>        > possibly requirements gathering, please?
>>        >
>>        > Regards,
>>        >
>>        > Franck
>>        >
>>        > ..
>>        > Franck Tanoh
>>        > BioCatalogue team
>>        > University of Manchester
>>        > +441612750145
>>        >
>>        >
>>        >
>>
>>
>>
>>
>>        --         "Science knows no country, because knowledge  
>> belongs to
>>        humanity, and is the torch which illuminates the world." -
>>        Louis Pasteur
>>         
>> ------------------------------------------------------------------------
>>
>>        _______________________________________________
>>        BioCatalogue-developers mailing list
>>        BioCatalogue-developers at rubyforge.org
>>        <mailto:BioCatalogue-developers at rubyforge.org>
>>        http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity,  
>> and is the torch which illuminates the world." - Louis Pasteur
>


From ericnzuo at ebi.ac.uk  Wed Sep  2 08:25:50 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Wed, 02 Sep 2009 13:25:50 +0100
Subject: [BioCatalogue-developers] wsdl parsing question
Message-ID: <4A9E644E.2040403@ebi.ac.uk>

Hi Guys,
While doing the work to integrate the WSDL parser from the embrace 
registry into BioCatalogue, I have come across a number of issues that I 
am not exactly sure how to resolve.

A question that has been bothering me is what exactly do we mean by the 
inputs/outputs of an operation?
According to wsdl spec, a request-response operation is specified as 
follows:

<wsdl:definitions .... >
    <wsdl:portType .... > *
        <wsdl:operation name="nmtoken" parameterOrder="nmtokens">
           <wsdl:input name="nmtoken"? message="qname"/>
           <wsdl:output name="nmtoken"? message="qname"/>
           <wsdl:fault name="nmtoken" message="qname"/>*
        </wsdl:operation>
    </wsdl:portType >
</wsdl:definitions>


One interpretation could be that since an operation input/output is 
always wrapped in the message, we take the messages as the 
inputs/outputs, meaning operations will always only have a single 
input/output. We could go a step further and expand the messages into 
their parts. Meaning the message parts would form what we will call 
inputs/outputs. We could go even further and expand the message parts 
into their constituent types. My question really is where should we end. 
I note here that useful meta data is often embedded in the types. I am 
not exactly sure what an input or  output of an operation should mean, 
and consequently how that maps to the wsdl.

Previously, we were not importing wsdl types information that was 
contained in an external schema. With the current work, we will be doing 
that and the question of what expansions we make is very relevant. My 
inclination was that message parts should map 1-1 with what we call 
inputs/outputs. But I am aware that there are issues there as to what 
tool kits do as Hamish pointed out to me.

Suggestion on what do here are most welcome.

Eric






From jits at cs.man.ac.uk  Thu Sep  3 05:30:16 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 03 Sep 2009 10:30:16 +0100
Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern
 module in the BioCatalogue
In-Reply-To: <31EB60F5-E079-46E4-9D85-5DAA218A0F85@cs.man.ac.uk>
References: <RT-Ticket-129246@broadinstitute.org>	
	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	
	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>	
	<d0ee827d0909020234r7f6894a2y1365840830cf8b6@mail.gmail.com>	
	<4A9E4295.5070806@cs.man.ac.uk>
	<d0ee827d0909020328x3dc5d349oc04e13ad6baa68b1@mail.gmail.com>
	<4A9E4BAD.6030803@cs.man.ac.uk>
	<31EB60F5-E079-46E4-9D85-5DAA218A0F85@cs.man.ac.uk>
Message-ID: <4A9F8CA8.4050708@cs.man.ac.uk>

Franck Tanoh wrote:
> >My concerns were raised from your quick email conversation with 
> Michael Reich below,
> my mistake then,  will try next time to handle a bit better 
> Shakespeare's language  : -)

LOL... noo Franck, that's not what I meant! :-) You did the right thing 
by engaging with them. You can understand my concerns with committing to 
any new work :-)

Jits


>
> Franck
>
> On 2 Sep 2009, at 11:40, Jiten Bhagat wrote:
>
>> Hi Franck,
>>
>> Okay, that's fair enough. Just pointing out that we should not commit 
>> to anything yet. We have a habit in our teams/projects to committing 
>> to collaborate with many "big names" without properly considering 
>> resources and without proper plans of action :-)
>>
>> My concerns were raised from your quick email conversation with 
>> Michael Reich below, which already hints at a commitment on our part 
>> to support GenePattern (ie: that the decision has been made to 
>> support GenePattern). But like you say, we should treat this as a 
>> listening exercise first and foremost.
>>
>> Cheers,
>> Jits
>>
>>
>> Franck Tanoh wrote:
>>> Hi Jits,
>>>
>>> The purpose of the meeting is for us to be familiar with 
>>> GenePattern, know what their requirements are and who to contact...
>>> Maybe we don't even need to right a code to have their services in 
>>> the BioCatalogue or they may right the code themselves...
>>> My point is, at this stage it is more a listening exercise than a 
>>> commitment to more work.  We're overburdened, that's absolutely true 
>>> BUT we should still listen, specially to these big names in the domain.
>>>
>>> Cheers,
>>> Franck
>>>
>>>
>>>
>>> 2009/9/2 Jiten Bhagat <jits at cs.man.ac.uk <mailto:jits at cs.man.ac.uk>>
>>>
>>>    Hi Franck,
>>>
>>>    I'm fine with having a quick overview chat with them BUT I think
>>>    we first need to clear some resources with Carole/Rodrigo/Steve
>>>    before we commit to actually doing any work to support
>>>    GenePattern. As things stand right now, we are overburdened and
>>>    overcommitted with work and it's not a good idea to commit to
>>>    anything else.
>>>
>>>    Otherwise, those dates are fine for me.
>>>
>>>    Cheers,
>>>    Jits
>>>
>>>
>>>    Franck Tanoh wrote:
>>>
>>>        Hello guys,
>>>
>>>        Are you available the week of 14/sept for a meeting with the
>>>        GenePattern team. This is an opportunity for us to see how we
>>>        could bring their services (modules) in the biocat.  The face
>>>        2 face is 14 and 15 so best date for me are 17 and 18.
>>>        Some background about GenePattern can be found here:
>>>        
>>> http://www.broadinstitute.org/cancer/software/genepattern/index.html
>>>
>>>        cheers,
>>>        Franck
>>>
>>>
>>>
>>>        ---------- Forwarded message ----------
>>>        From: *Michael Reich via RT* <gp-help at broadinstitute.org
>>>        <mailto:gp-help at broadinstitute.org>
>>>        <mailto:gp-help at broadinstitute.org
>>>        <mailto:gp-help at broadinstitute.org>>>
>>>        Date: 2009/9/1
>>>        Subject: [rt.broad #129246] GenePattern module in the 
>>> BioCatalogue
>>>        To: ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>>>        <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>>
>>>
>>>
>>>        Franck,
>>>
>>>        Thanks for your message - we are familiar with BioCatalogue
>>>        and will be
>>>        glad to discuss how to post GenePattern modules there. We should
>>>        probably have a technical discussion about how to classify the
>>>        way to
>>>        connect to the public GenePattern server via Web services - it
>>>        is not
>>>        straight WSDL-based.
>>>
>>>        We are working on a grant deadline now - are you available the
>>>        week of
>>>        9/14 to discuss?
>>>
>>>        Best,
>>>        Michael
>>>
>>>        > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>
>>>        <mailto:ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>> -
>>>        Tue Sep 01 08:18:35 2009]:
>>>
>>>        >
>>>        > Hello,
>>>        >
>>>        > The BioCatalogue team led by Prof. Carole Goble from the 
>>> myGrid
>>>        project and
>>>        > Rodrigo Lopez from the European Bioinformatics Institute (
>>>        EBI) would
>>>        really
>>>        > like to investigate the possibility to bring GenePattern's
>>>        modules and
>>>        > annotations in the BioCatalogue 
>>> (http://www.biocatalogue.org/).
>>>        > The BioCatalogue project aims to create a curated catalogue
>>>        of life
>>>        science
>>>        > Web Services. Through the BioCatalogue, the community can
>>>        meet and contact
>>>        > the maintainers of life science services.
>>>        > It is also a place where service provider can advertise and
>>>        monitor the
>>>        > usage of their services. The project is funded by the BBSRC
>>>        (Biotechnology
>>>        > and Biological Sciences Research Council).
>>>        > Since its launch in June, the BioCatalogue has more than
>>>        1000 services (
>>>        > SOAP, REST, BioMoby, Soaplab).
>>>        >
>>>        > I strongly believe that the BioCatalogue can serve as a
>>>        platform to
>>>        > advertise GenePattern and its modules to the community.
>>>        >
>>>        > Could you point me to the person(s) to contact to start the
>>>        discussion and
>>>        > possibly requirements gathering, please?
>>>        >
>>>        > Regards,
>>>        >
>>>        > Franck
>>>        >
>>>        > ..
>>>        > Franck Tanoh
>>>        > BioCatalogue team
>>>        > University of Manchester
>>>        > +441612750145
>>>        >
>>>        >
>>>        >
>>>
>>>
>>>
>>>
>>>        --         "Science knows no country, because knowledge 
>>> belongs to
>>>        humanity, and is the torch which illuminates the world." -
>>>        Louis Pasteur
>>>        
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>>        _______________________________________________
>>>        BioCatalogue-developers mailing list
>>>        BioCatalogue-developers at rubyforge.org
>>>        <mailto:BioCatalogue-developers at rubyforge.org>
>>>        http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>>
>>>
>>>
>>>
>>> -- 
>>> "Science knows no country, because knowledge belongs to humanity, 
>>> and is the torch which illuminates the world." - Louis Pasteur
>>
>


From noreply at rubyforge.org  Thu Sep  3 06:04:06 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  3 Sep 2009 06:04:06 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2782] Tooltip hover issues
Message-ID: <20090903100406.7E7971858200@rubyforge.org>

Task #2782 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Tooltip hover issues
Complete: 0%
Status: Open

Description: As reported by Sergey:

"I've just noticed that the tooltips over 'Latest Services Feed' and > the 'Follow me on Twitter' icons in the action bar appear under these > icons themselves (this doesn't normally happen with other tooltips - at > least not that I've seen)."

