This paper presents a thermal analysis and control framework for a cubesat which can serve as an on-orbit experimental platform on living mammalian tissues. In particular, the Bio-CubeSat will be used to study long term effects of space radiations and microgravity on a living sample of mammalian bone tissue contained in a bio housing. This housing will provide the adequate ex-vivo environment for the tissue to survive during the few weeks to perform the experiments. It will also contain the set of sensors to assess the health of the sample and its structural change and chemical degradation due to the harsh space environment. One of the most stringent requirements, for the survivability of the bone sample, relates to maintaining the housing temperature fluctuation within a narrow range during the orbit. In this work we describe the development of a framework to execute the thermal analysis of an orbiting cubesat. Our ultimate goal is to identify, for a given Bio-cubesat orbit, the external coating materials and attitude control law, during the Sun exposure, that limit the temperature fluctuation within an admissible range.