Introduction

BioCocoa is an open source Cocoa framework for bioinformatics written in Objective-C. We intend to provide Cocoa programmers with a full suite of tools for handling and manipulating biological sequences. Cocoa 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 Cocoa classes that are specific for molecular biology and biofinformatics. At this time, BioCocoa offers model classes for biological sequences, controller classes for alignment, sequence manipulation and I/O, interfacing with ENTREZ and view classes that let you easily display and work with sequences in your own applications.

BioCocoa at WWDC 2006

BioCocoa was present at the recent Worldwide Developers Convention in San Francisco. There was a poster, a podcast, and a demonstration. You can view a copy of the poster here. A link to the podcast will be added soon.

Versions

BioCocoa 2.0 is a completely new framework structure that consists 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 was in BioCocoa 1.x has been or will be moved to this new structure. Version 2.0 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, eg swiss-prot, ncbi, fasta.
• Tools to manipulate and obtain information about sequences.
• An NSTextView based class to display sequences.
• BioCocoa 2.0 can be used to create applications that run on both PPC and Intel based Macs.

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.

More information on BioCocoa's progress can be found here.

Download

Version 2.0 is now available for download here.

For the most recent code, you can also browse the source code in our Subversion repository. To checkout the repository, issue the following command in the Terminal:

svn checkout svn+ssh://bioinformatics.org/svnroot/BioCocoa

Documentation

The documentation is still very much work in progress. Make sure to have a look at the design page and the short tutorial.

The documentation for version 1.x is still available.

Progress & To-Do

See this page for more information on the framework's progress. A To-Do list is available as well.