BioCocoa is an open source OpenStep (GNUstep/Cocoa) framework for bioinformatics written in Objective-C. We intend to provide OpenStep programmers with a full suite of tools for handling and manipulating biological sequences. OpenStep is a great framework for rapid application development and it is therefore often used to create innovative bioscientific apps. To speed up development even more, BioCocoa wants to offer reusable OpenStep classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa includes:
- A set of model objects to represent biological sequences that are both easy to use, yet very powerful and lightweight.
- I/O classes to import and export sequences to and from a variety of commonly used formats including BEAST, Clustal, EMBL, Fasta, GCG-MSF, GDE, Hennig86, NCBI, NEXUS, NONA, PDB, Phylip, PIR, Plain/Raw, Swiss-Prot and TNT.
- Tools to manipulate and obtain information about sequences.
- Efficient caching so that large sequences maintained in files can be analyzed without loading them all into memory.
- Parsing classes for other biological data such as microarray gene expression, biomedical ontologies and metabolic models.
- An NSTextView based class to display sequences.
- BioCocoa can be used to create applications Apple Mac OSX using Cocoa, and on Linux and Windows using GNUstep.
The BioCocoa project is continually expanding. It consists of two major parts: BCFoundation and BCAppKit. BCFoundation provides the non-GUI classes while BCAppKit provides GUI classes, thus allowing both command-line utility programs and graphically-based applications to be developed.
BioCocoa 2.0 is a completely new framework structure that consists of BCFoundation and BCAppKit. BCFoundation introduces new classes, such as BCSequence, which form the basis for the rest of the framework. All functionality that was in BioCocoa 1.x has been or will be moved to this new structure. Version 2.0 includes:
BioCocoa 1.x was the original version of the framework, developed by Peter Schols. This framework contains classes for sequence I/O, fetching sequences from Entrez and displaying them. This 1.x version of the framework represents sequences as strings. You can find this version of the framework in in source repository under Tags/1.7.
Bio Cocoa | Edit Page | Page History | Recent Changes | (All) | Powered by PmWiki
Page last modified on February 18, 2011, at 05:33 PM