[Biococoa-dev] BioCocoa and CoreData

[Koen van der Drift]

Ahhh, the infamous 'killer app'  :)

Yes, using CD for meta data is indeed a good suggestion, and is
something that can be kept outside of the sequence data (which are
basically plain text files in most cases. Core Data could then maybe
be used to store relationships between sequences, group them together
based on various criteria (organism, function), etc etc.

- Koen.



On Mon, May 30, 2011 at 12:21 PM, Scott Christley <schristley at mac.com> wrote:
> Hello Koen,
>
> I don't have much experience with CoreData, but my understanding is that it is simple way to build database-type functionality without requiring the heavy backend database like Mysql or Postgres.  You can manage data (objects) in either a flat file or a local sqlite file.
>
> It isn't clear to me how to use it directly by BioCocoa, but I could imagine its use at the application level.  For example, let's say you had a simple application that manages all of your sequence experiments, so you could use CoreData to save information about sample prep, experimental protocols, etc. as well as maybe information on sequence files names, where they are stored etc.  So CoreData manages the "meta-data" while BioCocoa operates on the sequence data directly.
>
> This actually isn't too far off from the "killer app" I've been wanting to develop, right now all the biologists I know who are doing initial forays into high-throughput sequencing, are all doing ad-hoc workflows for managing data.
>
> cheers
> Scott
>
> On Jun 8, 2009, at 8:26 AM, Koen van der Drift wrote:
>
>> Hi,
>>
>> I haven't been doing a lot of programming in a while, but with the
>> WWDC starting and all the news and twittering around it, I couldn't
>> resist to open up Xcode. One thing I read a lot about recently is Core
>> Data (yes, I know, I'm slow, it's been out for a few years now :-),
>> and at first glance it looks like a very useful technique. So I
>> thought to write a small demo app like a simple sequence editor for
>> BioCocoa that uses CoreData, just as an exercise. The excellent
>> tutorial at MacResearch.org also deals with molecules, so that was
>> promising. But when I thought more about it, I came to the conclusion
>> that an editor is actually not a good example to use with CoreData
>> (please correct me if I'm wrong). It get's more interesting when the
>> app deals with more than one sequence at a time, eg when aligning
>> them, or when dealing with digests from a main sequence. On top of
>> that, if I use BCSequence as an attribute for my Sequence entity, I
>> still need to go to all the BioCocoa classes for I/O, use all the
>> accessors, etc.
>>
>> So, just out of curiosity, I was wondering if anyone has used CoreData
>> in combination with BioCocoa? Should/can BioCocoa be adapted to be
>> more CoreData friendly?
>>
>> cheers,
>>
>> - Koen.
>>
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>
>