Occurs in FF and IE apparently.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2782&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Sep  3 09:18:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu,  3 Sep 2009 09:18:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2783] Check UI for instances of
	non activated users showing up
Message-ID: <20090903131841.6471F1858249@rubyforge.org>

Task #2783 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Check UI for instances of non activated users showing up
Complete: 0%
Status: Open

Description: There is a potential bug!

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2783&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Mon Sep  7 06:48:03 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 07 Sep 2009 11:48:03 +0100
Subject: [BioCatalogue-developers] New Phusion Passenger Release (v2.2.5)
Message-ID: <4AA4E4E3.1000606@cs.man.ac.uk>

Hi guys,

Doesn't look urgent, but...

Phusion Passenger v2.2.5

http://blog.phusion.nl/2009/09/01/phusion-passenger-2-2-5-released/

Cheers,
Jits

From jits at cs.man.ac.uk  Mon Sep  7 06:51:22 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 07 Sep 2009 11:51:22 +0100
Subject: [BioCatalogue-developers] [URGENT} Upgrade to Rails 2.3.4
Message-ID: <4AA4E5AA.7080502@cs.man.ac.uk>

Hi guys,

I will be updating the trunk to Rails 2.3.4 due to a recently fixed XSS 
vulnerability in Rails.

For reference:

http://groups.google.com/group/rubyonrails-security/msg/7f57cd7794e1d1b4?pli=1

http://brian.mastenbrook.net/display/36

http://arstechnica.com/security/news/2009/09/ruby-on-rails-vulnerability-affects-twitter-ie8-immune.ars

I'm hoping to finish the Soaplab Server work soon and then we can get a 
release out. Hope this is okay.

Jits

From ericnzuo at ebi.ac.uk  Mon Sep  7 07:32:03 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 07 Sep 2009 12:32:03 +0100
Subject: [BioCatalogue-developers] New Phusion Passenger Release (v2.2.5)
In-Reply-To: <4AA4E4E3.1000606@cs.man.ac.uk>
References: <4AA4E4E3.1000606@cs.man.ac.uk>
Message-ID: <4AA4EF33.10408@ebi.ac.uk>

Should we upgrade to this release?

Eric


Jiten Bhagat wrote:
> Hi guys,
>
> Doesn't look urgent, but...
>
> Phusion Passenger v2.2.5
>
> http://blog.phusion.nl/2009/09/01/phusion-passenger-2-2-5-released/
>
> Cheers,
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From jits at cs.man.ac.uk  Mon Sep  7 07:34:19 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 07 Sep 2009 12:34:19 +0100
Subject: [BioCatalogue-developers] New Phusion Passenger Release (v2.2.5)
In-Reply-To: <4AA4EF33.10408@ebi.ac.uk>
References: <4AA4E4E3.1000606@cs.man.ac.uk> <4AA4EF33.10408@ebi.ac.uk>
Message-ID: <4AA4EFBB.5070007@cs.man.ac.uk>

I'll have a closer look later tonight to figure out if it affects us.

But right now I think it's something we should only worry about post F2F 
next week.

Cheers,
Jits


Eric Nzuobontane wrote:
> Should we upgrade to this release?
>
> Eric
>
>
> Jiten Bhagat wrote:
>> Hi guys,
>>
>> Doesn't look urgent, but...
>>
>> Phusion Passenger v2.2.5
>>
>> http://blog.phusion.nl/2009/09/01/phusion-passenger-2-2-5-released/
>>
>> Cheers,
>> Jits
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>


From jits at cs.man.ac.uk  Mon Sep  7 09:04:56 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 07 Sep 2009 14:04:56 +0100
Subject: [BioCatalogue-developers] [URGENT} Upgrade to Rails 2.3.4
In-Reply-To: <4AA4E5AA.7080502@cs.man.ac.uk>
References: <4AA4E5AA.7080502@cs.man.ac.uk>
Message-ID: <4AA504F8.5080603@cs.man.ac.uk>

Turns out this will require two version bumps (we're currently on 
v2.3.2), so might take a little longer (I would like to have some basic 
unit tests in place beforehand).

Jits


Jiten Bhagat wrote:
> Hi guys,
>
> I will be updating the trunk to Rails 2.3.4 due to a recently fixed 
> XSS vulnerability in Rails.
>
> For reference:
>
> http://groups.google.com/group/rubyonrails-security/msg/7f57cd7794e1d1b4?pli=1 
>
>
> http://brian.mastenbrook.net/display/36
>
> http://arstechnica.com/security/news/2009/09/ruby-on-rails-vulnerability-affects-twitter-ie8-immune.ars 
>
>
> I'm hoping to finish the Soaplab Server work soon and then we can get 
> a release out. Hope this is okay.
>
> Jits
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Tue Sep  8 10:24:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 10:24:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2761] service page slow to load
Message-ID: <20090908142409.59EA4197827D@rubyforge.org>

Task #2761 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: service page slow to load 
Complete: 50%
Status: Open

Description: the service page takes a bit too long to load ... i was trying to load the following service which has only 5 operations: http://www.biocatalogue.org/services/2059-mrbws_619207 

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 14:24
By: jits

Comment:
This was potentially due to the monitoring tab, which has now been improved.

We need to look into doing more performance improvements though.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2761&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 10:26:20 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 10:26:20 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2582] Store extra log info during
	searches
Message-ID: <20090908142620.C601F16782AC@rubyforge.org>

Task #2582 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Store extra log info during searches
Complete: 100%
Status: Closed

Description: Add search results count and any other info to ActivityLog after search...

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 14:26
By: jits

Comment:
As part of the REST API work, the HTTP referer, user agent, format and so on are now stored. This should be good for now.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2582&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 10:26:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 10:26:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2571] Add google analytics
Message-ID: <20090908142639.68DF5197827D@rubyforge.org>

Task #2571 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add google analytics
Complete: 100%
Status: Closed

Description: Need to add google analytics to the website

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 14:26
By: jits

Comment:
Done

-------------------------------------------------------
Date: 2009-03-11 13:02
By: jits

Comment:
Have the EBI registered for a Google Analytics account as Rodrigo mentioned?

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2571&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 10:32:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 10:32:47 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2777] Log all filters acces on
	/services
Message-ID: <20090908143247.709601978284@rubyforge.org>

Task #2777 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Log all filters acces on /services
Complete: 100%
Status: Closed

Description: ... incl any search queries used on /services. This should also record a "search" event log.

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 14:32
By: jits

Comment:
All done in the REST API branch.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2777&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 10:54:09 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 10:54:09 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2783] Check UI for instances of
	non activated users showing up
Message-ID: <20090908145410.13AA018581FC@rubyforge.org>

Task #2783 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Check UI for instances of non activated users showing up
Complete: 50%
Status: Open

Description: There is a potential bug!

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 14:54
By: jits

Comment:
An initial check has been done. However, a proper audit needs to take place at some point.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2783&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 12:00:21 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 12:00:21 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2461] Improve login failure
	information
Message-ID: <20090908160021.EE9A71978282@rubyforge.org>

Task #2461 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Improve login failure information
Complete: 100%
Status: Closed

Description: the login failure message should be different depending on if the login details are wrong or if the account hasn't been activated.

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 16:00
By: jits

Comment:
A friendlier error message is now shown BUT no distinction is made between an incorrect login email or password or account activation, so as not to give away any information to potential hackers.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2461&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 12:02:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 12:02:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2784] Potentially change names of
	providers
Message-ID: <20090908160214.50549197827D@rubyforge.org>

Task #2784 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Potentially change names of providers
Complete: 0%
Status: Open

Description: At the moment, providers have names like "ebi.ac.uk". This looks like a URL and is confusing. Instead change to a scheme like "ebi-ac-uk".

This requires:
1. Update the existing provider's names.
2. Update the submission code to appropriately build the provider's name.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2784&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep  8 12:35:00 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue,  8 Sep 2009 12:35:00 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2784] Potentially change names of
	providers
Message-ID: <20090908163500.94A63197827D@rubyforge.org>

Task #2784 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Potentially change names of providers
Complete: 100%
Status: Closed

Description: At the moment, providers have names like "ebi.ac.uk". This looks like a URL and is confusing. Instead change to a scheme like "ebi-ac-uk".

This requires:
1. Update the existing provider's names.
2. Update the submission code to appropriately build the provider's name.

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-08 16:35
By: jits

Comment:
Done, in revision 1078

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2784&group_id=6901&group_project_id=12540

From twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com  Tue Sep  8 12:36:34 2009
From: twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com (Twitter)
Date: Tue, 8 Sep 2009 16:36:34 +0000
Subject: [BioCatalogue-developers] Jeni is now following you on Twitter!
Message-ID: <4aa688125a75f_310d15ab3337f7f030915ee@mx007.twitter.com.tmail>

Hi, BioCatalogue Test (biocat_test).

 Jeni (yoyo4eeyge) is now following your tweets on Twitter.

Check out  Jeni's profile here:
  http://twitter.com/yoyo4eeyge

You may follow  Jeni as well by clicking on the "follow" button.
Best,
Twitter

--
Turn off these emails at: http://twitter.com/account/notifications
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From ericnzuo at ebi.ac.uk  Thu Sep 10 05:10:01 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 10 Sep 2009 10:10:01 +0100
Subject: [BioCatalogue-developers] unable to attach slides to wiki
In-Reply-To: <d0ee827d0909090859n1cf2eba4mea74b4e723856d08@mail.gmail.com>
References: <d0ee827d0909090859n1cf2eba4mea74b4e723856d08@mail.gmail.com>
Message-ID: <4AA8C269.1080707@ebi.ac.uk>

hi Frank,

Did you get an error message? Could you send the slides to me to try 
uploading?

Eric


Franck Tanoh wrote:
> Hi guys,
>
> I  unsuccessfully tried to attach the ISMB demo slides and the poster 
> to the event page on the wiki  ... 
> http://www.biocatalogue.org/wiki/doku.php?id=public
> please check.
>
> cheers,
> Franck
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From noreply at rubyforge.org  Thu Sep 10 05:56:42 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 10 Sep 2009 05:56:42 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2785] Refresh of Stats page
	generates exception
Message-ID: <20090910095642.7611D1D78802@rubyforge.org>

Task #2785 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Refresh of Stats page generates exception
Complete: 0%
Status: Open

Description: Refreshing the stats page on the live site  throws an exception.  

