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Quick Introduction to BIRCH
by Brian Fristensky, University of Manitoba

BIRCH is a resource for molecular biology, consisting of software and databases

Most of the programs and databases of BIRCH have been unified through bioLegato. bioLegato is best thought of as a program that runs other programs. As new programs are added to BIRCH, they appear as menu items in bioLegato. bioLegato takes care of all the "behind the scenes" tasks, such as interconverting file formats, allowing the user to concentrate on the science.

biolegato window containing protein 4-coumarate coA ligase protein coding sequences (CDS) extracted from GenBank entries using FEATURES. Translation of the sequences is shown at the bottom of the window. The two highlighted sequences were compared by a P1HOM, a matrix similarity program. P1HOM output appears in the pop-up window. The degree of local similarity is indicated by letters in the diagonal (A=100%, B=98-99% .. Z= 50-51%).

Using BIRCH at the command line

Most BIRCH programs can be run at the command line. Below is an example of DIGEST, which calculates restriction fragments resulting from multiple enzyme digests.

DIGEST session, showing fragments resulting from double digestion of a linear DNA fragment with AatII and BsmI. The left colum lists five fragments shown, in descending order of size. The locations of fragment ends are indicated in the two rightmost columns.
 
 
BIRCH makes it easy to take data from one program to the next, allowing the user to tailor the flow of analysis for a given problem.  This figure illustrates the steps in construction of a phylogenetic tree, from raw GenBank entries to trees replicated by bootstrapping.  At each step in the process, the user can choose one of several programs. biolegato takes care of moving data from one program to the next.

click here for an example

 

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BIRCH is seamlessly integrated into a complete desktop environment

BIRCH programs run within the larger context of the Unix system,  a comprehensive body of applications is available, including 


BIRCH Desktop

The applications software base for Unix is now so extensive that users who wish to abandon the Windows platform altogether can do all computing on an easy to use Unix desktop, eliminating most of the problems encountered in the PC world (rapid hardware obsolescence, backups, poor security, inconsistent system administration, software/hardware incompatibility etc.)

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Access BIRCH at work, at home, when travelling



VNC stands for Virtual Network Computing.  In essence, when you run an X-Windows session on from an X-terminal, Unix creates a screen image on the terminal, which displays on your monitor. VNC creates a screen image at the server, which can be viewed from anywhere, using the VNC Viewer. VNC Viewers are available for Unix, PCs, and there is even a Java version that runs in any Java-enabled Web browser. Con sequently, no matter where you go, you can run a full X-window session, from any PC.

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BIRCH is free

Students, staff and faculty at the U. of M., as well as at other BIRCH installations, have free access to BIRCH. Simply obtain a Unix userid and set up your account as described on the BIRCH web site.

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Questions and comments regarding this page should be sent toi psgendb@cc.umanitoba.ca