Physics 434, 2014: Scripts

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Back to Physics 434, 2014: Information Processing in Biology.

Scripts:

• HW1.m -- first homework problem simulation
• HW2_5.m -- second homework, problem 2 simulation
• Ecoli.m -- E. coli motion simulation
• LuriaDelbruck.m -- Luria-Delbruck simulated experiment.
• LDexpt.mat -- Luria-Delbruck experimental data; courtesy of Phil Nelson
• gillespie_bd.m -- Birth-death process, Gillespie simulation
• langevin_bd.m -- Birth-death process, Langevin simulation
• gillespie_mrna.m -- bursty mRNA expression, Gillespie simulation
• my_entropy.m -- entropy calculation for a discrete distribution
• mutual.m -- mutual information calculation for a discrete 2-variable distribution
• joint_pdf.m -- calculating the joint distribution from the conditional and the marginal
• CherryAdler.m -- phase portrait of the toggle switch, courtesy of Phil Nelson
• lac_switch_det.m -- deterministic dynamics of a simplified model of the lac bistable switch
• lac_switch.m -- Gillespie stochastic dynamics of the same simplified model of the lac bistable switch

Data files:

• neural-3neurons.mat -- activity of three coupled simulated neurons
• neural-calabrese.txt -- experimental neural activity of 6 neurons from a leech heart