Code behind the work "Single Cortical Neurons as Deep Artificial Neural Networks", published in Neuron 2021

Finite State Projection algorithms for chemical reaction networks

Development version of phaseR, an R package for phase plane analysis of one- and two-dimensional autonomous ODE systems

iCodon customizes gene expression based on the codon composition

Code behind the work "Multiple Synaptic Contacts Combined with Dendritic Filtering Enhance Spatio-Temporal Pattern Recognition of Single Neurons", bioRxiv 2022

In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes

Virtual population generation, fitting, and benchmarking.

Python toolkit for Bayesian parameter inference, model calibration, and model selection using Nested Sampling

A Game Theoretic Approach For Rendering Immersive Experiences In The Metaverse

A repository for the final project in MathBio class, exploring the dynamics of natural pattern adaptation through the lens of a cellular automata model. Contains code, documentation, and resources related to the project.

Implementation of a PINN solver for biological differential equations

An object-oriented model of the workings of the human body written in java and scala

4 dimensional model for neuronal modelling in Julia

Simulation of agents competing for resources with different strategies

Methods and Tools to Facilitate RE:IN Modeling and Analysis of GRNs

Bayesian inference of stochastic cellular processes with and without memory in Python.

Mini project (5ECTS) as part of the MSc Biology (University of Groningen), aiming to increase the efficeincy and speed of DAISIE model simulations.

Streaming over networks

PAR2 Activation and calcium signaling Reaction Model in PySB

Enhancing Boolean networks with continuous logical operators and edge tuning: smoothing simulations