A computerized system for modeling biological pathways is provided. The system comprises a database having a knowledge database for storing at least one attribute of at least one entity and a pathway database for storing at least one pathway diagram; a user interface for creating, querying, manipulating and viewing data from the database; a process system having a modeling module for simulating or analyzing the behavior of an attribute on a pathway diagram and a pathway editor module for retrieving, editing and saving at least one pathway diagram. The invention may be implemented on a web-based system that provides end users with the ability to create new pathway models, edit or manipulate existing pathway models, perform sequence searches and data queries, and generate reports.
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