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2785&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Thu Sep 10 06:59:11 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 10 Sep 2009 11:59:11 +0100
Subject: [BioCatalogue-developers] unable to attach slides to wiki
In-Reply-To: <d0ee827d0909100354m4f2a5e94p8e7e95dd71081c46@mail.gmail.com>
References: <d0ee827d0909090859n1cf2eba4mea74b4e723856d08@mail.gmail.com>	
	<4AA8C269.1080707@ebi.ac.uk>	
	<d0ee827d0909100341q52b20e67na14abbf4d607caf4@mail.gmail.com>
	<d0ee827d0909100354m4f2a5e94p8e7e95dd71081c46@mail.gmail.com>
Message-ID: <4AA8DBFF.6020307@ebi.ac.uk>

I think I have the ISMB files. I also saw them  on Jits' drop box.  But 
I do not seem to understand why the upload is apparently not working. 
Just guessing they may have exceeded the limit of the attachment sizes 
but not error messages are generated!  I will have another look.

Eric



Franck Tanoh wrote:
> Eric,
> i'll send you the file via skype .. don't seem to work by e-mail
>
> Franck
>
> 2009/9/10 Franck Tanoh <ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk>>
>
>     Hi Eric,
>
>     no error message, it seems to load fine but can't find it anywhere...
>     poster and slides attached.
>
>        *
>           There were a BioCatalogue demo and poster at DILS 2009
>           <http://www.cs.manchester.ac.uk/DILS09/>, on 20th July 2009,
>           by Jiten Bhagat and Franck Tanoh. Slides: <poster file her>
>
>        *
>           The BioCatalogue <http://www.biocatalogue.org/> was
>           successfully launched at ISMB 2009
>           <http://www.iscb.org/ismbeccb2009/>, on 1st July 2009, by
>           Jiten Bhagat and Franck Tanoh. Slides:<ISMB ppt here>
>
>     Franck
>
>
>     2009/9/10 Eric Nzuobontane <ericnzuo at ebi.ac.uk
>     <mailto:ericnzuo at ebi.ac.uk>>
>
>         hi Frank,
>
>         Did you get an error message? Could you send the slides to me
>         to try uploading?
>
>         Eric
>
>
>         Franck Tanoh wrote:
>
>             Hi guys,
>
>             I  unsuccessfully tried to attach the ISMB demo slides and
>             the poster to the event page on the wiki  ...
>             http://www.biocatalogue.org/wiki/doku.php?id=public
>             please check.
>
>             cheers,
>             Franck
>
>             -- 
>             "Science knows no country, because knowledge belongs to
>             humanity, and is the torch which illuminates the world." -
>             Louis Pasteur
>             ------------------------------------------------------------------------
>
>             _______________________________________________
>             BioCatalogue-developers mailing list
>             BioCatalogue-developers at rubyforge.org
>             <mailto:BioCatalogue-developers at rubyforge.org>
>             http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>              
>
>
>
>
>
>     -- 
>     "Science knows no country, because knowledge belongs to humanity,
>     and is the torch which illuminates the world." - Louis Pasteur
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur


From noreply at rubyforge.org  Mon Sep 14 06:58:47 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 14 Sep 2009 06:58:47 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2786] Add annotations for provider
	profile page
Message-ID: <20090914105848.090BC1858254@rubyforge.org>

Task #2786 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Add annotations for provider profile page
Complete: 0%
Status: Open

Description: Like for services... need to be able to annotate with info on contact details, names etc

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2786&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 14 07:00:46 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 14 Sep 2009 07:00:46 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2787] Build a leaner list for the
	search results
Message-ID: <20090914110046.E708B1978284@rubyforge.org>

Task #2787 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: Build a leaner list for the search results
Complete: 0%
Status: Open

Description: To improve on search results performance

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2787&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 14 07:38:03 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 14 Sep 2009 07:38:03 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2788] More profiling on search
Message-ID: <20090914113803.EB97B16782AA@rubyforge.org>

Task #2788 has been updated. 

Project: BioCatalogue
Subproject: Pilot
Summary: More profiling on search
Complete: 0%
Status: Open

Description: Need to do more profiling and optimisations on the search, from the solr retrieval to mapping to building the views.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2788&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Thu Sep 17 04:53:45 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 17 Sep 2009 09:53:45 +0100
Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module
 in the BioCatalogue
In-Reply-To: <d0ee827d0909020811q68476e3awfc74c0946b118b42@mail.gmail.com>
References: <RT-Ticket-129246@broadinstitute.org>	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>
	<d0ee827d0909020811q68476e3awfc74c0946b118b42@mail.gmail.com>
Message-ID: <4AB1F919.4050103@ebi.ac.uk>

Did we agree to meet Michael  of GenePattern today?

Eric


Franck Tanoh wrote:
> Hello Michael,
>
> Thanks for your reply, 
> 9/17 or 9/18  between 13.00-15.00 GMT is fine with us.  Is that ok 
> with you?
>
> Regards,
> Franck
>
> 2009/9/1 Michael Reich via RT <gp-help at broadinstitute.org 
> <mailto:gp-help at broadinstitute.org>>
>
>     Franck,
>
>     Thanks for your message - we are familiar with BioCatalogue and
>     will be
>     glad to discuss how to post GenePattern modules there. We should
>     probably have a technical discussion about how to classify the way to
>     connect to the public GenePattern server via Web services - it is not
>     straight WSDL-based.
>
>     We are working on a grant deadline now - are you available the week of
>     9/14 to discuss?
>
>     Best,
>     Michael
>
>     > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk> - Tue Sep 01
>     08:18:35 2009]:
>     >
>     > Hello,
>     >
>     > The BioCatalogue team led by Prof. Carole Goble from the myGrid
>     project and
>     > Rodrigo Lopez from the European Bioinformatics Institute ( EBI)
>     would
>     really
>     > like to investigate the possibility to bring GenePattern's
>     modules and
>     > annotations in the BioCatalogue (http://www.biocatalogue.org/).
>     > The BioCatalogue project aims to create a curated catalogue of life
>     science
>     > Web Services. Through the BioCatalogue, the community can meet
>     and contact
>     > the maintainers of life science services.
>     > It is also a place where service provider can advertise and
>     monitor the
>     > usage of their services. The project is funded by the BBSRC
>     (Biotechnology
>     > and Biological Sciences Research Council).
>     > Since its launch in June, the BioCatalogue has more than 1000
>     services (
>     > SOAP, REST, BioMoby, Soaplab).
>     >
>     > I strongly believe that the BioCatalogue can serve as a platform to
>     > advertise GenePattern and its modules to the community.
>     >
>     > Could you point me to the person(s) to contact to start the
>     discussion and
>     > possibly requirements gathering, please?
>     >
>     > Regards,
>     >
>     > Franck
>     >
>     > ..
>     > Franck Tanoh
>     > BioCatalogue team
>     > University of Manchester
>     > +441612750145
>     >
>     >
>     >
>
>
>
>
> -- 
> "Science knows no country, because knowledge belongs to humanity, and 
> is the torch which illuminates the world." - Louis Pasteur
> ------------------------------------------------------------------------
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>   


From ytanoh at cs.man.ac.uk  Thu Sep 17 05:07:46 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Thu, 17 Sep 2009 10:07:46 +0100
Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module
	in the BioCatalogue
In-Reply-To: <4AB1F919.4050103@ebi.ac.uk>
References: <RT-Ticket-129246@broadinstitute.org>	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>
	<d0ee827d0909020811q68476e3awfc74c0946b118b42@mail.gmail.com>
	<4AB1F919.4050103@ebi.ac.uk>
Message-ID: <B477D7B0-CA4C-41FD-B0AB-BC1458561DBE@cs.man.ac.uk>

Hi Eric,

i didn't hear from them ... will chase it up again.
so the meeting won't be today; maybe tomorrow or next week. Let's see  
what he says.

cheers,
Franck

On 17 Sep 2009, at 09:53, Eric Nzuobontane wrote:

> Did we agree to meet Michael  of GenePattern today?
>
> Eric
>
>
> Franck Tanoh wrote:
>> Hello Michael,
>>
>> Thanks for your reply, 9/17 or 9/18  between 13.00-15.00 GMT is  
>> fine with us.  Is that ok with you?
>>
>> Regards,
>> Franck
>>
>> 2009/9/1 Michael Reich via RT <gp-help at broadinstitute.org <mailto:gp-help at broadinstitute.org 
>> >>
>>
>>    Franck,
>>
>>    Thanks for your message - we are familiar with BioCatalogue and
>>    will be
>>    glad to discuss how to post GenePattern modules there. We should
>>    probably have a technical discussion about how to classify the  
>> way to
>>    connect to the public GenePattern server via Web services - it  
>> is not
>>    straight WSDL-based.
>>
>>    We are working on a grant deadline now - are you available the  
>> week of
>>    9/14 to discuss?
>>
>>    Best,
>>    Michael
>>
>>    > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk> - Tue Sep 01
>>    08:18:35 2009]:
>>    >
>>    > Hello,
>>    >
>>    > The BioCatalogue team led by Prof. Carole Goble from the myGrid
>>    project and
>>    > Rodrigo Lopez from the European Bioinformatics Institute ( EBI)
>>    would
>>    really
>>    > like to investigate the possibility to bring GenePattern's
>>    modules and
>>    > annotations in the BioCatalogue (http://www.biocatalogue.org/).
>>    > The BioCatalogue project aims to create a curated catalogue of  
>> life
>>    science
>>    > Web Services. Through the BioCatalogue, the community can meet
>>    and contact
>>    > the maintainers of life science services.
>>    > It is also a place where service provider can advertise and
>>    monitor the
>>    > usage of their services. The project is funded by the BBSRC
>>    (Biotechnology
>>    > and Biological Sciences Research Council).
>>    > Since its launch in June, the BioCatalogue has more than 1000
>>    services (
>>    > SOAP, REST, BioMoby, Soaplab).
>>    >
>>    > I strongly believe that the BioCatalogue can serve as a  
>> platform to
>>    > advertise GenePattern and its modules to the community.
>>    >
>>    > Could you point me to the person(s) to contact to start the
>>    discussion and
>>    > possibly requirements gathering, please?
>>    >
>>    > Regards,
>>    >
>>    > Franck
>>    >
>>    > ..
>>    > Franck Tanoh
>>    > BioCatalogue team
>>    > University of Manchester
>>    > +441612750145
>>    >
>>    >
>>    >
>>
>>
>>
>>
>> -- 
>> "Science knows no country, because knowledge belongs to humanity,  
>> and is the torch which illuminates the world." - Louis Pasteur
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>


