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LON-CAPA uses a powerful and flexible "cascading parameter" system. A "parameter" is anything that can be set for a problem in a course, such as a due date. LON-CAPA parameters can be set for the "entire course", for "all problems in a particular sequence", or for an "individual problem". Fully independently of that, they can be set for "everyone in a course", for "everyone in a section", or for "a single person". More specific parameter settings override more general ones.

Some of the more common parameters include "open date" (when a problem becomes visible for the student to complete), "due date" (the time the student must have the problem done by), "answer date" (an optional date where the solution to the problem becomes visible if they did not complete it earlier), and "weight" (the point value of the problem). Different problem types can also take different parameters; for instance, the instructor can override the "tolerance" for a numerical problem (how close the student must come for a numerical problem to be considered correct), or control the style of the problem (for instance, the system has an "exam" mode where it will give the student multiple choices for a numerical problem, which is useful for printed exams). Problems can also export arbitrary other parameters, which may give instructors the ability to control the difficulty level or select a specific varient of the problem, depending on how the problem was authored.

This parameter system makes most common manipulations of these parameters very easy. If a specific section missed a lab because of a fire drill, that section can have its due date extended for the week without affecting any other section with a single operation. A single student can have their problems opened earlier if they're going to be gone for some excused reason. An entire self-paced learning course can have a global due-date set at the beginning of the course.