[Biococoa-dev] Re: New goodies - BCStandaloneReader

Peter Schols peter.schols at bio.kuleuven.be
Fri Mar 3 05:16:19 EST 2006

Wow BioCocoa is back alive, that's great!

Alex and Tom, first of all, congratulations on the new versions of  
iRNAi and EnzymeX 3 (almost)!
The extended BCReader class is fantastic. I think everyone will agree  
with Koen's comment that we could easily incorporate this into the  
main BioCocoa project, just by switching to a BCSequenceArray  
(although I can understand why Alex did not change this for use in  
his apps).
As far as I can see from the BCReader code, Alex did not only add the  
DNAStrider and GCK formats, he also incorporated my "GNUStep code"  
for reading Hennig, TNT, ... files, which is great as well ;-)
I promised to do this almost a year ago, but still had not done it -  
shame on me...

The KDTextView is awesome! It looks already very polished to me (I  
like the fancy overlays showing position and selection, those are  
brilliant). This is exactly what I need for a small in-house project  
I'm planning to do for my former lab.

A bit on my own situation (feel free to skip this paragraph): I  
stopped working at the university of Leuven on January 1st 2006 and  
founded Orbicule, my own 'software company' (sounds too big because  
right now it's just me). I finally figured out that writing software  
and designing apps is really what I want to do.
Right now, I'm working on consumer software such as Undercover  
(because I really like to do consumer software and because it's a  
good way to start the company) but I'm also planning to continue  
writing science-related applications such as iMap. And finally - to  
come back to BioCocoa - I'm planning to do some BioCocoa-work again.  
I will be presenting Undercover at the SoHo Apple store in NY later  
this month so things will be quite busy until then. Starting in  
April, I will have more time to work on BioCocoa.

I have been thinking about BioCocoa and this is what I think we could  
do next:
- First of all, we should move to SVN.
I'm running my own in-house Subversion server on a Mac OS X machine  
for almost two years now and it is not even in the same league when  
compared to CVS. Moving to SVN would be great for several reasons  
(better support for binary files (nibs!), easier to create branches,  
great svnx front-end for Mac OS X, better Xcode integration, ...),  
and it will definitely encourage us to submit more to the repository.  
Since bioinformatics.org recently announced support for svn, I'm  
willing to move the project to svn. The only problem is that I can't  
login on the Bioinformatics.org homepage. I always get the not logged  
in error message. I have tried several things in 3 different  
browsers, but always the same error... could someone verify this with  
their account?

-  I have to enhance and cleanup my BLAST and Entrez classes and add  
them to BioCocoa.
I have a working demo app in which you can do a BLAST query on the  
Net and get results in an NSTableView with only 3 lines of code. I'll  
need to incorporate more BLAST settings into this BLAST classes  
though to increase usefulness.

- During some tests of the BLAST classes with ObjectAlloc (don't ask  
me why) I noticed what could be a memory leak in BCSequence. I was in  
a hurry back then (it was right before WWDC) but I'll do some more  
testing and see if it's still there ;-)

- As Koen suggested, we should move the BCReader code into the main  
project and switch to BCSequenceArray. Koen proposed to do this and  
that would be great! I'm always willing to help.

- Koen and Alex, any chance you will be donating the KDTextView to  
the project?

- Later on, it would also be worth discussing CoreData and if/how we  
could use it in BC.

These are just a few thoughts, I'm sure many of you have their own to- 
do lists and plans. Feel free to comment!


PS: If anybody is interested in a license key for Undercover, please  
drop me a line

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