ProcessDB Reference Manual
If you want more information about any ProcessDB tool or label, look it up here alphabetically.
Absolute Tolerance
Additional Output tab
Algorithm
All Parameters
All Residuals
Amount
...and this end time:
Assignment
At Time
Best OFV
Bleach end time
Bleach start time
Bleached state
Bolus
Bolus Inputs tab
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 :
Diagram pane
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:
How protocol is defined
ID of modified process
ID of modified state
ID of tagged molecule
ID of traced state
Import...
Infusion/Biosynthesis tab
Initial OFV
Iteration
Keep Best Parameters
Marquee Zoom
Marque 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.
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
PA pulse end time
PA pulse start time
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:
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 (<math>experiment weight \cdot datum
weight</math>). 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
- Y Residual
- Residual
- Fractional Residual
- Weighted
Search:
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
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.
X Residual
X Residual is a column of the Residuals tab in the Optimizer window. For details refer to Residuals tab.