Application: BioLingua is a novel concept in client-server programmability for computational biology and bioinformatics. Lisp is the most natural programming language in which to implement the symbolic computations that are crucial to modern systems biology. Lisp ability to manipulate code as data made the unique properties of BioBike very easy to implement. The Allegro CL compiler and garbage collector are probably the best of any Lisp implementation; Allegro CL code compares favorably against nearly every other non-C language, and often 10 times faster than the next nearest competitor. Franz has done a superb job with program-development tools, with packages to support important machinery such as threads, database access, and web server capabilities. BioBike is in use in a number of laboratories around the world. We strongly believe that the facilities that it offers in support of important biological science would not have been possible without a Lisp implementation of the quality of ACL.
Application: Encyclopedia of E. coli Genes and Metabolism
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is linked to other biological databases containing protein and nucleic-acid sequence data, bibliographic data, protein structures, and descriptions of different E. coli strains. In addition, the Pathway Tools software that underlies EcoCyc is not specific to E. coli, but has been applied to manage genomic and biochemical data for a variety of organisms.
MDL Information Systems
Application: MDL Information Systems uses Lisp and Allegro CL to help pharmaceutical companies create new drugs.
SRI International, Artificial Intelligence Center, Bioinformatics
Application: Pathway Tools by SRI.
SRI International offers innovative tools for modeling and analyzing genomes, metabolic pathways, and regulatory networks to support activities in drug discovery, agriculture, and biotechnology. These tools accelerate research and lead to a greater understanding of biological systems. SRI's unique Omics Viewers support visualization and analysis of large omics datasets on genome-scale cellular network diagrams. BioCyc and Pathway Tools are freely available for academic research.
Harvard Children's Hospital Informatics Program
Application: SNPer -- Harvard's Children's Hospital Informatics Program uses Lisp and Allegro CL to power SNPer, a web-based application that provides scientists with a variety of tools that greatly speed up the analysis process of SNPs (Single Nucleotide Polymorphisms). Using SNPper, scientists can now accomplish the same amount of work in a day that used to take weeks to complete.
Principles of Biomedical
Informatics, Second Edition
Application: The code examples in this book:
Lisp is the main programing language in this edition, as in the first. It is by far the best for achieving the goals of the book, to present biomedical informatics as a systematic set of formal ideas and methods that are naturally expressed as computations on well-defined representations. In Chapter 1, the basic ideas of symbolic computing are introduced gradually as needed. The Appendix has been expanded to include more tutorial material as well as references to aid the reader who is not so familiar with Lisp. All the code that appears in this book is available at the author's web site at the University of Washington, http://faculty.washington.edu/ikalet/
Application: 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.
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