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A framework for the visualization of multi-layer networks
MuLaViTo is a multi-layer visualization framework which allows to visualize relations between multiple graphs in derived applications. Moreover, it provides helpful means like k-shortest path algorithms, running algorithms in a separate thread, ...
***** Discontinued (may still work but will not be updated and supported anymore) *****
This extension connects the simulation platform NetLogo with the statistical analysis software R via Rserve. It adds some new primitives to NetLogo, which offers the interchange of data with R and the call of R functions from NetLogo. See the documentation for more details.
There is a similar extension, which use a direct connection to R via rJava/JRI, see http://r-ext.sourceforge.net. This extension is a little bit more complicated to set up but offers some more functionalities (e.g. interactive shell, more plotting functionalities).
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Please have also a look on our info page about other NetLogo extensions at http://www.uni-goettingen.de/en/315075.html.
PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.
NetBuilder' is a tool for building, visualizing, and simulating multi-layered biological networks, structured as hierarchical Petri-nets. It has a built-in stochastic simulator, but also provides easy access to other simulation and analysis.
Zwicker's Loudness Calculation (ISO532B) Tools. The project includes a loudness calculation program based on Zwicker's Method, and a WAV file analyzer generating data files for loudness calculation. Documentation and test files are also provided.
Combines Blender's graphical interface and rendering capabilities with MBDyn's multi-body dynamics, aerodynamics, and aeroelastics simulation and analysis, for rapid modeling and realistic rendering of physics based multi-body simulations.
General purpose discrete event simulation (DES) framework for the Python programming language. Khronos gathers ideas from other simulation software and tries to provide a simple and poweful toolset for simulation of discrete systems.
Siafu simulates individual agents and their context, from home to city-wide scenarios. As a developer, you use the API to write your simulation for the purposes of data-set generation, test or visualization, optionally hooking it to your own application.
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.
Guanxi is a robust analysis and simulation application for Social Network Analysts. Guanxi allows researchers in the field to create, import, and export an endless array of networks, analyze their structure, and run custom dynamics over them.
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures.
Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html
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.
Use SASSIE to generate and manipulate large numbers of molecular structures and then calculate the SAXS, SANS, and neutron reflectivity profiles from atomistic structures. Use for intrinsically disordered proteins. We need alpha-testers and developers.
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.
Java package to study a clustering model described in the paper \"Novel Clustering Algorithm Based Upon Games on Evolving Network\" by Q. Li, Z. Chen, Y. He and J-P. Jiang (in arxiv: http://arxiv.org/pdf/0812.5064v1), generalizations and similar issues.
PyMaTi is a simple and easy to use GUI for numerical and scientific computing in Python. It surrounds well know packages NumPy and Matplotlib and provides possibility to immediately play with numerical python from intuitive user interface.
A real-time graph plotter. While your application is computing and logging results to a CSV file using the LiveGraph Writer API, the plotter lets you visualise and monitor the results live - by instantly plotting charts and graphs of the data.
The Model Interaction Environment for Neuroscience provides tools for development, searching, editing, execution, and visualization of biophysical models, abstract mathematical models, and experimental protocols used in neuroscience research.
PetriKit is a modular toolkit for Petri Net analysis. It allows the extraction of basic properties, extraction of invariants, and generation of reachability graph. Results can be formatted in plain text, HTML or XML files.