How to: Enzymes with Linux.

**ENigma885** · March 30th, 2009

I was searching for a program to plot a Michaelis-Menten graph of Catalase vs. [Hydrogen peroxide] as a substrate for a university mini-research.
And it took me some days to find this one BioGraph (click to download) a pretty simple and easy to use enzyme plotting program. Plots like

Michaelis-Menten enzyme kinetics (Also it calculates MM constant Km and maximum velocity Vmax automatically and displays them on the graph) ,
pH and
temperature effects on the enzyme activity

can be drawn in such a nice-looking graphs like those ones:-

and

I also face some problems to get it to work. But finally, it worked and here's how:
i'm not sure if i understand every step, a friend helped me, but here's wat i did:-

1. Installed Apache, PHP5, Imagemagick, and Gnuplot.
2. Checked Apache with http://localhost/ and i got "It works!".
3.

Code:

cd /var/www

4.

Code:

sudo chmod 777 .

5. Copied bioGraph extracted folder to /var/www
6. In an internet browser, probably Firefox, paste "http://localhost/bioGraph_1.0/"
7. Using

Code:

whereis gnuplot

and

Code:

whereis convert

to localize gnuplot and convert to c if there's a need to modify config.php
and in my case the defaults works fine; /usr/bin/gnuplot and /usr/bin/convert correct places.
8. 1st run i got error log containing something like

Code:

Warning: chdir() [function.chdir]: No such file or directory (errno 2) in /var/www/bioGraph_1.0/mmgraph.php on line 32
Warning: fopen(/home/vimal/public_html/biograph/upload/tmp/file4646.dat) [function.fopen]: failed to open stream: No such file or directory in /var/www/bioGraph_1.0/mmgraph.php on line 34

9. In Terminal window

Code:

sudo gedit /var/www/bioGraph_1.0/config.php

Edited the temporary directories, last 3 lines, to

Code:

$TMP_DIR ="/var/www/bioGraph_1.0/tmp";

$CACHE_DIR ="/var/www/bioGraph_1.0/cache";

$URL_PATH = "http://localhost/bioGraph_1.0/cache";

10. WORKED PERFECTLY

I'm sure it will help any biochemistry newbies overthere. Just thought of sharing it. =)

**nateperson** · March 31st, 2009

Nice,

On a similar point, I just found nice paper in pubmed couple of days ago,

PMID: 18031997

That may be of interest to people
Its a review paper, focusing on bacterial bioinformatic tools and databases.

Just thought I'd chime in with some post lunch slump reading for anyone interested.