a modeling environment tailored to parameter estimation in dynamical systems

STAPLE (Shared Tools for Automatic Personalised Lower Extremity modelling) consists of a collection of methods for generating skeletal models from three-dimensional bone geometries, usually segmented from medical images. The methods are currently being expanded to create complete musculoskeletal models.

EPIDEMIC is an easy-to-run educational toolkit for epidemiological analysis.

Gillespie Stochastic Simulation Algorithm

"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.

PteraControls is a tool for designing control systems for flapping wing vehicles.

Implemented a static compressed sensing algorithm using orthogonal matching pursuit.

SoBioS is an easy-to-run code to compute Sobol' indices for biological systems.

ARBO is a package for simulation and analysis of arbovirus nonlinear dynamics.

MATLAB package for codon usage bias and NGS analysis

Hierarchical Model Reduction

Automated image analysis tool to analyze seedling kinematics

This repository contains companion codes, developed for use with the CRC Press Book "An Introduction to Systems Biology" by Karthik Raman

Code to accompany the paper: "Computational quantification and characterization of independently evolving cellular subpopulations within tumors is critical to inhibit anti-cancer therapy resistance"

A computational oncology application that analyzes and presents 3D MRI data of tumor growth in rat brains.

This project aims at running Monte Carlo Simulations to simulate life on earth.

Graduate Student Mathematical Modeling Camp

Power BI resources for reading and visualizing bioinformatics and genomics files

Software for inferring the intrinsic fitness landscape of poliovirus capsid protein (vp1) and comparing it with that of analogous proteins in HIV

A prior learning and sampling model informed tool for learning with Single Cell RNA-Seq data