[Biococoa-dev] More goodies!!

Peter Schols peter.schols at bio.kuleuven.be
Mon Mar 6 07:33:17 EST 2006

Hi Alex and other listers,

This BCAppkitTest works great and it will be a great addition to  
Over the weekend, I have worked with the - very helpful - people at  
Bioinformatics.org to solve my login problems (it turned out to be a  
proxy issue that was caused by a bug on their end, they have been  
able to fix it).
As a result, I am totally ready to start the subversion repository  
and do the initial import.

The main question I have now is: how should we organise the  
repository and the BioCocoa website? There are several scenarios:

1. Checkout the latest version of the BioCocoa framework from CVS and  
use that as the initial import for SVN. Make the BCAppkitTest  
available as a download on our website (both source and compiled app)  
but wait to put it in the repository until it's adapted to use the  
classes in our own framework.

2. Checkout the latest version of the BioCocoa framework from CVS and  
use that as the initial import for SVN. Make a second repository (I  
think this is possible @ bioinformatics.org) and put BCAppkitTest in  

3. Checkout the latest version of the BioCocoa framework from CVS,  
add the BCAppkitTest somewhere in the hierarchy of that same BioCocoa  
folder and check this hybrid framework in to one repository.

I think I'd prefer solution number 1 (or 2) because
- it seems a bit weird to have part of a framework that does not use  
the base classes available in the rest of the framework
- it might confuse users of the framework
- we should aim to integrate BCAppkitTest into BioCocoa asap, this  
won't be a huge undertaking

Please let me know your preference and I would be glad to create the  
Subversion repository and send instructions on using it. I'd also be  
glad to update the website and make the BCAppkitTest available.


On 06 Mar 2006, at 11:08, Alexander Griekspoor wrote:

> Hi guys,
> With EnzymeX3 now in beta testing phase it's time to share the  
> wealth...
> I've thrown together a very simple demo app showing the three  
> goodies I would like to donate back to the BioCocoa project:
> 	- BCReader, the standalone BCReader classes for sequence file IO  
> (original version Peter Schols)
> 	- EntrezController, a controller plus view for browsing and  
> fetching NCBI's Entrez Database
> 	- KDTextView+, a custom NSTextView for displaying biological  
> sequences (original version Koen van der Drift)
> Download and enjoy at: http://www.mekentosj.com/biococoa/ 
> BCAppkit_Test.dmg
> Of course all feedback and bug reports are welcome (or not  
> depending on how you interpret this sentence ;-)
> Also, coming back to Koen's remark. There are a few things I/we  
> could do.
> First, it would be nice if it had these views mentioned as  
> available on the website and the code given a place on the svn server.
> Second, we could perhaps post a small announcement (few lines) on  
> cocoa-dev to notify other cocoa developers, also letting them know  
> about BioCocoa again.
> Finally, we could compose a little message to MacResearch  
> describing the BioCocoa project and also the availability of this  
> code.
> Alternatively, I can inform them about it when we release the  
> EnzymeX final version. I believe Tom spoke a few times with the  
> guys behind MacResearch, so we could inform them directly.. Let me  
> know what you guys think.
> Cheers,
> Alex
> *********************************************************
>                     ** Alexander Griekspoor **
> *********************************************************
>               The Netherlands Cancer Institute
>               Department of Tumorbiology (H4)
>          Plesmanlaan 121, 1066 CX, Amsterdam
>                    Tel:  + 31 20 - 512 2023
>                   Fax:  + 31 20 - 512 2029
>                   AIM: mekentosj at mac.com
>                  E-mail: a.griekspoor at nki.nl
>               Web: http://www.mekentosj.com
>               4Peaks - For Peaks, Four Peaks.
>        2004 Winner of the Apple Design Awards
>                Best Mac OS X Student Product
>              http://www.mekentosj.com/4peaks
> *********************************************************
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