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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.
MANIKK is a toolkit for generating numerical interaction parameters -- describing the interaction between metallic atoms in a coherent lattice -- and for performing numerical Monte Carlo-simulations of physical properties of alloy systems.
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
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KU1K is a set of tools for 4D,5D and 6D compact U(1) lattice gauge theory Monte Carlo simulation using the Skipis-Vantzos algorithm. As the calculations involved, even for the 4D case, are consuming, the project is modular so as to run on the Grid.
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.
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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.
SimForge is a web-based Agent Based Model of an Open Source Ecosystem implemented in Python with Django. Developers act on randomly drawn preferences to create, collaborate, and use software.
aVolve is an evolutionary/genetic algorithm designed to evolve single-cell organisms in a micro ecosystem. It currently uses the JGAP Genetic algorithm, but does include a primitive genetic algorithm written in Python.
PyAero is a toolkit developped at andheo for CFD software :
post-processing, curve generation, …
Currently PyAero focuses on ONERA's code "Cedre".
PyAero is powered by Qt, Python, PySide, enthought and pyLot.
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.
Create a series of programs to help ABAQUS users from creating models to retrieve results.
Partially dump the slow and resource-consuming CAE interface.
Python program devoted to study the relationship between cells during inmune response. It is based on a 3D periodic boundary conditions grid where cells see each other and react according to certain movement, growth and interaction rules.
Python-based GUI for discrete-event system modeling and simulation
DEVSimPy is an advanced wxPython GUI for the modeling and simulation of systems based on the DEVS (Discrete EVent system Specification) formalism. Features include powerful built-in editor, advanced modeling approach, powerful discrete event simulation algorithm, import/export DEVS components library and more.