Open Source Python Simulation Software - Page 4

C++QED is an application-programming framework for simulating open quantum dynamics in general. It has demonstrated the ability to simulate full Master equation of up to several thousand, and quantum trajectories of up to several hundred thousand dimensions. The basic idea is to allow users to build arbitrarily complex interacting quantum systems out of free subsystems and interactions (elements), and simulate their time evolution with a number of available time-evolution drivers. C++QEDv2 specifies a small grammar to describe composite quantum systems. Apart from providing a number of elements out of the box, there are tools which facilitate the implementation of new elements. These are being added continuously, as the need arises. The principal concept of the design of C++QEDv2 is that all information available at compile time should be processed as such, with the help of TMP. The framework is very sensitive to performance both in computer resources and coding/design.

PySCeS CBMPy is a new platform for constraint based modelling and analysis. It has been designed using principles developed in the PySCeS simulation software project: usability, flexibility and accessibility. CBMPy supports the latest standards for encoding CBM models encoding, SBML L3 FBC, COBRA as well as MIRIAM compliant RDF and custom annotations. Its architecture is both extensible and flexible using data structures that are intuitive to the biologist while transparently translating these into the underlying mathematical structures. . CBMPy implements popular analyses such as FBA, FVA, element/charge balancing, network analysis and model editing as well as advanced methods developed for the ecosystem modelling. CBMPy supports user interaction via: - interactive console or as a library for advanced use - GUI, visual representation of the model, analysis methods - a SOAP based webAPI exposes high level functionality via web services

CHLone is a CGNS/SIDS compliant mapping on HDF5. You can read/write CGNS/HDF5 files and access to node through a C API interface or using a Python module.

Cellicone is a project to develop an artificial life organism with the necessary components to make it comparable to biological life as we know it. This includes components ranging from proteins to cells to organs to limbs, and many steps between.

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.

Charybdis is a Python-driven set of applications for solving partial differential equations on irregular domains.

A toolkit in C++ and python to process both experimental and simulation data of colloidal particles. Includes among others * a multiscale particle tracking algorithm [1] whose C++ implementation is optimised for 3D confocal data. Python implementation is more versatile (2D and 3D data). * a Leica file reader, * Steindhard bond orientational order calculation * a VTK file writer 1. Leocmach, M. & Tanaka, H. A novel particle tracking method with individual particle size measurement and its application to ordering in glassy hard sphere colloids. Soft Matter 9, 1447–1457 (2013). https://dx.doi.org/10.1039/C2SM27107A (http://arxiv.org/pdf/1301.7237.pdf)

Crujisim is a tool to allow Air Traffic Controllers trainees to practice in a radar environment. Different users connect to a hosting server to act either as controllers for adjacent positions or pseudopilots.

Dielectrophoresis for microfluidic applications, especially those biological, implemented in python

Distributions Networks Analyzer (DNA) is a tool for simulating (power flow) and analyzing electrical distribution networks. Users can easily implement and test their own power flow, optimal power flow and control algorithms.

Emulica provides manufacturing control engineers and researchers with generic modeling components to build industry-scale virtual (emulated) shop floor systems, and thus test control approaches.

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".

experimaestro is an experiment manager, and is composed of (1) a job scheduler that handles dependencies and locking (2) a modular experiment description framework, that allows easy description of the various parts of an experiments.

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.

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.

This is the first force-matching software published with the ability to do general coarse-graining for molecular systems.

A language and a compiler for the solution of differential equations (ODE). Both lumped and distributed variables (PDE) will be possible. The ability to solve DAEs is a long term goal. The compiler generates a Python program that does the computation.

Free HyperSim is a generic simulator (simulink like) platform adapted for shared projects. Components (icons) are plugins (python code, batch or executable files) which can be shared between users.

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.

GAI is a graphical GIS based front end to ANUGA which allows convenient and visual tools for setting up hydrodynamic models. GAI depends on ANUGA to run the models created by GAI.

"gtdev" is an open source tool which assists the engineer in developing a new gas turbine (1D Thermo- and Aerodynamics). It is created by the student research group "Hummingbird - TUM Gas Turbines" placed at the LFA, TU Munich: http://www.hummingbird.tum.de

GemSIM is a software package for generating realistic simulated next-generation sequencing reads with quality score values. Both Illumina and Roche/454 reads (single or paired end) can be simulated using appropriate empirical error models.

Gene-Environment iNteraction Simulator 2 (GENS2) simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. GENS2 is based on data with realistic patterns of linkage disequilibrium, and imposes no limitations either on the number of individuals to be simulated or on number of non-predisposing genetic/environmental factors to be considered. The GENS2 tool is able to simulate gene-environment and gene-gene interactions. To make the Simulator more intuitive, the input parameters are expressed as standard epidemiological quantities. GENS2 is written in Python language and takes advantage of operators and modules provided by the simuPOP simulation environment. It can be used through a graphical or a command-line interface.

Hermes -- a set of libraries and tools for the support of scientific simulation and data archival.

Analysis software for Nbody/SPH or SPH simulations (e.g. performed with Gadget II). See http://sourceforge.net/apps/wordpress/hyplot/about and http://sourceforge.net/apps/trac/hyplot/wiki for more information.