C-ImmSim is one of the most advanced computational models of the immune system. The software resorts to (bit or amino acid) strings to represent the “binding site” of cells and molecules. C-ImmSim is an agent-based model that includes the major classes of immune cells of the lymphoid lineage and some of the myeloid lineage. Helper T cells are divided into five phenotypes. B cells and plasma B are also divided into two phenotypes. All these entities interact with each other following a set of “rules” that describe the different phases of the recognition and response of the immune system against a pathogen. C-ImmSim accounts for phagocytosis, presentation, cytokine release, cell activation from the inactive or anergic state, cytotoxicity, and antibody secretion and incorporates the following immunological mechanisms: the clonal selection theory, the clonal deletion theory, the hypermutation of antibodies, the Hayflick limit, T cell anergy, Ag-dose induced tolerance in B cells, the danger theory, the idiotypic network theory.
C-ImmSim is one of the most detailed models of the human immune response. Considering its modularity and flexibility, it has the potential to reproduce the dynamics of the immune response to specific pathogens (bacteria and viruses) and diseases (e.g. cancer, autoimmune diseases, diabetes, among others). The ability to use amino acid strings has been a big step forward in modeling the immune system. It lays the foundation for developing commercial products for drug discovery pipelines, vaccinology, and in-silico clinical trials. In the long term, it has the potential to become one of the leading in-silico models for personalized treatment of diseases and pathologies in which the immune system plays a central role.