- Table of Contents
- 1. Introduction
- 2. The ModelDesigner Client architecture
- 2.1. Modules
- 3. Model Builder
- 3.1. Main window
- 3.2. Modeler frame
- 3.2.1. Creating a new model
- 3.2.2. Editing a model
- 3.2.3. Saving a model
- 3.2.4. Opening an existing model
- 3.2.5. Scanning a sequence database
- 3.2.6. Uploading a sequence database on the server
- 3.2.7. Models and active model
- 3.3. Templates frame
- 3.4. Commands reference
- 3.4.1. Main frame toolbar
- 3.4.2. Main frame menus and commands
- 4. Model Analyzer
- List of Tables
- 3-1. Commands accesible througth the Model Builder main frame toolbar. parameters
- 3-2. Commands available from the menu (Model Builder module).
- 3-3. Commands available from the menu (Model Builder module).
- 3-4. Commands available from the menu (Model Builder module).
- 3-5. Commands available from the menu (Model Builder module).
- 3-6. Commands available from the menu (Model Builder module).
- 4-1. Commands available from the menu (Model Analyzer module).
- 4-2. Commands available from the menu (Model Analyzer module).
- List of Figures
- 3-1. Model Builder.
- 3-2. Model Builder showing the Templates frame.
- 4-1. Model Analyzer.
Chapter 1. Introduction
1.1. Purpose of the document
The present document aims at explaining how the ModelDesigner client is organized and how to use it.
Chapter 2. The ModelDesigner Client architecture
2.1. Modules
The ModelDesigner Client (MD-C) allows an end-user to graphically create a sequence model, execute that model against a sequence database and analyse the results. For that purpose, MD-C provides the user with a graphical interface organized on two modules: Model Builder and Model Analyzer.
Model Builder allows a user to prepare a query execution. It propose the necessary functions to create a sequence model, to provide the user with the list of available sequence databases and to start a query execution on the ModelDesigner Server.
Model Analyzer provides the user with a graphical interface to easily explore the results of a query execution.
Chapter 3. Model Builder
3.1. Main window
Like all classic GUI-based software, Model Builder proposes a set of menus (
) and a toolbar (
) that give access to the softwares commands. Its main window is horizontally divided in two internal frames: Templates (
) and Modeler (
). It is worth noting that the Modeler frame caption bar displays between brackets the molecular type of model (DNA or protein).
Just after starting the software, the Templates frame is hidden (only its caption bar is visible) while the Modeler frame is fully visible (well it is just an empty blue panel since no model is displayed).
3.2. Modeler frame
The Modeler frame is the place where the user creates his/her models. After starting ModelDesigner, this frame is empty but it can be populated with several model panels as explained below.
3.2.1. Creating a new model
A new model can be created by selecting from the menu. As a result a new model panel is created within the Modeler frame: use this panel to start editing a new model.
3.2.2. Editing a model
Model editing can be done quite easily as follows. First, select the left part of the new model: it is either a NH2 (protein model) or a 5' entity (DNA model). Then, click on one of the available model entities listed in a toolbar under the panel' caption bar. Alternatively, you can right click on a selected entity, then choose a new model entity from the floating menu. Finally, the new entity is added after the selected one.
Each new entity is added within a model with default properties. They can be modified quite easily with convenient graphical editors: just double click on the entity you want to modify. Alternatively, you can right click on a selected entity, then choose in the floating menu.
A new view can be added to a model by right clicking on the model panel, then choosing in the floating menu. Conversely, an existing view can be removed from a model by right clicking on the right entity (either a COOH entity for protein model or a 3' entity for a DNA model) of the view to remove, then choosing in the floating menu.
The menu proposes some commands to copy, cut and paste entities between models; please note that these operations only apply to a single entity.
Be aware that all edit operations are undoable!
3.2.3. Saving a model
At any time during the edition of a model, it can be saved in a file by selecting from the menu. You can also save an already saved model with a different file name by selecting from the menu.
3.2.4. Opening an existing model
Select from the menu to open an existing model. ModelDesigner will then display this model in a new model panel.
3.2.5. Scanning a sequence database
To start a sequence database scanning with a model, first select the model use. This is done by clicking on the caption bar of the model panel containing the model of interest. Then, select from the menu. Model Designer will display the list of available sequence databases. Select one of them, then click on the [Ok] button to start the scan. Finally, Model Designer displays a dialog box stating that the query has been sent (succesfully or not) to the Model Designer server.
