Pathway Tools at SRI

Pathway Tools provides a powerful and comprehensive set of features for querying, visualization, analysis, and curation of the BioCyc database collection. Pathway Tools combines representation and inference techniques from artificial intelligence to extract additional information from genomes, and encode that information within a sophisticated ontology. Pathway Tools can operate on the BioCyc collection of PGDBs available through SRI, and on locally created PGDBs, such as for proprietary genomes. It can also operate on more than 1,700 PGDBs created by third parties, including those listed in SRI’s Registry of Pathway/Genome Databases at

To date, SRI has licensed Pathway Tools to more than 3,000 academic and industrial groups.


BioBike is a web-based, fully programmable research environment and biological knowledge base.

BioBike system is a biology-specific programming language embedded in an integrated biological knowledge-base, all accessible through the web. In the best case, biologists themselves would be able to log into the system and write their own programs to ask novel biological questions without the help of (or with very little help from) software engineers.

First published in 2002, BioBike is Common Lisp from top to bottom. The team chose Lisp because it is the most natural language in which to write complex symbolic reasoning programs. Common Lisp features such as macros are critical when extending the syntax to create the BioBike language.


StructureLab is a computational system which has been developed to permit the use of a broad array of approaches to the analysis of the structure of RNA. The goal of the development is to provide a large set of tools that can be well integrated with experimental biology to aid in the process of the determination of the underlying structure of RNA sequences.

The approach taken views the structure determination problem as one of dealing with a data base of many computationally generated structures and provides the capability to analyze this data set from different perspectives. Many algorithms are integrated into one system which also utilizes a heterogeneous computing approach permitting the use of several computer architectures to help solve the posed problems. These different computational platforms make it relatively easy to incorporate currently existing programs as well as newly developed algorithms and to match these algorithms to the appropriate hardware.


Marco Ramoni and his team at Harvard and Boston Children’s Hospital used LispWorks to develop both CAGED and BEST.

CAGED (Cluster Analysis of Gene Expression Dynamics) is a program for the analysis of temporal profiles of gene expression data. CAGED is distributed free of charge to academic and non-profit organisations. BEST (Best Enumeration of SNP Tags) is a program designed to identify the minimum set of SNPs tagging an haplotype block.