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From mekentosj at gmail.com  Sun Jan 27 20:25:18 2008
From: mekentosj at gmail.com (Alexander Griekspoor)
Date: Mon, 28 Jan 2008 01:25:18 +0000
Subject: [Biococoa-dev] [BiO Mail] BioCocoa, Leopard etc
In-Reply-To: <E1JIoLc-0008Vq-QL@dallas0.bioinformatics.org>
References: <E1JIoLc-0008Vq-QL@dallas0.bioinformatics.org>
Message-ID: <95E00BE9-10E3-4B7D-B82B-8E604D8B72AE@gmail.com>

Hi Peter,

Unfortunately the BioCocoa project is no longer (very) active due to a  
lack of time and to some extent need by the core developers. That  
doesn't mean it's completely dead but what is missing is one or two  
people who very actively like to push the project forward and which  
have a need for a BioCocoa framework and the time to develop it. So  
for instance it's indeed not pushed forward to 10.5, but you should be  
easily able to checkout the project change the target SDK to 10.4 or  
10.5 in XCode.

I don't know what formats Vector NTI support, and what it is you wish  
to convert exactly. We have a simple GCK read method but it only takes  
the sequence (not the vector map). Since the GCK file format is closed  
(and binary) it won't be easy to get all data out that you might wish,  
unless you're only interested in the raw sequence.

If you are still interested Koen should probably be able to help you  
out with the CVS issue.

Finally, regarding 4Peaks and contigs, we'd love to do that one day if  
time permits, we'll do our best.
Best wishes,
Alex & Tom
Mek & Tosj

On 26 jan 2008, at 16:57, Peter Ulvskov wrote:

> ----------------------------------------------------------------------------
> The following message was sent to you via the Bioinformatics.Org  
> email form.
> The sender is user Peter Ulvskov <p.ulvskov at dias.kvl.dk>.
> To report abuse, please forward this message to <abuse at bioinformatics.org 
> >.
> ----------------------------------------------------------------------------
> Dear Alexander,
>
> I hope that you can spare the time for a few questions:
>
> I have signed up at bioinformatics.org because of BioCocoa. My new
> username/password works fine for login, but I am rejected when I do  
> this:
> export CVSROOT=':ext:Ulvskov at bioinformatics.org:/cvsroot'
> cvs checkout BioCocoa -P
> ...and enter my password
> Does it take more than signing up at bioinformatics.org to download
> BioCocoa?
>
> I then did the download manually, and got the 10.3.9 SDK error,  
> which raises
> the question whether BioCocoa is an active project? Are efforts  
> being made at
> moving BioCocoa forward to 10.5? What does it entail changing the  
> SDK to
> Leopard (in other words, can I do this myself)?
>
> Finally, the problem I wanted to solve using BioCocoa is writing a  
> file
> conversion utility which will convert Gene Construction Kit files to  
> Vector NTI
> files. Is it correct that BioCocoa will help me get there?
>
> By the way, one of the reasons why Vector NTI is making its way into  
> the lab
> (under Windows XP (ouch!) on our Intel Macs) is the need for a contig
> assembly program. Judging from your FAQ-page at Mekentosj, this is  
> one of
> the most frequently requested features for 4Peaks. Any chance that  
> you will
> be swayed by the prayers?
>
> Thanks for your time, best regards,
>
> Peter
>
> (My Bioinformatics.Org username is Ulvskov.)
>
>
> __________________________________________________
> D O T E A S Y - "Join the web hosting revolution!"
>             http://www.doteasy.com

**********************************************
          ** Alexander Griekspoor  PhD **
**********************************************
           mekentosj.com

            EnzymeX - To cut or not to cut
  2006 Winner of the Apple Design Awards
          Best Mac OS X Scientific Solution
        http://www.mekentosj.com/enzymex
**********************************************



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From kvddrift at earthlink.net  Sun Jan 27 21:04:36 2008
From: kvddrift at earthlink.net (Koen van der Drift)
Date: Sun, 27 Jan 2008 21:04:36 -0500
Subject: [Biococoa-dev] [BiO Mail] BioCocoa, Leopard etc
In-Reply-To: <95E00BE9-10E3-4B7D-B82B-8E604D8B72AE@gmail.com>
References: <E1JIoLc-0008Vq-QL@dallas0.bioinformatics.org>
	<95E00BE9-10E3-4B7D-B82B-8E604D8B72AE@gmail.com>
Message-ID: <D898B343-2F37-4754-9266-8352B981F857@earthlink.net>

