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The Automatic Model Optimization Reference Implementation, AMORI, is a framework that integrates the modelling and the optimization processes by providing a plug-in interface for both. A genetic algorithm and Markov simulations are currently implemented.
This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
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edef - A small simulation framework for logic circuits, autoregressive processes, digital controller circuits and many more. Also there is a GUI application, that integrates a simple development environment and a circuit editor.
STOCHSIM is a stochastic simulator for biochemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. Simple spatial structures can be built.
Pysolar is a Python library for calculating the position of the sun relative to the earth as a function of latitude, longitude, and time. There is also code included for other problems related to the development of photovoltaic systems. Still in alpha.
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Poor Man's HPC is a framework that allows distributing and running code on a server farm. pmHPC is a scaled down and simplified version of distributed computing projects such as SETI, so is a perfect fit for enthusiasts and universities.
pyPulsar is a program for simulation and fitting of solid-state NMR spectra. It provides scripting facilities using Python.
(This project was not developed for a long time: It will be soon moved in a new project currently developed)
This project simulates a multi-agent system (swarm) behavior both graphically and not. The purpose of this project is to research the properties suggested in "stability analysis of swarms" V.Gazi & K.M.Passino. Using the vpython library for 3D modeling
Esse projeto é uma reimplementação dos processadores hipotéticos descritos no livro "Fundamentos de Arquitetura de Computadores" de Raul Fernando Weber, usados em diversas faculdades no sul do Brasil, incluindo o Instituto de Informática da UFRGS.
OpenWWTP is wastewater treatment plant simulator based on (modified) Activated Sludge Model (ASM2d) The project is in very beginning stage (help wanted).
Cellogica is a cellular logic analysis tool. It incorporates sequential logic and finite state machine to elucidate the relationship between transcription factors and corresponding gene expression.
gCoder is a GUI, server-client based dyanmic programing contest controler built in Python. Its a programing contest controller like pc^2 and TopCoder(TM) areana. It use system test module, which can actually test contestent codes without any human interf
A collection of modules and enduser tools designed to help design, test and use system models. While my research (hence, the examples) is focused on hydro-ecological systems, the program can be used on any system characterized by ODEs (and soon PDEs?)
SimED is a user-friendly Differential Equation simulation software. It can integrate numerically ODEs (Ordinary Differential Equations) using several methods, plot time and phase-space diagrams for variables, and interactively choose initial conditions.
FEVal, the Finite Element Evaluator written in Python, provides easy conversion for many Finite Element data formats (both binary and ascii). Mesh modification is very easy. Values of model results can be accessed given coordinates in physical space.
Simulator for large neuronal networks using leaky INF as its basic element. Simple few line scripts will enable rapid creation of large networks with different connectivities. Aimed at researchers interested in quickly testing large networks of neurons.
Freeode is a compiler for the SIML programming language. It is a specialized language to solve differential equations. The compiler creates a python program that uses Numpy and Scipy to do the numerical computations.