Parasim GUI
Parasim provides an alternate interface to experiments management (via file system and text editor) and analysis (see Parasim CLI) in the form of swing application. This application has one very important feature: Experiments created using its project manager are fully compatible with parasim CLI, i.e. it is possible to create experiments using parasim GUI and execute them in batch using parasim CLI (note: reverse may not apply unless certain naming and placement conventions are maintained).
On unix-like operating systems parasim may be executed using the parasim-gui.sh script (parasim has to be built).
For user convenience, experiments are aggregated into projects. A project comprises a single model and a collection of experiments, properties and configurations associated with this model. Parasim GUI may be used to manage and edit all project components, with two exceptions:
- model -- model file is asthe sumed to be the basis project and as such is presumed not to change during model analysis, therefore, it cannot be edited or managed by parasim GUI.
- properties -- properties (STL formulae) are too complex to be edited by this simple GUI, therefore, it is used only to manage (i.e. add, rename and delete) properties associated with parasim project.
In a file system, a project always constitues a directory.
Note: Parasim is not designed to edit model files, as there are several usable SBML editors. So far, model file may be edited (for its location see naming and placement conventions), however, parasim GUI does not adjust configuration after the model change, which may result in loss of project integrity when the number of variables (or parameters) is altered.
Simulation configuration comprises settings which pertain to numeric simulation of the model, such as precision configuration. Generally, default settings should satisfy most needs, however, some tweaking may be necessary to obtain desired outcome.
Perturbation configuration is directly connected to robustness analysis. It specifies which variables/parameters should be perturbed, in which intervals and how may samples should be used for initial iteration.
Experiment is an executable analysis corresponding to experiment executed in parasim CLI. It constitutes of simulation configuration, perturbation configuration (see above), property, analysis settings (timeout and iteration limit). Additionaly, it may contain annotation, i.e. a short description of experiment.
- iteration limit -- limits precision of robustness analysis method. Generally, 10 should be more than sufficient.
- timeout -- when running simulation exceeds timeout, it terminates.
Parasim GUI consists of project manager window and logger window. Logger window prints messages and keeps track of running simulation time. It is mostly non-interactive, as its main aim is to convey information to the user. Therefore, the key part of parasim gui is the project manager. Additionally, projection plotter is displayed when an analysis finishes.
parasim right after launching
parasim with running simulation
After parasim is launched, only toolbar and menubar are visible in the project window. A project has to be created or loaded in order to display all manager components.
To load a project, its directory has to be specified. Loading dialog checks whether the selected directory contains model file.
To create a new project, a model file and an empty directory has to by specified. The alternate way is moving a model file to a new directory and then open it (which, actually, is what project creator does).
A project consists of several types configurations: experiments, simulation configuration and perturbation configuration. There may be many instances of each configuration type, all of which are named. However, only one instance of each configuration type is displayed at a time.
Instances of one configuration type are managed via the name panel, which is located at the bottom of given configuration panel.
Configuration name panel (red frame) at the bottom of perturbation configuration panel.
The currently displayed (and edited) configuration is selected via the drop-down list. There also are several buttons to manage configurations.
| new | Create a new unnamed configuration, which is identical to the selected configuration. |
| save/rename | When the current configuration is not named, save it as a named configuration. Otherwise, rename the current configuration. |
| remove | Remove current configuration. |
| use (optional) | Experiment refers to a simulation and perturbation configuration. This button may be used to select this configuration for the current experiment (as an alternate method to drop-down list). |
Simulation configuration panel is located at the bottom left corner of the project manager window.
Field names are self-explanatory and default values are sufficient in most cases. There are, however, several peculiarities.
Simulation start and simulation end only affect what parts of simulation are displayed, simulation times are specified by used property.
Time step and maximum relative error affect the simulation precision. Lowering these values should make the simulation more precise while increasing analysis time.
The remaining values are specified for each model variable. Maximum absolute error need not be set in most cases. Minimum and maximum bounds on the variables limit "wild" behaviour of simulations -- when a trajectory exceeds this bounds, it is discarded.
Perturbation configuration panel is located at the bottom right corner of the project manager window.
Whether a variable or parameter is perturbed is set using checkboxes at the bottom of the panel. When it is not perturbed, default value is used. Perturbed variables/parameters are shown at the top of the panel. For each perturbed variable/parameter, interval over which they are perturbed must be set, as well as number of initial samples (the robustness analysis algorithm will create more samples in the places where property satisfaction is uncertain.
Properties panel is located at the top right corner of the project manger window.
| Import | Import a new property from external file. This button will open an "import property" dialog. |
| Remove | Remove selected property from this project. |
| Rename | Change the name of selected property. |
| Use | Use the selected property in current experiment. |
For user convenience, formula specifying a property is displayed as a tooltip when mouse pointer hovers over the property.
Experiments panel is located at the top left corner of the project manager window.
The field names are self-explanatory. Property, Simulation configuration and Perturbation configuration fields refer to the other configurations included in the project. They may be selected via the drop-down list. The ">>" button shows the selected configuration in corresponding configuration panel.
The blank text area at the bottom of the panel contains experiment annotation -- a short description.
When current experiment (i.e. experiment shown in experiment panel) is complete, it may be launch using the Launch Experiment button in the toolbar. When existing experiment results are available, they may be displayed using Show Last Results button in the toolbar.
Note: When experiment configuration or associated perturbation or simulation configurations are changed, the saved results may no longer correspond to the experiment. Therefore, it should be analysed anew.