[Biophp-dev] New question from the Newbie

[Nico Stuurman]

Hi Sean,

Great to hear from you again!

> I've been meaning to pack up a copy of the current 'reasonably usable'
> sections of the bioinformatics.org BioPHP code and make it available as
> a 'regular download' instead of making everyone go through CVS.

That is a great idea.  I would advice to get the structure of the 
biophp cvs such that you can simply do a 'cvs export' and have a nice 
biophp library ready for distribution.

> (Right now that would be, as I recall, the original "GenePHP-BioPHP" 
> modules
> from Serge, the import modules and 'seqFactory', and (in the other 
> section) my

That is now all in the biophp/genephp cvs if I am not mistaken.

> eSearch, eSummary, local BLAST, and ncbi BLAST frontends, and the 
> supporting
> modules for those (the 'core' XML parser from which the BLAST, 
> eSearch, and
> eSummary results parsers derive, and a small module for submitting POST
> queries to websites.)

Is that in biophp/sean/semi-official?  It would be great if you could 
move this into biophp/genephp (which we should simply rename to 
biophp/biophp or even biophp/).

What is the local BLAST module?  I wrote an interface to primer3 which 
I now put into biophp/genephp/interfaces.  I guess that this is 
conceptually similar to a local BLAST interface (and for that matter, 
an interface to clustalw, and hmm, there must be more out there that we 
need to interface to).

> As to BioPHP-GenePHP and BioPHP-Bioinformatics.org, I'm not sure 
> 'merging'
> the two projects is necessarily feasible or even desirable due to 
> differing
> goals, but I WOULD like to see more active 'cross-pollination'... 
> wonder how
> hard it would be to set up a "cvs changelog" mailing list which would
> show activity for both projects at the same time.

The way I see it they are the same thing.  What is now in the 
biophp/genephp cvs is basically the genephp code with soem changes by 
you and me and the addition of the parser classes.  There has not been 
any activity in the genephp cvs in about 10 months.  Nevertheless, I am 
sure that somethings have been going on with that code (see earlier 
mails from Serge).  If that work does not end up in cvs, there is not 
much anyone else can do with it.  I simply would like to end the 
confusion and have a single cvs repository that everyone agrees to work 
with (it looks, for instance, as if Fred started working with the 
original genephp code, which I would highly discourage since so much 
nice infrastructure has been added for file parsing in the 
biophp/genephp cvs).

The way it was last summer was that the bioinformatics cvs could not be 
accessed from Serge's windows box.  I will fire up the old beast in the 
basement this weekend and figure out if that is still the case.  If so, 
I propose to move the cvs repository to sourceforge so that everyone 
can contribute.  If not (that is bioinformatics cvs now works with 
windows), I invite everyone interested in biophp to contribute their 
code to that cvs.  In any case, Sean (and I, I guess) will need to do 
some re-organization of the code in cvs such that there is a logical, 
extendable structure in place.

> Sometime later today, I'll try to get an email out to the list with an
> overview of the importing modules (interfaces implemented by the 
> individual
> 'file-type import' modules, and what needs to be added to the central
> import class for e.g. auto-detection).


Great!


best,

Nico