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Introduction

First Steps

Loading a Model
Workbench Panel
The Species Tab
The Parameters Tab
The Parameter Sets Tab
The Data Browser Tab
The Sensitivity Tab
The Fit Tab
Running a Data Fit
Data Fit Result Window
Plotting the Data Fit
Sensitivity Analysis
Sensitivity Analysis Result Window
Links

Calling the BioPARKIN.bat for Windows (or python BioPARKIN.py) starts the BioPARKIN GUI. The user has several options to choose from. There is the menue bar, the icon bar and the model/workbench panel. The menue bar offers the following items:
  1. File:
    Open-open an SBML file
    Save-save current SBML
    model
    Save As-save current SBML
    via file browser
    Close-close current SBML
    file
    List of recently-
    opened SBML files
    Quit-quit BioPARKIN
  2. Actions:
    Simulate-runs the simulation
    of the current model
    with the active parameters
    Compute-computes the
    Sensitivitysensitivity of each
    Overviewspecies wrt the
    parameters
    Compute-gives a detailed
    Detailedsummary
    Sensetivity
    Estimate-estimates the
    Parameter Valuesparameter selected
  3. Tools:
    Show-opens a window
    generateddisplaying the ODEs and
    ODEsadditional information
  4. Help:
    About - opens a help dialog
Right below the menue the icon bar is placed.
the open dialog icon
saves the current project/model under a new file name
save the current project/model
opens a window with generated ODEs and additional info
opens a window displaying all current errors and warnings

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