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This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
Data mining tool for sequences (e.g. trajectories on a map, visited web pages, etc.) that creates a succinct description of the sequences, given a taxonomy (e.g. regions and sub-regions in the map, categories and sub-categories of pages, etc.).
A Java package that provides several computations related to the edit distance of strings. Other than the basic Levenshtein, this algorithm can rearange words when comparing. The class can also provide details of how words could be transformed.
transpose is a fast and efficient command-line tool that transposes (the rows become the columns, the columns become the rows) or reshapes a matrix in plain text. Inputs and outputs can be files or streams.
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curl-benchmark is an open-source tool written in C-language that generates multiple and simultaneous HTTP/HTTPS requests and returns data for performance analysis.
JTHERGAS (a JAVA implementation of THERGAS) estimates thermodynamic information from two dimensional graphical representations of molecules and radicals based on the Benson additivity method.
A simple program that solves linear equation systems. As of now only numerical coefficients are supported. The program is very simple and not suited for big matrices, since it uses laplace's method.
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A strong, yet minimalistic Math-oriented Programming Language (MML) providing an easy-to-use console and a command-line script interpreter, targetted towards fast calculations for extremely big numbers, and bundled with a number of math libraries.
The Fortran program MOLLY generates atomic positions in a molecule from those of a small number of prototype atoms and the molecule's point symmetry. It is intended as a time-saving aid in preparing input data for computational physics software.
Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
OSM XML to CSV conversion. POI only, polygons (and polylines, but not recommended) are approximated by centroid. Result is a 3-column table with lon, lat and value (for a particular key to be chosen beforehand).
Covered is a Verilog code coverage utility using VCD/LXT/FST dumpfiles (or VPI interface) and the design to generate line, toggle, memory, combinational logic, FSM state/arc and assertion coverage report metrics viewable via GUI or ASCII format.
This project is ported to github and can be found at:
https://github.com/chiphackers/covered
The Regional Urban Growth Model (RUG).
RUG Development Team
c/o Todd BenDor
Department of City and Regional Planning
University of North Carolina at Chapel Hill
CB #3140, New East Building
Chapel Hill, NC 27599-3140
bendor AT unc.edu
Porcupine2 is a small wearable sensory unit for logging motion data and doing low-level activity recognition. The project includes electronic schematics for the hardware, software for the microcontroller and client-side software for hardware-interaction.
A set of commandline tools to extract, manipulate, and present multidimensional data. These tools are targeted specifically at summarizing results of simulation experiments.
This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. "Novel computational methods for increasing PCR primer design effectiveness in directed sequencing". BMC Bioinformatics 2008, 9:191.
Methods and testing of methods for automatic analysis of in situ cyclic
voltammetry data.
This, at least initially, is the code from my masters thesis, which was
done as a contribution to a larger project called Aevum. Aevum is being
developed at t