| A | B | C | D | E | F | G | H | I | J | K | L | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ||||||||||||
2 | Leonard A. Harris | |||||||||||
3 | ||||||||||||
4 | Action | File types | Allowed arguments | Argument description | Default value | Available since | Example | |||||
5 | action({arg=>val,...}) | arg=>val_type | ||||||||||
6 | generate_network | .net | prefix=>"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=>0/1 | Verbose output. | 0 | |||||||||
9 | overwrite=>0/1 | Overwrite existing NET file. | 0 | |||||||||
10 | print_iter=>0/1 | Write NET file at every iteration. | 0 | |||||||||
11 | max_agg=>int | Max # of molecules in a complex. | 1e9 | |||||||||
12 | max_iter=>int | Max # 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=>0/1 | Write reactions with BNG-style species strings (human readable). | 0 | |||||||||
15 | TextSpecies=>0/1 | Write BNG-style species strings (human readable). | 1 | |||||||||
16 | generate_hybrid_model | .bngl | prefix=>"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=>0/1 | Verbose output. | 0 | |||||||||
19 | overwrite=>0/1 | Overwrite existing BNGL file. | 0 | |||||||||
20 | actions=>["string", "string",...] | List of actions to append to bottom of generated hybrid model. | "writeXML()" | |||||||||
21 | execute=>0/1 | Execute actions in hybrid model. | 0 | |||||||||
22 | safe=>0/1 | Enable safe mode (works with any value of "lumping rate constant"). | 0 | 2.2.4-testing | ||||||||
23 | simulate | .cdat | Recognizes all arguments to 'simulate_ode', 'simulate_ssa', 'simulate_pla', and 'simulate_nf', plus... | |||||||||
24 | All-purpose simulator. | .gdat | prefix=>"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=>0/1 | Verbose output. | 0 | ||||||||
27 | method=>"string" | Simulation method (currently supported methods are "ode", "ssa", "pla", and "nf"). | None (required) | types | ||||||||
28 | argfile=>"string" | Input file containing action arguments (Note: arguments defined within the model file take precendence). | undef | begin seed s | ||||||||
29 | continue=>0/1 | Signals that a simulation is a continuation of the previous simulation. | 0 | 2.1.8 | ||||||||
30 | t_start=>float | Start time for simulation. | 0.0 | |||||||||
31 | t_end=>float | End time for simulation. | max(sample_times)' if 'sample_times' defined and 'n_steps' NOT defined. Otherwise, must be user defined. | |||||||||
32 | n_steps=>int | Number of time points at which to output uniformly between 't_start' and 't_end'. | 1 | |||||||||
33 | n_output_steps=>int | Same as 'n_steps'. | 1 | 2.2.0-stable | ||||||||
34 | sample_times=>[float,...] | Specific time points at which to output (Notes: 'n_steps' takes precedence if defined; 't_start' still defaults to 0.0, not 'sample_times[0]'). | undef | |||||||||
35 | output_step_interval=>int | Number of simulation steps between outputs. | INFINITY | 2.2.0-stable | ||||||||
36 | max_sim_steps=>int | Upper limit on # of simulation steps. | INFINITY | 2.2.0-stable | ||||||||
37 | stop_if=>"string" | Logical condition for terminating simulation. | undef | 2.2.1-stable | ||||||||
38 | print_on_stop=>0/1 | Output system state to file upon satisfaction of 'stop_if' condition. | 1 | 2.2.1-stable | ||||||||
39 | print_end=>0/1 | Output network with final species concentrations to '_end.net' file. | 0 | |||||||||
40 | print_net=>0/1 | Output network to '_save.net' file at every output step (useful for restarting in the event of an unexpected interruption). | 0 | |||||||||
41 | save_progress=>0/1 | Same as 'print_net'. | 0 | 2.2.0-stable | ||||||||
42 | print_CDAT=>0/1 | Output species concentrations to CDAT file (if disabled, only initial and final concentrations output). | 1 | 2.2.0-stable | ||||||||
43 | print_functions=>0/1 | Output global function values to GDAT file. | 0 | 2.2.0-stable | ||||||||
44 | netfile=>"string" | NET file to use for simulation. | "[model_name].net" | |||||||||
45 | seed=>int | Random 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. | .gdat | atol=>float | Absolute error tolerance. | 1.0E-08 | |||||||
