We announce the availability of CHROMINFO, a tool to create, maintain
and display top-level chromosome mapping data, via anonymous ftp from
ncbi.nlm.nih.gov.
What is CHROMINFO?
----------------------------
CHROMINFO sprang from the needs of one of us (Steve Reeders) to
organize data on Chromosome 16 coming in from centers around the
world, and maintain it in a form that would be useful to co-ordinate
research between different centers., as well as for submission to the
Human Gene Mapping Workshop (including generation of the consensus
map diagram from the database rather than drawing it by hand).
CHROMINFO works with top-level chromosome data. considers locus
order to be the most critical aspect of chromosome mapping. Order
information is central to all types of mapping including genetic linkage,
somatic cell hybridization, radiation and restriction maps. CHROMINFO
maintains a backbone of unequivocally ordered loci (Landmarks) from the
p-terminus to the q-terminus.
CHROMINFO also allows the storage of ambiguous information such as
partial maps.
At the most primitive level, CHROMINFO acts like an electronic
reference. However, you can ask it many questions regarding order and
distance information on loci. More important, CHROMINFO lets a user
add value to her/his personal copy of the database through the addition of
notes.
What you need to run CHROMINFO
---------------------------------------------
CHROMINFO runs on the Apple Macintosh and requires the commercial
Mac database program 4th Dimension (4D) to run. We recommend at least
a Mac II, 4MB RAM and a 13S monitor. CHROMINFO will use color if
you have it; if you donUt, set your Mac to display at least 16 shades of
gray.
How to get it
----------------
after anonymous ftp login to ncbi.nlm.nih.gov, type
cd repository/chrominfo
You should see a file README is in text form, and two directories,
program and data. Both these directories contain MacBinary files; set your
ftp mode to binary if you wish to get at these.
All files in both directories are Stuffit self-uncompressing archives, which
after downloading, will appear as applications. Double-click on an
application to unpack its contents.
Contents of the program directory
-----------------------------------------
There is a single file, program.sit, with the following contents:
-- chrominfo manual., a manual in Microsoft Word format
-- chrominfo.comp, a compiled version of the program (it still requires 4D
to run).
-- chrominfo, the uncompiled (interpreted/source) version. This will be
useful for those who are curious to see what we did, and who wish to
make modifications or use the program and data in power-user mode,
without the menus.
-- proc.ext, a collection of RexternalS (machine-code) routines used by
CHROMINFO.
-- 4dDataDict, a folder containing a 4D database without any menus that is
a data dictionary for CHROMINFO. Apart from a detailed description of
the tables and fields, it also explains why we took certain design decisions.
You can use this structure to document your own databases (which may
have been built with Sybase, for example).
Contents of the data directory
------------------------------------
All files have the form chr-xx.sit,
where xx is the name of the chromosome.
We can vouch for the currency of information on chromosome 16;
information on other chromosomes is valid only as of HGM 11.
Updates to CHROMINFO
-------------------------------
Updates to both the program and the data will be posted periodically. See
the file README for what we have added; at the least, this file will hold
the dates of the last updates to the files.
As far as data is concerned, the only file that we ourselves will update is
the chromosome 16 data file, since we are lack the resources to manage
data for the other chromosomes.
What we would like from you
-------------------------------------
CHROMINFO is in late beta (0.8); that is, the program wonUt crash on you
or give you wrong answers; however, it may not have all the features you
need. We want your feedback: tell us what you like about it, what you
donUt., what you would like to see in it. We make no promises; but if
request for a feature reaches critical mass, it will be incorporated.
We are looking for lead users, who are in the position of co-ordinating the
gathering of data on a single chromosome from several centers, to play
with CHROMINFO and tell us where CHROMINFO is on and off target.
If any one volunteers to maintain the consensus data for a particular
chromosome, and is prepared to share it by posting it periodically on the
NCBI server, weUll be only too glad to work closely with her/him.
Copyright Notice and Disclaimer
----------------------------------------
CHROMINFO is copyrighted by its authors, Prakash Nadkarni and Steve
Reeders; we encourage users to distribute the software, data files and
manual freely provided the copyright messages in the program and manual
are not altered.
Modifications, enhancements and customizations are encouraged; users
who make changes are encouraged to submit the same to the authors for
possible inclusion in future releases. Such enhancements will be gratefully
acknowledged.
You are welcome to lift any good idea out of CHROMINFO for
implementation in your own applications, provided that you acknowledge
the fact.
We have tried everything to ensure that CHROMINFO will substantially
perform as billed, but software and data that is free cannot come with
warranties.
Thanks
---------
-- to Mark Shifman and Perry Miller of the Yale Center for Medical
Informatics for logistic support; Mark has also been a useful devilUs
advocate;
-- to Ed Hildebrand and Christian Burks of LANL for moral support and
feedback in the early phases of development;
-- to Jim Ostell and Scott Federhen of NCBI; we were going crazy mailing
CHROMINFO out on floppies until we sought their help.
Prakash Nadkarni / Stephen Reeders
