  Computer simulations have become a very powerful tool for scientific
research. Given the vast complexity that comes with many open scientific
questions, a purely analytical or experimental approach is often not viable.
For example, biological systems (such as the human brain) comprise an extremely
complex organization and heterogeneous interactions across different spatial
and temporal scales. In order to facilitate research on such problems, the
BioDynaMo project (\url{https://biodynamo.web.cern.ch/}) aims at a general
platform for computer simulations for biological research. Since the scientific
investigations require extensive computer resources, this platform should be
executable on hybrid cloud computing systems, allowing for the efficient use of
state-of-the-art computing technology. This paper describes challenges during
the early stages of the software development process. In particular, we
describe issues regarding the implementation and the highly interdisciplinary
as well as international nature of the collaboration. Moreover, we explain the
methodologies, the approach, and the lessons learnt by the team during these
first stages.
