An easy-to-use tool for computatio …
An easy-to-use tool for computational neuroscientists that facilitates the following tasks: creating, editing and visualizing models and other objects; interacting with neuronal databases; interacting with simulation systems such as GENESIS; and collaborating with other modelers using simultaneous shared editing and visualization.
A realistic neuronal model represents a modeler's understanding of the structure and function of a part of the nervous system. As the number of neurobiologists constructing realistic models continues to grow, and as the models become ever more sophisticated, they collectively represent a significant accumulation of knowledge about the structural and functional organization of nervous systems. But at the same time, locating appropriate models and interpreting them becomes increasingly more difficult as the number of online model and experimental databases grows. The central motivation for the Modeler's Workspace project is to address these problems.
With support from The Human Brain Project, we began by exploring the construction of a brain database based on our existing neural simulation system, GENESIS. This was a feasibility study for a novel approach to neural database construction, organization, and interaction.
The Modeler's Workspace was originally conceived as the user interface to this system. As the design has evolved, the creation of a next-generation interface for collaborative neural simulations has become our goal. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies).
The Modeler's Workspace is a collection of software tools that enable users to interact over the WWW with databases of models and data. It provides facilities for: searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs.
The central motivation for the Modeler's Workspace project is to address these problems of locating and interpreting models by creating software for assisting computational neuroscientists. The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler's Workspace is designed to provide the following:
-Search and retrieval facilities for interacting with databases of models and other information;
-Facilities for creating, editing and visualizing the characteristics of models;
-Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON;
-Facilities for managing a personal database where a user can collect models and other objects; and
-Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared database and communicate with each other using real-time chat.
The Modeler's Workspace is written in Java for portability and extensibility. It is modular in design and uses pluggable components for supporting different data formats, which means that new data types can be supported by loading an appropriate plug-in. To increase the probability that the Modeler's Workspace will be compatible with future databases and tools, we are using the eXtensible Markup Language (XML) as the interchange format for communicating with databases.
A Workspace Database contains objects that represent different types of entities such as models or bibliographic references. Each database object is structured according to a particular template. A template defines the format of an object, including its attributes and subattributes and the permitted types of data that can be stored in each attribute. Templates have names, and different templates are used to define different types of objects. Some of the basic types of objects predefined by the Modeler's Workspace are ``Author, ``Reference, ``Data, ``Neuron Model and ``Ion Channel Model.