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
