pioreactor/config.dev.ini at master · Pioreactor/pioreactor · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
[PWM]
# map the externals to the PWM
# hardware PWM are available on channels 1 & 3.
1=stirring
2=waste
3=media
4=alt_media
5=heating


[leds]
A=IR
B=white_light
C=
D=


[bioreactor]
# efflux_tube_volume_ml is determined by the volume that just touches the outflow tube. I.e. if you
# where to keep running the waste pump, what would the stable volume be.
# see docs
efflux_tube_volume_ml=14
initial_volume_ml=14
initial_alt_media_fraction=0.0


[stirring.config]
initial_target_rpm=500
initial_duty_cycle=15
pwm_hz=200
use_rpm=True
duration_between_updates_seconds=23
post_delay_duration=0.25
pre_delay_duration=0.25
enable_dodging_od=true
target_rpm_during_od_reading=0
target_rpm_outside_od_reading=500


[dosing_automation.turbidostat]
biomass_signal=auto

[stirring.pid]
Kp=0.007
Ki=0.0
Kd=0.0


[od_config.photodiode_channel]
1=REF
2=90

[od_reading.config]
# how many samples should the ADC publish per second?
samples_per_second=0.2
turn_off_leds_during_reading=1
pd_reference_ema=0.4

ir_led_intensity=auto

ref_normalization=unity


# apply a smoothing penalizer
smoothing_penalizer=6.0

duration_between_led_off_and_od_reading=0.1

[storage]
database=.pioreactor/storage/pioreactor.sqlite
temporary_cache=.pioreactor/storage/local_intermittent_pioreactor_metadata.sqlite
persistent_cache=.pioreactor/storage/local_persistent_pioreactor_metadata.sqlite
number_of_backup_replicates_to_workers=0

[logging]
log_file=./pioreactor.log
ui_log_file=./pioreactor.log

# See Python's logging module for possible values
#TODO: move this to another section
ui_log_level=DEBUG
console_log_level=DEBUG

[cluster.topology]
leader_hostname=localhost
leader_address=localhost


[ui.overview.settings]
filtered_od_lookback_minutes=240
raw_od_lookback_minutes=240
log_display_count=65
time_display_mode=hours

[ui]
port=4999
proto=http


[ui.overview.charts]
# show/hide charts on the PioreactorUI dashboard
# 1 is show, 0 is hide
implied_growth_rate=1
implied_daily_growth_rate=0
fraction_of_volume_that_is_alternative_media=1
normalized_optical_density=1
raw_optical_density=1
fused_optical_density=1
temperature=1

[ui.overview.cards]
# show/hide cards on the PioreactorUI dashboard
# 1 is show, 0 is hide
dosings=1
event_logs=1
profiles=1


[dosing_automation.pid_morbidostat]
Kp=5
Ki=0
Kd=0


[temperature_automation.thermostat]
Kp=.01
Ki=.01
Kd=.01

[temperature_automation.fir]
mlx_address=0x3A
sample_period_s=1.0
default_estimator_name=fir_temperature_estimator_linear_mlx_ambient_pcb_v1

[mqtt]
username=pioreactor
password=raspberry
broker_address=localhost
broker_ws_port=9001
broker_port=1883
ws_protocol=ws
use_tls=0

[dosing_automation.config]
pause_between_subdoses_seconds=0.5
waste_removal_multiplier=2.0
max_volume_to_warn=17.0
max_volume_to_stop=18.0
max_subdose=1.0
experimental_pump_malfunction_tolerance=0.2
experimental_detect_pump_malfunction=False

[growth_rate_calculating.config]
# these next two parameters control the length and magnitude
# of the variance shift that our Kalman filter performs after a dosing event
ekf_outlier_std_threshold=3.0
samples_for_od_statistics=35