BNG_actions_and_args
 Share
The version of the browser you are using is no longer supported. Please upgrade to a supported browser.Dismiss

 
View only
 
 
ABCDEFGHIJKL
1
2
**Last updated on 10/29/15 by:Leonard A. Harris
3
4
ActionFile typesAllowed argumentsArgument descriptionDefault valueAvailable sinceExample
5
action({arg=>val,...})arg=>val_type
6
generate_network.netprefix=>"string"Change the base filename for output."[model_name]"
7
Generate species and reactions by iterative application of rules, starting from the seed species.suffix=>"string"Suffix added to output base filename.""
8
verbose=>0/1Verbose output.0
9
overwrite=>0/1Overwrite existing NET file.0
10
print_iter=>0/1Write NET file at every iteration.0
11
max_agg=>intMax # of molecules in a complex.1e9
12
max_iter=>intMax # of iterations of rule application.100
13
max_stoich=>{"string"=>int, "string"=>int,...}Max # of molecules of specified type(s) in a complex.undef
14
TextReaction=>0/1Write reactions with BNG-style species strings (human readable).0
15
TextSpecies=>0/1Write BNG-style species strings (human readable).1
16
generate_hybrid_model.bnglprefix=>"string"Change the base filename for output."[model_name]"2.2.0
17
Write hybrid particle/population model to reduce NFsim memory use.suffix=>"string"Suffix added to output base filename."hpp"
18
verbose=>0/1Verbose output.0
19
overwrite=>0/1Overwrite existing BNGL file.0
20
actions=>["string", "string",...]List of actions to append to bottom of generated hybrid model."writeXML()"
21
execute=>0/1Execute actions in hybrid model.0
22
safe=>0/1Enable safe mode (works with any value of "lumping rate constant").02.2.4-testing
23
simulate .cdat Recognizes all arguments to 'simulate_ode', 'simulate_ssa', 'simulate_pla', and 'simulate_nf', plus...
24
All-purpose simulator. .gdatprefix=>"string"Change the base filename for output."[model_name]"
25
Available since BNG 2.2.0-stable[_end.net]suffix=>"string"Suffix added to output base filename.""
26
[_save.net]verbose=>0/1Verbose output.0
27
method=>"string"Simulation method (currently supported methods are "ode", "ssa", "pla", and "nf").None (required)method=>"nf" since 2.2.6-testing
28
argfile=>"string"Input file containing action arguments (Note: arguments defined within the model file take precendence).undef2.2.0-stable
29
continue=>0/1Signals that a simulation is a continuation of the previous simulation.02.1.8
30
t_start=>floatStart time for simulation.0.0
31
t_end=>floatEnd time for simulation.max(sample_times)' if 'sample_times' defined and 'n_steps' NOT defined. Otherwise, must be user defined.
32
n_steps=>intNumber of time points at which to output uniformly between 't_start' and 't_end'.1
33
n_output_steps=>intSame as 'n_steps'.12.2.0-stable
34
sample_times=>[float,...]Specific time points at which to output (Note: 'n_steps' takes precedence if defined).undef
35
output_step_interval=>intNumber of simulation steps between outputs.INFINITY2.2.0-stable
36
max_sim_steps=>intUpper limit on # of simulation steps.INFINITY2.2.0-stable
37
stop_if=>"string"Logical condition for terminating simulation.undef2.2.1-stable
38
print_on_stop=>0/1Output system state to file upon satisfaction of 'stop_if' condition.12.2.1-stable
39
print_end=>0/1Output network with final species concentrations to '_end.net' file.0
40
print_net=>0/1Output network to '_save.net' file at every output step (useful for restarting in the event of an unexpected interruption).0
41
save_progress=>0/1Same as 'print_net'.02.2.0-stable
42
print_CDAT=>0/1Output species concentrations to CDAT file (if disabled, only initial and final concentrations output).12.2.0-stable
43
print_functions=>0/1Output global function values to GDAT file.02.2.0-stable
44
netfile=>"string"NET file to use for simulation."[model_name].net"
45
seed=>intRandom seed (method=>"ssa"/"pla"/"nf").floor(rand(2**31))
46
simulate_ode.cdat Recognizes all arguments to 'simulate' (except 'method'), plus...
47
Simulate reaction network using SUNDIALS CVODE ordinary differential equation integrator..gdatatol=>floatAbsolute error tolerance.1.0E-08
48
( Called as simulate({method=>"ode", ...}) )[_end.net]rtol=>floatRelative error tolerance.1.0E-08
49
[_save.net]sparse=>0/1Use sparse Jacobian/iterative solver.0
50
steady_state=>0/1Perform steady-state check on species concentrations.0
51
simulate_ssa.cdat Recognizes all arguments to 'simulate' (except 'method'), plus...
52
Simulate reaction network using Gillespie's stochastic simulation algorithm (direct method w/ propensity sorting)..gdatseed=>intRandom seed.floor(rand(2**31))
