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Models published in the literature
Curated models: original Biomodels version and Biocham ODE curated version
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Models published in the literature
Curated models: original Biomodels version and Biocham ODE curated version
(1 of 1)
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Commands
Loading, listing and exporting models
Biocham files
load(<<input_file>>).
add(<<input_file>>).
clear_biocham.
load_biocham(<<input_file>>).
add_biocham(<<input_file>>).
list_model.
export_biocham(<<output_file>>).
expand_biocham(<<input_file>>).
export_init(<<output_file>>).
export_param(<<output_file>>).
SBML files
export_sbml(<<output_file>>).
export_sbml3(<<output_file>>).
load_sbml(<<input_file>>).
add_sbml(<<input_file>>).
curate_sbml(<<input_file>>).
curate_sbml(<<input_file>>,<<output_file>>).
ODE files
export_ode(<<output_file>>).
export_ode_latex(<<output_file>>).
load_ode(<<input_file>>).
add_ode(<<input_file>>).
curate_model.
Graphics files
export_dimacs(<<output_file>>).
export_dot(<<output_file>>).
export_dot(<<output_file>>,<<list_of_options>>).
dot.
draw_reactions.
json_reactions.
Other files
export_nusmv(<<output_file>>).
export_lotos(<<output_file>>).
export_prolog(<<output_file>>).
export_biopepa(<<output_file>>).
Listing and editing rules and events
Rules
list_rules.
list_rules(<<reaction>>).
expand_rules.
expand_rules(<<reaction>>).
add_rules(<<reaction>>).
add_rule(<<reaction>>).
add_rules(<<set_of_reactions>>).
add_rule(<<set_of_reactions>>).
delete_rules(<<reaction>>).
delete_rules(<<set_of_reactions>>).
clear_rules.
rule(<<int>>).
rule(<<reaction_name>>).
pathway(<<list_of_ints>>).
pathway.
list_ODE.
list_ODE(<<object>>).
Events
add_event(<<condition>>,<<parameter>>,<<kinetics>>).
add_event(<<condition>>,<<list_of_parameters>>,<<list_of_kinetics>>).
add_time_event(<<kinetics>>,<<condition>>,<<parameter>>,<<kinetics>>).
add_time_event(<<kinetics>>,<<condition>>,<<list_of_parameters>>,<<list_of_kinetics>>).
delete_event(<<condition>>,<<parameter>>,<<kinetics>>).
delete_event(<<condition>>,<<list_of_parameters>>,<<list_of_kinetics>>).
delete_time_event(<<kinetics>>,<<condition>>,<<parameter>>,<<kinetics>>).
delete_time_event(<<kinetics>>,<<condition>>,<<list_of_parameters>>,<<list_of_kinetics>>).
delete_events.
list_events.
Hybrid boolean-differential models
add_boolean_state(<<int>>,<<list_of_boolean_variables>>).
set_initial_boolean_state(<<int>>).
add_boolean_transition(<<transition>>,<<int>>,<<int>>).
add_interface(<<transition>>,<<condition>>,<<list_of_parameters>>,<<list_of_kinetics>>).
Hybrid stochastic-differential models
compose_ode_stochastic(<<input_file>>,<<input_file>>,<<output_file>>,<<volume>>,<<time>>).
compose_ode_stochastic(<<input_file>>,<<input_file>>).
Listing and defining initial states, molecules and locations
Initial state
list_initial_state.
list_all_initial_states.
clear_initial_state.
present(<<object>>).
present(<<set_of_objects>>).
present(<<object>>,<<concentration>>).
present(<<object>>,<<parameter>>).
absent(<<object>>).
absent(<<set_of_objects>>).
undefined(<<object>>).
undefined(<<set_of_objects>>).
make_present_not_absent.
make_absent_not_present.
set_initial_state(<<state>>).
set_initial_state(<<set_of_states>>).
