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).
Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc
Perl module for reading/writing QuickBooks IIF files.
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.
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.
Group of small samples meant to simply illustrate and explore different concepts in computer science.
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.
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!"
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.
RYUON : many-particle simulation suite
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.
The project aims at defining standard for common approach of indexing various types of data in peer-to-peer networks. Among content data following categories can be distinguished: multimedia video, images and audio recordings.
Magnetostatic finite differences simulation tool based on GNU Octave and a Perl/Tk user interface.
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.