ProcessDB Reference Manual

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If you want more information about any ProcessDB tool or label, look it up here alphabetically.

Contents

Absolute Tolerance

A parameter to the simulator that controls how small a number must be during simulation before it is equivalent to zero. See Simulator#Choosing Tolerances

Add (Graphs menu)

In the Parameter Explorer window, the Graphs menu Add button allows you to add a new graph to your displayed collection of graphs. This graph is added to the bottom of the graph page, so you may need to scroll down to see it. The added graph will have a default title (e.g. Graph 1) and five default variables plotted. Right click anywhere in the displayed graph and select Edit to modify its title, to choose semi-log instead of linear, to enter labels for the x-axis and y-axis, to set x and y minimum and maximum values for the graph axes, to remove plots, to add plots, and to change the color of a particular plot.

Add (Edit Graph Settings)

In the Edit Graph Settings dialog in the "Plots:" pane, click Add to add a new variable to the list of variables you want to plot in this graph. If necessary drag the column divider to see the full names of variables. You can also drag the edge of the Edit Graph Settings dialog to make it larger. Click the variable name in the newly added row to display an alphabetical list of the model variables you can plot. Use the mouse wheel or scroll to the variable you want to plot and click to select it. Click the Save button at the bottom of the Graph Settings Dialog to save your changes.

Additional Output tab

Algorithm

All Parameters

All Residuals

Amount

...and this end time:

Arrange Places

Arrange Places Automatically

Assignment

At Time

Best OFV

Bleach end time

Bleach start time

Bleached state

Bolus

Bolus Inputs tab

Connect

Current model

In ProcessDB the Current model is the model that is currently displayed in the Diagram pane.

Database pane

Data Sets

Data set ID

Data set name

Data Set Name :

Delete

Diagram pane

At the top of the Diagram pane is the Diagram Tool Bar: Diagram pane tool bar.png This tool bar appears when any model is loaded into the Diagram pane. Each tool is represented by an icon and the name of the tool appears as a tool tip when your cursor rolls over the icon. For details on the usage and capabilities of these tools, follow the links in this list: from left to right the tools are: Undo, Redo, Arrange Places Automatically, Select, Arrange Places (Manually), Pan, Interactive Zoom, Marquee Zoom, Navigate Edges, Zoom Fit, Connect, Hierarchical Layout, Symmetric Layout, Orthogonal Layout, Incremental Layout, Overview, and Delete.

Display

Display is the name of a drop down menu (located just below the list of Models in the Models tab of the main ProcessDB window) that allows you to select which models will be displayed in your Models tab. The choices are My Models, Shared, or Public. My models displays the names of all models owned by you. These are typically models that you created yourself, but have not made public. Shared displays models created and owned by other ProcessDB users, but shared with you. The owner must explicitly share such a model with you in order for it to appear in your Shared model display. You have complete authority over any model that has been shared with you, with the exception that you cannot delete it. Public displays models that have been shared with all ProcessDB users. Some Public models are examples used in ProcessDB Workshops; others are published models. There are no restrictions. Any ProcessDB user can make any of their models Public. You can run and Public model as is, but if you wish to modify it you must make a copy of your own.

Equations tab

Events tab

Experimental Data

Experimental measurements and data tab

Experimental measurements made during this experiment

Experiments tab

Forcing Function

Forcing Functions tab

Forcing Function enforced between this initial time:

Forcing functions are defined over some interval of time. For periods of time not covered by the forcing function, solution of the normal system differential equations will determine the values of the variable. The initial time defined here is the time value of the first datum used to define the time course of the variable as seen by the rest of the model. See also "...and this end time."

How protocol is defined

Hierarchical Layout

ID of modified process

ID of modified state

ID of tagged molecule

ID of traced state

Import...

Incremental Layout

Infusion/Biosynthesis tab

Initial OFV

Interactive Zoom

Iteration

Keep Best Parameters

Marquee Zoom

Marquee Zoom is a tool on the Diagram Pane Toolbar. Its icon is Marquee zoom icon.jpg. Click this icon to activate marquee zoom, which allows you to drag a rectangle over a region of interest in a diagram and zoom in to see the details in that region. To exit Marquee Zoom click the Select tool Select tool icon.png.

Max Iter

Model tree structure pane

The Model tree structure pane is the lower left pane of the main ProcessDB window. It provides an expandable and contractible outline of the structure of the Current model. When you first Load a model, its tree structure appears collapsed like thisCollapsed Model tree structure.png. Click the + (Process tree expansion icon.png) to the left of the word Processes to display the full list of processes in the current model. It will look something like this: Process tree expanded.png. Each process has a curvy arrow icon (Process icon.png), the name of the process assigned by the person who created the process, and the ProcessDB ID of the process.

MOE Functions tab

Molecules and Complexes tab

Name of modified process

Name of modified state

Name of traced state

Navigate Edges

Num Failed OF Evals

Num OF Evals

Num Parameters

OFV Tol

Orthogonal Layout

Overview

The Overview tool Overview icon.png is available on the Diagram pane tool bar when a model is displayed. Clicking this tool opens a small window displaying an overview or bird's-eye view of the entire current model. In this overview window Overview window.png you will see a blue rectangle that indicates what portion of the model is currently visible in the full diagram pane. You will see that this blue rectangle changes as you zoom in or out using any of the Zoom tools or a mouse-wheel.

