[Biococoa-dev] hello!

Julian Blow j.j.blow at dundee.ac.uk
Fri Feb 4 09:02:15 EST 2005

Dear Biococoa-dev Subscribers,

just a quick word to let you know I've added myself to the mailing 
list as suggested by Koen. I'll keep an eye on what's going on, and 
will contribute if and when I think I can add something.



>Dear Julian,
>Thanks for your reply. Too bad you don't have enough time right now 
>to join the development of BioCocoa - I completely understand it 
>though, all current developers work on BioCocoa on the side. So 
>either solution you suggested works fine for me. An alternative 
>could be for you to for now only join the mailing list. This way you 
>get an idea of the current developments in the project, and you can 
>jump in in case there is a subject that is in your field. But it is 
>completely up to you.
>- Koen.
>On Jan 31, 2005, at 7:28 AM, Julian Blow wrote:
>>Dear Koen
>>I've had a look at what you're up to, and I think it sounds very 
>>worthwhile. I'd be keen to support and help your project if I 
>>could. However, I don't think I'd be much help in doing coding at 
>>present. The main problem is that programming is only a sideline 
>>for me (it has to be squeezed into my 'spare time' either late at 
>>night or early in the morning) and most of my energy is directed to 
>>running my lab. I already have two major software projects I'm 
>>committed to at present; I guess these will take up most of my 
>>coding time for the next 6 months at least.
>>So what should I do? I'm happy to join if it would help you, but I 
>>really would not be active, at least not until I've finished my 
>>other projects. Alternatively, I could leave you my goodwill, and 
>>you could contact me should you need anything you think I could 
>>specifically help with, or I could contact you when my current 
>>projects are done and I have coding time on my hands.
>>>Dear Julian,
>>>I found your name on the CocoaDev mailing list. I am one of the 
>>>core developers of the BioCocoa project, an open source Cocoa 
>>>framework for reading, writing, and manipulating various 
>>>biological sequences. Originally the framework only focused on 
>>>reading and writing sequences, and was also aimed at GNUStep, 
>>>which is still the official version that you can download from the 
>>>website at http://bioinformatics.org/biococoa/. A few months ago a 
>>>couple of mac loving bioscientists joined the project, and it was 
>>>transformed in a Cocoa-only framework, and extended to be able to 
>>>do other things with sequences than reading and writing. You could 
>>>say that it is trying to be the Cocoa/ObjC sibling of BioJava, 
>>>BioPerl, etc.
>>>So far we have created a set of new classes, that we believe 
>>>should be a solid base for extending the whole framework. However, 
>>>we still have many discussions  what would be the best design. For 
>>>instance, currently we have a core class BCSequence, with various 
>>>subclasses for DNA, RNA, and proteins. We have had many 
>>>discussions whether we actually should subclass BCSequence 
>>>(compare eg BioJava which doesn't subclass it's main sequence 
>>>class). As an alternative, recently we have been discussing if 
>>>maybe we should use the class cluster design for the various 
>>>sequence classes,
>>>At the moment we are only a small group of developers, mainly with 
>>>a scientific background. Based on the description on the CocoaDev 
>>>webpage, it seems you could be a valuable addition to the BioCocoa 
>>>project. So we were wondering if you would be interested in 
>>>joining the development team, and the discussions on our mailing 
>>>list (see http://bioinformatics.org/project/?group_id=318 for more 
>>>info). To download the source code from CVS, please follow these 
>>>* First, log in by typing the following. When prompted for the 
>>>password, just press Enter.
>>>cvs -d:pserver:anonymous at bioinformatics.org:/cvsroot login
>>>* Then, type the following to download the project:
>>>cvs -d:pserver:anonymous at bioinformatics.org:/cvsroot checkout -P BioCocoa
>>>Feel free to have a look at the code and the current discussions, 
>>>and let me or one of the other developers know if you are 
>>>interested. We look forward to your reply,
>>>On behalf of the BioCocoa Team,
>>>Best regards,
>>>Koen van der Drift

Prof. J. Julian Blow, FRSE
Cancer Research UK Chromosome Replication Research Group
Wellcome Trust Biocentre, University of Dundee
Dow Street, Dundee  DD1 5EH, Scotland, UK
Tel: (+44) (0)1382-345797    Fax: (+44) (0)1382-348072
E-mail: j.j.blow at dundee.ac.uk

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