I migrated a year ago from Windows to Ubuntu "Edgy Eft" Linux which quickly became my main operating system. It's there that I got the problem that each migrant gets at one point: How do I replace those specific softwares which I so badly need for work?

I was well accustomed (addicted?) to Vector NTi (Developed by Invitrogen), the reference for DNA/Protein sequences management and edition softwares in the Windows environment. Here, I write about a software which is a good alternative to Vector NTi for basic needs, and works in the Linux, Windows and Mac OS environments, please let me introduce CLC Free Workbench.

Vector NTi is a nice piece of software for biological sequences edition. A free version with basic functionalities is even proposed to students. This software only runs on Windows and was the last reason I was keeping Windows with a dual boot configuration. Of course, I don't have to stress too much how rebooting only for one specific program can be inefficient and annoying over time.

A first workaround was offered by VMware Server, a virtualization software which is able to run Windows from its partition in Linux. This allowed me to just switch from one system to the other through a simple window switch... Sounds perfect?... Well, that was just no good! VMware has to boot and run Windows on the same resources as Linux resulting in a mutual slowdown, and giving a software (a wonderful software by the way, but programmed by humans nonetheless) direct write permissions to your raw partition is really hard for the nerves....

After several months of struggle, I digged a little further in an alternative solution which had not worked in some first trials because of my inexperience with Linux: CLC Free Workbench. This review is about this nice biological sequence editor developed by CLC Bio which has nearly all the functions I need: A nice and easy graphical interface, a simple database to manage the sequences of genes and plasmids and basic notions of molecular biology (ORF finding, restriction analysis, etc...).

CLC Free Workbench 4.0.2

CLC Free Workbench is a free and basic version of the CLC Combined Workbench by CLC Bio. It was developed in Java and therefore runs on either Windows, MacOS X or any Linux system on which the Java interpreter is installed.

Installation

Sun Java Development Kit installation

CLC Free Workbench was developed in Java and may therefore be run on either Windows, MacOS X, or any Linux system on which the Java interpreter is installed. So first things first, one needs to install Sun's Java packages on his linux distribution (Here described for Kubuntu "Gutsy Gibbon") before attempting anything else. This is made easy with the following command in a console:

$ sudo apt-get install sun-java6-jdk

A quick check that the Sun Java platform is activated by default is recommended:

$ sudo update-alternatives --config java

If it is not, instructions are given to activate it.

CLC Free Workbench 4.0.2 installation

CLC Free Workbench may be downloaded on CLC Bio's website. The installer comes as a single .sh file which must be made executable before it may be launched as root to be granted with access to the system folders:

$ chmod a+x CLCFreeWorkbench_4_0_2.sh
$ sudo ./CLCFreeWorkbench_4_0_2.sh

A wizard guides the user through easy intallation steps. Accept the invitation to start CLC Free Workbench to accept the license (you are still root). One small trap: do not start right away to use the software as everything will be saved in root's folder and with root privileges. You may relaunch it later as a simple user through the installed shortcuts or through the command:

$ clcfreewb4