With the growth of computational power and with the increase in the use of dis- tributed computing, new possibilities to simulate complex biological systems came out. To perform these simulation biological systems need to be modeled first. Mod- eling biological systems require a deep understanding in their biological mechanisms. Understand all the mechanisms to be modeled is difficult mainly for a reason: studies and researches in biology often focus on sub-fields that can describe only some por- tion of the complex system. An effort in understanding the interconnections between knowledge coming from different sub-fields is required. This lack in understanding mechanisms at the edge of the various sub-fields is reflected also in the various for- mats born in these last years to describe biological models.