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

	30-10-2007 20:01
	CLC free workbench 4.0.3 A new version (4.0.3) of CLC free workbench has been released mainly to fix some bugs. The installation procedure and the interface are still the same.

thegeek

	13-12-2007 07:17
	Vector NTI runs very well in wine Btw, thanks to some work myself and others have done in the previous year, Vector NTI actually runs very well in Wine, and this is definitely an alternative for people using Ubuntu. Basically, it's as simple as really just double-clicking on the installer if you have Wine installed (just "sudo aptitude install wine" first will do); if you'd like a little more of the tools menu (Web ordering) you'll have to dig around for mfc42.dll on google and (i) run "wine" with no parameters to create ~/.wine, (ii) copy mfc42.dll to ~/.wine/drive_c/windows/system32, and (iii) double-click on the installer. Only real big thing not working is online help. Hope this helps.

misha680

	13-12-2007 13:33
	Thanks for the precision I must say I only tried more than a year ago to run Vector NTi under Wine. By the time, it was not working as simply and I did not check for news since then. It's really good to hear that it may now be run under Linux! Thanks for the post.    A tiny question though: what version of Vector NTi runs now in Wine (if not all)?

molgyk

	15-01-2008 00:27
	Which version? Sorry didn't mention the version number. The latest that is downloadable from Invitrogen Vector NTI Advance 10 now works very well (perfectly except no online help index/searching, only context-based) on wine. I use it almost every day.

misha680

	08-04-2008 07:03
	Geneious doesn't only include a demo When you download Geneious, it runs as Geneious Pro for 14 days and then reverts to Geneious Basic. You can continue to use Geneious Basic for as long as you want, so it's not just a demo as you say.    Also, unlike CLC the free version of Geneious will occasionally (about once in 8 days I think, but not in regular intervals) give you free use of the Pro features - it's called "Geneious Day".    Also, a new version 3.6.2 of Geneious is out and contains loads of new features and improvements.

Geneious Developer

	14-04-2008 22:03
	Geneious Thanks for the comment.    My post is becoming a bit old. Still, when I tested Geneious (I should have mentioned the version), I just thought the free "demo" version was not suitable for the simple everyday needs of a molecular biologist.    That said, I'll be glad to test the new features of Geneious soon!

molgyk

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