BiSDL - A new Biological Systems Description Language

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. Indeed the simulation of a biological system functioning require a language that describes the model and acts as interface between biologists and computer. The existing languages are mainly machine-readable formats, based on the Extensible Markup Language (XML). In this work we make an effort in creating a human-readable language able to describe complex biological systems, trying to overcome the weaknesses of existing formats. We focus mainly in the Ontogeny field, because is enough complex to make us able to describe multiple complex mechanisms. One of our requirement was flexibility to avoid the creation of another language too focused in a biological sub-field. We also choose a new formalism that can describe these complex systems, in contrast to the Ordinary Differential Equations (ODEs), mainly exploited when modeling biological mechanisms, we adopt the Net Within Net (NWN) formalism.