Toolbox for parameter estimation of the Standard Model of diffusion in white matter

CHARM, a model that estimates the GHG impacts and land-use requirements of forestry

This toolbox allows to simulate interactions between neural mass potentials (resonating at 40Hz) in the structural connectome. Here, a single brain region is seen as an oscillator whose dynamics is explained by a Stuart Landau Equation (Hopf Bifurcation including time delay).

Feed-forward neural network that predicts cytokine dynamics of T-cells in response to antigens

Python toolbox for creating and validating single-cell neuronal models with active dendrites.

Nitrogen balance model components and test procedures

Biophysical modeling of ribosome motion during mRNA translation using TASEP and ballistic models, including analytical derivations and validation with simulation and Ribo-seq data.

Materials for the PANGEOS Uncertainty Quantification workshop

GPyTool, a Bayesian framework developed to estimate the diffusive properties of a stochastic time trajectory

These are python version of codes that I wrote to analyze images and videos of a macromolecule, that I took via fluorescence microscopy, in my research in grad school.

Processing agro-environmental data

Simulation of an FtsZ filament in C++

Model of BG components to learn more about mechanisms of DBS

Bottom-up dynamical modeling of biological systems using ordinary, partial, and stochastic differential equations.

Large-scale thalamocortical network model for simulating physiological and paroxysmal brain rhythms: version 1

Large-scale thalamocortical network model for simulating physiological and paroxysmal brain rhythms: version 2

Data and figures (R-notebooks) for the in-silico biodiversity experiment using DART biophysical model

Jupyter widgets for use with NeuroML

Review paper describing how a systems modelling approach can help predict how biological systems respond to extreme heat