[Biococoa-dev] Re: New goodies - BCStandaloneReader

Alexander Griekspoor a.griekspoor at nki.nl
Fri Mar 3 05:29:57 EST 2006

Hi Peter,

Nice to hear you're doing so well!

> Wow BioCocoa is back alive, that's great!
Alive is a big word perhaps, still certainly good to hear there's  
still interest!
> Alex and Tom, first of all, congratulations on the new versions of  
> iRNAi and EnzymeX 3 (almost)!
Haha, thanks!
> 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...
Ho ho ho, I just copied those from the BioCocoa website (I was to  
lazy to look it up in the code), guess I have to be ashamed here..
> 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.
Very nice, I kind of made the same decision (software development  
rather than wetlab bio), but in a different way, I'm going to the  
European Bioinformatics Institute to a group who works on  
textmining... ;-) But great to hear that Orbicule goes so well, seems  
you have things organized very well, kudos! Also very cool the  
presentation in the SoHo store, be sure to share some pictures (and  
update your blog a bit more often, just nitpicking ;-)
> 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?
Good plan, I don't have much experience here, but Charles is the king  
(at least in my world ;-)..
Charles perhaps you also want to inform these guys on the project  
you're doing with Drew..
> -  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.
That's awesome, I once had an idea for some BLAST app, which in the  
end wasn't feasible, but perhaps some code/ideas still can be used..
> - 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?
I promised that already, so yes. But first I want to finish EnzymeX  
for the simple reason that I will probably find bugs still in the  
Textview class that can be fixed first. For instance, I now added a  
unit property as it didn't make sense that the textview shows   
166-182 (16bp) while I had 16 aminoacids selected ;-)
> - Later on, it would also be worth discussing CoreData and if/how  
> we could use it in BC.
I still have to dive in that whole thing, soooon ;-)

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

Definitely!! But I'm for sure willing to pay for it as well Peter,  
have been considering to buy a license already...

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                     ** 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

                             iRNAi, do you?


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