start using biojava Was: [Biojava-l] NetBlast for java?

[Matthew Pocock]

Hi John,

A whole new chunk of tutorials and examples should appear over the next 
week as the bootcamp materials go on line (I sincerely hope they will be 
posted...). This will be a good way to get started with the basic 
classes. However, I'm guessing that you are modelling genes and gene 
families at a different level of granularity than 'features located on a 
genome'. There is a pressing need for BioJava objects that represent the 
semantics of and links between genes.

Anyone: I don't think we even have a GO client - can this be easily 
rectified?

If you are keen to integrate with BioJava, we could discuss your 
schema/object model and what functionality you want to add to it, or 
what functionality you would want to add to BioJava. For example, what 
you store in your "genes" table, and what you would like to associate 
with genes that you can't currently handle.

All the best,

Matthew

ozborn@UVic.CA wrote:
> I also a question.  What is the best way to start using biojava?  I have
> lurked on this list for over a year, but the project I am working on
> doesn't use biojava at all, although there are many places it could.  (My
> project is a poxvirus database for the Center for Disease Control,
> although it will eventually hold information on other viruses, and
> possibily bacteria).
> 
> Right now the database only has complete genomes, genes, and gene families
> but no sequences.  I want to add bio-java sequences to the database, and
> features which is also not there (it's all in the "genes" table).  The
> problem is I don't really know how all the packages in biojava fit
> together, or where to just start using it in a productive way.  Do I just
> use bio.seq.db?  From what I have looked at, I can't really see the
> advantage of doing so at this point.  Can anyone give me some pointers on
> getting started?
> 
>  -John
> 
> 
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