|the little b language: shared models built from reusable parts
The little b project is an effort to provide an open source language which allows scientists to build mathematical models of complex systems. The initial focus is systems biology. The goal is to stimulate widespread sharing and reuse of models.
The little b language enables scientists to build models from shared parts and create custom notations which make models easier to read and write. Currently, libraries have been developed for building ODE models of molecular networks in multi-compartment systems such as cellular epithelia.
Aneil Mallavarapu is the author and inventor of little b, and runs the project. Little b is based in Common Lisp. The environment is text-based, interactive and programmable, and contains mechanisms for rule-based reasoning, symbolic mathematics and object-oriented definitions. The syntax is designed to be terse and human-readable to facilitate communication.
Last update: Sept. 6, 2008
- Official release of little b 1.6.0, Sept 6, 2008 - console application,
Council for Systems Biology awards 2008 Merrimack Prize for development of little b
- Updated little b course materials posted (Aug 28, 2008)
- Download - Version 1.5.11 (Aug 24, 2008)
Ars Technica covers little b (July 29, 2008)
Wired Blog: Open-Source Biomodels. Molecules First, Then the World (July 22, 2008)
- Programming with Models: Modularity and abstraction provide powerful capabilities for systems biology (pdf)
Syntax for Describing Molecular Complexes (pdf)
- Presentation Jun 19, 2008
- Little b 1.5.8 source code: Bug Fixes and Numerica support
- Paper: Modular Model Building (Oct 18, 2007)
- Little b 1.5.5 source code released (Dec. 2007): Bug fixes, CLisp support, molecular complexes (Nov 22, 2007)
- Source code released on SourceForge - see download page for more information.
- Symbolic substitution in model building - Presentation
- Main tutorial - a walk through the language, beginning with core concepts and syntax, and working up to representation of biological objects and mathematics.
- Quickstarts - simple code samples.
- Introduction - motivation for and challenges of building a modular shareable modeling language.
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- post questions and feedback.
- Other sections are currently under development. Check back later for downloads, an online manual, and models.