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This study aims at highlighting the collaborative activity of two high school students (age 14) in the cases of modeling the complex biological process of plant growth with two different tools: the "paper & pencil" concept mapping technique and the computer-supported educational environment "ModelsCreator". Students' shared activity in both cases is carried out in the presence of a facilitator providing technical as well as cognitive support when necessary. The objective of the study is to highlight the ways in which the collaborating students are engaged in the plant growth modeling activity in the two cases and also identify the activity's similar and different aspects in each one. Our analysis is carried out on two complementary axes, the first of which concerns the "process" of collaboratively creating a plant growth model with each different tool, while the second has to do with the students' conceptualizations of the biological aspect of the modeling task in each case. A two-level analytic tool for the modeling process has been derived within the theoretical framework of "activity theory" on the basis of the "OCAF" scheme for "basic modeling operations" and the scheme of Stratford et al. [Stratford, S. J., Krajcik, J., & Soloway, E. (1998). Secondary students' dynamic modeling processes: analyzing, reasoning about, synthesizing, and testing models of stream ecosystems. "Journal of Science Education and Technology," 7(3), 215-234.] for "higher-order modeling actions." According to our results, four major "modeling actions (analysis, synthesis, testing-interpreting, technical and cognitive support)" performed through a plethora of "modeling operations" define the steps of the modeling process in both cases, while specific qualitative differences can be actually identified. Finally, the students' conceptualizations of the biological aspect of the modeling task in the two-case activity is analyzed in regard with their capability of shifting reasoning between macro- and micro-levels, while educational implications are also discussed.