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Snap (snap-pari) is a computer program for studying arithmetic invariants of hyperbolic 3-manifolds. See: Computing arithmetic invariants of 3-manifolds by Coulson, Goodman, Hodgson and Neumann, Experimental Mathematics Vol.9 (2000) 1.
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
Converts Digital Terrain Elevation Data from one level to another. (Currently only converts DTED1>DTED2) No longer in development due to personal time constraints. If there are features you desperately need, feel free to ask, or write it your self :)
On December 8, 2009 the UK Met Office released records of worldwide land surface temperature readings. This project analyzes these records and produces output files that can be read by gnuplot and Google Earth to show temperature trends.
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Maximally flat (maxflat) digital filter design in Java, with arbitrary numbers of poles and zeros. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi.
dprimer is a command line utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
Maximally flat (maxflat) digital filter design for Octave and Matlab. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi. Handles arbitrary numbers of poles and zeros.
DawNLITE is a Natural-Language-based Image Transmoding Engine. The software transforms an image to a video as recorded by a virtual camera panning and zooming over the image, following a natural language text description of the image.
cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files
vcif is an open source software for validation of Crystallographic Information Files. It supports lexical, parser and dictionary validation (DDL 1 and 2 are fully supported, DDLm draft partially supported)
An efficient implementation of the Smith-Waterman algorithm that takes advantage of SIMD instruction sets in modern CPUs. The Smith-Waterman algorithm is used for sequence alignment in bioinformatics.
A cross platform Open Source implementation of Digi's "Digi Discovery" utility as well as a Java library providing the features of the ADDP (Advanced Digi Discovery Protocol) protocol. The protocol is documented at http://qbeukes.blogspot.com/search/label/advanced%20digi%20discovery%20protocol
SystemML is an XML format for exchange of mathematical systems for numerical simulation. This toolbox offers support for the SystemML infrastructure. It is included in the distributions of SystemML execution clients, but can be installed separately.
pyOBD-II (a.k.a. "pyobd2") is a Python library for communicating with OBD-II vehicles. Its goal is to make writing programs for vehicle diagnostics and monitoring vehicle data as easy as possible. Relies on pySerial to communicate with ELM scanners.
Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.
This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.
A logging shell that can log commands from a shell. Designed to act as an automated lab-book for people that conduct experiments in their standard shell environments. Users can log and re-run experiments with little/no manual effort or interference.