LSDCAS Server Configuration
The design of LSDCAS allows it to be easily developed into a multi-microscope. multi-user live cell imaging facility. If the needed components (e.g., PostgreSQL and Resin) are combined with a web server (like Apache 2), a complete web application environment and relational database system facilitates data sharing, experimental data archiving, and post-acquisition analysis. Even for smaller installations, certain system configuration is needed. This document will provide you with the necessary steps to accomplish this task.
Hardware Configuration
If you are setting up a small installation, it is likely that the same machine used for data acquisition can be used for the database and web application installation. For larger installations, such as for a shared live cell imaging facility, you will probably want to set up a highly available multi-server system, although such configurations are not required for LSDCAS. If you are interested in Linux-based high availability systems, you can get ample information on the worldwide web (e.g., see http://www.linux-ha.org). At this point, we will assume that an appropriate system has been installed and configured. If you haven't already installed all of the software in the cas2 repository, do that before continuing (see [LsdcasInstallation]).
The first thing we will do is create a new system user that will be responsible for owning all of the data associated with LSDCAS (we use a userid of 'lsdcas'). Dedicating a single userid for data acqusition is highly recommended for security reasons.
This command will create the user:
$ sudo adduser lsdcas
Just answer yes to all default questions here. If you are going to be using this machine to acquire data using your camera and stage controller, the lsdcas user must also have the necessary permissions. So, execute the following command (I will assume that the userid is 'lsdcas' as before):
$ sudo usermod --groups disk,dialout,video lsdcas
These group memberships are needed to access the serial port for the stage controller (group 'dialout'), and the firewire hardware (groups 'disk' and 'video').
Installing PostgreSQL
Regardless of the complexity of the server configuration, you'll need to install a PostgreSQL server. This is used for cataloging information for experimental data acquired using LSDCAS.
Setting up of the actual database is outside the scope of this document. There are many great tutorials on the web for doing this. However, if you're using Ubuntu Linux, the following procedure should be all you need.
Now that we have our LSDCAS user account set up, we need to set up a corresponding database.
$ sudo su postgres -c "createdb lsdcasdb" CREATE DATABASE $ sudo su postgres -c "createuser lsdcas" Shall the new role be a superuser? (y/n) n Shall the new role be allowed to create databases? (y/n) n Shall the new role be allowed to create more new roles? (y/n) n CREATE ROLE
Securing the LSDCAS Database
To Do
Next, install the tsearch2 functions
$ sudo su postgres -c "psql lsdcasdb < /usr/share/postgresql/8.2/contrib/tsearch2.sql"
Now initialize the LSDCAS database structure (we assume you have downloaded the LSDCAS source as described in LsdcasInstallation)
# cd lsdcas/trunk/cas2/sql $ sudo su postgres -c "psql lsdcasdb < lsdcasdb.sql"
Your database should now be initialized and ready for use.
Setting up PostgresQL permissions/security
To Do
Setting up Apache Web Server
To Do
Setting up Resin
To Do
Putting It All Together
Now you are ready to try using the LSDCAS acquisition program 'casBasicAcquisition'. Note that LSDCAS data acquisition is highly configurable using this program. More complex configurations can be implemented relatively easily due to the modular nature of the software design.
See '[AcquiringDataUsingLsdcas]'
