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Volta is a suite of development tools for distributed, hard real-time systems. It includes Cascade, a control flow analysis tool for Java, and Clepsydra, a worst-case execution time analyzer. Also included is a Clepsydra plug-in for jEdit.
Simulates data from a gaussian/beta/piecewise-linear species response function on an environmental gradient, with different sampling (error) distributions. See "Cline (biology)" on wikipedia.org.
A collection of compact, powerful programs and functions, written in C, for the analysis and transformation of data. No object or structure dependencies, no fancy interfaces - just good tools.
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The goal of this project is to develop converter from OCAD map format to open PFM(Polish Map Format) for further use with cGPSmapper compiler. This allows easy use of OCAD maps in Garmin GPS receivers.
GISpatialNet is a Java-based tool for mapping network data (nodes and edges between them) to spatial coordinates; reformatting network and spatial data together; and calculating spatial network measures.
Install by saving to c:\ drive and typing the following in a commandline:
java -jar c:\GISpatialNet-0.9b.jar
haggies is an optimizing code generator. It can read in expressions in common notation and generate output for many programming languages including C/C++, Java, Fortran, Python and many others.
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.
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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.
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.
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
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
FONZIE is a bioinformatic tool written in Python developed for the genetic cartography speciality. FONZIE allow as well to find markers on a set of sequences than to find associate oligonucleotides. http://www.biomedcentral.com/1756-0500/3/322/abstra
An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.