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Tips of GENESIS/kinetikit


GENESIS/kinetikit is a powerfull simulator of signal transduction. You can constract models of synaptic plasticity, MAP kinase cascades, Ca2+ oscillation, etc. with GUI interfaces. There are a lot of modules of singal transduction pathways in examples in GENESIS/kinetikit.


How to get GENESIS/kinetikit?

GENESIS/kinetikit is a GPL lisence software, and you can get and use it right now. The latest kinetikit is available at http://www.ncbs.res.in/~bhalla/kkit/download.html. GENESIS ftp site (http://www.genesis-sim.org/GENESIS/) has also kinetikit, but it is not the latest.



How to compile GENESIS/kinetikit?

You don't have to compile it because Dr. Bhalla distributes a binary excutable file for Linux. I recommend you to use the binary file. However, you can compile by yourself ...

A Linux PC is needed. Get genesis2.2.tar.gz from GENESIS ftp site, and type the following command to unzip the downloaded file

$ tar zxvf genesis2.2.tar.gz

A list of unzipped files is displayed. Read README files in "src" directory carefully. Edit MAKEFILE before compiling. The original format is MAKEFILE.dist.

$ cd genesis/src/
$ cp MAKEFILE.dist MAKEFILE.
$ emacs ./MAKEFILE &

Delete comment-outs for linux PC to activate the configuration for a compiler. Don't touch the file, MAKEFILE.linux.

$ su
Password: xxxxxxxx
# make
Finished successfully!
# exit
$

When the compile proceedure finished successfully, you will get genesis/.simrc file. Copy the file to your home directry.

$ cp genesis/.simrc ~

Finally, confirm the paths in the ~/.simrc.



How to understand GENESIS/kinetikit?

Two books will help you very much.
The Book of GENESIS 2nd edition: Exploring Realistic Neural Models with the GEneral NEural SImulation System, by James M Bower and David Beeman.
Computational Neuroscience: Realistic Modeling for Experimentalists, edited by Erik De Schutter



Getting started

Core dump whenever we are trying to save kinetikit scripts.
Use the latest binaries released by Prof. Bhalla (http://www.ncbs.res.in/~bhalla/kkit/download.html) instead of your compiled genesis executive file.

GENESIS says, "RAINBOW is not found".
Did you copy .simrc from genesis directory to your home directry? GENESIS/kinetikit requires this config file in your home directory.

The counter of Current Time seems not to run.
Your .simrc file does not work well. Do not comment out "schedule" and "include escapelist."

Some plot data of the time course of a molecular concentration drop out at random.
I know the problem, but I don't know solve it. It depends on environment in your PC.



For advanced users

What is a command to save the time course of a molecular concentration?
"do_save_named_plot" saves a time course in a xgraph of GENESIS/kinetikit.
genesis #0 > do_save_named_plot /graphs/conc1/Glu.Co {"Glu_ver1.plot"}
genesis #1 > do_save_named_plot /graphs/conc2/mGluR.Co {"mGluR_ver1.plot"}
genesis #2 > do_save_named_plot /moregraphs/conc3/PLCbeta.Co {"PLCbeta_ver1.plot"}
genesis #3 > do_save_named_plot /moregraphs/conc4/IP3.Co {"IP3_ver1.plot"}


How to run GENESIS/kinetikit without GUI interface?
Just run GENESIS with -nox option:
$ genesis -nox yourscripts.g
When you don't need GUI or any commands after starting GENESIS/kinetikit, add -notty option:
$ genesis -nox -notty yourscripts.g