Exemplary embodiments of the present invention comprise a tool kit for the design and execution of research protocols, for example, comprising a web-based research protocol composer for generating a data processing protocol; a collector for collecting data entered via an internet based questionnaire; a database for data; and a protocol processing routine for processing data and generating an output. For example, the toolkit suitably serves as a "hub" of a global research environment (e.g., connected via the Internet or other network) that creates and connects communities of researchers and facilitates the sharing of software and results. Additionally, the present invention provides standardized and custom online "programs" or "scripts" (referred to herein as "protocols") that define and guide events in experiments, clinical trials, surveys, and other kinds of studies. These protocols are created and executed online.