feigenbaum is a set of project scripts purposed to ensure that our 2 gene ratio experiment actually terminates; It will be composed of projects much like before with a few tweaks. Specifically,the experiments have different population sizes, which will be done until I find a 'sweet' spot where the simulation equilibriates reliably. Maybe do some tests to come up with a score cut off instead of a generational cut off.
For now, there will be no weight given to expression error.
bin/ contains the higher order scripts that manipulate the control model and execute the output model project scripts. iterations/ contains the experiment folders for each iteration, and the csv output for each iteration. paper/ contains what I have completed so for of the paper. plotting/ contains plot utilities (written in R) and plots.
1) Run bin/replace_script.sh and input iteration number (this creates a directory in the iteration/date and iteration/experiments folders with
the specified iteration name) EX: 1st, 2nd, 3rd, etc
2) Ensure that the codons are correct in data/model_codons.csv - the script bin/make_experiments.sh changes this file by incrementing 'TAT'
3) Run bin/make_experiments.sh to create the experiment folders in iterations/experiments
4) Run sed -e 's/[old name]/[new name]/g' bin/execute_[old name].sh > execute_[new name].sh to make the new execution script
5) chmod +x bin/execute_[new name].sh to run all experiments.
1) experiment has W=0, N=50, terminated at approx. 500 for 1ratio
2) experiment has W=0, N=50, terminated at approx. 506 for 1ratio
3) experiment has W=0, N=50, terminated at approx. 504 for 1ratio
4) experiment has W=0, N=10, terminated at approx. 35 for 1ratio
5) experiment has W=0, N=10, terminated at approx. 33 for 1ratio
6) experiment has W=0, N=50, terminated at approx. 506 for 1ratio
7) experiment has W=0, N=50, terminated at approx. 505 for 1ratio
8) experiment has W=0, N=100, terminated at approx. 505 for 1ratio
9) experiment has W=0, N=100, terminated at approx. 504 for 1ratio
10) experiment has W=0, N=100, terminated at approx. 506 for 1ratio
11) experiment has W=0, N=100, terminated at approx. 507 for 1ratio
12) experiment has W=0, N=10, terminated at approx. 41 for 1ratio
13) experiment has W=0, N=10, terminated at approx. 34 for 1ratio
14) experiment has W=0, N=10, terminated at approx. 36 for 1ratio
Next, choose parameter N=50 and try multiple weights.
15) experiment has W=.25, N=50,
16) experiment has W=.25, N=50,
17) experiment has W=.25, N=50,
18) experiment has W=.25, N=50,
19) experiment has W=.25, N=50,
20) experiment has W=.50, N=50,
21) experiment has W=.50, N=50,
22) experiment has W=.50, N=50,
23) experiment has W=.50, N=50,
24) experiment has W=.50, N=50,
25) experiment has W=.75, N=50,
26) experiment has W=.75, N=50,
27) experiment has W=.75, N=50,
28) experiment has W=.75, N=50,
29) experiment has W=.75, N=50,
30) experiment has W=1.0, N=50,
31) experiment has W=1.0, N=50,
32) experiment has W=1.0, N=50,
33) experiment has W=1.0, N=50,
34) experiment has W=1.0, N=50,
35) experiment has W=1.25, N=50,
36) experiment has W=1.25, N=50,
37) experiment has W=1.25, N=50,
38) experiment has W=1.25, N=50,
39) experiment has W=1.25, N=50,
40) experiment has W=1.5, N=50,
41) experiment has W=1.5, N=50,
42) experiment has W=1.5, N=50,
43) experiment has W=1.5, N=50,
44) experiment has W=1.5, N=50,
45) experiment has W=1.75, N=50,
46) experiment has W=1.75, N=50,
47) experiment has W=1.75, N=50,
48) experiment has W=1.75, N=50,
49) experiment has W=1.75, N=50,
50) experiment has W=2.0, N=50,
51) experiment has W=2.0, N=50,
52) experiment has W=2.0, N=50,
53) experiment has W=2.0, N=50,
54) experiment has W=2.0, N=50,
Directories have structure: ── experiments └──── pp_amount └── pp_rate ├── 50_expression_error │ ├── weight_0 │ │ ├── 1st_iteration │ │ ├── 2nd_iteration │ │ ├── 3rd_iteration │ │ ├── 4th_iteration │ │ └── 5th_iteration │ ├── weight_1 │ │ ├── 1st_iteration │ │ ├── 2nd_iteration │ │ ├── 3rd_iteration │ │ ├── 4th_iteration │ │ └── 5th_iteration │ ├── weight_2 │ │ ├── 1st_iteration │ │ ├── 2nd_iteration │ │ ├── 3rd_iteration │ │ ├── 4th_iteration │ │ └── 5th_iteration │ ├── weight_3 │ │ ├── 1st_iteration │ │ ├── 2nd_iteration │ │ ├── 3rd_iteration │ │ ├── 4th_iteration │ │ └── 5th_iteration │ └── weight_99 │ ├── 1st_iteration │ ├── 2nd_iteration │ ├── 3rd_iteration │ ├── 4th_iteration │ └── 5th_iteration └── init_expression_error └── weight_0 ├── 1st_iteration ├── 2nd_iteration ├── 3rd_iteration ├── 4th_iteration └── 5th_iteration
22 directories