a modeling environment tailored to parameter estimation in dynamical systems
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Updated
Jul 18, 2024 - MATLAB
a modeling environment tailored to parameter estimation in dynamical systems
ARBO is a Matlab/C++ package for simulation and analysis of arbovirus nonlinear dynamics.
SoBioS is an easy-to-run Matlab code to compute Sobol' indices for biological systems.
CE-ABC is a code to simulate the epidemic outbreaks with mechanistic models through a cross-entropy approximate Bayesian framework.
EPIDEMIC is an easy-to-run Matlab/Octave educational toolkit for epidemiological analysis.
Image processing and analysis tool to measure growth kinematics of Arabidopsis seedlings
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.
Command-line program and scheduled GitHub action for publishing the ModelDB model repository to BioSimulations
Mathematical modelling of microglial cells for the neuroscience community
The files in this repository reproduce all the simulations and graphs in the paper, Fofana & Hurford 2022, Parasite-induced shifts in host movement may explain the transient coexistence of high- and low-pathogenic disease strains, J Evol Biol.
MATLAB package for codon usage bias and NGS analysis
FASTA Alignment search for BsaI and BsmBI restriction sites in the ORF6 protein to verify assertions made by Bruttel, et. al. in "Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2."
Power BI resources for reading and visualizing bioinformatics and genomics files
Code to accompany the paper: "Computational quantification and characterization of independently evolving cellular subpopulations within tumors is critical to inhibit anti-cancer therapy resistance"
Utilizes Markov Models to predict protein coding genes
Search for and find thermodynamic advantages for product synthesis using metabolic single-species community models
"Scutoids are a geometrical solution to three-dimensional packing of epithelia" - https://www.nature.com/articles/s41467-018-05376-1.
"A quantitative principle to understand 3D cellular connectivity in epithelial tubes" Gomez-Galvez et al
This repository contains companion codes, developed for use with the CRC Press Book "An Introduction to Systems Biology" by Karthik Raman
PteraControls is a tool for designing control systems for flapping wing vehicles.
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