From ericnzuo at ebi.ac.uk  Thu Sep 17 05:10:23 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 17 Sep 2009 10:10:23 +0100
Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module
 in the BioCatalogue
In-Reply-To: <B477D7B0-CA4C-41FD-B0AB-BC1458561DBE@cs.man.ac.uk>
References: <RT-Ticket-129246@broadinstitute.org>	<d0ee827d0909010518x7d0fd261m90e0ca3b088d12c0@mail.gmail.com>	<rt-3.4.5-34294-1251825123-1546.129246-6-0@broadinstitute.org>
	<d0ee827d0909020811q68476e3awfc74c0946b118b42@mail.gmail.com>
	<4AB1F919.4050103@ebi.ac.uk>
	<B477D7B0-CA4C-41FD-B0AB-BC1458561DBE@cs.man.ac.uk>
Message-ID: <4AB1FCFF.10401@ebi.ac.uk>

As we need a meeting booked here at EBI, I would prefer next week as 
that gives us a better chance of obtaining a suitable one.

Eric


Franck Tanoh wrote:
> Hi Eric,
>
> i didn't hear from them ... will chase it up again.
> so the meeting won't be today; maybe tomorrow or next week. Let's see 
> what he says.
>
> cheers,
> Franck
>
> On 17 Sep 2009, at 09:53, Eric Nzuobontane wrote:
>
>> Did we agree to meet Michael  of GenePattern today?
>>
>> Eric
>>
>>
>> Franck Tanoh wrote:
>>> Hello Michael,
>>>
>>> Thanks for your reply, 9/17 or 9/18  between 13.00-15.00 GMT is fine 
>>> with us.  Is that ok with you?
>>>
>>> Regards,
>>> Franck
>>>
>>> 2009/9/1 Michael Reich via RT <gp-help at broadinstitute.org 
>>> <mailto:gp-help at broadinstitute.org>>
>>>
>>>    Franck,
>>>
>>>    Thanks for your message - we are familiar with BioCatalogue and
>>>    will be
>>>    glad to discuss how to post GenePattern modules there. We should
>>>    probably have a technical discussion about how to classify the 
>>> way to
>>>    connect to the public GenePattern server via Web services - it is 
>>> not
>>>    straight WSDL-based.
>>>
>>>    We are working on a grant deadline now - are you available the 
>>> week of
>>>    9/14 to discuss?
>>>
>>>    Best,
>>>    Michael
>>>
>>>    > [ytanoh at cs.man.ac.uk <mailto:ytanoh at cs.man.ac.uk> - Tue Sep 01
>>>    08:18:35 2009]:
>>>    >
>>>    > Hello,
>>>    >
>>>    > The BioCatalogue team led by Prof. Carole Goble from the myGrid
>>>    project and
>>>    > Rodrigo Lopez from the European Bioinformatics Institute ( EBI)
>>>    would
>>>    really
>>>    > like to investigate the possibility to bring GenePattern's
>>>    modules and
>>>    > annotations in the BioCatalogue (http://www.biocatalogue.org/).
>>>    > The BioCatalogue project aims to create a curated catalogue of 
>>> life
>>>    science
>>>    > Web Services. Through the BioCatalogue, the community can meet
>>>    and contact
>>>    > the maintainers of life science services.
>>>    > It is also a place where service provider can advertise and
>>>    monitor the
>>>    > usage of their services. The project is funded by the BBSRC
>>>    (Biotechnology
>>>    > and Biological Sciences Research Council).
>>>    > Since its launch in June, the BioCatalogue has more than 1000
>>>    services (
>>>    > SOAP, REST, BioMoby, Soaplab).
>>>    >
>>>    > I strongly believe that the BioCatalogue can serve as a 
>>> platform to
>>>    > advertise GenePattern and its modules to the community.
>>>    >
>>>    > Could you point me to the person(s) to contact to start the
>>>    discussion and
>>>    > possibly requirements gathering, please?
>>>    >
>>>    > Regards,
>>>    >
>>>    > Franck
>>>    >
>>>    > ..
>>>    > Franck Tanoh
>>>    > BioCatalogue team
>>>    > University of Manchester
>>>    > +441612750145
>>>    >
>>>    >
>>>    >
>>>
>>>
>>>
>>>
>>> -- 
>>> "Science knows no country, because knowledge belongs to humanity, 
>>> and is the torch which illuminates the world." - Louis Pasteur
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>


From ericnzuo at ebi.ac.uk  Thu Sep 17 05:12:59 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 17 Sep 2009 10:12:59 +0100
Subject: [BioCatalogue-developers] Embrace test script data
Message-ID: <4AB1FD9B.6010303@ebi.ac.uk>

Hi Jits,

Is is possible for me to get a dump of the test script data from the 
embrace registry?

Eric


From jits at cs.man.ac.uk  Thu Sep 17 05:25:12 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 17 Sep 2009 10:25:12 +0100
Subject: [BioCatalogue-developers] Embrace test script data
In-Reply-To: <4AB1FD9B.6010303@ebi.ac.uk>
References: <4AB1FD9B.6010303@ebi.ac.uk>
Message-ID: <4AB20078.7050700@cs.man.ac.uk>

Hi Eric,

Sure, I'll get you the db dump of what I had in June. You can use that 
for now if that's okay.

I'll put it on DropBox and then message you on Skype.

Jits


Eric Nzuobontane wrote:
> Hi Jits,
>
> Is is possible for me to get a dump of the test script data from the 
> embrace registry?
>
> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From ericnzuo at ebi.ac.uk  Thu Sep 17 05:27:28 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Thu, 17 Sep 2009 10:27:28 +0100
Subject: [BioCatalogue-developers] Embrace test script data
In-Reply-To: <4AB20078.7050700@cs.man.ac.uk>
References: <4AB1FD9B.6010303@ebi.ac.uk> <4AB20078.7050700@cs.man.ac.uk>
Message-ID: <4AB20100.8040106@ebi.ac.uk>

That is perfectly fine. Thanks!

Eric


Jiten Bhagat wrote:
> Hi Eric,
>
> Sure, I'll get you the db dump of what I had in June. You can use that 
> for now if that's okay.
>
> I'll put it on DropBox and then message you on Skype.
>
> Jits
>
>
> Eric Nzuobontane wrote:
>> Hi Jits,
>>
>> Is is possible for me to get a dump of the test script data from the 
>> embrace registry?
>>
>> Eric
>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Thu Sep 17 06:16:38 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 17 Sep 2009 06:16:38 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2511] Annotations: check the
	setting of "source" when creating
Message-ID: <20090917101638.7E33B185824F@rubyforge.org>

Task #2511 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Annotations: check the setting of "source" when creating
Complete: 0%
Status: Open

Description: Currently the create method will set the source to the current_user if no source data is provided in the params hash. Should we allow setting an arbitrary source via params? How about having a configuration setting "restricted_source_types" that prevents creation of annotation (via params) that have those source types.

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-17 10:16
By: jits

Comment:
Also, maybe by default you no "User" should be set as source via params in the create method.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2511&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Sep 17 06:34:41 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 17 Sep 2009 06:34:41 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2789] Upgrade to latest
	memcache-client
Message-ID: <20090917103441.B6A91185824C@rubyforge.org>

Task #2789 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Upgrade to latest memcache-client
Complete: 0%
Status: Open

Description: Some speed improvements have been promised for this!

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2789&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Thu Sep 17 06:54:17 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Thu, 17 Sep 2009 06:54:17 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2790] Add a "Services I have
	annotated" tab in user profile
Message-ID: <20090917105417.6F0EF185824C@rubyforge.org>

Task #2790 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Add a "Services I have annotated" tab in user profile
Complete: 0%
Status: Open

Description: At the moment there is now way to see what services someone has annotated.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2790&group_id=6901&group_project_id=12540

From ytanoh at cs.man.ac.uk  Fri Sep 18 07:06:38 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 18 Sep 2009 12:06:38 +0100
Subject: [BioCatalogue-developers] report for annotator
Message-ID: <d0ee827d0909180406v4bc4b8a8s491ab38defa3f7af@mail.gmail.com>

Hi guys,

I guess we'll at some point discuss the annotation tool... before that
I've listed the number of reports which would be extremely useful to
have as part of the tool.

1-	New services added
2-     Recently updated services
3-	Services that don?t work anymore
4-	Anything picks up by the monitor (notify me when amber or red)
5-	Most viewed services
6-	Less viewed services
7-	Most farourited services
8-	Most annotated services
9-	Services without any description
10-	List of services non-categorized
11-	New members
12-	Members detail and contact mail
13-	Member with the most annotation
14-	Member with the most submitted service
15-	New comments added
16-	Updated service description by members
17-	Service providers list
18-	Service submitter list
19-	Recently annotated services
20-  Recently deleted service

cheers,
Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From jits at cs.man.ac.uk  Fri Sep 18 07:17:39 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 18 Sep 2009 12:17:39 +0100
Subject: [BioCatalogue-developers] report for annotator
In-Reply-To: <d0ee827d0909180406v4bc4b8a8s491ab38defa3f7af@mail.gmail.com>
References: <d0ee827d0909180406v4bc4b8a8s491ab38defa3f7af@mail.gmail.com>
Message-ID: <4AB36C53.7080807@cs.man.ac.uk>

Thanks Franck that's very useful.

