DNA WorkBench version 0.40 is now available.
Summary of New Features:
* Mac version now easy to install and full-featured.
* Automatically obtain, process, and install databases
and programs from ftp sites.
* Internet services more reliable.
Available by anonymous ftp at
cbil.humgen.upenn.edu:/pub/dnaworkbench
(130.91.180.83)
Here is the beginning of the ANNOUNCE file available at the site above:
Announcing:
DNA WorkBench
A program for sequence searching and manipulation.
* It's free.
* It runs on Unix and Macs (and PCs - see below) with internet connections.
* Powerful and fast searches on Genbank and other databases.
* Client-server: access remote databases and programs.
* Parallel distributed processing for huge databases of the near future.
* Full automatic control: by script, command-line or standard input.
* Enhancable - run your own programs on databases and search results.
* Handles most sequence file formats silently - reformats easily.
* Many sequence manipulation functions.
* Convenient user interface, complete on-line help.
* Automates the retrieval, processing, and installation of
updated databases and programs from ftp sites.
HOW TO GET IT
ftp cbil.humgen.upenn.edu (or, ftp 130.91.180.83)
login as "anonymous", give your email address as a password
For UNIX:
cd /pub/dnaworkbench
mget ANNOUNCE INSTALL README (and, if you want, CHANGES and PERL-FAQ)
(Answer "yes" to the prompts)
cd unix
get dnaworkbench
quit
For MAC:
fetch /pub/dnaworkbench/mac/DNA_WorkBench.bin in automatic or macbinary
You may also want /pub/dnaworkbench/mac/MacInstall for more information,
as well as:
/pub/dnaworkbench/ANNOUNCE
/pub/dnaworkbench/INSTALL
/pub/dnaworkbench/README
and, if you want, CHANGES and PERL-FAQ
For PC: get the following files:
/pub/dnaworkbench/msdos/dnaworkbench
/pub/dnaworkbench/ANNOUNCE
/pub/dnaworkbench/INSTALL
/pub/dnaworkbench/README
and, if you want, CHANGES and PERL-FAQ
Please send mail to tisdall at cbil.humgen.upenn.edu if you install
the program. You will then be informed of program updates and other
information.
( ... )
Here is the latest entry in the CHANGES file:
version 0.40 Jan 25 1994
Backward compatibility added to server for previous versions of client.
New treatment of GenBank cumulative updates:
TEXT and SEQUENCE commands - "gball" no longer includes "gbnew"
ID ACCESSION KEYWORDS ORGANISM that use indices can be tuned:
By default they search release + updates.
The following command sets to search only updates:
perl $UPDATES = 'UPDATES'
The following command sets to search only release:
perl $UPDATES = 'RELEASE'
The following command resets default, updates+release:
perl $UPDATES = ''
Socket communication improved:
In client, sockets closed and reopened more frequently.
In server, socket timeout increase from 10 to 60 minutes.
Internet addresses may now be given as numbers as well as names.
MacIntosh version improved:
Now handles 30 sockets, so e.g. "text watson gball gbnew" okay.
Distributed as single executable file, easy installation.
Improved handling of out-of-memory conditions.
SEQUENCE command bug - did not handle "^" correctly (regular expression
match to beginning of string) - fixed in server code.
dnaworkbench -DBUPDATE dbupdate.conf
Read a configuration file to automate the fetching, processing,
and installation of updated databases and programs from
ftp sites. Good for running on a Unix server via "cron".
For details, see the program code, "sub DBupdate".
======================================================================
James Tisdall
Departments of Genetics and Computer and Information Science
Computational Biology and Informatics Laboratory, Human Genome Project
510 Blockley Hall
University of Pennsylvania
tisdall at cbil.humgen.upenn.edu
215-573-3113
fax 215-573-3111
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