53
( Called as simulate({method=>"ssa", ...}) )[_end.net]
54
[_save.net]
55
simulate_pla .cdat Recognizes all arguments to 'simulate' (except 'method'), plus...
56
Simulate reaction network using the “partitioned-leaping algorithm” (a tau-leaping variant)..gdatseed=>intRandom seed.floor(rand(2**31))
57
( Called as simulate({method=>"pla", ...}) )[_end.net]pla_config=>"string"PLA simulation configuration.fEuler|pre-neg:sb|eps=0.032.2.0-stable
58
[_save.net]pla_output=>0/1PLA-specific output (currently only rxn classifications to '.classif' file).02.2.1-stable
59
simulate_nf.cdat Recognizes all arguments to 'simulate' (except 'method'), plus...
60
Simulate rule-based model using network-free stochastic simulator NFsim..gdatseed=>intRandom seed.floor(rand(2**31))
61
( Called as simulate({method=>"nf", ...}) ).xmlcomplex=>0/1Turn on complex bookkeeping (method=>"nf").1
62
.speciesnocslf=>0/1Disable evaluation of complex-scoped local functions. (method=>"nf")0
63
notf=>0/1Disable on-the-fly observable calculation (method=>"nf").0
64
binary_output=>0/1Write output to binary format (method=>"nf").0
65
gml=>intSet global molecule limit (method=>"nf").100000
66
equil=>floatAmount of time to simulate (equilibrate) before beginning output (method=>"nf").0.0
67
get_final_state=>0/1Output final system state (method=>"nf").1
68
utl=>intSet the universal traversal limit (method=>"nf").Size of the largest reactant pattern in the rule set.
69
param=>"string"Additional NFsim arguments not recognized by BNG (see NFsim manual).""param=>"-dump [0;5]"
70
parameter_scan.cdatSame as 'simulate''parameter_scan' calls 'simulate', passing all valid arguments. N/A
71
Perform a parameter scan (all methods supported)..gdatparameter=>"string"Parameter to be scanned.None (required)
72
[_end.net]par_min=>floatMin value of parameter for scan.None (required if 'par_scan_vals' not defined)
73
[_save.net]par_max=>floatMax value of parameter for scan.None (required if 'par_scan_vals' not defined)
74
.scann_scan_pts=>int# of values in scan, uniform between 'par_min' and 'par_max'.None (required if 'par_scan_vals' not defined)
75
log_scale=>0/1Distribute scan points uniformly between log10('par_min') and log10('par_max').0
76
par_scan_vals=>[float,...]Specific values of the parameter to be scanned overNone (required if 'par_min', 'par_max', and 'n_scan_pts' not defined)2.2.6-stable
77
reset_conc=>0/1Reset concentrations after each simulation in the scan.12.2.6-testing
78
bifurcate_bifurcate_[OBS_NAME].scanSame as 'parameter_scan' except 'reset_conc', which is set to 0. 'bifurcate' calls 'parameter_scan' twice, once scanning from 'par_min' to 'par_max', and the second scanning in the opposite direction. The output of the scans is processed, generating one output file per observable. Each file contains three columns: scan pts, forward scan result, reverse scan result.reset_conc=>02.2.6-testing
79
Perform a bifurcation analysis (all methods supported).(one output file per observable)
80
81
readFile.bnglfile=>"string"File to read (absolute path).None (required)
82
Read model from file..netblocks=>["string",...]An optional list of blocks to be imported from a file.None (by default, all blocks are imported)2.2.6-testing
83
.xml (SBML)atomize=>0/1Extract implicit molecular structure from an input SBML model file02.2.6-testing
84
skip_actions=>0/1Skip all actions in a .bngl file0
85
writeFile.bnglformat=>"string"select output format (currently supported formats are "bngl", "net", "xml")."net"2.2.0-stable
86
All-purpose method for writing models to file..netprefix=>"string"set prefix of output file name."[model_name]"
87
(Use writeModel, writeNetwork, or writeXML when possible).xml (BNG-XML)suffix=>"string"set suffix of output file name.""
88
evaluate_expressions=>0/1evaluate math expressions output as numbers.0
89
include_model=>0/1include model blocks in output file.1
90
include_network=>0/1include network blocks in output file.1
91
overwrite=>0/1allow writeFile to overwrite exisiting files.1
92
pretty_formatting=>0/1write output in "pretty" form.1
93
TextReaction=>0/1write reactions as BNGL strings.0
94
TextSpecies=>0/1write species as BNGL string.1
95
writeModel .bngl Same as 'writeFile', with the following defaults:2.2.0-stable
96
Write rule-based model in BNGL format.format=>"bngl"
97
include_model=>1
98
include_network=>0
99
evaluate_expressions=>0
100
pretty_formatting=>1
Loading...
 
 
 
Sheet1