Jits


Franck Tanoh wrote:
> Hi guys,
>
> I guess we'll at some point discuss the annotation tool... before that
> I've listed the number of reports which would be extremely useful to
> have as part of the tool.
>
> 1-	New services added
> 2-     Recently updated services
> 3-	Services that don?t work anymore
> 4-	Anything picks up by the monitor (notify me when amber or red)
> 5-	Most viewed services
> 6-	Less viewed services
> 7-	Most farourited services
> 8-	Most annotated services
> 9-	Services without any description
> 10-	List of services non-categorized
> 11-	New members
> 12-	Members detail and contact mail
> 13-	Member with the most annotation
> 14-	Member with the most submitted service
> 15-	New comments added
> 16-	Updated service description by members
> 17-	Service providers list
> 18-	Service submitter list
> 19-	Recently annotated services
> 20-  Recently deleted service
>
> cheers,
> Franck
>
>   


From noreply at rubyforge.org  Fri Sep 18 08:02:08 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 18 Sep 2009 08:02:08 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2791] biocatalogue
	statistics-report
Message-ID: <20090918120208.485B416782A9@rubyforge.org>

Task #2791 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: biocatalogue statistics-report
Complete: 0%
Status: Open

Description: BioCatalogue will have a better reporting mechanism through the annotator tools and other tools. In the mean time, we will produce stats on:

1-	New services added
2-     Recently updated services
3-	Services that don?t work anymore
4-	Anything picks up by the monitor (notify me when amber or red)
5-	Most viewed services
6-	Less viewed services
7-	Most farourited services
8-	Most annotated services
9-	Services without any description
10-	List of services non-categorized
11-	New members
12-	Members detail and contact mail
13-	Member with the most annotation
14-	Member with the most submitted service
15-	New comments added
16-	Updated service description by members
17-	Service providers list
18-	Service submitter list
19-	Recently annotated services
20-  Recently deleted service

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2791&group_id=6901&group_project_id=12540

From ericnzuo at ebi.ac.uk  Fri Sep 18 13:13:32 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Fri, 18 Sep 2009 18:13:32 +0100
Subject: [BioCatalogue-developers] libraries for test scripts
Message-ID: <4AB3BFBC.3030009@ebi.ac.uk>

Hi Steve,
Would be possible to give me a list of the libraries and their version 
that are needed for the test script environment? I did find some 
information here
http://www.embraceregistry.net/content/information-service-providers

but it is not clear what the complete set is.

Systems would like this list in order to set up the machines.

cheers,

Eric


From steve.pettifer at manchester.ac.uk  Sat Sep 19 14:13:06 2009
From: steve.pettifer at manchester.ac.uk (Steve Pettifer)
Date: Sat, 19 Sep 2009 19:13:06 +0100
Subject: [BioCatalogue-developers] libraries for test scripts
In-Reply-To: <4AB3BFBC.3030009@ebi.ac.uk>
References: <4AB3BFBC.3030009@ebi.ac.uk>
Message-ID: <D048606D-E317-4397-8D22-AA07ECFF6670@manchester.ac.uk>

> http://www.embraceregistry.net/content/information-service-providers
>
> but it is not clear what the complete set is.

That *is* the complete set :)

Steve

From noreply at rubyforge.org  Sun Sep 20 16:30:32 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 20 Sep 2009 16:30:32 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2792] Move smtp settings into a
	seperate file
Message-ID: <20090920203032.A91DE16782A9@rubyforge.org>

Task #2792 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Move smtp settings into a seperate file
Complete: 0%
Status: Open

Description: Currently the SMTP settings are hard coded. They need to be moved out and configurable for other instances outside of the EBI.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2792&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Sun Sep 20 17:15:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Sun, 20 Sep 2009 17:15:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2793] Annotations plugin: update
	versioning
Message-ID: <20090920211507.3074416782A9@rubyforge.org>

Task #2793 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Annotations plugin: update versioning
Complete: 0%
Status: Open

Description: In main codebase we have applied this: http://github.com/jmckible/version_fu/commit/6621b379f96591c3299d69ae60d720b3214a9f16

Look to using a newer version_fu in the Annotations plugin master GitHub master repo.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2793&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 21 05:38:48 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 21 Sep 2009 05:38:48 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2794] Implement delete button for
	services
Message-ID: <20090921093849.078A2185824E@rubyforge.org>

Task #2794 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Implement delete button for services
Complete: 0%
Status: Open

Description: Currently you cannot delete services

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2794&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 21 05:42:12 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 21 Sep 2009 05:42:12 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2795] Possibly implement ordering
	curation of annotations
Message-ID: <20090921094213.1E9E81858253@rubyforge.org>

Task #2795 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Possibly implement ordering curation of annotations
Complete: 0%
Status: Open

Description: Up/down buttons for people to specify where they think the annotation belongs in the list. Like votes. Like in ServerFault and StackOverflow.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2795&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 21 05:43:24 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 21 Sep 2009 05:43:24 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2796] Implement mechanism and UI
	for "Recommended Services"
Message-ID: <20090921094325.1EC951858252@rubyforge.org>

Task #2796 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Implement mechanism and UI for "Recommended Services"
Complete: 0%
Status: Open

Description: Have Franck etc be able to set certain services as "Recommended for..... x y z" (where xyz are for specific tasks) and then those recommended services are highlighted in listings (much like they do on the FireFox and Thunderbird addons site).

Also have a "All recommended services" list.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2796&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 21 10:44:58 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 21 Sep 2009 10:44:58 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2797] Clarify requirements for
	test script environment
Message-ID: <20090921144458.92D3D167829F@rubyforge.org>

Task #2797 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Clarify requirements for test script environment
Complete: 0%
Status: Open

Description: Present systems with a complete list of requirements for the test script environment. 

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2797&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Mon Sep 21 10:46:35 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Mon, 21 Sep 2009 10:46:35 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2798] Test Harness & wrapper port
Message-ID: <20090921144636.1C9A91858267@rubyforge.org>

Task #2798 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Test Harness & wrapper port
Complete: 0%
Status: Open

Description: Examine and possibly port the test harness and wrapper from the embrace services registry

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2798&group_id=6901&group_project_id=12540

From ytanoh at cs.man.ac.uk  Mon Sep 21 11:03:53 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 21 Sep 2009 16:03:53 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
Message-ID: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>

here is the list:

kwolstencroft
kwolstencroft

tlaurent
th.laurent
tlaurent

rodrigoluk
Rodrigo Lopez

I'll check with Katy the one she's currently using; Thomas-you can
remove one of the duplicated name or just change the display name.
Rodrigo's one seems ok for me. People are allow to have more than 1
account, aren't they?

Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From tlaurent at ebi.ac.uk  Mon Sep 21 11:35:12 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Mon, 21 Sep 2009 16:35:12 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
In-Reply-To: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>
References: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>
Message-ID: <4AB79D30.1080204@ebi.ac.uk>

I have deactivated my extra accounts in the database. They still show up 
if we search for them in the UI, but I think next time we'll reindex the 
db, they'll disappear.

Thomas

Franck Tanoh wrote:
> here is the list:
> 
> kwolstencroft
> kwolstencroft
> 
> tlaurent
> th.laurent
> tlaurent
> 
> rodrigoluk
> Rodrigo Lopez
> 
> I'll check with Katy the one she's currently using; Thomas-you can
> remove one of the duplicated name or just change the display name.
> Rodrigo's one seems ok for me. People are allow to have more than 1
> account, aren't they?
> 
> Franck
> 

From noreply at rubyforge.org  Tue Sep 22 06:32:42 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 06:32:42 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2799] check apache logs
Message-ID: <20090922103242.EE7081D78809@rubyforge.org>

Task #2799 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: check apache logs
Complete: 0%
Status: Open

Description: Check apache logs for error that point to local host. Error message with " the message for
example says to contact the server administrator at
<<root at localhost>>."

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2799&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep 22 06:35:49 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 06:35:49 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2697] Wrap the wsdl parsing in a
	timeout
Message-ID: <20090922103549.ECF9E185826D@rubyforge.org>

Task #2697 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Wrap the wsdl parsing in a timeout
Complete: 0%
Status: Closed

Description: Use SystemTimer instead of the built in Ruby timer.

Look in /lib/bio_catalogue/util.rb for examples.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2697&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep 22 06:53:11 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 06:53:11 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2800] Improve solr indexing by
	using the solr types config option
Message-ID: <20090922105311.CC4031858275@rubyforge.org>

Task #2800 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Improve solr indexing by using the solr types config option
Complete: 0%
Status: Open

Description: Currently all fields indexed are treated as solr "text" fields which have the full ngramtokenizer treatment applied to them. However we might want certain fields to be indexed as they are and not split into tokens (potentially fields like "category"). Look into doing this using syntax such as:

acts_as_solr :fields => [ { :price => :range_float } ]

The available field types are:
- :float
- :integer
- :boolean
- :date
- :string
- :range_integer
- :range_float

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2800&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Tue Sep 22 07:01:54 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 22 Sep 2009 12:01:54 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
In-Reply-To: <4AB79D30.1080204@ebi.ac.uk>
References: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>
	<4AB79D30.1080204@ebi.ac.uk>
Message-ID: <4AB8AEA2.1060304@cs.man.ac.uk>

Thomas Laurent wrote:
> I have deactivated my extra accounts in the database. They still show
> up if we search for them in the UI, but I think next time we'll
> reindex the db, they'll disappear.

This is actually a bug, thanks for picking it up. I've committed a fix
to the codebase (revision 1091) to only index activated users.

This needs testing on the test server.

Jits


>
> Thomas
>
> Franck Tanoh wrote:
>> here is the list:
>>
>> kwolstencroft
>> kwolstencroft
>>
>> tlaurent
>> th.laurent
>> tlaurent
>>
>> rodrigoluk
>> Rodrigo Lopez
>>
>> I'll check with Katy the one she's currently using; Thomas-you can
>> remove one of the duplicated name or just change the display name.
>> Rodrigo's one seems ok for me. People are allow to have more than 1
>> account, aren't they?
>>
>> Franck
>>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers


From noreply at rubyforge.org  Tue Sep 22 07:33:14 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 07:33:14 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2801] Test UI  users
Message-ID: <20090922113314.887621D7880F@rubyforge.org>

Task #2801 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Test UI  users
Complete: 0%
Status: Open

Description: Only activated users should show up in the UI. 

