The invention relates to a web-based instrument and data management system and method including software executing on an instrument controller computer system that receives a web file from a web browsing software executing on a remote computer. The web-based interface also extracts a user identifier and a requested action, determines with the user is authorized for the requested action and performs the action is the user is authorized. If not the web-based interface generates and transmits a web file indicating that the user is not authorized for the requested action.