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The Caml Hump: Science :: Biology

Stable

Scientific software
Sumo [14-Apr-2003, Stable]
A system for extracting structural and possibly functional similarities in 3D structures of proteins.
Author: Martin Jambon.

Beta

Native OCaml libraries
MyCGR [03-Jul-2006, version 0.98, Beta] Has a tutorial
This software implements the researches of the thesis of Peggy Cénac. Use the CGR to build a new family of tests of structure of sequences (i.i.d., markovian), empirically check the level and power of the tests and apply them on DNA sequences. Generalize the dinucleotide abundance profile to a CGR-based relative abundance profile and use this profile on DNA sequences to build taxonomy trees. Define CGR-trees, which are Digital Search Trees built from sequences, and check that the empirical longest branches, shortest branches and insertion level match the theorical results of the thesis.

Development code

Native OCaml libraries
BioCaml [12-Aug-2002, Development code]
BioCaml aims to be a library of useful functions for bioinformatics, written in the Objective Caml (OCaml) language.
Native OCaml libraries
Camlspikes [05-May-2009, Development code]
Library for the (possibly distributed) simulation of networks of spiking neurons, with an emphasis on the quick and easy implementation of one's own neuron or synapse model.
Author: Guillaume Hennequin.