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2801&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep 22 07:36:07 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 07:36:07 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2802] better error reporting
Message-ID: <20090922113607.BBF6B1D7880F@rubyforge.org>

Task #2802 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: better error reporting 
Complete: 0%
Status: Open

Description: We need a better error reporting when a service submission fails. At the moment it is a localhost type error message.
e.g. using this service: http://biomoby.org/services/wsdl/xml.nig.ac.jp/Blastp_SearchSimple

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2802&group_id=6901&group_project_id=12540

From noreply at rubyforge.org  Tue Sep 22 10:34:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Tue, 22 Sep 2009 10:34:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2802] better error reporting
Message-ID: <20090922143439.DE93A19780E6@rubyforge.org>

Task #2802 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: better error reporting 
Complete: 0%
Status: Open

Description: We need a better error reporting when a service submission fails. At the moment it is a localhost type error message.
e.g. using this service: http://biomoby.org/services/wsdl/xml.nig.ac.jp/Blastp_SearchSimple

Follow-Ups:

-------------------------------------------------------
Date: 2009-09-22 14:34
By: jits

Comment:
This is a potential issue arising at the Apache web server level, not within the Rails app.

-------------------------------------------------------
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From ytanoh at cs.man.ac.uk  Wed Sep 23 10:40:40 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 23 Sep 2009 15:40:40 +0100
Subject: [BioCatalogue-developers] biocat focus group
Message-ID: <d0ee827d0909230740s1b7a7086q159813947cec9c42@mail.gmail.com>

Hello,

I propose for the focus group  we individually talk to a number of
users or possible users here in Manchester and at the EBI.
in Manchester i can go through the site with Paul, Katy, Peter Li, one
or 2 people at the MIB.
at EBI, Eric can go trough the website with Duncan, and one or 2
people who are user or possible user of the catalogue.
Added to that i can ask the new PALS for feedback via phone or by e-mail.
we should be able to gather enough feedback for the report that way.

what do you think?

Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From jits at cs.man.ac.uk  Wed Sep 23 11:22:14 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Wed, 23 Sep 2009 16:22:14 +0100
Subject: [BioCatalogue-developers] biocat focus group
In-Reply-To: <d0ee827d0909230740s1b7a7086q159813947cec9c42@mail.gmail.com>
References: <d0ee827d0909230740s1b7a7086q159813947cec9c42@mail.gmail.com>
Message-ID: <4ABA3D26.2040407@cs.man.ac.uk>

Hi Franck,

This sounds okay to me, BUT it might be worth posting this to the main
BioCatalogue list so that Carole/Rodrigo give their views on this.

Also it would be useful if you put together a list of the different
things you will be asking and what kind of information you will be
collecting. So we can get an idea early one whether that is required for
the report or something else.

Cheers,
Jits


Franck Tanoh wrote:
> Hello,
>
> I propose for the focus group  we individually talk to a number of
> users or possible users here in Manchester and at the EBI.
> in Manchester i can go through the site with Paul, Katy, Peter Li, one
> or 2 people at the MIB.
> at EBI, Eric can go trough the website with Duncan, and one or 2
> people who are user or possible user of the catalogue.
> Added to that i can ask the new PALS for feedback via phone or by e-mail.
> we should be able to gather enough feedback for the report that way.
>
> what do you think?
>
> Franck
>
>   


From jits at cs.man.ac.uk  Thu Sep 24 13:39:34 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Thu, 24 Sep 2009 18:39:34 +0100
Subject: [BioCatalogue-developers] Easier annotations UI
Message-ID: <4ABBAED6.1030801@cs.man.ac.uk>

Hi Franck,

I've put together an easier way of adding annotations in the
BioCatalogue. Please check this out on http://sandbox.biocatalogue.org/

For example, if you go to:
http://sandbox.biocatalogue.org/services/2059-mrbws_619207 you will now
see text boxes to easily add annotations in each section and in the tag
clouds (you need to be logged in). All adds should now do it inline
inside of causing a full refresh. I've also spent ages figuring out a
way of automatically expanding the text boxes when you add text in them.

Please play around with this and let me know what you think. Note that
the URL above is my sandbox site so feel free to add any crappy data for
testing purposes. We're hoping to get this released to the live site
next week (or potentially the week after).

Thomas, Eric - it would be great to get your feedback too.

Cheers,
Jits

From ytanoh at cs.man.ac.uk  Fri Sep 25 05:42:46 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Fri, 25 Sep 2009 10:42:46 +0100
Subject: [BioCatalogue-developers] Easier annotations UI
In-Reply-To: <4ABBAED6.1030801@cs.man.ac.uk>
References: <4ABBAED6.1030801@cs.man.ac.uk>
Message-ID: <d0ee827d0909250242r698cffeai3b8db4c47562ebec@mail.gmail.com>

Hi Jits,

looking really good... thanks
Instead of having the forms for adding description or tags visible by
default will it be possible to hide them? The interface looks very
clutter with all these forms when you sign in.
Did you leave thing like 'name alias', 'other annotation' on purpose?
Also updating a description still the same as before.

 >I've also spent ages figuring out a way of automatically expanding
the text boxes when you add text in them.
At the moment i can expand it with the arrow on my keyboard but I
agree, it will extremely be useful if that can be done automatically.

Cheers,
Franck

2009/9/24 Jiten Bhagat <jits at cs.man.ac.uk>:
> Hi Franck,
>
> I've put together an easier way of adding annotations in the
> BioCatalogue. Please check this out on http://sandbox.biocatalogue.org/
>
> For example, if you go to:
> http://sandbox.biocatalogue.org/services/2059-mrbws_619207 you will now
> see text boxes to easily add annotations in each section and in the tag
> clouds (you need to be logged in). All adds should now do it inline
> inside of causing a full refresh. I've also spent ages figuring out a
> way of automatically expanding the text boxes when you add text in them.
>
> Please play around with this and let me know what you think. Note that
> the URL above is my sandbox site so feel free to add any crappy data for
> testing purposes. We're hoping to get this released to the live site
> next week (or potentially the week after).
>
> Thomas, Eric - it would be great to get your feedback too.
>
> Cheers,
> Jits
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From noreply at rubyforge.org  Fri Sep 25 11:27:39 2009
From: noreply at rubyforge.org (noreply at rubyforge.org)
Date: Fri, 25 Sep 2009 11:27:39 -0400 (EDT)
Subject: [BioCatalogue-developers] [Task #2805] Track when users were last
	active
Message-ID: <20090925152739.C3C9015B8025@rubyforge.org>

Task #2805 has been updated. 

Project: BioCatalogue
Subproject: Main
Summary: Track when users were last active
Complete: 0%
Status: Open

Description: Add a "last_active" field to users model and on every request update the user model (but only the one field) to show when a user was last active.

-------------------------------------------------------
For more info, visit:

http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2805&group_id=6901&group_project_id=12540

From jits at cs.man.ac.uk  Fri Sep 25 11:39:43 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Fri, 25 Sep 2009 16:39:43 +0100
Subject: [BioCatalogue-developers] Socket connections question
Message-ID: <4ABCE43F.4080404@cs.man.ac.uk>

Hi guys,

I'm implementing OpenID (and Facebook, Twitter, Google etc)
authentication and wanted to check something. Will I hit the EBI sockets
issue if I use the following code:

require 'net/http'
require 'net/https'

request = Net::HTTP::Post.new(some_path)

Thanks,
Jits

From jits at cs.man.ac.uk  Mon Sep 28 04:44:47 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 28 Sep 2009 09:44:47 +0100
Subject: [BioCatalogue-developers] Socket connections question
In-Reply-To: <4ABCF262.80203@ebi.ac.uk>
References: <4ABCE43F.4080404@cs.man.ac.uk> <4ABCF262.80203@ebi.ac.uk>
Message-ID: <4AC0777F.8030709@cs.man.ac.uk>

Okay thanks Eric.

I'm actually using a plugin to do this for me so I might have to modify
the plugin to use the proxy. I'm hoping that the Net::HTTP libraries
automatically look for the PROXY setting...

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Jits,
> I would not think so, as I suppose that request is over http/https.
> However, at EBI connection to the web servers are via proxy, so the
> post may have to take some configuration parameters.
>
> cheers,
>
> Eric
>
>
>
> Jiten Bhagat wrote:
>> Hi guys,
>>
>> I'm implementing OpenID (and Facebook, Twitter, Google etc)
>> authentication and wanted to check something. Will I hit the EBI sockets
>> issue if I use the following code:
>>
>> require 'net/http'
>> require 'net/https'
>>
>> request = Net::HTTP::Post.new(some_path)
>>
>> Thanks,
>> Jits
>>   
>


From jits at cs.man.ac.uk  Mon Sep 28 08:43:11 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 28 Sep 2009 13:43:11 +0100
Subject: [BioCatalogue-developers] RPX (to allow login/register using OpenID,
 Yahoo ID, Facebook, Twitter, Google Account, etc)
Message-ID: <4AC0AF5F.7050700@cs.man.ac.uk>

Hi,

This morning I mentioned I'm building support in the BioCatalogue for
login/register using OpenID, Yahoo ID, and other single sign on
providers out there. I thought I would share how I am doing this. I
strongly feel that we should have this in myExperiment too!

I'm using an online service called RPX - https://rpxnow.com/, which is
developed and provider by Jan Rain - the same people who provide
myOpenID. As you can see from their website, many different companies
already use them.

At the moment I've signed up for the free package which restricts it to
6 different providers.

To provide nicer integration with the Rails app I'm using a plugin -
http://github.com/grosser/rpx_now/

I'm still in the middle of implementing this, so if anyone has any
queries let me know. If this fails drastically for some reason then I'll
let everyone know!

Cheers,
Jits

From ytanoh at cs.man.ac.uk  Mon Sep 28 09:30:04 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Mon, 28 Sep 2009 14:30:04 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
In-Reply-To: <4AB8AEA2.1060304@cs.man.ac.uk>
References: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>
	<4AB79D30.1080204@ebi.ac.uk> <4AB8AEA2.1060304@cs.man.ac.uk>
Message-ID: <d0ee827d0909280630yd7171d8y43f9b7cc2f4e00a6@mail.gmail.com>

Hi guys,
Katy doesn't use the following account: http://www.biocatalogue.org/users/79
can you remove it please?