Molecules
add_declaration(<<molecule_declaration>>).
list_declarations.
delete_declaration(<<molecule_name>>).
list_molecules.
list_molecules(<<object>>).
list_molecules(<<set_of_objects>>).
list_all_molecules.
list_all_molecules(<<object>>).
list_all_molecules(<<set_of_objects>>).
check_molecules.
Locations
volume(<<location>>,<<kinetics>>).
volume(<<location>>).
list_volumes.
Listing and declaring parameters, macros and invariants
Parameters
parameter(<<parameter>>,<<parameter_value>>).
parameter(<<parameter>>).
parameter_list(<<list_of_pdeclarations>>).
list_parameters.
delete_parameter(<<parameter>>).
Macros
macro(<<macro>>,<<kinetics>>).
macro(<<macro>>).
list_macros.
delete_macro(<<macro>>).
Algebraic invariants, conservation laws and P-invariants
conservation(<<set_of_objects>>).
conservation(<<conservation_list>>).
check_conservations.
delete_conservation(<<set_of_objects>>).
delete_conservation(<<conservation_list>>).
delete_conservations.
list_conservations.
search_conservations.
search_conservations(<<int>>).
Simulations
Boolean simulator
boolean_simulation.
boolean_simulation(<<count>>).
boolean_enumeration.
ODE and stochastic simulations
numerical_method.
numerical_method(<<simulation_method>>).
numerical_simulation.
numerical_simulation(<<time>>).
continue(<<time>>).
Parameters of ODE simulations:
step_size.
step_size(<<step>>).
step_doubling.
step_doubling(<<num>>).
no_step_doubling.
Parameters of stochastic simulations:
conversion_factor.
conversion_factor(<<int>>).
critical_reaction_threshold.
critical_reaction_threshold(<<int>>).
Plotting the result of simulations
keep_plot.
plot.
plot(<<object>>,<<object>>).
plot(<<object>>,<<object>>,<<object>>).
export_plot(<<output_file>>).
show_molecules(<<object>>).
show_molecules(<<set_of_objects>>).
hide_molecules(<<object>>).
hide_molecules(<<set_of_objects>>).
show_macros.
show_macros(<<set_of_macros>>).
hide_macros.
show_parameters.
show_parameters(<<set_of_parameters>>).
hide_parameters.
show_hide.
set_color(<<object>>,<<int>>).
set_color(<<macro>>,<<int>>).
test_plot.
set_xmin(<<num>>).
set_xmax(<<num>>).
set_ymin(<<num>>).
set_ymax(<<num>>).
fit_xmin.
fit_xmax.
fit_x.
fit_ymin.
fit_ymax.
fit_y.
get_max_from_trace(<<molecule>>).
get_min_from_trace(<<molecule>>).
get_period_from_trace(<<molecule>>).
set_init_from_trace(<<num>>).
Boolean temporal properties
CTL specification
add_spec(<<biocham_query>>).
add_specs(<<set_of_biocham_queries>>).
delete_spec(<<biocham_query>>).
delete_specs(<<set_of_biocham_queries>>).
list_spec.
clear_spec.
Checking CTL properties
check_ctl(<<biocham_query>>).
why.
check_why(<<biocham_query>>).
check_spec.
check_why_spec.
check_all_spec.
fairness_path.
no_fairness_path.
nusmv_dynamic_reordering.
nusmv_disable_dynamic_reordering.
nusmv_direct.
nusmv_non_direct.
Inferring CTL properties
genCTL.
genCTL(<<input_file>>).
add_genCTL.
Model reductions preserving CTL properties
reduce_model.
reduce_model(<<reaction>>).
reduce_model(<<set_of_reactions>>).
Learning rules from a CTL specification
learn_one_addition(<<reaction>>).
learn_one_addition(<<set_of_reactions>>).
learn_one_deletion(<<reaction>>).
learn_one_deletion(<<set_of_reactions>>).
learn_one_deletion.
revise_model.
revise_model(<<reaction>>).
revise_model(<<set_of_reactions>>).
revise_model_interactive.
revise_model_interactive(<<reaction>>).
revise_model_interactive(<<set_of_reactions>>).
