Fermini

What is Fermini?

Fermini is system for monitoring yeast fermentations.

In 2010, participating in a yeast phenotyping project, I took the initiative to design a system to store data obtained from small volume fermentations.

• The Fermini system is dedicated to fermentation in small volumes (300 mL) that do not require a kinetic monitoring
• It facilitates the data management (weighing and sampling);
• The data are securerely stored in a database;
• Data can be exported in "one-click" in a file in ODS format (spreadsheet);

Dependencies

For Debian/Ubuntu:

$ su -
aptitude install apache2 mysql-server mysql-client phpmyadmin

Install Perl modules from CPAN:

cpan -i CPAN::Bundle YAML Term::ReadLine::Perl Device::SerialPort DBI OpenOffice::OODoc

Install

Download project

Clone from GitHub:

cd /var/www
git clone https://github.com/bigey/Fermini.git
cd Fermini

Or download sources from GitHub:

unzip Fermini-master.zip
mkdir /var/www/Fermini
mv -r Fermini-master/* /var/www/Fermini
cd /var/www/Fermini

Create Fermini database

Edit the scrip create_fermentation_db.sh:

cd /var/www/Fermini/Install
nano create_fermentation_db.sh

Set the password for the root MySQL account:

DB_ROOT_USER='root'
DB_ROOT_PASS=<root-mysql-user-password>

Edit the scrip fermini_db_creation.sql:

cd /var/www/Install
nano fermini_db_creation.sql

Set the password for the www-data (apache2) user accessing the Fermini database in the line bellow:

CREATE USER 'www-data'@'localhost' IDENTIFIED BY 'password';

Then create the database:

bash /var/www/Fermini/Install/create_fermentation_db.sh

Edit the scrip constantes.php:

cd /var/www/Fermini
nano /var/www/Fermini/constantes.php

Set password in the line bellow:

define("USER","www-data");
define("PASS", "password");

Edit the scrip export_2_oocalc.pl:

cd /var/www/Scripts
nano export_2_oocalc.pl

Set the password in the line bellow:

my $user="www-data";
my $password="password";

Setup the configuration for your balance

The balance used here is OHAUS model Adventurer Pro AV812C (Max: 810 g, d: 0.01 g), which is an entry level balance. You can use any other manufacturers or models supporting a serial communication.

In order to access the serial port you need to add the user www-data to the dialout group:

adduser www-data dialout

In the Perl script /Scripts/balance_ohaus.pl

Change the serial port accordingly (eg. /dev/ttS0, /dev/ttS1):

my $device = "/dev/ttyS0";

In function initDevice bellow, change baudrate, parity, databits, stopbits, handshake according to your manufacturer specification:

sub initDevice {

	my $port = shift;
	my $PortObj = shift;

	$PortObj = Device::SerialPort->new($port) or die "Can't start $port\n";

	# Serial device parameters
	$PortObj->baudrate(2400);      # \
	$PortObj->parity("none");      #  |
	$PortObj->databits(7);         #  |Change parameters here!
	$PortObj->stopbits(1);         #  |
	$PortObj->handshake("xoff");   # /
	$PortObj->write_settings;

	$PortObj->save("Ohaus.conf");

	return $PortObj;
}

In function parseWeight bellow, change the parsing regex according to the output format of you balance:

sub parseWeight {

	my $string = shift;
	my $weight;

	if ($string =~ m/(\d+\.\d\d) g \r\n/) { # <- change the regex here
		$weight = $1;
		return($weight);
	} else {
		warn "Weight parsing error!";
		return(undef);
	}
}

Set a regular backup of database (optional)

mkdir /home/<user>/bin
cp -a /var/www/Fermini/Install/mysqldump.sh /home/<user>/bin

Create an entry in crontab:

crontab -e

# m h dom mon dow   command
0 */2 * * * /home/<user>/bin/run-mysqldump.sh
Ctl+D