Franck

2009/9/22 Jiten Bhagat <jits at cs.man.ac.uk>:
> Thomas Laurent wrote:
>> I have deactivated my extra accounts in the database. They still show
>> up if we search for them in the UI, but I think next time we'll
>> reindex the db, they'll disappear.
>
> This is actually a bug, thanks for picking it up. I've committed a fix
> to the codebase (revision 1091) to only index activated users.
>
> This needs testing on the test server.
>
> Jits
>
>
>>
>> Thomas
>>
>> Franck Tanoh wrote:
>>> here is the list:
>>>
>>> kwolstencroft
>>> kwolstencroft
>>>
>>> tlaurent
>>> th.laurent
>>> tlaurent
>>>
>>> rodrigoluk
>>> Rodrigo Lopez
>>>
>>> I'll check with Katy the one she's currently using; Thomas-you can
>>> remove one of the duplicated name or just change the display name.
>>> Rodrigo's one seems ok for me. People are allow to have more than 1
>>> account, aren't they?
>>>
>>> Franck
>>>
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From ericnzuo at ebi.ac.uk  Mon Sep 28 12:39:15 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 28 Sep 2009 17:39:15 +0100
Subject: [BioCatalogue-developers] Google Analytics stats
Message-ID: <4AC0E6B3.50405@ebi.ac.uk>

Hi Jits,

Could you please give us access to the google analytics statistics for 
BioCatalogue? That way we can see how they compare with the stats 
collected here at EBI.

cheers,

Eric

From jits at cs.man.ac.uk  Mon Sep 28 12:42:29 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Mon, 28 Sep 2009 17:42:29 +0100
Subject: [BioCatalogue-developers] Google Analytics stats
In-Reply-To: <4AC0E6B3.50405@ebi.ac.uk>
References: <4AC0E6B3.50405@ebi.ac.uk>
Message-ID: <4AC0E775.1080108@cs.man.ac.uk>

Hi Eric,

Sure! I thought I had already done that but when I looked closely it was
Thomas who had access. In any case I've added you (through your gmail
account: ericnzuo at googlemail.com).

Cheers,
Jits


Eric Nzuobontane wrote:
> Hi Jits,
>
> Could you please give us access to the google analytics statistics for
> BioCatalogue? That way we can see how they compare with the stats
> collected here at EBI.
>
> cheers,
>
> Eric


From ericnzuo at ebi.ac.uk  Mon Sep 28 12:46:55 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Mon, 28 Sep 2009 17:46:55 +0100
Subject: [BioCatalogue-developers] Google Analytics stats
In-Reply-To: <4AC0E775.1080108@cs.man.ac.uk>
References: <4AC0E6B3.50405@ebi.ac.uk> <4AC0E775.1080108@cs.man.ac.uk>
Message-ID: <4AC0E87F.2060607@ebi.ac.uk>

Thanks!

Eric

Jiten Bhagat wrote:
> Hi Eric,
>
> Sure! I thought I had already done that but when I looked closely it was
> Thomas who had access. In any case I've added you (through your gmail
> account: ericnzuo at googlemail.com).
>
> Cheers,
> Jits
>
>
> Eric Nzuobontane wrote:
>   
>> Hi Jits,
>>
>> Could you please give us access to the google analytics statistics for
>> BioCatalogue? That way we can see how they compare with the stats
>> collected here at EBI.
>>
>> cheers,
>>
>> Eric
>>     


From tlaurent at ebi.ac.uk  Tue Sep 29 04:44:43 2009
From: tlaurent at ebi.ac.uk (Thomas Laurent)
Date: Tue, 29 Sep 2009 09:44:43 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
In-Reply-To: <d0ee827d0909280630yd7171d8y43f9b7cc2f4e00a6@mail.gmail.com>
References: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>	
	<4AB79D30.1080204@ebi.ac.uk> <4AB8AEA2.1060304@cs.man.ac.uk>
	<d0ee827d0909280630yd7171d8y43f9b7cc2f4e00a6@mail.gmail.com>
Message-ID: <4AC1C8FB.4000603@ebi.ac.uk>

I have inactivated this account in the database.

Cheers,
Thomas

Franck Tanoh wrote:
> Hi guys,
> Katy doesn't use the following account: http://www.biocatalogue.org/users/79
> can you remove it please?
> 
> Franck
> 
> 2009/9/22 Jiten Bhagat <jits at cs.man.ac.uk>:
>> Thomas Laurent wrote:
>>> I have deactivated my extra accounts in the database. They still show
>>> up if we search for them in the UI, but I think next time we'll
>>> reindex the db, they'll disappear.
>> This is actually a bug, thanks for picking it up. I've committed a fix
>> to the codebase (revision 1091) to only index activated users.
>>
>> This needs testing on the test server.
>>
>> Jits
>>
>>
>>> Thomas
>>>
>>> Franck Tanoh wrote:
>>>> here is the list:
>>>>
>>>> kwolstencroft
>>>> kwolstencroft
>>>>
>>>> tlaurent
>>>> th.laurent
>>>> tlaurent
>>>>
>>>> rodrigoluk
>>>> Rodrigo Lopez
>>>>
>>>> I'll check with Katy the one she's currently using; Thomas-you can
>>>> remove one of the duplicated name or just change the display name.
>>>> Rodrigo's one seems ok for me. People are allow to have more than 1
>>>> account, aren't they?
>>>>
>>>> Franck
>>>>
>>> _______________________________________________
>>> BioCatalogue-developers mailing list
>>> BioCatalogue-developers at rubyforge.org
>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
> 
> 
> 

From ytanoh at cs.man.ac.uk  Tue Sep 29 04:51:32 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 29 Sep 2009 09:51:32 +0100
Subject: [BioCatalogue-developers] Google Analytics stats
In-Reply-To: <4AC0E775.1080108@cs.man.ac.uk>
References: <4AC0E6B3.50405@ebi.ac.uk> <4AC0E775.1080108@cs.man.ac.uk>
Message-ID: <d0ee827d0909290151o54256d93jc4576548139c0396@mail.gmail.com>

Can  I have access too pls ?
my gmail account: franck at mygrid.org.uk

cheers,

Franck

2009/9/28 Jiten Bhagat <jits at cs.man.ac.uk>:
> Hi Eric,
>
> Sure! I thought I had already done that but when I looked closely it was
> Thomas who had access. In any case I've added you (through your gmail
> account: ericnzuo at googlemail.com).
>
> Cheers,
> Jits
>
>
> Eric Nzuobontane wrote:
>> Hi Jits,
>>
>> Could you please give us access to the google analytics statistics for
>> BioCatalogue? That way we can see how they compare with the stats
>> collected here at EBI.
>>
>> cheers,
>>
>> Eric
>
> _______________________________________________
> BioCatalogue-developers mailing list
> BioCatalogue-developers at rubyforge.org
> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From ytanoh at cs.man.ac.uk  Tue Sep 29 04:53:05 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 29 Sep 2009 09:53:05 +0100
Subject: [BioCatalogue-developers] member with more than 1 account ....
In-Reply-To: <4AC1C8FB.4000603@ebi.ac.uk>
References: <d0ee827d0909210803g52bc38d1q19b8edc5ddb43949@mail.gmail.com>
	<4AB79D30.1080204@ebi.ac.uk> <4AB8AEA2.1060304@cs.man.ac.uk>
	<d0ee827d0909280630yd7171d8y43f9b7cc2f4e00a6@mail.gmail.com>
	<4AC1C8FB.4000603@ebi.ac.uk>
Message-ID: <d0ee827d0909290153i6dedfdb1l48f27459e77c7bba@mail.gmail.com>

Thanks Thomas,

Franck

2009/9/29 Thomas Laurent <tlaurent at ebi.ac.uk>:
> I have inactivated this account in the database.
>
> Cheers,
> Thomas
>
> Franck Tanoh wrote:
>>
>> Hi guys,
>> Katy doesn't use the following account:
>> http://www.biocatalogue.org/users/79
>> can you remove it please?
>>
>> Franck
>>
>> 2009/9/22 Jiten Bhagat <jits at cs.man.ac.uk>:
>>>
>>> Thomas Laurent wrote:
>>>>
>>>> I have deactivated my extra accounts in the database. They still show
>>>> up if we search for them in the UI, but I think next time we'll
>>>> reindex the db, they'll disappear.
>>>
>>> This is actually a bug, thanks for picking it up. I've committed a fix
>>> to the codebase (revision 1091) to only index activated users.
>>>
>>> This needs testing on the test server.
>>>
>>> Jits
>>>
>>>
>>>> Thomas
>>>>
>>>> Franck Tanoh wrote:
>>>>>
>>>>> here is the list:
>>>>>
>>>>> kwolstencroft
>>>>> kwolstencroft
>>>>>
>>>>> tlaurent
>>>>> th.laurent
>>>>> tlaurent
>>>>>
>>>>> rodrigoluk
>>>>> Rodrigo Lopez
>>>>>
>>>>> I'll check with Katy the one she's currently using; Thomas-you can
>>>>> remove one of the duplicated name or just change the display name.
>>>>> Rodrigo's one seems ok for me. People are allow to have more than 1
>>>>> account, aren't they?
>>>>>
>>>>> Franck
>>>>>
>>>> _______________________________________________
>>>> BioCatalogue-developers mailing list
>>>> BioCatalogue-developers at rubyforge.org
>>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>>
>>
>>
>>
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From jits at cs.man.ac.uk  Tue Sep 29 05:00:31 2009
From: jits at cs.man.ac.uk (Jiten Bhagat)
Date: Tue, 29 Sep 2009 10:00:31 +0100
Subject: [BioCatalogue-developers] Google Analytics stats
In-Reply-To: <d0ee827d0909290151o54256d93jc4576548139c0396@mail.gmail.com>
References: <4AC0E6B3.50405@ebi.ac.uk> <4AC0E775.1080108@cs.man.ac.uk>
	<d0ee827d0909290151o54256d93jc4576548139c0396@mail.gmail.com>
Message-ID: <4AC1CCAF.8060707@cs.man.ac.uk>

Sure thing Franck. Done. You can now login with your Google Account to
Google Analytics and you should see the BioCatalogue there.

