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README

              	Kinetics Modeling in GENESIS 

The kinetics C-code library and kinetikit.
Version 7
By Upinder S. Bhalla
Copyright 1994-2000
National Centre for Biological Sciences, Bangalore, INDIA

Kinetikit is a utility for modeling large numbers of chemical reactions
such as occur in biochemical signaling pathways. It consists of two
sections: the C-code library kinetics, which gets compiled and linked with
GENESIS, and the script interface for Kinetikit, also known as kkit.

These files are copylefted, that is, copyrighted under the GNU Public
License (the kinetics library is copyrighted under the GNU Library
Public License, which is very similar, only it applies to libraries rather
than stand-alone programs). Please see the file COPYRIGHT for details.

kkit 7 requires GENESIS version 2.1 or greater, plus the kinetics library.
The new transporter object requires GENESIS 2.2 for proper operation.
As of GENESIS version 2.1, the kinetics library is compiled into GENESIS by
default.  The installation procedure for older versions of GENESIS is
described in the kinetikit distribution, available from the usual GENESIS
distribution sites.

Changes from previous versions of Kinetikit are described in CHANGES.

Further information about Kinetikit and examples may be obtained from
http://www.ncbs.res.in/~bhalla/kkit/index.html

=============================================================================

In addition to the scripts used for running Kinetikit this directory contains
the following files or directories:

README			- You're reading it!
tutorial.doc		- A tutorial document in Microsoft Word 6.0
COPYRIGHT		- The copyright notice.
GPL-2.0			- The GNU GENERAL PUBLIC LICENSE
Kkit.help               - The directions for kkit, viewable from within kkit.
kkit.g                  - The main script for running kkit.
Kinetikit.g             - An alias for kkit.g
examples/               - Directory of example scripts for use with kkit.
examples/README         - Description of the example scripts.

=============================================================================

Using Kinetikit:

If you plan to use kinetikit frequently as a tool, add the kinetikit
directory to your SIMPATH in the .simrc file,just as you would for other
'kits' like Neurokit.  A typical path would now look like:

    setenv SIMPATH  {getenv SIMPATH} /home/myname/genesis/Scripts/kinetikit

To try out Kinetikit, go to the kinetikit directory (this one), and type
'genesis kkit'.  If the installation has been successful, then an information
note containing copyright information and the Statement on Models and
Experiments should appear while Kinetikit loads. Then the Kinetikit interface
should pop up, and you are set to start modeling.  Refer to the help file in
this directory (which is also accessible from within Kinetikit) for further
information on using it.

For further information about the use of Kinetikit and modeling of biochemical
kinetics, see Chapter 10, of "The Book of GENESIS", second edition.  The
documentation for the GENESIS objects pool, enz, reac, and concchan will be
helpful for using these kinetics objects in GENESIS simulations outside of
Kinetikit.

=============================================================================

Bug reports:
------------
Please send bug reports relating to kinetikit (and only to kinetikit) to 

bhalla@ncbs.res.in

I cannot guarantee a quick reply, but I will try to fix things as they
turn up. Please do _not_ send me general questions regarding GENESIS and
its installation. These are more appropriately addressed to the GENESIS
address: genesis@bbb.caltech.edu
=============================================================================
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