48 | ( Called as simulate({method=>"ode", ...}) ) | [_end.net] | rtol=>float | Relative error tolerance. | 1.0E-08 | |||||||
49 | [_save.net] | sparse=>0/1 | Use sparse Jacobian/iterative solver. | 0 | ||||||||
50 | steady_state=>0/1 | Perform 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). | .gdat | seed=>int | Random 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). | .gdat | seed=>int | Random seed. | floor(rand(2**31)) | |||||||
57 | ( Called as simulate({method=>"pla", ...}) ) | [_end.net] | pla_config=>"string" | PLA simulation configuration. | fEuler|pre-neg:sb|eps=0.03 | 2.2.0-stable | ||||||
58 | [_save.net] | pla_output=>0/1 | PLA-specific output (currently only rxn classifications to '.classif' file). | 0 | 2.2.1-stable | |||||||
59 | simulate_nf | .cdat | Recognizes all arguments to 'simulate' (except 'method'), plus... | |||||||||
60 | Simulate rule-based model using network-free stochastic simulator NFsim. | .gdat | seed=>int | Random seed. | floor(rand(2**31)) | |||||||
61 | ( Called as simulate({method=>"nf", ...}) ) | .xml | complex=>0/1 | Turn on complex bookkeeping (method=>"nf"). | 1 | |||||||
62 | .species | nocslf=>0/1 | Disable evaluation of complex-scoped local functions. (method=>"nf") | 0 | ||||||||
63 | notf=>0/1 | Disable on-the-fly observable calculation (method=>"nf"). | 0 | |||||||||
64 | binary_output=>0/1 | Write output to binary format (method=>"nf"). | 0 | |||||||||
65 | gml=>int | Set global molecule limit (method=>"nf"). | 100000 | |||||||||
66 | equil=>float | Amount of time to simulate (equilibrate) before beginning output (method=>"nf"). | 0.0 | |||||||||
67 | get_final_state=>0/1 | Output final system state (method=>"nf"). | 1 | |||||||||
68 | utl=>int | Set 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 | .cdat | Same as 'simulate' | 'parameter_scan' calls 'simulate', passing all valid arguments. | N/A | |||||||
71 | Perform a parameter scan (all methods supported). | .gdat | parameter=>"string" | Parameter to be scanned. | None (required) | |||||||
72 | [_end.net] | par_min=>float | Min value of parameter for scan. | None (required if 'par_scan_vals' not defined) | ||||||||
73 | [_save.net] | par_max=>float | Max value of parameter for scan. | None (required if 'par_scan_vals' not defined) | ||||||||
74 | .scan | n_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=>0/1 | Distribute 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 over | None (required if 'par_min', 'par_max', and 'n_scan_pts' not defined) | 2.2.6-stable | ||||||||
77 | reset_conc=>0/1 | Reset concentrations after each simulation in the scan. | 1 | 2.2.6-testing | ||||||||
78 | bifurcate | _bifurcate_[OBS_NAME].scan | Same 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=>0 | 2.2.6-testing | ||||||
79 | Perform a bifurcation analysis (all methods supported). | (one output file per observable) | ||||||||||
80 | ||||||||||||
81 | readFile | .bngl | file=>"string" | File to read (absolute path). | None (required) | |||||||
82 | Read model from file. | .net | blocks=>["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=>0/1 | Extract implicit molecular structure from an input SBML model file | 0 | 2.2.6-testing | |||||||
84 | skip_actions=>0/1 | Skip all actions in a .bngl file | 0 | |||||||||
85 | writeFile | .bngl | format=>"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. | .net | prefix=>"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=>0/1 | evaluate math expressions output as numbers. | 0 | |||||||||
89 | include_model=>0/1 | include model blocks in output file. | 1 | |||||||||
90 | include_network=>0/1 | include network blocks in output file. | 1 | |||||||||
91 | overwrite=>0/1 | allow writeFile to overwrite exisiting files. | 1 | |||||||||
92 | pretty_formatting=>0/1 | write output in "pretty" form. | 1 | |||||||||
93 | TextReaction=>0/1 | write reactions as BNGL strings. | 0 | |||||||||
94 | TextSpecies=>0/1 | write 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 | |||||||||||