simcov/simforager_null.config at 1a6e385de99efc3383c3ceb7556e5513945381aa · AdaptiveComputationLab/simcov · 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
; These are version 1.0 test of 'null' forager parameters for SIMCoV
; This means a parameter-based translation of SIMCoV into SIMForager without yet
; changing anything about the existing SIMCoV code base

; Dimensions: x y z (assuming grid spacing of 5 microns)
dim =                         500 500 1
; >> resulting in 225000000 total environment (epithelial) cells

; Whole lung dimensions: x y z (assuming grid spacing of 5 microns)
whole-lung-dim =              500 500 1

; Number of timesteps (assuming 1 min per timestep)
; Set to arbitrary small number to start
timesteps =                   14400
; >> ten days

; Location of initial infections (omit for no infections); can be:
;  list of space-separated coords x,y,z,timestep
;  uniform:N (where N is an int, for N uniformly distributed starting points at time 0)
;  random:N (where N is an int, for N randomly distributed starting points at time 0)
infection-coords =            uniform:22500
; >> this is .001% of total grid cells

; Number of virions at initial infection locations
; Chosen to guarantee that at least one cell is infected at the start - see infectivity
initial-infection =           1
; >> initially 1000 combined with number of initial infection sites, this should yield a 1:100 ratio of grid cells to algae cells

; Average number of time steps to expressing virions after cell is infected
incubation-period =           0

; Average number of time steps to death after apoptosis is induced
apoptosis-period =            3

; Average number of time steps to death after a cell starts expresssing
expressing-period =           1000000

; Factor multiplied by number of virions to determine probability of infection
infectivity =                 0.5
; SIMCoV paper default

; Multiplier reducing infectivity where inflammatory signal is present
; (the multiplier reducing infectivity should be between 0.9 and 0.7 based on values
; in literature demonstrating a reduction of cell death in vitro with IFN)
infectivity-multiplier =      1.0
; >> irrelevant

; Number of virions produced by expressing cell each time step
virion-production =           1.1
; this is SIMCoV default we're going with for now...

; Multiplier reducing virion production rate where inflammatory signal is present
; (the reduction should be represented by a multiplier betweeon 0.05 and 0.15)
virion-production-multiplier = 1.0

; Fraction by which virion count drops each time step
virion-clearance =            0.0
; >> effectively algae death rate; not considered here

; Fraction of virions that diffuse into all neighbors each time step
virion-diffusion =            0.0

; Amount of chemokine produced by expressing cells each time step
chemokine-production =        0.0

; Amount by which chemokine concentration drops each time step
chemokine-decay =             0.0

; Fraction of chemokine concentration that diffuses into all neighbors each time step
chemokine-diffusion =         1.0

; Minimum chemokine concentration that triggers a T cell
min-chemokine =               0.0
; >> this should allow fish (T-cells) to be present at start

; Impact of antibodies; multiplier for virion decay (setting to 1 means this has no effect)
antibody-factor =             1

; Number of time steps before antibodies start to be produced
antibody-period =             1000000
; >> WHAT!? NOBODY INVITED ANTIBODIES TO A REEF

; Number of tcells generated at each timestep for the whole lung
; This is scaled up 5000x from the mouse model (20 per minute)
tcell-generation-rate =       100
; >> for a stable population of fish (T-cells) throughout sim

; Number of time steps before T cells start to be produced
tcell-initial-delay =         0

; Average number of time steps to death for a T cell in the vasculature
tcell-vascular-period =       2

; Average number of time steps to death after a T cell extravasates
tcell-tissue-period =         1000000

; Number of time steps a T cell is bound to an epithelial cell when inducing apoptosis
tcell-binding-period =        2

; Max probability of a T cell binding to an infected cell in one time step
max-binding-prob =            1

; T cells in tissue follow the chemokine gradient
tcells-follow-gradient =      false

; Random seed
seed =                        29

; Number of timesteps between samples (set to 0 to disable sampling)
sample-period =               5

; Resolution for sampling
sample-resolution =           1

; Max. block dimension - larger means more locality but worse load balance. Set to 0 for largest possible.
max-block-dim =               10

; Output directory (automatically generated)
;  output =                   results