This guide shows the parts of the Structural Analysis Tool GUI and how to use them.
Load: Browse to open an SBML file. Multiple SBML files can be opened at the same time, and will be shown in the Models list.
Clear: Clears all the currently loaded models.
Exit: Closes the program.
Used to show or hide the panels in the program.
The SBW menu allows for transferring models between SBW-enabled applications without importing/exporting the models between programs.
To send models from the Structural Analysis Module, load a model into the Structural Analysis Module and select another program from the SBW Menu. The model will be sent to other program.
To send models to the Structural Analysis Module from another SBW module, select the Structural Analysis Module from the SBW Menu in another program. The model will be sent to the Structural Analysis Module.
The Models list shows a list of currently loaded models, their numbers of species and reactions, and their rank. Several models can be loaded at the same time.
Partially and Fully Pivoted LU models of existing models are also added to this list.
Clicking on one of the models makes the selected model’s information appear in all other panels.
Checking the Test Details box at the bottom of the Models panel will show or hide the Test Details.
The Test Details show the results of five tests that check the validity of the conservation laws. These check the rank of the generated matrices in a number of ways to ensure their correctness. If the generated conserved cycles have an error, the resultant matrices would not allow the ranks to match, and in particular, the product of the conservation matrix Gamma and the Stoichiometric matrix N would not be a zero matrix.
Checking the Matrix Chooser box at the bottom of the Models panel will show or hide the Matrix Chooser.
The Matrix Chooser shows a list of matrices (Stoichiometry matrix N, NR matrix, N0 matrix, L0 matrix, L matrix, Gamma matrix, K0 and Nullspace) and their dimensions. Clicking on a matrix type will display that type of matrix for the currently selected model in the panels on the right.
LU on Models
Model Name: shows a list of currently loaded models. Selecting one will display its information in the right panels.
Matrix Name: shows a list of matrix types. Selecting one will display the currently selected model as that type of matrix in the right panels.
Species Names: shows a list of species in the model. When the Display Data panel is selected and a species in this list is selected, the row associated with that species will be highlighted in the matrix visualization.
Reaction Names: shows a list of reactions in the model. When the Display Data panel is selected and a reaction in this list is selected, the column associated with that species will be highlighted in the matrix visualization.
All options below this, such as origin, display colors, and cell formatting, control how the matrix is displayed in the Display Data panel.
The summary panel shows information for the model currently selected in the Model list. Information shown includes the dimension, rank, number and names of independent and dependent species, and the conserved entities.
Checking the Show Matrix Grid box (located at the bottom of the Summary Panel) will show or hide the values of the currently selected matrix for the currently selected model. If this is selected, then the data for the matrices is displayed as the matrix values in the Summary Panel. If this is not selected, then the data is displayed as a visualization of the matrix in the Display Data panel.
Shows a visual representation of the currently selected matrix for the currently selected model.
The visualization of the matrix can be moved by clicking on it and dragging it.
The Copy Image button copies the matrix visualization to the clipboard so it can be pasted into other applications.
The toolbar has buttons for the matrices that can be displayed (N matrix (Stoichiometry), NR matrix, N0 matrix, L0 matrix, L matrix, Gamma (Conservation) matrix, K0 and Nullspace). Clicking these buttons displays the matrix visualization in the Display Data panel.
The Summary button displays the summary for the model in the Summary panel.
The Conserved Cycle button displays a list of conservation laws for the model in the Summary Panel.
The Use Partially Pivoted LU and Use Fully Pivoted LU create new models after having performed the specified decomposition on them. These models are added to the Models list.