Selecting from the menu displays a dialog box showing the status of the queries sent to the Model Designer server.
3.2.6. Uploading a sequence database on the server
It is possible to upload on the ModelDesigner server a user defined sequence database by selecting from the menu. A dialog box will be displayed where the set of sequences can be entered either by copy/paste or by opening a file. The only authorized file format is FASTA. The set of sequences will be sent to the ModelDesigner server by clicking on the [Ok] button.
Although there is no limit on the number of sequences that can be sent to the server, it is recommand to send no more than a few Mb of data.
3.2.7. Models and active model
The Modeler frame can contain several internal frames, each of them displaying a model. Only one of these internal frames does have a light blue caption bar (see for example Figure 3-1). This frame contains the active model, i.e. the model on which edition operations apply.
3.3. Templates frame
The Templates frame maintains a library of entities that can be used as building blocks to make models. By default, the frame is hidden and only its caption bar is visible. To show the current list of available templates, simply click on the small arrow located on the left of the Templates caption bar.
The Templates frame contains three sections: Types(), Entities () and Content(). The Types section displays the list of templates entities organized by their type. As a consequence, clicking on an entry in the Types section results in the display of the corresponding entities in the Entities section. Clicking on an entry in the Entities section results in the display of the properties of that entity in the Content section.
3.3.1. Editing a Template entity
Each template entity can be edited by selecting an entity in the Entities section, then choosing from the menu.
Since template entity edition directly affects an existing entity, you can first duplicate (i.e., copy) an existing template entity, then edit the copy. This is be done by selecting the entity to copy, then choosing from the menu.
3.3.2. Managing Template entities
The menu contains the commands to edit, duplicate and delete template entities. All these commands apply to the entity that is currently selected in the Entities section of the Templates panel.
The menu also contains a command to delete types. As a result all the entities of that type will be removed from the template library. This command applies to the selected entry of the Types section.
Be aware that the execution of these commands is undoable.
3.3.3. Saving/loading a library of Templates
The content of the Templates frame can be saved in a file by selecting the command from the menu. By default, the library is saved in a file which is the one that is automatically read by Model Designer at start up. This file is called the system library and is named either DNALibrary.xml or ProteinLibrary.xml (depending on the current running configuration of ModelDesigner: DNA or Protein model) and is located in the directory $USER_HOME/.mdesigner/conf, where $USER_HOME is the user home directory.
Since the command from the menu overrides the system library file without notice, the user should use it carrefully. Alternatively, the from the menu can be used to save a library in another file, the file name being specified by the user.
3.3.4. Adding Template entities into a model
Templates entities can be added to a model very easily by selecting an entity in the model being edited in the Modeler frame, then selecting in the Entities section the template entity to add in this model. Finally, selecting the command from the menu results in the addition of the Template entity in the model.
3.3.5. Adding models and entities into Templates
A model being edited in the Modeler frame can be copied to the Templates frame by selecting from the menu. Similarly, a model'entity can be copied to the Templates frame by selecting from the menu.
3.4. Commands reference
3.4.1. Main frame toolbar
Table 3-1. Commands accesible througth the Model Builder main frame toolbar. parameters
| Icon | Command |
|---|---|
 | Create a new model |
 | Save a model |
 | Edit the properties of a Template entity |
 | Copy a Template entity to the clipboard |
 | Delete a Template entity |
 | Edit the properties of an entity |
 | Copy an entity to the clipboard |
 | Cut an entity |
 | Paste the entity contained in the clipboard into a model |
 | Delete an entity |
Commands , and apply on the entity selected in the Entities section of the Templates frame.
Commands , , , and apply on the entity selected on the active model (see Section 3.2.7) of the Modeler frame.
3.4.2. Main frame menus and commands
The Model Builder main frame proposes the following menus: , , , and . The following tables list the commands available in these menus.
