Open Source Python Simulation Software - Page 2

The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.

ANUGA is a software implementation of a hydrodynamic model which is specifically designed to model wetting and drying processes. ANUGA is a joint development project between Geoscience Australia (GA) and the Australian National University (ANU). ANUGA is now being developed on github at https://github.com/anuga-community/anuga_core For information on ANUGA please go to http://anuga.anu.edu.au The ANUGA project is described on http://en.wikipedia.org/wiki/ANUGA_Hydro

An application programming (API) and graphical user interface (GUI) to facilitate the use of PENELOPE's program PENEPMA.

CEA Simplified is a GUI for a released version of NASA's CEA program from the 1970s. It is similar to the rocketCEA library for python or the ProPEP GUIs in that it attempts to provide an updated tool for using the same underlying software, but it is more focused on being beginner friendly.

The OpenCMISS-Zinc Library (opencmiss.org/zinc), or Zinc, is a software library for building interactive graphical modelling and visualisation applications. Models are represented in Zinc as mathematical fields defined over domains, including finite elements with support for high-order basis functions, complex parameter mappings and time variation, and image-based fields. Further fields can be defined by mathematical expressions and algorithms on existing fields, including image processing filters. Zinc model data structures are dynamic, supporting interactive applications which programmatically create, destroy and modify parts of models.

This is a sophisticated & integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). It supports symbolic math, optimization, continuation, data analysis, biological apps...

Computational electromagnetics software. Uses surface Method of Moments, enhanced by using the Multilevel Fast Multipole Method. Code is parallelized and runs on laptops, desktops and clusters. The code precision is adjustable, it is fast and uses little memory. CFIE is used for closed surfaces, and EFIE for open PEC surfaces. Can function on GMSH, GiD and ANSYS meshes.

Crystalsim is a simple freeware program with a neat graphical user interface for X-ray diffraction (XRD) data analysis . It can simulates all possible {hkl} planes data for the selected crystal. Crystallographic Information File (.cif) can also be used. Analyze both powder diffraction and single crystal data . Indexed at International Union of Crystallography (IUCR). Crystalline lattice parameters such as ‘a’, ‘b’, ‘c’ as well as interfacial angles such as alpha, beta, gamma can also be entered manually. Processed data can be saved as .csv file format. Designed by M Kanagasabapathy, Assistant Professor, Department of Chemistry, Rajus' College, Affiliated to Madurai Kamaraj University Rajapalayam (TN) India email: rrcmks(at)gmail.com

This application provides a web based visual browser for NetCDF files. The application provides a simple and friendly user interface for getting a quick overview of the data contained in the files.

StochPy - Stochastistic modeling in Python - is an easy-to-use package, which provides several stochastic simulation algorithms and unique analysis techniques, which can be used for stochastic simulations of biochemical systems.

NMEASIM sends NMEA 0183 sentences to a navigation SW such as OpenCpn via a serial com port or a UDP channel. These NMEA sentences simulate data coming from a GPS(sentence $GPRMC...) and an AIS receiver(sentence !AIVDM...) All the parameters : name, mmsi, initial position (lat/long), COG, SOG for my boat as well as for AIS targets, and I/O configuration (com port...) can be edited in the 'datasimul.json' (file created by the app with default values in V1.0) Just Download the nmeasim.exe file (green button above) and launch it. Be patient for a few seconds if you have a slow PC! Go to the 'Files' tab to look at the readme file and download any additional file if needed.

Do you work with chemical reactors? Are you curious about them? ASALI is the open-source code that you are looking for. Chemical reactor models, transport/thermodynamic properties of gases, equilibrium calculations. ASALI couples all these features with an user friendly graphical interface. Modeling chemical reactors has never been so easy.

Cantera is a suite of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and/or transport processes. It can be used from MATLAB, Python, C++, or Fortran.

xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by filtering the data using a modular, user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level.

VLE is a multi-modeling and simulation environment to study complex dynamic systems. VLE is based on the discrete event specification DEVS. and it implements the DSDE formalism (A merge of Dynamic Structure DEVS, DSDEVS, with Parallel DEVS, PDEVS). VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages.

Moved to https://github.com/rdiankov/openrave An open-source, cross-platform, plugin-based robot planning environment for autonomous robotics. Includes services like collision detection, physics, (inverse) kinematics, sensors, robot controls, python bindings, and a network scripting environment.

We experiment with Evolution of Artifical Neural Networks, combining the two fields of Evolutionary Computation and ANNs. Our methods are applied to a variety of interesting problems. To learn more, click on "Home Page", "Mail", or "Files".

Free 3D Acropolis is a model 3D in hight resolution of the Acropolis of Athens shortly after its construction.

The Modular System for Shelves and Coasts (MOSSCO) is a coupling framework for Earth System Models. It helps users to integrate their own numerical models with other developments. Quick Start: git clone git://git.code.sf.net/p/mossco/setups mossco-setups git clone git://git.code.sf.net/p/mossco/code mossco-code cd mossco-code cat QuickStart.md or read online https://sf.net/p/mossco/code/ci/master/tree/QuickStart.md Beware: this is alpha software, expect trouble! ------------------------- Better, read the full documentation online http://www.mossco.de/doc or make it yourself make doc acroread doc/mossco_documentation.pdf ---------------------- Why MOSSCO? MOSSCO, the "Modular System for Shelves and Coasts" is a framework for coupling processes or domains that are originally developed in standalone numerical models. The software MOSSCO implements this infrastructure in the form of a library of components and couplers, and of example coupled application.

PyAMS (Python for Analog and Mixed Signals) is used to simplify modeling analog elements and simulate electronic circuit The objectives of PyAMS is: - Drawing circuit by schematic (CAD approach); - Simulating the circuit; - Creating new symbols for models; - Creating new models of electrical elements by using Python language with pyams_lib; - Presenting simulation results in waveform or in probe; - PyAMS is developed with Python 3+, ElectronJS and NodeJs - Licensed under: PyAMS is free to use. GPLv3 . - Open source.

Biskit is a python library for structural bioinformatics research. It simplifies the analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories and offers a platform for the rapid integration of external programs. PLEASE NOTE: The Biskit source code as well as any later releases are now hosted on https://github.com/graik/biskit The sourceforge repo is only kept here for reference.

A general-purpose individual-based forward-time population genetics simulation environment

A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.

NGSolve is a general purpose Finite Element Library on top of Netgen. With the basic library one can solve heat flow equations, Maxwell equations, and solid mechanical problems. Several add-ons are available for particular application classes. New paper: J. Schöberl: "C++11 Implementation of Finite Elements in NGSolve", ASC Report 30/2014, Institute for Analysis and Scientific Computing, Vienna University of Technology, 2014 http://www.asc.tuwien.ac.at/~schoeberl/wiki/publications/ngs-cpp11.pdf

PySCeS is the Python Simulator of Cellular Systems. For a network of coupled reactions it does a stoichiometric matrix analysis, calculates the time course and steady state, and does a complete control analysis.