How is a virtual biological system defined?

All biological systems are formed by a finite number of biological elements (genes, proteins, metabolites…) interacting in a non-linear fashion and acting as a network to perform different tasks/functions.

Fascinatingly, biological systems are not static; they are continuously affected by external and internal factors, named stimuli, which promote the transition to new phenotypes (i.e. sets of measurable parameters: gene or protein expression levels, enzyme activity, metabolite concentration, size, color…), named responses. This is possible because the interactions among the systems' components transmit signals which affect the function of the whole network.

stimulus response

Examples of biological systems include tissues, organs or even whole organisms. The previous explanation is true for any of them, regardless of their complexity: organisms consist of several organs working in tight coordination; organs are composed of different tissues, and so on. At the base of these complex structures lays the cell, which is itself a biological system defined by interactions between genes/proteins. Thus, it is valid enough to assume that an assembly of cells, interconnected in a specific way, is an accurate representation of a tissue, organ or organism.

Taking into account the nature of biological systems, we can thus conclude that a biological system is defined and has to be characterized by:

  • - The number and type of its elements
  • - Its responses to the stimuli that it receives.

SIMScells characterize its virtual biosystems by manually curating scientific literature and by the use of high-throughput data obtained from publicly available microarrays (GEO database). The inclusion of the complete ensemble of stimulus-response pairs and the definition of the elements of a specific biological system in the Truth Table produce biological system specific models, i.e. the virtual biological system.

SIMScells puts at its users' disposal a list of virtual systems with different organization levels: the whole human organism, different cell types, etc. In order to make it possible, we have developed an ever-growing collection of cell types with biological relevance, in which a team of experts is continuously working to add even more cell types and refine the existing models. In addition, we encourage you to suggest us any further cell type of your interest.