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biology

Biology related models

covid19

model of how the infection may be spreading

csensapprox

Experiments with Sensitivity Approximation (SA) in C using the gsl ode solvers.

demomodel

A demonstration and testing model for sampling and model conversion

emacs-svg-images

This is me learning elisp and emacs

forking-workflow-exercise

Exercise to practice collaborative forking workflow.

mcmc_clib

c program for simplified manifold MALA sampling of ODE model parameters

model

Brainstorming for a new format for Systems Biology

ode_rmhmc

Sources for the MATLAB implementation of RMHMC using Newton-Raphson steady state finding and linear equation sensitivity analysis

rgsl

R gsl solver interface

rpn-derivative

Calculates the derivative of anexpression given in reverse polish notation

sbtabvfgen

Convert a Model written in SBtab, saved as an Open Document Spreadsheet to a VFGEN vector field file

simbiology-sbml-fix

simbiologyfluxfunction

a script that makes a flux function for simbiology models

systems-biology-scripts

Scripts that are useful for the processing of parameter samples of dynamic models

tsv2csv

converts tsv to a somewhat safe csv and back

vfgen

Source code generator for differential equation solvers.

workarounds

These are my workarounds for common problems

workshop-codetesting-ak

Workshop Example Repository for Automatic Code Testing