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Simple Molecular Interaction Potential Generator in Python
Molecular Interaction Potential Generator
MIPGEN is a python program that will calculate Molecular Interaction Potential grids
over a given molecule, that could be either a protein or a small organic compound (drug).
The output will be a series of grids with DX format (*.dx) that the user will be able
to visualize using any Molecular visualization program like VMD, PyMol, Chimera...
For more information on dependencies and usage, please read the Documentation.
Users are welcome...
pydaqtools provides a common interface to data-acquisition hardware for Python. Control analog/digital output or acquire analog/digital input for immediate analysis with Python for scientific, educational or engineering applications.
This project is a complete cross-platform (Windows, Linux) framework for Evolutionary Computation in pure python. See the project site at http://pyevolve.sourceforge.net or the blog at http://pyevolve.sourceforge.net/wordpress
ByoDyn (http://cbbl.imim.es/ByoDyn) is a software tool for the study of biochemical networks within the framework of systems biology. SBML compatible, ByoDyn is a group effort of the Computational Biochemistry and Biophysics Lab.
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Java based multi-agent platform built on an organizational model (agent, group, role). MadKit provides general agent facilities (lifecycle management, message passing, distribution, ...), and allows high heterogeneity in agents.
pyFoam is a Python front-end to the OpenFOAM (Open Source CFD Toolbox). It introduces interactivity into OpenFOAM, simplifies connection with third-party functionality and streamlines design of custom user solvers
FAUNUS is an object oriented class library for molecular simulation, written in C++. It contains routines and utility programs for, Metropolis Monte Carlo sampling (NVT, NPT, NmuT ensembles), Macromolecules, Proton Titration, Widom Analysis etc.
IFoam is an OpenFOAM derived framework. It uses Python programming language for definition of its API. Itegrates visual components for limited post-processing. Provides access to some GUI components for more efficient set up the simulation cases.
Translates OpenFOAM (Open Source CFD Toolbox, see http://sourceforge.net/projects/foam) data into MED format (see http://www.code-aster.org/outils/med). The initial goal to develop this utility was to be able integrate OpenFOAM functionality with SALOME
The Location Containment Object Model(LCOM) is a simulation framework written in Python. LCOM provides a rule-based solution to handling partial object containment, object migration, message passing, and simulation observation.
Programs to download and work with satellite measurements, calculate solar wind (SW) propagation time and compare data to other satellites. It uses and compares different modern techniques to determine the SW planar structures orientation.
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
Spyse is a software framework for building multi-agent systems. It allows Python developers to build distributed intelligent systems of multiple cooperative agents based on FIPA, OWL, SOA and many others. Spyse is designed for ease-of-use and fun.
This project is started out of the idea to simulate simple creatures like game of live. The goal is to build up an multi processor/host environment to simulate the building of simple live in given world environments.
Pydusa is a package for parallel programming using Python. It contains a module for doing MPI programming in Python. We have added parallel solver packages such as Parallel SuperLU for solving sparse linear systems.
"Blue Planet" is a research project simulating the behaviour and darwinian evolution of unicellular lifeforms, each controlled by its own genetic program. Moreover, "Blue Planet Inhabitants" are suited for swarm intelligence and swarm research.
PGAF provides a framework tuned, user-specific genetic algorithms by handling I/O, UI, and parallelism. It is designed for optimizing functions that take a "very long time" to evaluate.
CDNsim is a GNU/LINUX simulation tool for CDNs, written in C++ (core) and python (GUI wizard). It models: redirection policies, cache policies, TCP/IP, batch simulations, statistics extraction and more. CDNsim is uses the OMNet++ library
PyDocumentary, is a class file that allows for a straight forward movement of information in a python simulation to a latex report. It is not a form of literate programming.