CHROMINFO is available by anonymous ftp

prakash nadkarni nadkarni-prakash at CS.YALE.EDU
Wed Jun 3 18:02:05 EST 1992


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




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