Tuesday, November 29, 2005

CLC Bio Free Workbench 1.1

What are your needs for DNA and protein sequence analysis and management?

If your needs are extremely basic, CLCbio's new free offering, CLC Free Workbench might suit you.

Disclaimer: In our lab, we use MacVector 8 from Accelrys, and our primary needs are restriction enzyme predictions, oligonucleotide primer selection, and ORF map figure generation. Basically, we use DNA sequence analysis software for designing linear DNA fragments and plasmids in our studies with E. coli. Keep this in mind during my review.

Limited Functionality
CLC Free Workbench is the base module in a trio of products to be offered by CLCbio. There is currently a Protein module, and a Gene module is planned for Spring 2006. The Free Workbench is designed to be a sequence entry and data viewer module, with some other limited functionalities in sequence alignment, restriction enzyme site finding, and DNA editing. NCBI nucleotide and protein databases can be searched, and sequences can be downloaded from that interface or imported from a variety of file formats (genbank, fasta, etc.). Sequences can be aligned, and from those, basic phylogenetic trees constructed. One can generate the reverse-complement or protein sequence from DNA sequences, and there is a basic ORF-finder included.

Free Workbench is a Java-based application, which means it runs on Linux and Windows, and can have the Aqua interface of normal Mac OS X applications on a Mac, but there are some quirks. The program sports an interesting interface, where with a strong project-based focus. All data is enclosed within a database, so there aren't dozens of sequence files floating through your file system. This is a handy way to deal with the file overload that usually results from sequence analyses. Users of VectorNTI from Informax will probably be familiar with this concept. The downside is that you have to export files to send them to others.

The workspace is very modular, with "projects" and "toolbox" along the left-hand side. A toolbar extends across the top of the window. Opened sequences, alignments, and other analyses appear in a tabbed-like interface occupying the center and right of the window. Individual tabs can be dragged to two tab groups: one upper and one lower. These interfaces are probably helpful for managing a lot of open windows. Additionally,workspaces can be customized and saved, allowing certain windows to remain open through program restarts. Several workspaces can opened at once, allowing several simulataneous views of data at once.

Another nice feature is when you are doing batch alignments, restriction enzyme searches, and file downloads, all functions are added to a que, allowing you to pursue other studies while older items are completed.

However, the user interface needs a lot of work to be considered a quality Mac application. There are at least three "View" menus (accessed through the MenuBar, ToolBar, and Right Click) and they all have different available options. This leads to confusion when trying to follow the tutorial. Similarly, zooming in and out of a sequence requires pressing a button on the tool bar for changing this function. I would prefer holding the option key to alter the function, as is done in Photoshop and Illustrator.

Final Words

The other modules will carry a >2000USD price tag, but will apparently have much more functionality. This set of software would allow sequence entry, basic edit, and project set-up (more below) via the Free Workbench. These projects could then be sent to a computer that had the Gene or Protein module, a set of analyses would be performed, data generated, and then the project could be viewed again on the Free Workbench.

The approach is very interesting, giving basic functionality to all users on multiple operating system platforms, but charging for major features. When I first saw their software page, I assumed that the free software would be a hook to bring users to their platform, then upselling the major analysis components. However, I find that the Free Workbench is too limited to even consider using for my lab's purposes, so I won't be consider any of their other products. If you primarily need a way to do sequence alignments and tree building, perhaps this is for you.