Inducible oscilating pulse generator.

Dampening.

GRN with arrows!

And circuit thing logisym

Back up with references.

Edenborough part of IGEM site has defined repressors.

Logisym
Should be continuos
Explicitly state bistability from toggle switch
Say its fro mthe toggle switch

Solving analytically by examining the graphs.

No time scale separation for oscilators.

Repressilator and bi-stable toggle swtich

Project Description, Aaron Blotnick

Clear motivation, though some claims should be backed up by references (e.g., "these systems are
one of the most pervasive circuits seen in biology", circadian rhythm responding to "time and specific
inputs"). What do you mean by the oscillator becoming "out-of-phase" (with respect to what)? If the
system fails, the oscillation of each of the three elements C, D, and E will dampen to a steady-state
instead of changing their respective periods to become out-of-phase with each other. The project
scope is still somewhat undefined. It remains unclear why you are choosing to model the formation
of a callus as an oscillation, since there was no mention of periodic/cyclic (this is the key behavior of

an oscillator) up/down-regulation of callus forming/degrading pathways that would justify this choice.
An external reference would justify this claim that introducing an oscillating motif will accurately
recapitulate callus formation. Why did you choose a stochastic model (random/probabilistic such that
each run of a simulation will output different results given the same inputs) when temporal MATLAB
models are generally deterministic (such as the Biosystems framework we have been using)? Also,
are you planning on "numerically"/mathematically analyzing steady-state stability as you mentioned?
In class we have been doing this by looking at transfer functions/curves/graphs, nullclines, etc. Also,
be careful in your use of the term "bi-stability", as there is not really such thing as a bi-stable
oscillator.
Alternatively, you could propose that your oscillating system may accurately recapitulate callus
formation and acknowledge the feasibility of this in later assignments.