The goals of this paper are to describe some characteristics of the pedagogical project of the "Carbopolis" software and some programming solutions that were found during the computational implementation of this software. Relative to the first goal, some pedagogical features that are considered necessary to developing computerized learning materials for scientific education are analyzed. To that end, the design of scenarios is presented as a way of linking learning strategies, such as simulation, problem solving, and play. Related to the second goal, there is a brief description of some potential that JAVA technology holds for the computational implementation of pedagogical projects with such features. The context of the inclusion of the computational implementation using free software is also shown. Eventually, the programming solutions developed using a graphical interface, scenario mapping, data storage, bookmarking, notepad, browser (developed specifically for "Carbopolis"), and the software installation are described. In addition, some information obtained in two contexts of the pedagogical project evaluation is presented: one context attempted to evaluate conceptual learning; the second attempted to show the software usability in different school settings. (Contains 1 table and 4 figures.)