RGDS_Practical_Guide by Ronald/Daniel

The location for programs linked to the book <title> that will be published 2013. (simulation, pharmaceutical)

PK1IV1a

PK1IV1b

PK1IV1c

Renin-Angiotensin-System (RAS) model for SimBiology by Sven Mesecke

Provides a SimBiology model implementation of the Renin-Angiotensin-System (simbiology, pkpd, systems biology)

Continuous Stirred Tank Bioreactor (CSTR) SimBiology model by Sven Mesecke

SimBiology project containing a simple CSTR bioreactor model (simbiology, simbiology model, biotech)

Generic SimBiology Physiologically-based Pharmacokinetic (PBPK) model by Sven Mesecke

SimBiology implementation of a generic PBPK model. Human fasted, Human fed and Rat physiologies. (simbiology, simbiology model, pbpk)

calculateParacellularAbsorption(DrugLogP, DrugMolecularWeig...

calculateTissuePartition(...

Convert SimBiology(R) model to COBRA Toolbox model by Sven Mesecke

Use SimBiology for dynamic modeling and COBRA Toolbox algorithms for constraint-based modeling. (simbiology, simbiology export, systems biology)

sbioexportCobra(simbioModel,varargin)

BerkeleyMadonna model import function for SimBiology by Sven Mesecke

Imports ODE models in the BerkeleyMadonna(TM) format into a SimBiology(R) model (simbiology, simbiology import, systems biology)

sbioimportBerkeleyMadonna.m

SCOPE: interactively tabulate SEER excel variables by Rex Cheung

This takes SEER excel column data interactively, tabulate them, write back in table format. (data import, data export, optimization)

output=xls2tabulate2xls(xlsfilename)

Physiologically-based Pharmacokinetic (PBPK) model for SimBiology by Sven Mesecke

Provides a PBPK and a Renin-Angiotensin system model for SimBiology (simbiology, simbiology model, pbpk)

calculateParacellularAbsorption(DrugLogP, DrugMolecularWeig...

calculateTissuePartition(...

SimBiology implementation of PBPK model for Trichloroethylene (TCE) by Asawari Samant

SimBiology model describing the metabolism and distribution of TCE using a human PBPK model (pbpk, physiologicallybased, simbiology)

Using SimBiology for Mechanism-Based PK/PD Modeling in Preclinical & Discovery by Asawari Samant

Examples used in the March 2012 webinar: Using SimBiology for Mechanism-Based PK/PD Modeling (simbiology, pkpd, antibacterial)

antibioticDoseResponseGUI.m

doseResponse(mObj, drugName, strainName, PKPD, MIC)

doseResponsePlot(X1, Y1)

get reaction rates out of SimBiology by Frank Sommerhage

This tool pulls the reaction rates out of your SimBiology model. (simbiology, modeling, simulation)

rateout(time)

SimBiology model for PK/PD of anticancer drugs by Asawari Samant

SimBiology model describing the effect of anticancer drugs on tumor growth kinetics (simbiology, pkpd, tumor growth kinetics)

SimBiology model for Target-Mediated Drug Disposition (TMDD) by Asawari Samant

SimBiology implementation of the Target-Mediated Drug Disposition (TMDD) model (simbiology, pkpd model, tmdd)

SimBiology model for PK/PD of antibacterial drugs by Asawari Samant

SimBiology model for PK/PD of antibacterial drugs (pkpd, bacterial growth mode..., antimicrobial)

Modeling Biology with SimBiology: An Introduction for iGEM Teams by Asawari Samant

SimBiology model used in webinar: Modeling Biology with SimBiology: An Introduction for iGEM Teams (simbiology, igem, repressilator)

Fitting with MATLAB: Statistics, Optimization, and Curve Fitting by Richard Willey

Demo code and data for the "Fitting with MATLAB" webinar (outlier detection, censored data, deming regression)

evalTumorWeight(t , p)

objFcn(p , tObs, drug)

CensoredData.m

Chinese Matlab Digest: Matlab Technical Bulletin by Hong Zhang

Chinese Matlab Digest is the first matlab digest published in Chinese by www.iLoveMatlab.cn (digest, matlab digest, chinese digest)

SimBiology Tutorial by Asawari Samant

Files used in Online SimBiology Tutorial (simbiology, apoptosis model, tutorial)

ParameterEstimation.m

create_input_files.m by Marc Turcotte

Extracts ODE from model into stand-alone Matlab callable form (simbiology ode creato...)

create_input_files.m

create_input_files.m by Marc Turcotte

Extracts ODE from model into stand-alone Matlab callable form (simbiology ode creato...)

create_input_files.m