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Page last modified on March 01, 2011, at 04:00 PM
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March 01, 2011, at 04:00 PM
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!!!Welcome to the BioCocoa wiki!
March 01, 2011, at 03:50 PM
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The BioCocoa wiki is the main website for the [[BioCocoa/Overview|BioCocoa]] framework and other applications and frameworks part of the larger BioCocoa suite. Click on the links in the sidebar for more information.
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The BioCocoa wiki is the main website for the [[BioCocoa/Overview|BioCocoa]] framework, the [[BioSwarm/Overview|BioSwarm]] framework, and other applications part of the larger BioCocoa suite. Click on the links in the sidebar for more information.
February 18, 2011, at 05:44 PM
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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 [[http://bioinformatics.org/biococoa/ | BioCocoa website]].
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 [[http://bioinformatics.org/biococoa/ | BioCocoa website]].
to:
The BioCocoa wiki is the main website for the [[BioCocoa/Overview|BioCocoa]] framework and other applications and frameworks part of the larger BioCocoa suite. Click on the links in the sidebar for more information.
August 04, 2006, at 11:10 AM
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Added lines 1-15:
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 [[http://bioinformatics.org/biococoa/ | BioCocoa website]].
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 [[http://bioinformatics.org/biococoa/ | BioCocoa website]].
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