A particularly useful trick is to drag the blue rectangle around the overview window to find the portion of the full model that you want to examine in detail.

PA pulse end time

PA pulse start time

Pan

Parameters tab

Parameter Sets tab

Photoactivated state

Photoactivation tab

Photobleaching tab

Places tab

ProcessDB ID

The DB in ProcessDB stands for database. It is a unique feature of ProcessDB that everything about each model is stored in a professionally designed relational database. This gives ProcessDB enormous power that will speed your work. (see Features List Page). One consequence of this underlying design principle is that every important model component, such as a Process or a State, has a unique numerical ProcessDB ID. We consciously decided to make these ProcessDB IDs available to you even though many software developers would argue that database IDs should be hidden from the users. There were several reasons for this decision:

  • Precision communication. We designed ProcessDB to be a collaborative environment. We anticipated that multi-person teams would be working on a single model and we found in our own collaborations that the ideal way to be certain everyone understands which model or process or state or experiment you are talking about is to refer to it by its unique ProcessDB ID
  • .
  • Efficient search
  • Unambiguous notation in equations
  • ProcessDB window

    Processes tab

    Process protocols tab

    Rate

    Relative Tolerance

    A parameter to the simulator that controls how close two numbers must be relative to their magnitude before they are considered equivalent. See Simulator#Choosing Tolerances

    Remove Selected (Edit Graph Settings)

    To remove any variable you no longer want in this plot, click the checkbox beside its name and click the "Remove Selected" button. Click Save at the bottom of the Edit Graph Settings dialog to save your changes to this plot.

    Residuals tab

    A table of data related to the residuals is in this tab. The name and meaning of the columns are below.

    • Measurement - the name of the experimental measurement for the data to the right and below when the #All Residuals toggle button is on. see #Experimental measurements made during this experiment
    • Dataset - the name of the data set for the data to the right and below when the #All Residuals toggle button is on. see #Data Sets
    • Time - the time that the experimental data measurement was taken (the independent variable). see #Data Sets
    • Exp Datum - the measured experimental data point (the dependent variable). see #Data Sets
    • Sim Datum - the value of the simulation variable at the time from the experimental data. For orthogonal distance optimizers this is not defined yet. TODO: update this when data is defined for ODR problems.
    • X Residual (init) - the initial estimated error in the independent variable. Currently, this is always zero. see "Residual (init)" below for more.
    • Y Residual (init) - the initial estimated error in the dependent variable. More precisely described as the vertical distance between the data point and the simulation curve. If the simulation curve is precisely vertical at the point then the measurement is either the shorter of the distance between the top of the curve and the exp datum and the bottom of the curve and the exp datum or zero if the datum is in between the top and bottom of the curve. see "Residual (init)" below for more.
    • Residual (init) - same as Y Residua (init) as long as the X Residual (init) is zero. In the case of orthogonal distance optimizers (such as Odrpack95) this is redundant for the initial point. In the case of normal least squares optimizers (such as PSO), the Y Residual (init) is not given separately but is instead under this column.
    • Weighted (init) - the Residual (init) squared times the combined weight (experiment weight times the datum weight). In the case of Odrpack95, since the initial residual for the independent variable is always zero, the value here isn't different than PSO.
    • X Residual - the estimated error in the independent variable at the best estimate of the parameters after optimization is complete.
    • Y Residual - the estimated error in the dependent variable at the best estimate of the parameters after optimization is complete.
    • Residual - For PSO and other normal least squares optimizers, this is the same as the Y residual and the Y residual isn't displayed separately outside this column. For Odrpack95 and other orthogonal distance optimizers, this it the unweighted orthogonal distance: the square root of the sum of the x residual squared and the y residual squared.
    • Fractional Residual - this is the fractional residual at the best estimated parameters for the dependent variable only. It is the ratio of the dependent residual (as seen in the Y Residual column for Odrpack95 and the Residual column for PSO) to the exp datum in the Exp Datum column.
    • Weighted - for PSO this is the residual squared times the combined weight (weight of the experiment times the weight of the datum). For Odrpack95 this is the independent variable's residual squared plus the combined weight times the dependent variable's residual squared. Note, the weight for the independent variable is effectively 1.0. This is currently how Odrpack95 treats it, but this will likely change in the future to allow non-unity weights.

    Redo

    Search:

    Select

    Show Models

    Show Models appears as an option on three different context menus. If you select Show Models from the context menu for a molecule or complex, ProcessDB will find every model that includes that molecule or complex. If such models are found, an expansion plus sign will appear next to the molecule icon (Expansion plus sign for molecule.png). Click the plus sign to display the list of models. Double click any model in the list to Load it into the diagram pane. Show Models works the same way when selected from the context menu for a Process in the Processes tab or for a Place in the Places tab.

    Simulations tab

    Start Time

    Start Time:

    State modified

    State Name

    State protocols tab

    State where bolus is applied

    State where infusion is applied

    Symmetric Layout

    Tagged molecule name

    Tagged molecules used

    Traced Processes tab

    Traced States tab

    Tracer protocols tab

    Tree structure pane

    The Tree structure pane is short for Model tree structure pane. It is the lower left pane of the main ProcessDB window. For details see Model tree structure pane.

    Undo

    X Residual

    X Residual is a column of the Residuals tab in the Optimizer window. For details refer to Residuals tab.

    Zoom Fit