BM User's Guide 8.0

BM User's Guide 8.0 - Berkeley Madonna Users Guide Version...

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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
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-2 - Table of Contents INTRODUCTION. ............................................................................................................ 5 S YSTEM R EQUIREMENTS ............................................................................................... 5 BERKELEY MADONNA WINDOWS . .............................................................................. 5 T HE E QUATION W INDOW ............................................................................................... 5 T HE F LOWCHART W INDOW ............................................................................................ 7 T HE P ARAMETER W INDOW ............................................................................................. 8 T HE G RAPH W INDOW .................................................................................................... 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 T HE D ATASETS W INDOW ............................................................................................. 15 Importing Datasets. ............................................................................................. 15 Vector Datasets . ................................................................................................. 16 Matrix Datasets. .................................................................................................. 16 Modifying and Removing Datasets . .................................................................... 17 T HE N OTES W INDOW .................................................................................................. 17 Embedding Pictures and Objects. ....................................................................... 17 RUNNING MODELS. ..................................................................................................... 18 S INGLE R UN ............................................................................................................... 18 C ONTINUE R UN [W INDOWS ONLY ]................................................................................. 18 S LIDERS ..................................................................................................................... 18 B ATCH R UNS .............................................................................................................. 19 P ARAMETER P LOT ....................................................................................................... 20 C HECK DT . ................................................................................................................ 21
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-3 - F LOATING -P OINT E XCEPTIONS ..................................................................................... 21 EQUATION SYNTAX . ................................................................................................... 22 B ASIC S YNTAX ............................................................................................................ 22 D IFFERENTIAL E QUATIONS ........................................................................................... 23 D IFFERENCE E QUATIONS ............................................................................................. 24 D ISCRETE E QUATIONS ................................................................................................. 25 Conveyors. .......................................................................................................... 25 Ovens . ................................................................................................................ 26 Queues . .............................................................................................................. 27 R OOT F INDER E QUATIONS ........................................................................................... 28 Initial and Step Root Finders. .............................................................................. 29 The Root Finder Algorithm. ................................................................................. 29 Multidimensional Root Finders. ........................................................................... 30 L IMIT E QUATIONS ........................................................................................................ 30 O THER E QUATION T YPES ............................................................................................ 30 METHOD Statement. .......................................................................................... 31 DISPLAY Statement . .......................................................................................... 31 RENAME Statement. .......................................................................................... 31 B UILT - IN S YMBOLS ...................................................................................................... 31 O PERATORS ............................................................................................................... 33 B UILT - IN F UNCTIONS ................................................................................................... 34 ARRAYSUM, ARRAYMEAN, ARRAYSTDDEV. ................................................. 36 BINOMIAL, NORMAL, POISSON, RANDOM . .................................................... 36 DELAY. ............................................................................................................... 36 NETFLOW . ......................................................................................................... 36 STEPSIZE . ......................................................................................................... 37 MAXINFLOW, OUTFLOW, OSTATE, QPOP, QPOPS. ...................................... 37 A RRAY E QUATIONS ..................................................................................................... 37 D ATASET F UNCTIONS .................................................................................................. 40 Plotting Matrix Datasets. ..................................................................................... 40 R EGIONAL S ETTINGS [W INDOWS ONLY ]......................................................................... 41 R UNNING STELLA M ODELS ........................................................................................ 42 T IPS AND T ECHNIQUES ................................................................................................ 43 Creating Periodic Functions. ............................................................................... 43 Creating Piecewise-Linear Functions. ................................................................. 43 Non-negative Reservoirs and Unidirectional Flows . ........................................... 43 Simulating STELLA Conveyors, Ovens, and Queues. ........................................ 44
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-4 - INTEGRATION METHODS . .......................................................................................... 45 F IXED - STEPSIZE M ETHODS .......................................................................................... 45 V ARIABLE - STEPSIZE M ETHODS ..................................................................................... 45 U SING DTOUT. .......................................................................................................... 47 C USTOM DT M ETHOD ................................................................................................. 47 OTHER FEATURES. ..................................................................................................... 49 C HEMICAL R EACTIONS ................................................................................................. 49 Adding Other Equations. ..................................................................................... 50 C URVE F ITTER ............................................................................................................ 51 Multiple Fits. ........................................................................................................ 52 Specifying Initial Guesses. .................................................................................. 52 Floating-point Exceptions. ................................................................................... 53 O PTIMIZER ................................................................................................................. 53 B OUNDARY V ALUE S OLVER .......................................................................................... 53 S ENSITIVITY ................................................................................................................ 55 P LUG - IN F UNCTIONS AND I NTEGRATION M ETHODS ......................................................... 55 FLOWCHART REFERENCE. ........................................................................................ 55 A LIASES ..................................................................................................................... 55 S UBMODELS ............................................................................................................... 57 Creating and Deleting Submodels . ..................................................................... 57 Making Connections Between Submodels. ......................................................... 58 Moving Icons Between Submodels. .................................................................... 59 F LOWCHART T OOLBAR ................................................................................................ 60 F LOWCHART C OMMANDS ............................................................................................. 62 F LOWCHART P REFERENCES ......................................................................................... 64 C USTOMIZING I CONS ................................................................................................... 65 K NOWN B UGS AND L IMITATIONS ................................................................................... 66
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-5 - Introduction Berkeley Madonna is a program that numerically solves systems of ordinary differential equations (ODEs) and difference equations. It was originally developed to execute models written in STELLA® more quickly. Over time, we added our own unique features which have made Berkeley Madonna into a fast, self-contained, and easy-to-use modeling tool.
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This note was uploaded on 01/03/2012 for the course BI 170a taught by Professor List during the Fall '09 term at Caltech.

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BM User's Guide 8.0 - Berkeley Madonna Users Guide Version...

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