Biochemical processes mediate the interaction of cells with their environment and are responsible for most of the information processing inside the cell. Networks of interacting proteins underlie many of these processes. Three major types of biochemical processes are distinguished:


*†† Metabolic pathways are sequences of chemical reactions, each catalyzed by an enzymes, where certain product molecules are formed from other small substrates. Metabolites are usually small molecules while enzymes are proteins.


*†† Signal transduction networks are pathways of molecular interactions that provide communication between the cell membrane and intracellular end-points, leading to some change in the cell. Signals are transduced by modification of one proteinís activity or location by another protein.


*†† Gene regulation circuits determine whether or not a particular gene is expressed at any particular time. Transcription factors, proteins that promote or repress transcription, either directly or indirectly bind regulatory DNA elements.


Metabolic, transduction and regulatory circuits are interleaved and integrated. For example, gene regulation circuits are fed by external signals transmitted by signal transduction pathways. The high complexity of these systems makes their proper understanding difficult. The BioSPI project is addressing this challenge by developing a novel framework for the representation, simulation and analysis of biochemical processes in the pi-calculus and related process algebras.


*†† More info and resources on biochemical pathways can be found here.