The present talk deals with dynamical processes observed at the organismal level in conditions close to real-world environments. The relatively small amount of data and replicates available in such experiments poses specific challenges to the design, deployment and application of integrated computational tools for data management and analysis. They are exemplified by microcosm studies of phototrophic biofilms and in-vivo circadian rhythms of body temperature in mammalians. On the basis of these experiences, I will discuss potential alterations to common protocols of interdisciplinary collaboration, which might be useful in enhancing the efficiency of computational tools in knowledge discovery.