protocol archiving

Coady Michael coady at ERE.UMontreal.CA
Tue Mar 10 17:11:25 EST 1992

	Don Gilbert posted a message today about protocol archiving and 
I would like to put in my two cents worth.  I think that the protocol
archiving could be a great idea and have occasionally wondered why no one
had suggested one previously.  I would be curious to know, however, what
exactly is being set up and for whom.
	For instance, I used telnet to access the gopher service at today to try out the methods section at
IUBIO gopher service.  The methods are taken from Hypercard and so there
are control characters that showed up on my terminal as flashing numerals
rather than Greek letters or "degree signs".  Are the protocols intended to
be downloaded en masse into the user's Macintosh, or are the archives
intended to be a resource to which molecular biologists and their ilkl
can turn to download the particular protocol in which they are interested
that week?  If the former is correct, then I suppose that uploads of 
protocols should also be in Hypercard format whereas if the latter is
the envisioned plan for the archives, then a few things might need changing.
The most obvious is to have everything in ASCII format; anyone who downloads
something could then prettify it on their own computer.  More importantly
is the need to place the methods in a hierarchical format, which will become
a more serious problem as people send in their favourite methods of doing
something.  Each will have its own advantages and proponents; it may be
difficult to keep them out.  Just examining the different methods of minipreps
that are published in Biotechniques and NAR suggests that they could fill up
a fair-sized archive.  Thus, a hierarchical format will be needed for
anyone who logs in to download a few protocols without a clear idea of
exactly which ones they want.
	Perhaps this argument suggest that I'm not clear in what I want.  
Well, I hope that the protocol archive is a big success.  I look forward to
the day when people can download practically any protocol since we all
know labs with Maniatis, Current Protocols etc. which continue to use
binders with printouts of their favourite methods.  It would be easier
to modify these if they could be downloaded individually rather than 
typed in by grad students and other lower forms of life (:    But this
suggests that some more organization is unfortunately going to be needed
for the protocols if they could fulfill this use.  
	My hat is off to Don Gilbert and to Jim Brown for setting up this
service.  If I can type in any needed protocols I will, but I will also
caution folks that if this does turn into a big success, possibly limiting
sales of the molecular biology bibles (e.g. Maniatis), then those folks
might not appreciate their works being used as reference in this data
	Thanks for letting me spout.

MIke Coady

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