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