Mining the database for information

There are two different kinds of tools that can be used to find information in the GENESIS database. The database browser (see image) can be used to look through all the available data, and works similarly to a file directory browser - the data is sorted into a hierarchy of categories, and the user can explore this hierarchy by opening and closing folders.

The Workspace also provides a set of query interfaces which will allow a user to specify a number of restrictions on the data to be retrieved. These restrictions can be combined by using logical operators (such as and, or and not). In order to spare the user from learning the details of database query languages, the query interfaces will be based on a system of pull-down menus (see image).

Once the user has assembled a query using the interface shown above, all matching models will be retrieved from the database. In the case that there are several models that fit the criteria, they will all be displayed together. This lets the user see immediately how certain important parameters may vary over large sets of models. In the example below, the we have looked for models that contain L-type calcium channels. The display uses color-coding to represent the conductance density of this channel type throughout the model.

Visualizing different kinds of models

Once a model has been retrieved from the database, the proper visualizer is automatically launched to let the user examine the details of that model and its associated data.


An important goal of the Workspace project is to make it easier for researchers to understand models built by others. One way we intend to accomplish this is by encouraging and supporting the inclusion of guided tutorials with each model submitted to the database.

The image below shows the user interface for running tutorials from the Workspace. Each tutorial may be divided into different parts, each of which contains detailed instructions and an explanation of why the model behaves as it does. A number of slide bars may also be provided - these let the user manipulate certain sensitive parameters in the model and see the effect in the simulation.

Clicking on the "Start" button starts a GENESIS simulation, the parameters of which are stored in the database together with the tutorial.

The image below shows the result of a current clamp simulation that was run via the tutorial. In order to create this, the Modeler's Workspace

The colors in the cell display represent the membrane potential in the various comaprtments of the model, and indicate an active propagation of action potentials into the dendrites.