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bionet.molbio.gene-linkage FAQ in next post

Conan the Librarian rootd at ee.pdx.edu
Mon May 30 01:35:57 EST 1994

I'm sending out the 28may release of the bionet.molbio.gene-linkage
FAQ in my next post.  I wanted to make a couple comments.

This is a HUGE improvement over the 15may release, but only an
incremental improvement over the 21may release.  I will continue
to edit and improve the FAQ, but the improvements will be more
incremental in nature from now on.  I will post it once/month.

Many people sent me corrections/information.  Thank you all!
I hope that I've credited you all appropriately in the FAQ, but
if I've made a mistake, send me email and I will correct it.

There are a couple topics I'd like to comment on.

1) linkage programs available via anonymous ftp

	There are many useful programs available via
	anonymous ftp.  That's great!  The easy availability
	of the programs speeds up everyone's research.

	Unfortunately, there are many programs which are not
	available via anonymous ftp.  crimap, simlink, mkcrigen,
	and the crimap-utilities-package are excellent examples.
	In one case (mkcrigen) it appears that the source code
	has been "lost."  Executables still exist, but this
	excellent program will not be modified/recompiled unless
	source code can be found.

	The people who wrote these programs are to be thanked for
	their excellent contribution to the linkage community.
	The programs are useful, and generally delivered to anyone
	who asks for them without charge.

	Nevertheless, it would be easier if the programs were
	placed on anonymous-ftp sites.  I'm happy to hear that
	simlink and crimap will be placed on ftp sites "soon."
	I just want to encourage authors to place their work
	on ftp sites.

	An excellent example of a freely redistributed program
	is the Linkage package (Lathrop et al).  There are two
	seperate ftp sites (one for Jurg Ott to maintain the
	IBM versions, another for other platforms).  Tons of
	researchers use the package.  Another group converted
	it it C and improved the speed by an order-of-magnitude.
	By making the program available, research which uses the
	program has been greatly aided.

2) Archie indexing of ftp sites

	Archie is a database-server which logs into ftp sites
	and obtains a directory listing of the entire site.  Then
	users can telnet to an archie server and have it search
	all indexed ftp sites for a particular program.

	Ever waste time looking through serveral ftp sites for a program?
	Archie helps solve the problem, IF the ftp site with the
	program is indexed.  Archie only indexes ftp sites with the
	permission of the maintainer.  I'd like to encourage all
	ftp-site administrators to have their ftp site archie-indexed.

	FAQ question B2 explains how to use archie
	FAQ question B3 explains how to have your ftp site archie indexed

	With the inclusion of a ftp-site list in the FAQ, this is less
	important than before, but it will still be useful.

There are many ways you can help me improve the FAQ.  I'd like
to assemble a complete set of file format conversion programs
(to convert between ped.out, .gen, liped, linkage, simlink, and peddraw
formats).  If you find a good ftp, gopher, or www(mosaic) site, send me
the address and a brief description of the contents.  My FAQ is
notoriously defecient in "technical" questions/answers.

I'll be monitoring several bionet newsgroups and adding appropriate
information to the FAQ, but if each individual sends in one bit of
useful information the FAQ will be fabulous!

Thank you for your time, I hope you find the FAQ useful.

Darrell Root
rootd at ohsu.edu

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