Bioperl: MEDLARSII

[Ewan Birney]

On Thu, 22 Oct 1998, Paul Gordon wrote:

> Greeting all,
> 
> 	     I'm working with MEDLARSII formatted records from National
> Library of Medicine.  Those of you who work with Medline might know what
> I'm talking about.  I've started to write some Perl code to process the
> data format, and I have two questions.  First, has anyone already written
> such code? Second, if no one has, would it be useful to add this to the
> bioperl code base?  The MEDLARSII records are often cited in sequence
> database entries as the publication reference for the sequence.


Paul - that sounds great. Certainly I know that 'us' (if there is an us
at bioperl) would be very happy to help you distribute and maintain the
code. There are probably two options for this:

	a) provide your stuff as a standalone package which does
coordinate with other bioperl stuff if needed. We can help here on the
distribution and publicising of the code.

	b) check your stuff in as bioperl core module into the cvs
system. This will provide greater software source control by people who
have access to the repository (ie, some people might fix bugs for you as
well as find them!). 

In either case you probably want to be talking to chris dadigan about how
you can distribute stuff from bio.perl.org. (if you want to). If you want
to go for option b), I would suggest the following steps:

	a) checking out the bioperl cvs repository locally so that your
work can be automatically and painlessly kept in sync with the core.
		For this you need a) an account on bio.perl.org (see
chris), b) local installation of ssh (secure shell) and cvs.

	b) joining the 'guts' mailing list 

	c) talking over your plans about the object on the guts mailing
list. We don't code by committee but I find it very helpful to talk over
things first with people and people usually have good suggestions for what
should be done and what not. You don't have to if you don't want to though
;)

	d) using, if possible, the Bio::Root::Object system provided by
steve chervitz which really builds a much cleaner object system ontop of
perl's own system for objects (eg exception handling!). If you are an
emacs user I have written some lisp functions that make using this a real
walk in the park.


If you have any further questions - just post back to this list, or 
follow it up on the guts list or mail me directly. 


Thanks for posting the inquiry.

	

> 
> Kind Regards,
> 	Paul Gordon
> 	Institute for Marine Biosciences
> 	National Research Council of Canada
> 
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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