Hi Peter,

I'm not sure about the cvs error, but we've switched to using svn, see  
instructions here on how to get the source code from the repository:

http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.UsingSubversion

As Alex explained, there is not much activity going on with BioCocoa  
right now, but new blood is always welcome!  I've also included Peter  
Schols's name, since he was the original developer of BioCocoa, and  
may be able to help you out with your cvs errors.

cheers,

- Koen



On Jan 27, 2008, at 8:25 PM, Alexander Griekspoor wrote:

> Hi Peter,
>
> Unfortunately the BioCocoa project is no longer (very) active due to  
> a lack of time and to some extent need by the core developers. That  
> doesn't mean it's completely dead but what is missing is one or two  
> people who very actively like to push the project forward and which  
> have a need for a BioCocoa framework and the time to develop it. So  
> for instance it's indeed not pushed forward to 10.5, but you should  
> be easily able to checkout the project change the target SDK to 10.4  
> or 10.5 in XCode.
>
> I don't know what formats Vector NTI support, and what it is you  
> wish to convert exactly. We have a simple GCK read method but it  
> only takes the sequence (not the vector map). Since the GCK file  
> format is closed (and binary) it won't be easy to get all data out  
> that you might wish, unless you're only interested in the raw  
> sequence.
>
> If you are still interested Koen should probably be able to help you  
> out with the CVS issue.
>
> Finally, regarding 4Peaks and contigs, we'd love to do that one day  
> if time permits, we'll do our best.
> Best wishes,
> Alex & Tom
> Mek & Tosj
>
> On 26 jan 2008, at 16:57, Peter Ulvskov wrote:
>
>> ----------------------------------------------------------------------------
>> The following message was sent to you via the Bioinformatics.Org  
>> email form.
>> The sender is user Peter Ulvskov <p.ulvskov at dias.kvl.dk>.
>> To report abuse, please forward this message to <abuse at bioinformatics.org 
>> >.
>> ----------------------------------------------------------------------------
>> Dear Alexander,
>>
>> I hope that you can spare the time for a few questions:
>>
>> I have signed up at bioinformatics.org because of BioCocoa. My new
>> username/password works fine for login, but I am rejected when I do  
>> this:
>> export CVSROOT=':ext:Ulvskov at bioinformatics.org:/cvsroot'
>> cvs checkout BioCocoa -P
>> ...and enter my password
>> Does it take more than signing up at bioinformatics.org to download
>> BioCocoa?
>>
>> I then did the download manually, and got the 10.3.9 SDK error,  
>> which raises
>> the question whether BioCocoa is an active project? Are efforts  
>> being made at
>> moving BioCocoa forward to 10.5? What does it entail changing the  
>> SDK to
>> Leopard (in other words, can I do this myself)?
>>
>> Finally, the problem I wanted to solve using BioCocoa is writing a  
>> file
>> conversion utility which will convert Gene Construction Kit files  
>> to Vector NTI
>> files. Is it correct that BioCocoa will help me get there?
>>
>> By the way, one of the reasons why Vector NTI is making its way  
>> into the lab
>> (under Windows XP (ouch!) on our Intel Macs) is the need for a contig
>> assembly program. Judging from your FAQ-page at Mekentosj, this is  
>> one of
>> the most frequently requested features for 4Peaks. Any chance that  
>> you will
>> be swayed by the prayers?
>>
>> Thanks for your time, best regards,
>>
>> Peter
>>
>> (My Bioinformatics.Org username is Ulvskov.)
>>
>>
>> __________________________________________________
>> D O T E A S Y - "Join the web hosting revolution!"
>>             http://www.doteasy.com
>
> **********************************************
>          ** Alexander Griekspoor  PhD **
> **********************************************
>           mekentosj.com
>
>            EnzymeX - To cut or not to cut
>  2006 Winner of the Apple Design Awards
>          Best Mac OS X Scientific Solution
>        http://www.mekentosj.com/enzymex
> **********************************************
>
>
>




From info at orbicule.com  Mon Jan 28 05:32:25 2008
From: info at orbicule.com (Peter Schols)
Date: Mon, 28 Jan 2008 11:32:25 +0100
Subject: [Biococoa-dev] [BiO Mail] BioCocoa, Leopard etc
In-Reply-To: <D898B343-2F37-4754-9266-8352B981F857@earthlink.net>
References: <E1JIoLc-0008Vq-QL@dallas0.bioinformatics.org>
	<95E00BE9-10E3-4B7D-B82B-8E604D8B72AE@gmail.com>
	<D898B343-2F37-4754-9266-8352B981F857@earthlink.net>
Message-ID: <82220FC6-9C94-4A99-BE9A-F7382E3BE6F0@orbicule.com>

Hi Peter,

Good to see some activity on the BioCocoa list!

