Friday, May 11, 2007

Moved to Connectedbases

In case anyone ever reads this page, I have decided to move to my self-hosted blog at I continue to write about web-based tools for science, microbiology, and Macs.

Thanks for reading,

Brian Haugen

Thursday, February 09, 2006

Podcast subscription for bioscience & biotech researchers

Biowww blogger has compiled a list of Podcasts for bioscience & biotech researchers. This should make for some good listening.

List is below the fold:

Nature Podcast XML

The scientist podcast: XML

Science Magazine Podcast: XML

Invitrogen web seminars - bringing the latest developments and research results live and direct to your desktop. XML

The New Scientist podcast: XML

Introduction to Molecular and Cellular Biology Podcast: XML

ITC Biotech podcast: XML

Monday, January 09, 2006

Top 10 Dashboard Widgets for Biologists

The Dashboard of Mac OS X 10.4 "Tiger" is a great interface for a quick glance at reference materials or quick searches from frequently used resources. Research biologists often suffer from open window overload, so having a button to press to clear that all away to check a resource is great.

With that in mind, here's a collection of useful Dashboard Widgets (as well as some for the Yahoo Widget Engine):
  1. AbOrygen, the makers of BiOpen, provides 7 great widgets:

  2. Solutions from helps figure out solution compositions, and what is molecular biology if not a never ending series of molarity and dilution calculations. I am looking forward to more great widgets from these guys.
  3. PubMed Medline Search Widget is a basic search interface to PubMed, which is useful if you don't need all the features of the Entrez 1.1 widget from above.
  4. Protein Glimpse A great molecule viewer widget based on Jmol, though probably more useful as eye candy than as an investigative tool.

If you don't have Tiger, the Yahoo Widget Engine (formerly Konfabulator) has a few available widgets.
  1. NCBI Search, which allows searches of biological databases via pasted, typed, or drag-and-dropped text. Included are nucleotide and protein BLAST, PubMed, and the global Entrez searches.
  2. Pubmed Search The first public PubMed search widget for Konfabulator.
  3. BioMultiTool which has lots of tools available, including restriction digest and PCR reaction calculators. I would like to see an option to add 10% for the master mixes, since that is how I make sure I don't come up short on volume.

I have yet to find any Microsoft Gadgets for Microsoft Windows Live or for the Google Desktop Sidebar, but I am sure those will come. Please leave comments with any more widgets you find.

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.

Friday, June 10, 2005

Prism Support for Spotlight, Automator

Graphpad has announced support for Mac OS X 10.4 "Tiger" with a Spotlight importer that works for Prism 3 and 4, as well as an Automator action that works for Prism 4 only.

Since I only have Prism 3, I have only tried the Spotlight importer. Searching for statistical tests, and column titles works as expected. This is a great addition to the main statistics and graphing program I use.