Introduction

BioCaml aims to be a library of useful (and maybe not so useful :P) functions for bioinformatics, written in the Objective Caml (OCaml) language. OCaml is a wonderful functional language!

BioCaml has started out as a hobby project (and still is, I guess...), but our aims are high :). Development is in its early stages, and tends to be centered (at least for now) around what we need and feel useful, rather than what may be more useful for the public.

News

02/12/2003: Added IDL files for wrapping the MySQL C API

01/09/2003: Added code to translate codons to amino acids. (big deal! :-P)

06/18/2002: Working on some string indexing structures (MASCDAWG)

02/07/2002: Implemented K-Means clustering algorithm.

01/17/2002: Added bindings for libRmath - stand-alone math functions from the statistical package R

12/10/2001: Removed access restrictions for biocaml.org pages so everyone can see.

Misc.

• Source tarball
• Browse cvs repository
• Documentation via ocamldoc

TODO/IDEAS

• More careful consideration on the design of library
• Parallel processing (How? using OCamlMPI?)

Authors

• Hideo Bannai
• Yoshinori Tamada

Other bio-software written in Objective Caml

iPSORT

iPSORT is a simple predictor of N-terminal protein sorting signals.

SUMO

SuMo is a system for extracting structural and possibly functional similarities in 3D structures of proteins.

Links

• BioPerl, BioPython, BioRuby, BioJava, The Open Bioinformatics Foundation
• The Objective Caml Home
• Simple OCaml Introduction (In Japanese)
• HypothesisCreator
• Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo.