An important design goal of Nodus 3 was to have user friendly access to all variables, this was realized with popup menus. The selection of simulation parameters requires the combined use of several of popup menus and the user has some control over how these popup menus are organized.
The selection of a simulation parameter
Most simulation database parameters can be selected for graphic or text output (Fig. IV/22). The list of available simulation parameters includes values which are constant (like reversal potentials) or which are not available (like concentrations) in Nodus 3.1. These are included for future compatibility. In later versions of Nodus concentrations will be implemented and changing reversal potentials and maximum conductances will be possible.
The first step in selecting simulation parameters for output is to choose the type of parameter. This is done with the value type selection popup menu (Fig. IV/22); this popup menu figures in the View/Edit Parameters, Configure Plots and Text Output commands. Simulation parameters which are not present in the simulation database are dimmed.
Figure IV/22: the value type selection popup menu. With this menu a type of simulation
parameter is selected for output.
Usually a lot of parameters of a single type are available; the user has to select a specific parameter for output. In all the experiment commands the user also has to select parameters: for the Current Clamp and Voltage Clamp experiments compartments, for the Synaptic
Firing Times command postsynaptic sites and for Block Ionic Currents experiments
currents. All these output and experiment parameters are selected with the “selection popup row” (Fig. IV/23).
Neuron selection
Compartment preselection
Compartment selectionSubdefinition selection
A B C
Figure IV/23: three “selection popup rows”. In A a full set of 4 popup menus which deter-
mine a synapse parameter. In B a set of 3 popup menus which determine a membrane potential parameter. In C a popup row for an output parameter that is not in use.
The parameter selection popup menus are created from the data present in the source model definition files. The selection popup rows function only if the source model definition files are present in memory and if they have not changed too much since the simulation database was created (see also the last subsection). The parameter selection process basically maps the model data structure to the simulation database structure.
Each selection popup row makes the unambiguous selection of a single simulation parameter possible. Active selection popup rows consist of a set of 3 or 4 popup menus depending on the selected value type (Fig. IV/23). Parameters are selected from left to right, i.e. first select the appropriate item in the first popup menu then in the second one, etc. The neuron popup menu will show either not used when nothing is selected or the local name of a neuron present in the simulation model. Select the appropriate neuron, the compartment popup menu will change to show the first (appropriate) compartment of that neuron. The compartment popup menu shows the compartment number and its name if it has one, otherwise its structure type. Select the desired compartment with the compartment popup menu (the subdefinition popup menu will change). If the value type is a membrane potential the selection is complete, otherwise a subdefinition selection has to be made also. The subdefinition popup menu shows a memory ID-number (which is of no concern to the user) for the subdefinition and its name.
The use of the compartment preselection popup menu is explained in the next subsection.
The compartment popup menus are created selectively, except for experiment value types. The compartment popup menu will only show compartments were the selected value type is present; for example if ionic currents are selected only excitable compartments will be shown. The neuron popup and compartment preselection popup menus are not selective, they show all available items. If the selected neuron or compartment preselection contain no appropriate compartments an alert warning about an “empty selection” will be shown (Fig. IV/31); the popup menus will revert to the previous setting.
The selection popup rows for experiment value types are smaller. For injected currents they are similar to membrane potential selection rows with 3 popup menus (Fig. IV/23B). For vol-
tage clamps only the neuron popup menu is shown. For conductance blocking factors
the first popup menu is an ionic current popup menu and is the only popup menu shown.
The use of selection popup rows differs slightly between output commands (Fig. IV/24) and experiment commands (Fig. IV/25). In output dialog windows several selection popup rows are present (Fig. IV/24); each row represents one parameter for graphic or text output. The selection popup row can be active (it shows 3 or 4 popup menus that determine a simulation parameter) or not (it shows not used). The number of parameters that will be plotted or saved to the disk is determined by the number of active popup rows. Active and inactive selection popup rows may be interspersed, though this does not improve clarity!
Figure IV/24: the Configure Plots dialog window. Four selection popup rows are active,
In experiment dialog windows there is only one selection popup row (Fig. IV/25), which is always active. It is used to select the place (i.e. a compartment, postsynaptic site or current depending on the type of experiment) on which the experiment settings in the dialog window will operate. All experiment settings can be active at several places at once; for example currents can be injected in several different compartments. In most experiment dialogs (except in the
Voltage Clamp dialog) only one place in the model can be viewed; the Synaptic Firing Times dialog shows all firing times at one synaptic site, the Current Clamp command a
single current injection in one compartment, etc. Use the selection popup row to select other places in the model and view or edit the experiment settings there. Initially the dialog window will show a place in the model where a setting is active or the first available place in the model if no experiment settings are active. All experiment commands have a button to Delete all the settings at all places in the model.
Figure IV/25: the Synaptic Firing Times dialog window. Two firing times are preset at
the postsynaptic site shown in the selection popup row; other firing times might be preset at other postsynaptic sites.
The compartment preselection popup menu
Popup menus are a nice instrument to select parameters, but they should not be too long. Imagine selecting a compartment for membrane potential output in a 1000-compartments neuron model, a compartment popup menu showing all 1000 compartments would be hard to use! Therefore Nodus never shows more than 50 items in a popup menu. To select which set of 50 compartments in a 1000-compartment model will be shown in the compartment popup menu, the compartment preselection popup menu is used.
The compartment preselection popup menu is the second popup menu in the selection popup row (Fig. IV/27). It makes selection of a subrange in the compartment popup menu possible. The user has control over the compartment preselection process with 2 options in the
Preferences command.
The Select by structure type option in the Preferences dialog window forces Nodus to always display a structure type preselection popup menu (Fig. IV/26), corresponding to the
Structure type popup menu in the compartment dialog window (Fig. IV/13) (with an all comps menu item added). The compartment popup menu will then only show compartments
with the corresponding structure and where the requested value type is present. The all comps menu item will be dimmed for large neuron models. This option is useful if (most) compart- ments in the model have a structure type different from undefined. Note that in very large neuron models more than 50 compartments may have the same structure type.
The Show only named comparts option in the Preferences dialog window affects the compartment popup menu directly. Only compartments which have a compartment name (Fig. IV/13) will be shown, unnamed compartments cannot be selected. This option is useful if compartments were named selectively, so that only “interesting” ones are shown. The Show
Figure IV/26: Compartment preselection by structure type. The complete structure type
preselection popup menu is shown at the left. At the right the effect of a structure type preselection upon the compartment popup menu is shown in a membrane potential selection popup row.
The appearance of the compartment preselection popup menu depends on the size of the selected neuron model and the Select by structure type option (Fig. IV/27). If the neuron model is small and no structure type selection is requested, the words all comps will be shown instead of a preselection popup menu (Fig. IV/24). If the neuron model is large and no structure type selection is requested, a range preselection popup menu is shown (Fig. IV/27). The range preselection popup menu just contains subranges of compartment numbers, i.e. #1-#50, #51-
#52, etc. If the Select by structure type option is on, there will always be a structure type
preselection popup menu. The size of the neuron model determines whether the all comps menu item is available or not.
5-compartment neuron:
ionic current selection 109-compartment neuron:membrane potential selection Select by structure type is OFF
Select by structure type is ON
structure type preselection popup menu, all comps item is available
no preselection
popup menu range preselection popup menu
structure type preselection popup menu, all comps item is dimmed
Figure IV/27: four types of preselection popup menus are possible, depending on the size
of the neuron model and the Select by structure type option.
Error messages about parameter selection
A simulation parameter selection maps the model data structure to the simulation database structure. This process will work fine if the model and database structures coincide, otherwise Nodus will warn the user that there is a problem. Which error message is shown depends on the circumstances.
Errors during New Simulation
A new simulation database inherits its output and experiment settings from the “old” simulation database (if present, otherwise defaults are used). If the model used for the new simulation is quite different from the preceding one, some output and/or experiment settings may no longer be relevant.
For example graphic output of ionic currents will not work very well for a passive membrane model. Nodus warns that some simulation parameters could not be found and lists them all in the error message (Fig. IV/28)
Figure IV/28: error message during execution of a New Simulation command with a new
source definition file. The new model is too different from the preceding one; some simulation parameters no longer exist.
Correct the listed settings before running the simulation by executing the appropriate simulation output and/or experiment commands. When such an output or experiment command is activated an additional error message will be shown (Fig IV/30). If the settings are not corrected the simulation can run, but the involved output will be continuously zero and the concerned experi- ments will not work.
Errors during simulation output or experiment commands
The selection popup row in all simulation output and experiment dialogs is created from data in the source model definition files, which have to be in memory. If the source files are not in memory, Nodus will warn the user (Fig. IV/29). This condition can occur only after the user has Closed some definition windows or after an Open Simulation with the Open all
linked files check box switched off (Fig. IV/8).
Figure IV/29: error message warning that some source model definition files are not in
memory. This message will displayed when a View/Edit Parameters,
Configure Plots, Text Output, Current Clamp, Voltage Clamp, Synaptic Firing Times or Block Ionic Currents command is executed.
The best solution is to press Cancel and Open the required source model definition files before executing the required command again. For output commands one can Continue. After
Continue the output dialog windows will show the raw parameter selection numbers that
Nodus uses internally. These selection numbers are not documented, this option is available for emergency use only. The average user should never edit the raw parameter selection numbers! Experiment commands are not accessible; the Continue button is replaced with a Delete
experiment settings button.which clears the experiment completely when pressed
If the source model definition files are in memory, but have been edited since the compilation of the simulation database, some of the parameter settings may have become invalid. The changes in definition files causing this problem are usually deletions: deleting a compartment (Fuse
Compartments), removing a compartment “tie” to a subdefinition or removing a neuron in a
network. Any output or experiment setting referring to the deleted compartment or subdefinition has then become irrelevant. Deletions can cause two problems: either simulation parameters are no longer available and an error message (Fig. IV/30) will be shown or some settings will seem to have “shifted” and point to different simulation parameters (see ‘The initial value problem’).
Figure IV/30: error message displayed upon selecting an output or experiment command.
Discrepancies between the simulation database and the (edited) source model definition files make the display of a parameter selection popup row impossible.
Simulations will run without problems because the simulation database has not changed, but the parameter selection popup row can no longer display the correct popup menu item. Nodus warns the user which model structure was not found before displaying the simulation output or experiment command (Fig. IV/30). To prevent this problem one should keep original source model definition files, rename the file (and give it a new hidden ID-number) after large changes to the model structure by doing Save As.
If Continue is pressed the raw parameter selection numbers that Nodus uses internally will be shown for those parameters that are no longer present in the source model files. Do not try to edit these parameter selection numbers, but change any other parameter or popup menu as you like. The Continue & delete concerned settings button is useful when this happened after a New Simulation database compilation. As the concerned parameters are no longer in the simulation database either one has to change or delete them anyway. All parameter selections that are no longer relevant will be replaced by the not used setting, the other selections remain unchanged.
During popup menu parameter selections one may try to select a neuron or compartment pre- selection menu item that has no compartments with the requested value type. This could happen for example in a network simulation, when a synaptic current value type is selected and the user selects with the neuron popup menu (Fig. IV/23) a neuron that has only presynaptic sites. Then an alert like in Fig. IV/31 will be shown and the popup menus will revert to their previous setting. This may happen frequently if the Select by structure type option is active.
Figure IV/31: error message warning that the selected neuron or compartment pre-
selection popup menu item cannot be used for the requested value and structure type (in this case synaptic currents and neurites).
V. NODUS MENU COMMANDS
Apple Menu 5 5