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updated 17 days ago

App Builder for SimBiology Models by Asawari Samant

Tool to automate the process of creating standalone, model-exploration apps for SimBiology model (simbiology, pkpd, systems biology)

buildApp(inputSet, compileFlag)

createSlider(f, pNum, pInfo)

createUI(model, appName)

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updated 4 months ago

RGDS_Practical_Guide by Daniel/Ronald

MATLAB routines for the book: "Development of Innovative Drugs via Modeling with MATLAB". (simulation, pharmaceutical, simulink)

AUC

CTSbasics.m

DDEconst

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updated 1 year ago

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, DrugMolecularWe...

calculateTissuePartition(...

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updated 1 year ago

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)

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updated 1 year ago

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

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updated 1 year ago

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)

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updated 1 year ago

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, DrugMolecularWe...

calculateTissuePartition(...

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updated almost 2 years ago

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)

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updated 2 years ago

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)

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updated almost 3 years ago

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

Demo code and data for the "Fitting with MATLAB" webinar (poisson regression, logistic regression, orthogonal regression)

evalTumorWeight(t , p)

objFcn(p , tObs, drug)

CensoredData.m

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