[Biojava-l] biojava.dp doc/tutorials?

[Richard K. Belew]

hi matthew and samiul,

Matthew Pocock wrote:
> 
> I hope that UCSD is having better weather than we are. England seems to
> be totaly below water at the moment.

and i thought you Brit's enjoyed being all wet:)  we don't
have weather in SoCal, just the sort of stasis that breeds politicians,
like Ronald Reagan.

> The DP objects have changed a bit since the 1.01 release - and for the
> better. We should put up a new snapshot of the project on the web-site
> as soon as I fix a show-stopper bug in the alphabet indexing code. 

ah!  i am having problems running the SearchProfile demo:

> Loading sequences
> java.util.NoSuchElementException: There is no parser 'symbol' defined in 
>		alphabet PROTEIN+X
>         at org.biojava.bio.symbol.AbstractAlphabet.getParser(AbstractAlphabet.java:58)
>         at SearchProfile.readSequenceDB(SearchProfile.java:110)
>         at SearchProfile.main(SearchProfile.java:21)        

maybe this is related?

the new hacks you are developing sound very neat, so do let me know
when you are ready to let others play.  note that this is a relatively
intro course in our curriculum, so my goal is to use things like DP
to
understand how good, efficient designs can make java work even on
larger HMMs.  the ideal progression will be to let them work on
some small dataset (probably over DNA strings), then consider scaling
issues as the length of strings increases and we move to proteins.

> There is sadly almost no tutorial documentation. I think that Samiul is
> interested in writing some. He has been using the package to model
> histone binding sites, and I think he is the nearest persone we have to
> a user (as oposed to developer) at this time.

thanks Samiul for also replying!  can you point me to any prelim
writeups re: your use of these routines in your own work?  that might
help me slant what i develop (eg, towards data sets relevant to you)?

do you think it is worth bugging Durbin et al with this same question?
they'd be the sort of academics that i'd imagine also using this
in a class somewhere?  or are they all already listening in on biojava?

> Please feel free to bother me at any time about how the code works, why
> it looks like that, or tell me of any difficulties/bugs. 

thanks again, i'll probably take you up on that.

best,
	rik


-- 
Richard K. Belew                          rik@cs.ucsd.edu
                              http://www.cs.ucsd.edu/~rik
Computer Science & Engr. Dept.      
Univ. California -- San Diego       858 / 534-2601       
9500 Gilman Dr. (0114)              858 / 532-0702 (msgs)
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