Numerical temporal properties
LTL(R) specification
add_ltl(<<ltl_query>>).
add_ltl(<<set_of_ltl_queries>>).
delete_ltl(<<ltl_query>>).
delete_ltl(<<set_of_ltl_queries>>).
list_ltl.
clear_ltl.
Checking LTL(R) properties
Truth value of LTL(R) formulae
check_ltl(<<ltl_query>>).
check_ltl_spec.
check_ltl_spec(<<time>>).
FOLTL(R) constraints, validity domains, sensitivity and robustness
validity_domain(<<ltl_query>>).
satisfaction_degree(<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
Parameter sensitivity and robustness of FOLTL(R) properties
sensitivity(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
sensitivity_log(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
robustness(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
robustness_log(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
robustness_normal(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<count>>,<<time>>).
robustness_lognormal(<<list_of_parameters>>,<<list_of_nums>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<count>>,<<time>>).
Searching parameters from an LTL(R) specification
Simple parameter scanning method
landscape(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<count>>,<<time>>,<<output_file>>).
landscape(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<count>>,<<time>>,<<output_file>>,<<int>>).
landscape_log(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<count>>,<<time>>,<<output_file>>).
search_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<time>>).
search_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<ltl_query>>,<<time>>).
search_all_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<ltl_query>>,<<time>>).
search_all_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<time>>).
search_random_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<ltl_query>>,<<time>>).
search_random_parameters(<<list_of_parameters>>,<<list_of_intervals>>,<<count>>,<<time>>).
search_random_all_parameters(<<num>>,<<count>>,<<ltl_query>>,<<time>>).
search_random_all_parameters(<<num>>,<<count>>,<<time>>).
Parameter optimization using CMA-ES
search_parameters_cmaes(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
search_parameters_log_cmaes(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<time>>).
cmaes_params(<<count>>,<<num>>,<<num>>).
cmaes_params(<<count>>,<<num>>).
search_parameters_fss(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<num>>).
search_parameters_log_fss(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<num>>).
fss_params(<<count>>,<<count>>,<<num>>,<<num>>,<<num>>,<<int>>).
Multi-trace conditions
first_search_condition(<<list_of_parameters>>,<<list_of_intervals>>,<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<num>>).
add_search_condition(<<ltl_query>>,<<list_of_variables>>,<<list_of_nums>>,<<list_of_ppairs>>).
cmaes_multi_conditions.
Trace loading and simplification
load_trace(<<input_file>>).
set_simplification_trace(<<simplification_method>>).
set_simplification_trace(<<simplification_method>>,<<num>>).
rm_simplification_trace.
Abstractions
Model reductions
smerge(<<object>>,<<molecule>>).
smerge(<<set_of_objects>>,<<molecule>>).
sdelete(<<object>>).
sdelete(<<set_of_objects>>).
rdelete(<<reaction>>).
rdelete(<<set_of_reactions>>).
rmerge(<<reaction>>).
rmerge(<<set_of_reactions>>).
search_reduction(<<input_file>>,<<input_file>>).
search_all_reductions(<<input_file>>,<<input_file>>).
search_mreduction(<<input_file>>,<<input_file>>).
search_all_mreductions(<<input_file>>,<<input_file>>).
Dimensional analysis
list_dimensions.
set_dimension(<<parameter>>,<<signed_int>>).
Influence graph
list_influences.
export_influences_dot(<<output_file>>).
export_influences_ginml(<<output_file>>).
draw_influences.
Protein functions
list_functions.
Location neighborhood
list_neighborhood.
draw_neighborhood.
export_neighborhood_dot(<<output_file>>).
