We present the development of an integrated extendable web-based simulation environment called Computational Science and Engineering On-line (CSEO) that allows computational scientists to perform research using state-of-the-art tools, querying data from personal or public databases, discuss results with colleagues, and access resources beyond those available locally from a web browser. It is a user-driven web-based application tool. Currently, CSEO provides an integrated environment for multi-scale modeling of complex reacting systems. A unique feature of CSEO is in its framework that allows data to flow from one application to another in a transparent manner. A particular example is demonstrated to show how results from fundamental quantum chemistry simulations are used to calculate thermodynamic and kinetic properties of a chemical reaction, which subsequently are used in the simulation of a combustion reactor. Advantages, disadvantages, and future prospects of a web-based simulation approach are then discussed. CSEO can be accessed at http://cseo.net.