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Berkeley Madonna User's Guide

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Berkeley Madonna User's Guide Berkeley Madonna User’s Guide Version 8.0 March 23, 2000 Robert Macey George Oster Tim Zahnley University of California Department of Molecular and Cellular Biology Berkeley, CA 94720 http://www.berkeleymadonna.com Table of Contents INTRODUCTION .............................................................................................................5 SYSTEM REQUIREMENTS ...............................................................................................5 BERKELEY MADONNA WINDOWS ...............................................................................5 THE EQUATION WINDOW ...............................................................................................5 THE FLOWCHART WINDOW ............................................................................................7 THE PARAMETER WINDOW.............................................................................................8 THE GRAPH WINDOW ....................................................................................................9 Creating Multiple Graph Windows ........................................................................9 Specifying Which Variables to View......................................................................9 Changing Axis Settings.......................................................................................10 Creating Multiple Pages [Windows only].............................................................11 Using Graph Buttons...........................................................................................11 Printing Graphs and Tables ................................................................................13 Exporting Graphs and Tables .............................................................................13 Customizing Background Colors [Macintosh only]..............................................13 Oscilloscope Mode..............................................................................................14 Run Information ..................................................................................................14 Readout..............................................................................................................14 Initial Conditions .................................................................................................15 Fast-Fourier Transform.......................................................................................15 THE DATASETS WINDOW .............................................................................................15 Importing Datasets..............................................................................................15 Vector Datasets ..................................................................................................16 Matrix Datasets...................................................................................................16 Modifying and Removing Datasets .....................................................................17 THE NOTES WINDOW ..................................................................................................17 Embedding Pictures and Objects........................................................................17 RUNNING MODELS......................................................................................................18 SINGLE RUN ...............................................................................................................18 CONTINUE RUN [WINDOWS ONLY].................................................................................18 SLIDERS.....................................................................................................................18 BATCH RUNS..............................................................................................................19 PARAMETER PLOT.......................................................................................................20 CHECK DT .................................................................................................................21 -2- FLOATING-POINT EXCEPTIONS .....................................................................................21 EQUATION SYNTAX ....................................................................................................22 BASIC SYNTAX............................................................................................................22 DIFFERENTIAL EQUATIONS ...........................................................................................23 DIFFERENCE EQUATIONS .............................................................................................24 DISCRETE EQUATIONS.................................................................................................25 Conveyors...........................................................................................................25 Ovens .................................................................................................................26 Queues ...............................................................................................................27 ROOT FINDER EQUATIONS ...........................................................................................28 Initial and Step Root Finders...............................................................................29 The Root Finder Algorithm..................................................................................29 Multidimensional Root Finders............................................................................30 LIMIT EQUATIONS........................................................................................................30 OTHER EQUATION TYPES ............................................................................................30 METHOD Statement...........................................................................................31 DISPLAY Statement ...........................................................................................31 RENAME Statement ...........................................................................................31 BUILT-IN SYMBOLS......................................................................................................31 OPERATORS ...............................................................................................................33 BUILT-IN FUNCTIONS ...................................................................................................34 ARRAYSUM, ARRAYMEAN, ARRAYSTDDEV ..................................................36 BINOMIAL, NORMAL, POISSON, RANDOM .....................................................36 DELAY................................................................................................................36 NETFLOW ..........................................................................................................36 STEPSIZE ..........................................................................................................37 MAXINFLOW, OUTFLOW, OSTATE, QPOP, QPOPS.......................................37 ARRAY EQUATIONS .....................................................................................................37 DATASET FUNCTIONS ..................................................................................................40 Plotting Matrix Datasets......................................................................................40 REGIONAL SETTINGS [WINDOWS ONLY].........................................................................41 RUNNING STELLA MODELS ........................................................................................42 TIPS AND TECHNIQUES ................................................................................................43 Creating Periodic Functions................................................................................43 Creating Piecewise-Linear Functions..................................................................43 Non-negative Reservoirs and Unidirectional Flows ............................................43 Simulating STELLA Conveyors, Ovens, and Queues.........................................44 -3- INTEGRATION METHODS ...........................................................................................45 FIXED-STEPSIZE METHODS ..........................................................................................45 VARIABLE-STEPSIZE METHODS.....................................................................................45 USING DTOUT...........................................................................................................47 CUSTOM DT METHOD .................................................................................................47 OTHER FEATURES......................................................................................................49 CHEMICAL REACTIONS.................................................................................................49 Adding Other Equations......................................................................................50 CURVE FITTER............................................................................................................51 Multiple Fits.........................................................................................................52 Specifying Initial Guesses...................................................................................52 Floating-point Exceptions....................................................................................53
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