Pinned Repositories
binpacking
Distribution of weighted items to bins (either a fixed number of bins or a fixed number of volume per bin). Data may be in form of list, dictionary, list of tuples or csv-file.
COVID19CaseNumberModel
Fit the algebraic growth of case numbers in Mainland China with an SIR-containment model
epipack
Fast prototyping of epidemiological models based on reaction equations. Analyze the ODEs analytically or numerically, or run stochastic simulations on networks/well-mixed systems.
fisheye
The original fisheye function has a visual flaw due to discontiuities in its first derivative. Here, I present a fisheye function which is continuously differentiable and hence more pleasing to the eye.
netwulf
Interactive visualization of networks based on Ulf Aslak's d3 web app.
python-fisheye
Transform single points or arrays of points using several fisheye functions.
qsuite
command line tool to provide an easy framework to submit computer simulations of arbitrary variety in parameter space to various cluster frameworks
reaction-diffusion
Some Python examples to obtain reaction-diffusion results and animations.
smallworld
Generate and analyze small-world networks according to the revised Watts-Strogatz model where the randomization at β = 1 is truly equal to the Erdős-Rényi network model.
tacoma
Temporal networks in Python. Provides fast tools to analyze temporal contact networks and simulate dynamic processes on them using Gillespie's SSA.
benmaier's Repositories
benmaier/reaction-diffusion
Some Python examples to obtain reaction-diffusion results and animations.
benmaier/python-fisheye
Transform single points or arrays of points using several fisheye functions.
benmaier/fisheye
The original fisheye function has a visual flaw due to discontiuities in its first derivative. Here, I present a fisheye function which is continuously differentiable and hence more pleasing to the eye.
benmaier/phase_space_example
Examples on how to integrate ODE systems with Python and how to plot trajectories in phase space.
benmaier/better_understanding
A track made with Sonic Pi
benmaier/couzinswarm
Simulating fish swarming behavior using the model by Iain Couzin et al.
benmaier/cividis
Register `cividis` with matplotlib, a color map optimized for color vision deficiency, as published in Nuñez, et al. (2018), PLoS ONE 13(7): e0199239 .
benmaier/cThredgeCorr
For fast generation of edge lists from the thresholded edge correlation model.
benmaier/GTOM
Computes the general topological overlap measure for undirected and unweighted networks
benmaier/3d-fractals
create 3D fractals in blender
benmaier/BiasedRandomWalks
Provides classes around biased random walks on networks.
benmaier/boarding_school_SIR
Fit SIR dynamics to the prevalence curve of an H1N1 outbreak of a British boarding school in 1978.
benmaier/cNetworkDiff
For fast diffusion simulation (or random walks) on networks.
benmaier/diese-visuelle-welt
ruby script for the track "Diese visuelle Welt" written in Sonic Pi
benmaier/DynGillEpi
Runs Gillespie contagion processes on time dependent contact networks.
benmaier/LyXTufteThesis
A LyX template for PhD theses at HU Berlin
benmaier/network-properties
Package to easily compute and wrap a bunch of network properties for a given graph
benmaier/nwDiff
Simulates diffusion processes on networks.
benmaier/RK45js
JavaScript implementation of Runge-Kutta-Fehlberg numerical integration for the browser
benmaier/BFMaierFBnetwork
Facebook friendship network of author B.F. Maier with himself removed
benmaier/buehne
Ambient track made in Sonic Pi
benmaier/CSSS18_Lindenmayer_Shirt
Builds a fractal structure from a base png
benmaier/csss2018
benmaier/curved-edges
playing around with curved edges and arrows in force-directed graph visualizations
benmaier/D3-Opinion-Dynamics
Implementation of the adaptive voter model and copan:Exploit in d3
benmaier/FoxDot
Python driven environment for Live Coding
benmaier/grayscott-js
Gray-Scott system in JavaScript, sadly without webGL support and hence a bit slow
benmaier/lmfit-py
Non-Linear Least Squares Minimization, with flexible Parameter settings, based on scipy.optimize.leastsq, and with many additional classes and methods for curve fitting
benmaier/pytisean
Python wrapper for TISEAN
benmaier/TemporalGillespieAlgorithm
C++ code for implementations of the temporal Gillespie algorithm.