ProcessDB Reference Manual
If you want more information about any ProcessDB tool or label, look it up here alphabetically.
Absolute Tolerance
Controls how small a number must be during simulation before it is equivalent to zero. See Simulator#Choosing Tolerances
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: 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 . 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 .
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 this. Click the + () to the left of the word Processes to display the full list of processes in the current model. It will look something like this: . Each process has a curvy arrow icon (), 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
Num Failed OF Evals
Num OF Evals
Num Parameters
OFV Tol
Orthogonal Layout
Overview
The Overview tool 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 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:
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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
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 (). 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.