A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.
A neural network package for Octave! Goal is to be as compatible as possible to the one of MATLAB(TM).
RYUON : many-particle simulation suite
Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
Plasmodium Typing Utility Software
The goal of PlaTypUS is to establish a unified Plasmodium whole genome analysis tool, that aligns short read sequences in an agreed upon manner, with many quality control steps, and calls both SNVs and CNVs in a community agreed standard way. We also seek to provide this analysis in a stand-alone graphic user interface so that labs around the world can analyze their own whole genome sequencing data, rather than relying on outside institutes.
The Sound Description Interchange Format (SDIF) is an established standard for the interchange of sound descriptions and analysis data. This project provides libraries, SDIF (in C) and Easdif (in C++), tools, and wrappers to read and write SDIF files.
A way to use XFOIL for airfoil analysis with MATLAB. Utilizes Perl to provide a pty to interface with XFOIL and to parse results to send back to MATLAB. "MatPerlXFOIL: Half MATLAB, Half Perl. Half XFOIL. EXELSIOR!"
APEX Tools is a collection of utilities used in conjunction with the processing of airborne hyperspectral data developed for the ESA-Prodex supported Airborne Prism EXperiment (APEX).
Biolet is project aimed to analyze genomic DNA sequences using wavelets. Of additional interest may be a batch processing tool for doing round-robin scheduling of jobs on a beowulf cluster. For that checkout the project robin from the CVS.
Build system And Software Implementation Standard
The CMake Build system And Software Implementation Standard makes it easy to create sharable software and libraries that work together. This is accomplished by combining and documenting some of the best practices and utilities available. More importantly, BASIS supplies a fully integrated suite of functionality to make the whole process seamless! Check out the web site for more information. The Git repository of this project is hosted on GitHub. Some interesting facts about this project can be found on Ohloh at https://www.ohloh.net/p/cmake-basis.
Perl module for reading/writing QuickBooks IIF files.
IT-Students Project to probe collaboration in software development
This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data
A collection of m-files enhancing Matlab experience
The M-lab toolbox is a collection of m-files enhancing Matlab experience. It provides several useful tools for scientist, engineers and students. The tools range from very simple functions to very developped classes and high-level gestion of Matlab's interface. A transparent gestion of Matlab's path is provided in a project-oriented architecture.
Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.
A set of utilities for manipulating ICTP's RegCM3 input and output data.
Design and develop Recommendation and Adaptive Prediction Engines to address eCommerce opportunities. Build a portfolio of engines by creating and porting algorithms from multiple disciplines to a usable form. Try to solve NetFlix and other challenges.
Magnetostatic finite differences simulation tool based on GNU Octave and a Perl/Tk user interface.
This project deals with algorithms on Matrices.
Lattice simulation of biochemical reactions and diffusion
This site hosts code investigating the role of spatial heterogeneity in biochemical signaling. Motivated by several biological examples, we study the behavior of covalent modification networks when the activating component is localized to a planar membrane in either a random or clustered configuration. Reactions and diffusion are implemented on a three-dimensional lattice.