COGENT Version 2.3 Help

Research Programmes

Cognitive models are rarely static things. In general, they develop and evolve over time in response to empirical and/or theoretical inadequacies. COGENT supports this kind of model evolution via the concept of a Research Programme (Cf. Lakatos, 1970). A research programme consists of a set of related models. Often those models will have been created by successive modifications of some initial model. COGENT provides a number of facilities for managing research programmes, including editing functions (e.g., to create and delete models), a display facility (in which a research programme is represented graphically as a "family tree" showing all models in the research programme's development and the historical relations between them) and archive facilities.

The Research Programme Manager

When COGENT is started, it presents the user with the top-level Research Programme Manager window. This window provides access to COGENT's research programme management facilities and its model development tools. The Research Programme Manager window consists of three regions (see figure 1). Along the top are buttons. Beneath these buttons are (on the left) a region displaying the list of current research programmes and (on the right) a set of panels for displaying the contents of the currently selected research programme.

Figure 1: The Research Programme Manager Window

The buttons along the top of the window allow access to:

Note that COGENT must be correctly configured for the What's New... and Help... buttons to find the correct data files. If the window that pops up after pressing either of these buttons is empty, check that you have copies of all help files and that these files are located in the appropriate folder. This folder may be set or checked by selecting the File locations item from the Preferences... window.

The research programme list on the left of the main window contains an alphabetically sorted list of all of your existing research programmes. (If you don't have any research programmes then this list will be empty.) Individual research programmes in this list may be selected by left-clicking on them. Once a research programme is selected, its details (including its history, description and model list) are displayed in the panels on the right of the Research Programme Manager.

Pages within the Research Programme Manager Window

The right hand side of the Research Programme Manager window shows details of the currently selected research programme. These details include the research programme's name, the date it was created, and a brief one-line description of the programme. Beneath these details there is a set of panels in the form of a "notebook". The pages in the notebook correspond to:

It is possible to switch between the pages at any time. However, if a programme description is modified it must be saved before switching to either of the other pages or closing the research programme. If a modified description is not explicitly saved, COGENT will ask whether it should be saved before closing the Programme Description page.

The Programme Description Page

The Programme Description page is a free-format text area provided for purely documentation purposes. It consists of a panel where plain unformatted text describing the research programme may be entered and saved. The text might describe the motivation for the research programme, or give an over-view of the component models.

The Diagrammatic History Page

COGENT displays a research programme's history in its top-level window as an annotated time-line. (See Figure 1 above.) Annotated nodes correspond to individual models within the research programme. Each model is represented as a little COGENT icon with its name or creation date. If the research programme consists of just a single model, then there will be just one icon. If the research programme comprises multiple models then a number of icons will be shown. The time-line which connects the icons may be linear, indicating a sequence of models that have developed cumulatively from a single ancestry, or it may branch, indicating points at which different modifications to a model have been considered. This allows, for example, a range of modifications to a single model to be explored.

The diagrammatic history panel is sensitive to the position of the mouse, and when the mouse is moved over a model's icon some details of the model (when it was created, last edited, and last run) will appear in a window beneath the icon. The panel is also sensitive to mouse clicks. Models may be selected by left-clicking on their icons and operated on by selecting a function from the menu bar at the top of the panel. The following functions are available:

File / Open:Open the model in COGENT's box and arrow editor, either in View... or Edit... mode.
File / New Model:Create a new, empty, model. Clicking on this button will pop up a dialogue window that queries some basic model information. When the information is given and the dialogue closed, a new model based on that information is created. This will be reflected by a new icon appearing on the diagrammatic history. Note that the new model will be completely blank, and effectively represent a new line in the research programme unrelated to any existing models. Thus, this method of creating a new model is not appropriate when one is merely modifying an existing model. To modify an existing model without destroying the model, use the Edit / Create Copy menu item described above.

File / Print:Print the selected model. A window will popup asking which details of the model should be printed and allowing the user to select a print format.
File / Webify:Create HTML files and associated graphics for the whole model, as used in WebCOGENT. This menu item is only available in the registered version of COGENT
Edit / Select / None: Deselect all models within the research programme.
Edit / Select / Invert: Invert the selection of models within the research programme.
Edit / Select / All: Select all models within the research programme.
Edit / Create Copy:Create a new model by copying the selected model. The new model may then be modified without destroying the original model.
Edit / Delete/Cut:Delete the model from the research programme. The deleted model will be placed on COGENT's clipboard, from where it can be pasted into another research programme if desired.
Edit / Paste:Move a model from COGENT's clipboard back into the selected research programme.
Edit / Set Parent:Alter the parent model of the selected model, and hence alter the arrow relations between the corresponding nodes.
View / Grid:Display a feint grid on the diagrammatic history canvas, to allow easier manual alignment of icons. (This option is only available in the registered version of COGENT, where it is possible to position icons by dragging them across the canvas.)
View / Arrange / Autospace: Spaces icons equally across the horizontal dimension of the diagram. (Note that in the registered version of COGENT it is also possible to position icons by dragging them across the canvas.)
View / Arrange / Scale: Scale the horizontal distance between icons to fit with the creation dates of the corresponding models. (Note that in the registered version of COGENT it is also possible to position icons by dragging them across the canvas.)
Help...:Open a web browser showing this help information.

