Many file formats exist for sequence analysis and phylogenetics. Users of bioinformatics software often expect applications to read all of these file formats. For developers, however, this means, implementing their own I/O methods, a time consuming and error prone task. The disadvantage for end users is that they can be betrayed by inconsistently and incorrectly implemented import and export procedures.
The BioCocoa framework provides developers with the opportunity to add support for reading and writing including BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT files by writing only a few lines of code. The framework is written in Cocoa (Objective-C) and can be used in any Cocoa application, intended for Mac OS X. The framework is licensed under the Creative Commons ShareAlike Attribution and is freely available.
The BioCocoa project is still very much under construction. It consists of two major parts that are - at least for now - two separate code bases.
First of all, there is BioCocoa 1.x which contains classes for sequence I/O, fetching sequences from Entrez and displaying them. This 1.x version of the framework represents sequences as strings.
At the same time, we are working on a completely new framework structure that will consist of BCFoundation and BCAppKit. BCFoundation will introduce new classes, such as BCSequence, which will form the basis for the rest of the framework. You can view the current state of this new framework in the Trunk directory of the Subversion repository.
All functionality that is now in BioCocoa 1.x will be moved to this new structure. If you need this functionality right now, however, we recommend to use the string-based 1.x version.
More information can be found on the BioCocoa website.
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Page last modified on August 02, 2006, at 09:28 AM