As far as I know, CVS can no longer be used to get access to the  
latest version of BioCocoa.
You should use SVN to get at the latest source code.

Best wishes,

Peter




On 28 Jan 2008, at 03:04, Koen van der Drift wrote:

> Hi Peter,
>
> I'm not sure about the cvs error, but we've switched to using svn, see
> instructions here on how to get the source code from the repository:
>
> http://www.bioinformatics.org/biococoa/wiki/pmwiki.php?n=Main.UsingSubversion
>
> As Alex explained, there is not much activity going on with BioCocoa
> right now, but new blood is always welcome!  I've also included Peter
> Schols's name, since he was the original developer of BioCocoa, and
> may be able to help you out with your cvs errors.
>
> cheers,
>
> - Koen
>
>
>
> On Jan 27, 2008, at 8:25 PM, Alexander Griekspoor wrote:
>
>> Hi Peter,
>>
>> Unfortunately the BioCocoa project is no longer (very) active due to
>> a lack of time and to some extent need by the core developers. That
>> doesn't mean it's completely dead but what is missing is one or two
>> people who very actively like to push the project forward and which
>> have a need for a BioCocoa framework and the time to develop it. So
>> for instance it's indeed not pushed forward to 10.5, but you should
>> be easily able to checkout the project change the target SDK to 10.4
>> or 10.5 in XCode.
>>
>> I don't know what formats Vector NTI support, and what it is you
>> wish to convert exactly. We have a simple GCK read method but it
>> only takes the sequence (not the vector map). Since the GCK file
>> format is closed (and binary) it won't be easy to get all data out
>> that you might wish, unless you're only interested in the raw
>> sequence.
>>
>> If you are still interested Koen should probably be able to help you
>> out with the CVS issue.
>>
>> Finally, regarding 4Peaks and contigs, we'd love to do that one day
>> if time permits, we'll do our best.
>> Best wishes,
>> Alex & Tom
>> Mek & Tosj
>>
>> On 26 jan 2008, at 16:57, Peter Ulvskov wrote:
>>
>>> ----------------------------------------------------------------------------
>>> The following message was sent to you via the Bioinformatics.Org
>>> email form.
>>> The sender is user Peter Ulvskov <p.ulvskov at dias.kvl.dk>.
>>> To report abuse, please forward this message to <abuse at bioinformatics.org
>>>> .
>>> ----------------------------------------------------------------------------
>>> Dear Alexander,
>>>
>>> I hope that you can spare the time for a few questions:
>>>
>>> I have signed up at bioinformatics.org because of BioCocoa. My new
>>> username/password works fine for login, but I am rejected when I do
>>> this:
>>> export CVSROOT=':ext:Ulvskov at bioinformatics.org:/cvsroot'
>>> cvs checkout BioCocoa -P
>>> ...and enter my password
>>> Does it take more than signing up at bioinformatics.org to download
>>> BioCocoa?
>>>
>>> I then did the download manually, and got the 10.3.9 SDK error,
>>> which raises
>>> the question whether BioCocoa is an active project? Are efforts
>>> being made at
>>> moving BioCocoa forward to 10.5? What does it entail changing the
>>> SDK to
>>> Leopard (in other words, can I do this myself)?
>>>
>>> Finally, the problem I wanted to solve using BioCocoa is writing a
>>> file
>>> conversion utility which will convert Gene Construction Kit files
>>> to Vector NTI
>>> files. Is it correct that BioCocoa will help me get there?
>>>
>>> By the way, one of the reasons why Vector NTI is making its way
>>> into the lab
>>> (under Windows XP (ouch!) on our Intel Macs) is the need for a  
>>> contig
>>> assembly program. Judging from your FAQ-page at Mekentosj, this is
>>> one of
>>> the most frequently requested features for 4Peaks. Any chance that
>>> you will
>>> be swayed by the prayers?
>>>
>>> Thanks for your time, best regards,
>>>
>>> Peter
>>>
>>> (My Bioinformatics.Org username is Ulvskov.)
>>>
>>>
>>> __________________________________________________
>>> D O T E A S Y - "Join the web hosting revolution!"
>>>           http://www.doteasy.com
>>
>> **********************************************
>>        ** Alexander Griekspoor  PhD **
>> **********************************************
>>         mekentosj.com
>>
>>          EnzymeX - To cut or not to cut
>> 2006 Winner of the Apple Design Awards
>>        Best Mac OS X Scientific Solution
>>      http://www.mekentosj.com/enzymex
>> **********************************************
>>
>>
>>
>
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev

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