Cheers,
Jits


Franck Tanoh wrote:
> Can  I have access too pls ?
> my gmail account: franck at mygrid.org.uk
>
> cheers,
>
> Franck
>
> 2009/9/28 Jiten Bhagat <jits at cs.man.ac.uk>:
>   
>> Hi Eric,
>>
>> Sure! I thought I had already done that but when I looked closely it was
>> Thomas who had access. In any case I've added you (through your gmail
>> account: ericnzuo at googlemail.com).
>>
>> Cheers,
>> Jits
>>
>>
>> Eric Nzuobontane wrote:
>>     
>>> Hi Jits,
>>>
>>> Could you please give us access to the google analytics statistics for
>>> BioCatalogue? That way we can see how they compare with the stats
>>> collected here at EBI.
>>>
>>> cheers,
>>>
>>> Eric
>>>       
>> _______________________________________________
>> BioCatalogue-developers mailing list
>> BioCatalogue-developers at rubyforge.org
>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers
>>
>>     
>
>
>
>   


From ericnzuo at ebi.ac.uk  Tue Sep 29 08:36:49 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 29 Sep 2009 13:36:49 +0100
Subject: [BioCatalogue-developers] version dependencies in test scripts
Message-ID: <4AC1FF61.5050409@ebi.ac.uk>

Hi Steve,

As I was going through the test scripts from the embrace registry, I 
realized that some perl scripts do not run against certain versions of  
XML::Compile::WSDL11 library.  Could you advise what version of the 
library runs on the embrace registry test box? Are you aware of any 
other version dependencies? If you have that kind of information, it 
would be nice if you could share as it will help me be more efficient in 
setting up the environment for running the test scripts.

cheers,

Eric


From ericnzuo at ebi.ac.uk  Tue Sep 29 10:57:37 2009
From: ericnzuo at ebi.ac.uk (Eric Nzuobontane)
Date: Tue, 29 Sep 2009 15:57:37 +0100
Subject: [BioCatalogue-developers] version dependencies in test scripts
In-Reply-To: <0DF7750A-92FC-4D4D-8DA7-CF04B1E1AF81@manchester.ac.uk>
References: <4AC1FF61.5050409@ebi.ac.uk>
	<0DF7750A-92FC-4D4D-8DA7-CF04B1E1AF81@manchester.ac.uk>
Message-ID: <4AC22061.1050102@ebi.ac.uk>

Thanks Steve!
If you run this little perl script, it should make it clearer what xml 
modules & versions are available

perl -MFile::Find=find -MFile::Spec::Functions -lwe 'find { wanted => 
sub { print canonpath $_ if /\.pm\z/ }, no_chdir => 1 }, @INC' | grep XML


Example

/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Util.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Iterator.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Translate.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema/Specs.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema/Instance.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema/BuiltInTypes.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema/NameSpaces.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Schema/BuiltInFacets.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Translate/Writer.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Translate/Template.pm
/usr/lib/perl5/vendor_perl/5.8.8/XML/Compile/Translate/Reader.pm




Steve Pettifer wrote:
> Here's a list of all the stuff installed (XML compile is part of 
> XML-parser I believe)
>
> Python:
> - PyXML 0.8.4
> - SOAPpy 0.12.0
> - ZSI 2.1-a1
> - fpconst 0.7.2
>
> Perl:
> Archive-Tar      [0.072  ] module for manipulation of tar archives.
> Compress-Zlib    [1.08   ] Interface to zlib compression library
> Digest-MD5       [2.11   ] Perl interface to the MD5 Algorithm
> File-CounterFile [0.12   ] Persistent counter class
> Font-AFM         [1.18   ] Interface to Adobe Font Metrics files
> HTML-Parser      [3.19   ] SGML parser class
> HTML-Tagset      [3.03   ] Data tables useful in parsing HTML
> HTML-Tree        [3.11   ] HTML syntax tree builder
> MIME-Base64      [2.11   ] Encoding and decoding of base64 strings
> PPM              [2.1.9  ] Perl Package Manager: locate, install, upgrade
>                           software packages.
> SOAP-Lite        [0.46   ] Library for Simple Object Access Protocol 
> (SOAP)
>                           clients and servers in Perl
> URI              [1.11   ] Uniform Resource Identifiers (absolute and 
> relative)
> XML-Element      [1.07   ] Base element class for XML elements
> XML-Parser       [2.27   ] A Perl module for parsing XML documents
> libnet           [1.07.03] Collection of Network protocol modules
> libwin32         [0.17.2 ] A collection of extensions that aims to provide
>                           comprehensive access to the Windows API.
> libwww-perl      [5.51   ] Library for WWW access in Perl
>
>
>
> 2009/9/29 Steve Pettifer <steve.pettifer at manchester.ac.uk 
> <mailto:steve.pettifer at manchester.ac.uk>>:
>> ... for both python and perl please
>>
>> Ta
>>
>> Steve
>>
>>
>
>
> On 29 Sep 2009, at 13:36, Eric Nzuobontane wrote:
>
>> Hi Steve,
>>
>> As I was going through the test scripts from the embrace registry, I 
>> realized that some perl scripts do not run against certain versions 
>> of  XML::Compile::WSDL11 library.  Could you advise what version of 
>> the library runs on the embrace registry test box? Are you aware of 
>> any other version dependencies? If you have that kind of information, 
>> it would be nice if you could share as it will help me be more 
>> efficient in setting up the environment for running the test scripts.
>>
>> cheers,
>>
>> Eric
>>
>>
>


From ytanoh at cs.man.ac.uk  Tue Sep 29 11:02:33 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 29 Sep 2009 16:02:33 +0100
Subject: [BioCatalogue-developers] need some name for biocat jamboree
Message-ID: <d0ee827d0909290802p700c2b83jcf603a5b60b69167@mail.gmail.com>

Hi,

I want to invite one or 2 persons from the EBI for the annotation
jamboree on Nov 27.
Any suggestion please?

cheers,
Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From rls at ebi.ac.uk  Tue Sep 29 11:17:01 2009
From: rls at ebi.ac.uk (Rodrigo Lopez)
Date: Tue, 29 Sep 2009 16:17:01 +0100
Subject: [BioCatalogue-developers] need some name for biocat jamboree
In-Reply-To: <d0ee827d0909290802p700c2b83jcf603a5b60b69167@mail.gmail.com>
References: <d0ee827d0909290802p700c2b83jcf603a5b60b69167@mail.gmail.com>
Message-ID: <4AC224ED.5030808@ebi.ac.uk>

List of potential contacts:

Bruno Aranda: baranda at ebi.ac.uk
Ying Cheng: ycheng at ebi.ac.uk
Phil Jones: pjones at ebi.ac.uk
Richard Cote: rcote at ebi.ac.uk
Alan Horne: hornead at ebi.ac.uk
Chen Li: chenli at ebi.ac.uk
Mahmut Uludag: uludag at ebi.ac.uk
Misha Kapushesky: ostolop at ebi.ac.uk
Paula de Matos: pmatos at ebi.ac.uk
Sam Patient: spatient at ebi.ac.uk

Note: Some of the above are coordinators and the invitation should imply 
that if they cannot attend themselves, then to nominate someone. I'd be 
surprised if you get more than 3 positive replies for the initial 
jamboree. People are *very* busy these days...

R:)

Franck Tanoh wrote:
> Hi,
> 
> I want to invite one or 2 persons from the EBI for the annotation
> jamboree on Nov 27.
> Any suggestion please?
> 
> cheers,
> Franck
> 

From ytanoh at cs.man.ac.uk  Tue Sep 29 11:29:52 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Tue, 29 Sep 2009 16:29:52 +0100
Subject: [BioCatalogue-developers] need some name for biocat jamboree
In-Reply-To: <4AC224ED.5030808@ebi.ac.uk>
References: <d0ee827d0909290802p700c2b83jcf603a5b60b69167@mail.gmail.com>
	<4AC224ED.5030808@ebi.ac.uk>
Message-ID: <d0ee827d0909290829y2e56c89aw1156e42fb429d15@mail.gmail.com>

Thanks,

Franck



2009/9/29 Rodrigo Lopez <rls at ebi.ac.uk>:
> List of potential contacts:
>
> Bruno Aranda: baranda at ebi.ac.uk
> Ying Cheng: ycheng at ebi.ac.uk
> Phil Jones: pjones at ebi.ac.uk
> Richard Cote: rcote at ebi.ac.uk
> Alan Horne: hornead at ebi.ac.uk
> Chen Li: chenli at ebi.ac.uk
> Mahmut Uludag: uludag at ebi.ac.uk
> Misha Kapushesky: ostolop at ebi.ac.uk
> Paula de Matos: pmatos at ebi.ac.uk
> Sam Patient: spatient at ebi.ac.uk
>
> Note: Some of the above are coordinators and the invitation should imply
> that if they cannot attend themselves, then to nominate someone. I'd be
> surprised if you get more than 3 positive replies for the initial jamboree.
> People are *very* busy these days...
>
> R:)
>
> Franck Tanoh wrote:
>>
>> Hi,
>>
>> I want to invite one or 2 persons from the EBI for the annotation
>> jamboree on Nov 27.
>> Any suggestion please?
>>
>> cheers,
>> Franck
>>
>



-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur

From ytanoh at cs.man.ac.uk  Wed Sep 30 07:00:27 2009
From: ytanoh at cs.man.ac.uk (Franck Tanoh)
Date: Wed, 30 Sep 2009 12:00:27 +0100
Subject: [BioCatalogue-developers] new terms and conditions
Message-ID: <d0ee827d0909300400g7e976bb5xc869b9d45815db81@mail.gmail.com>

Hi guys,
please, do update our terms and conditions when doing the next release.

cheers,
Franck

-- 
 "Science knows no country, because knowledge belongs to humanity, and
is the torch which illuminates the world." - Louis Pasteur