Little b is a modeling language built to help systems biologists construct shareable ODE mathematical models representing systems of biochemical reactions.
Users write descriptions of molecules and reactions, and annotate the reactions with kinetic data and rate equations. The language dynamically infers new molecules implied by the reactions and provides facilities for generating mathematical models in MatLab.

Checkout the wiki for an overview of how to write little b code.

Getting up and running with the little b source code

This file explains how to get little b running in a Lisp implementation of your choice. A development environment containing little b is also available at http://littleb.org.

I Installing the Source Tree:

1) Checkout little b if you haven't already:

cvs -z3 -d:pserver:[email protected]:/cvsroot/littleb co -P b1 
=> creates the folder b1/

2) Checkout LISA and graph-tools inside the b1 folder:

   a) Switch to the b1 folder:
	   cd b1      
    
   b) Either execute the script/batch file found in the b1 folder: 
                  get-cvs-modules.bat (on windows)
                  bash get-cvs-modules.sh (on unix)

       The cvs program will need to be in the Shell's path.

       Or, do it manually:
	cvs -z3 -d :pserver:[email protected]:/cvsroot/littleb co -P lisa
    	 => creates the folder lisa/ inside b1/
	cvs -z3 -d :pserver:[email protected]:/cvsroot/littleb co -P graph-tools
    	 => creates the folder graph-tools/ inside b1/

When you're done, the b1 folder should look like this:

b1
  \asdf			<--- contains the ASDF defsystem 
  \graph-tools		<--- the graph-tools library
  \libraries		<--- little b system and examples libraries
  \lisa			<--- the LISA reasoning system
  \src			<--- the main little b source tree 
  \support			<--- initialization files
  .cvsignore
  b1.asd			<--- the ASDF system specification file 
  LICENSE.txt		<--- software license 
  CHANGELOG.txt		<--- CVS comments
  SOURCES.txt		<--- how to work with the sources
  RELEASE.txt           <--- release notes (bugs / what's new)
  README.txt 		<--- this file
  littleb.lisp		<--- loads little b 

II Loading Little b:

1. Open your Lisp implementation, at the prompt, load the littleb.lisp file,
changing "path/to/b1/" to point to the location of your b1 folder:

      (load "path/to/b1/littleb.lisp") 


2. If you have trouble loading, you may want to try the following steps:

(asdf:delete-binaries :b1)
(asdf:delete-binaries :lisa)
(asdf:delete-binaries :graph-tools)
(b:delete-library-binaries 'b) ;; this may not be possible depending on how the load went
(load "path/to/b1/littleb.lisp")

III Lisp Implementations

Little b is known to run in * Allegro CL 8.x * Lispworks 4.x and 5.x * CLISP 2.41 and higher (buggy - produces bad math!)

IV Dependencies:

Little b depends on LISA (Lisp Intelligent Software Agents) and the Graph-tools library, both of which can be obtained from SourceForge.

V Bug Reports:

Any bug reports should be submitted to http://sourceforge.net/tracker/?atid=851502&group_id=169724 Any feature requests should be submitted to http://sourceforge.net/tracker/?group_id=169724&atid=851505