[Biojava-dev] SNP analyses in Biojava2

[Matthew Pocock]

Hi,

Bruno Aranda - eBioIntel wrote:

>Hello everybody,
>
>We are endeavouring a project about SNP and related stuff and, of course,
>it will be using BioJava. It is a long term project and we are now in
>early design. What I would like it to do is to analyze the SNPs with
>summary statistics,  neutrality tests, coalescent and other things. As we
>are just in the earliest thoughts and it will be using J2SE 1.5 I think
>that all this SNP api would be a good contribution to Biojava 2. So, is
>  
>
Sounds interesting. SNPs are definitely something I'd like us to support 
- biojava 2 is about data integration and handling many more types of 
data, so SNPs are a good example.

>there any specification about, for instance, how to do statistical
>equation classes in Biojava 2 (just the classes with the equations to
>process statistics)... it is too early for this? Of course I can do it
>  
>
We don't have anything yet. This is a perfect time to find out what 
people would need. For example, what classes do you want to see? What 
API would you like to talk to for the statistical equations? Would you 
like to be able to pass in a string like "p(x) = p(x | y)" and have it 
produce code? Would you pass around Strategy objects for different 
probability distributions? And so on.

>aside BioJava but, if I make all these classes with the bjv2 phylosophy,
>then it will be easier to include them...
>  
>
Agreed. At the moment I've got basic data integration and query working, 
and a 1st cut at the biological features API. Everything else is up for 
grabs. The core design principles are now in the README on the trunk, 
and scatterd on different package.html files in the source.

Matthew

>Any appreciation is welcome,
>
>Bruno Aranda
>
>
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>  
>