Table 3-2. Commands available from the menu (Model Builder module).
| Command | Description |
|---|---|
| New | Create a new model |
| Open | Open an existing model available on disk |
| Open prosite | Converts a Prosite expression into a ModelDesigner model |
| Save | Save the active model on disk (see Section 3.2.7) |
| Save as | Save the active model on disk using a new file name |
| Close | Close the frame containing the active model |
| Save library | Save the content of the Templates frame in the system library file (see Section 3.3.3) |
| Save library as | Save the content of the Templates frame on disk using a file name specified by the user |
| Dump SVG | Converts the active model into the ModelDesigner syntax, SVG (String Variable Grammar) |
| Exit | Close ModelDesigner |
Table 3-3. Commands available from the menu (Model Builder module).
| Command | Description |
|---|---|
| Edit properties | Edit the properties of a Template entity (see Section 3.3.1) |
| Duplicate | Duplicate a Template entity (see Section 3.3.2) |
| Delete | Delete a Template entity (see Section 3.3.2) |
| Add into model | Add a Tamplate entity in the active model (see Section 3.3.4) |
| Delete type | Delete a Template Type (see Section 3.3.2) |
Table 3-4. Commands available from the menu (Model Builder module).
| Command | Description |
|---|---|
| Edit properties | Edit the properties of an entity (see Section 3.2.2) |
| Copy entity | Copy an entity to the clipboard |
| Copy model | Copy the active model to the clipboard (see Section 3.2.7) |
| Paste | Paste the entity contained in the clipboard into a model |
| Cut entity | Cut an entity |
| Delete | Delete an entity |
| Add Entity to Templates | Copy an entity to the Template library |
| Add Model to Templates | Copy the active model to the Template library (see Section 3.2.7) |
Table 3-5. Commands available from the menu (Model Builder module).
| Command | Description |
|---|---|
| Send | Send the active model to the ModelDesigner server. This command is the entry point to start a database scanning (see Section 3.2.5) |
| Check status | Display the execution status of queries (see Section 3.2.5) |
| Upload database | Upload on the ModelDesigner server a user defined sequence database (see Section 3.2.6) |
Chapter 4. Model Analyzer
4.1. Main window
The main goal of the Model Analyzer module is to display the result of a query execution. Its main window contains a single frame named Results that can contain several internal frames each of them displaying the result of a query.
There are two ways to acces to this module from Model Builder: either by selecting the command from the menu or via the Query Status dialog box (accessible by choosing the command from the menu).
4.2. Opening a query result from the Model Builder module
A first convenient way to open the results of a query execution consists in choosing the command from the menu of Model Builder. You end up with a dialog box listing the queries sent to the ModelDesigner server along with their execution status. As soon as the status of a query is set to 'done', the associated results can be displayed by clicking on the [Fetch] button located at the bottom of the dialog box. ModelDesigner will then download the result from the server; this procedure may take some times depending on the size of the result. When the download ends, ModelDesigner automatically switchs from the Model Builder to the Model Analyzer module.
It is worth noting that during the download procedure, ModelDesigner copies the result from the server on your local disk. It means that any further accesses to a result already downloaded will be faster since ModelDesigner gets it from the local disk.
4.3. Opening a query result from the Model Analyzer module
A second way to open a result file is by selecting the command from the menu of the Model Analyzer module. The module displays a dialog box listing all the queries sent to the ModelDesigner server. To display the results of a particular query, select it in the list, then click on the [Ok] button. ModelDesigner will then download the result from the server; this procedure may take some times depending on the size of the result.
It is worth noting that during the download procedure, ModelDesigner copies the result from the server on your local disk. It means that any further accesses to a result already downloaded will be faster since ModelDesigner gets it from the local disk.
4.4. Exploring query results
The results of a query are displayed in a frame containing two tabs, Summary and Results, located at the bottom of this frame. By clicking on these tabs you can display either the Summay or the Results panel.
4.4.1. Summary panel
This panel displays some general data related to a query: the name of the model used to scan the sequence database, the name and size of this database and the number of matches (positive hits) and mismatches (negative hits).
4.4.2. Results panel
This panel displays the database sequences matching the model. The sequences are displayed in a tabular form and the model is displayed above the table. Each row in the table corresponds to a sequence database. On the right, a graphical display summarizes the location of the model within each sequence. That display can be replaced by the sequence display by clicking on the column' header.
In order to explore the model'matches within each sequence, it is possible to select separately each entity constituting the model. As a result, only the matches corresponding to the selection are displayed.
4.5. Menus and commands
The Model Analyzer main frame proposes the following menus: and . The following tables list the commands available in these menus.
Table 4-1. Commands available from the menu (Model Analyzer module).
| Command | Description |
|---|---|
| Open | Open a query result |
| Close | Close a query result frame |
| Export | Export the hit table in a file using a format suitable for spreadsheet (such as Excel) |
| Exit | Close ModelDesigner |