Biology students need exposure to modern research techniques relatively early in their educational careers. Computer multimedia simulation tools have been developed to address the challenge of providing all students with hands-on laboratory research experience. This paper presents a learner-centered approach to the design and development of a multimedia simulation for biology education. We present our methodology and a multimedia simulation tool designed and developed using the methodology. Out tool has been widely adopted by biological science educators for teaching molecular biology subjects in a wide range of undergraduate biology courses. We believe that our methodology can be adopted or adapted by learner communities in other disciplines.