I am involved in a modelling task of a biological process described as follows:
-- "Objective: to model behavior of a sender receiver type system
The process goes as follows
Pre-signal [PS] is in media
Pre-signal diffuses into bacteria
Pre-signal binds to activator as a co-activator
Co-activator activator complex binds to DNA and starts transcription of enzyme mRNA
Enzyme mRNA is transcribed then translated into enzyme
Enzyme begins converting Pre-signal to signal [S]
Signal diffuses out of the cell into media
Signal diffuses into receiver cell from media
Signal binds to repressor inducing activation of reporter gene
Questions for model:
What concentrations of signal will be required to get a response from receiver cell?"
My questions are: what kind of mathematical/computational model or simulation tool is more suitable for this task? is it neccesary to model every step, or can some of these be ignored? I know the basics of ODEs, so I wonder if these are enough or something else would be required. Any other advice about how to go through the modelling is welcome.