Difference between revisions of "ProcessDB Reference Manual"
| Line 1: | Line 1: | ||
If you want more information about any ProcessDB tool or label, look it up here alphabetically. | If you want more information about any ProcessDB tool or label, look it up here alphabetically. | ||
| + | == Absolute Tolerance == | ||
== Additional Output tab == | == Additional Output tab == | ||
== Algorithm == | == Algorithm == | ||
== All Parameters == | == All Parameters == | ||
== All Residuals == | == All Residuals == | ||
| − | + | == Amount == | |
| − | + | == ...and this end time: == | |
| + | == Assignment == | ||
| + | == At Time == | ||
== Best OFV == | == Best OFV == | ||
| + | == Bleach end time == | ||
| + | == Bleach start time == | ||
| + | == Bleached state == | ||
| + | == Bolus == | ||
| + | == Bolus Inputs tab == | ||
| − | + | == Data Sets == | |
| − | + | == Data set ID == | |
| − | + | == Data set name == | |
| + | == Data Set Name : == | ||
== Display == | == 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. | '''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 == | == 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 == | == Initial OFV == | ||
| Line 23: | Line 47: | ||
== Max Iter == | == Max Iter == | ||
| + | == MOE Functions tab == | ||
== Molecules and Complexes tab == | == Molecules and Complexes tab == | ||
| − | + | == Name of modified process == | |
| + | == Name of modified state == | ||
| + | == Name of traced state == | ||
== Num Failed OF Evals == | == Num Failed OF Evals == | ||
| Line 35: | Line 62: | ||
== OFV Tol == | == OFV Tol == | ||
| + | == PA pulse end time == | ||
| + | == PA pulse start time == | ||
== Parameters tab == | == Parameters tab == | ||
| + | == Parameter Sets tab == | ||
| + | == Photoactivated state | ||
| + | == Photoactivation tab == | ||
| + | == Photobleaching tab == | ||
== Places tab == | == Places tab == | ||
== Processes tab == | == Processes tab == | ||
| − | + | == Process protocols tab == | |
| + | == Rate == | ||
| + | == Relative Tolerance: == | ||
== Residuals tab == | == Residuals tab == | ||
| + | == Search: == | ||
== Show Models == | == 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 ([[File: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. | '''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 ([[File: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 == | == 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 == | ||
Revision as of 11:08, 5 June 2015
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
Data Sets
Data set ID
Data set name
Data Set Name :
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
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
Processes tab
Process protocols tab
Rate
Relative Tolerance:
Residuals tab
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.