Where a function operates on a model, the function may be applied to multiple models by selecting multiple models before selecting the function. Multiple models may be selected by pressing the shift key and keeping it pressed while left-clicking on multiple icons.

Double-clicking on an icon provides a shortcut to the default menu option. Initially this is Open in Edit... mode, so initially double clicking on an icon will open the corresponding model. The various functions may also be accessed by right-clicking on the diagrammatic history panel and selecting from the menu that pops up.

The Model List Page

The Model List page provides an alternative way of viewing the models in a research programme. The models are displayed as a simple list, with dates and model descriptions given for each model in the list. Clicking on an element in the list will select the corresponding model. Clicking with the right mouse button will pop up the standard menu for model manipulation described in the documentation above for the Diagrammatic History page.

Archive Facilities

What is an Archive?

Archives are single files that contain entire COGENT research programmes. In COGENT's normal mode of operation, the models within a research programme are each contained in a separate folder within the user's project folder. This makes transferring models and/or complete research programmes between machines difficult, because you need to transfer the contents of an entire folder. It also makes uploading and downloading research programmes from the web more difficult than necessary. By stuffing all of the relevant files into a single file, archives provide a convenient portable format for transfer and exchange of complete research programmes.

The Archive Browser

The archive browser is an interface tool that allows research programmes to be transformed into archive files and vice versa. The browser window (shown below) consists of a list of research programmes (on the left) and a list of archives (on the right), with two buttons between the list for transforming one format into the other. To archive a research programme, select the desired research programme and click on the >>Archive>> button. To extract an archive, select the desired archive and click on the <<Extract<< button. Preferences relating to archives (e.g., the format in which archives will be created, the locations of archives and research programmes, and whether research programmes/archives should be retained after they are transformed) may also be set from the archive browser. (See Archive Preferences.)

Figure 2: The Archive Browser

Supported Archive Formats

COGENT supports several archive formats:

CARThis is the default, and preferred, format for COGENT archives. CAR files are ASCII text files that contain all files within a research programme. While they may be examined with a text editor such as emacs or notepad, it is not advisable to attempt to edit them. One disadvantage of CAR files is that they tend to be rather large.
COGThe COG format was introduced with the original version of COGENT for windows. In that version of COGENT, it was the native file format: when COGENT was installed files ending in .cog would be automatically opened with COGENT. The COG format only includes one model (rather than an entire research programme) in an archive, and cannot by generated by recent versions of COGENT. However, COGENT can still extract models from COG files into the format used by the rest of the system. This means that COG files created in WinCOGENT can be translated into research programmes for use by the current version of COGENT.
TARThis format will be familiar to UNIX users. The archive file is a standard tar (tape archive) file, built by using the tar command to package the research programme folder into a single file. TAR archives have two disadvantages: most Windows machines don't have tar (and so they tend to be UNIX specific); and the archive file includes the research programme's name, so changing the file's name won't change the name of the extracted research programme (and may confuse COGENT slightly). On Windows programmes such as WinZip may be used to extract TAR archives.
TGZThis format will be familiar to UNIX users. The archive file is a standard compressed tar archive, built by first using tar to package the research programme folder into a single file and then compressing that file with gzip. TGZ archives have one advantage and two disadvantages. Since they are compressed they tend to be smaller than equivalent archives in other formats. However, most Windows machines don't have tar or gzip (and so TGZ archives tend to be UNIX specific), and TGZ archive files include the research programme's name, so changing the archive file's name won't change the name of the extracted research programme (and may confuse COGENT slightly). On Windows, programmes such as WinZip may be used to extract TGZ archives.

Each archive format has pros and cons. The CAR format is most portable, and generally recommended. CAR and COG files may be renamed, and the archive will then extract into a research programme of the new name. TAR and TGZ files contain the names of the research programme within them, and so renaming these files will not alter the name of the extracted research programme. Furthermore, TAR and TGZ formats are not supported under Windows. However, the TGZ format is most compact.

If archive file size is an issue, be sure to reinitialise all models in the research programme before archiving it (this generally ensures that message logs and current contents files are small). For reductions in archive size can be obtained by compressing CAR files (using a zip utility), though they must of course be uncompressed before COGENT can extract the contents.

The format of an archive is indicated by the last three characters of the file's name. COGENT uses these characters to work out which extraction routine should be applied to the file. Don't change them!

The Online Model Archive

The Online Model Archive is a web site that contains models created by members of the COGENT community. COGENT includes a browser for the online model archive so that users may download and upload models from within COGENT at the click of a button. The browser, which is accessed from the Programme Manager window by selecting CogWeb... from the View menu, is shown in Figure 3.

Figure 3: The Online Model Archive Browser

To browse the online archive, ensure the web site address is valid (the official online archive is at: and click on the Reload button. If you are connected to the net, COGENT will query the online model archive site and display, in the Contributed Research Programmes frame, a list of models available for download. To download a model, select it and click on the Download button.

Trusted users may also upload research programmes to the site for download by other COGENT users. To upload a research programme, select the programme from the panel on the left of the browser, and the click on the Upload button. This facility is limited to trusted users to avoid the possibility of anonymous users uploading malicious models.

COGENT Version 2.3 Help