Examples
cell_cycle_Tyson_6Var
tyson91_fss_parameter_search_2.bc
tyson91_fss_parameter_search_8_dim.bc
tyson91_fss_parameter_search.bc
tyson91_global_sensitivity_analysis.bc
tyson91_parameter_search_examples_2.bc
tyson91_parameter_search_examples_8_dim.bc
tyson91_parameter_search_examples_old.bc
tyson91_parameter_search_examples.bc
tyson91_test.bc
tyson91.bc
cell_cycle_Tyson_multiple_conditions
tyson91_multi_search_commands.bc
tyson91_multi.bc
cell_cycle
cell_cycle_pattern.bc
cell_cycle_test.bc
cell_cycle.bc
init_state2.bc
events
ball.bc
events_test.bc
ssa.bc
time_events.bc
generic_test
generic_test.bc
hybrid
cell_cycle_bool.bc
cell_cycle_interface.bc
cell_cycle_ode.bc
cell_cycle_test.bc
input_ode.bc
input_stoch.bc
T7_hybrid.bc
T7_stochastic.bc
kinetics
2g_test.bc
2g.bc
add_biocham_test.bc
add_biocham2_test.bc
circ.bc
circa_hong2.bc
circa_test.bc
enzyme_test.bc
enzyme-ai.bc
enzyme-i.bc
enzyme-s.bc
event_test.bc
event.bc
kt_test.bc
kt.bc
lv_test.bc
lv.bc
mapk.bc
MM_test.bc
MM.bc
order_test.bc
order1.bc
order2.bc
stiff_test.bc
stiff.bc
locations
notch4n36c.bc
p53Mdm2_test.bc
p53Mdm2.bc
MAPK
mapk_test.bc
mapk.bc
MPRI
BIOMD0000000021_curated.bc
BIOMD0000000021.bc
BIOMD0000000071_curated.bc
BIOMD0000000071.bc
PreyPredator.bc
Switch.bc
Trypsin.bc
TrypsinQE.bc
TrypsinQSSA.bc
ode
MM_test.bc
MM.bc
small_cell_cycle
initial_state.bc
small_cell_cycle_test.bc
small_cell_cycle.bc
small
pepa.bc
pinv_test.bc
pinv1.bc
pinv2.bc
pinv3.bc
pinv4.bc
small_test.bc
small.bc
stoch
simple_test.bc
simple.bc
T7bacteriophage.bc
tyson_test.bc
transcriptional_cascade
cascade_analysis.bc
cascade.bc
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Server examples
cell_cycle_Tyson_6Var
tyson91_fss_parameter_search_2.bc
tyson91_fss_parameter_search_8_dim.bc
tyson91_fss_parameter_search.bc
tyson91_global_sensitivity_analysis.bc
tyson91_parameter_search_examples_2.bc
tyson91_parameter_search_examples_8_dim.bc
tyson91_parameter_search_examples_old.bc
tyson91_parameter_search_examples.bc
tyson91_test.bc
tyson91.bc
cell_cycle_Tyson_multiple_conditions
tyson91_multi_search_commands.bc
tyson91_multi.bc
cell_cycle
cell_cycle_pattern.bc
cell_cycle_test.bc
cell_cycle.bc
init_state2.bc
events
ball.bc
events_test.bc
ssa.bc
time_events.bc
generic_test
generic_test.bc
hybrid
cell_cycle_bool.bc
cell_cycle_interface.bc
cell_cycle_ode.bc
cell_cycle_test.bc
input_ode.bc
input_stoch.bc
T7_hybrid.bc
T7_stochastic.bc
kinetics
2g_test.bc
2g.bc
add_biocham_test.bc
add_biocham2_test.bc
circ.bc
circa_hong2.bc
circa_test.bc
enzyme_test.bc
enzyme-ai.bc
enzyme-i.bc
enzyme-s.bc
event_test.bc
event.bc
kt_test.bc
kt.bc
lv_test.bc
lv.bc
mapk.bc
MM_test.bc
MM.bc
order_test.bc
order1.bc
order2.bc
stiff_test.bc
stiff.bc
locations
notch4n36c.bc
p53Mdm2_test.bc
p53Mdm2.bc
MAPK
mapk_test.bc
mapk.bc
MPRI
BIOMD0000000021_curated.bc
BIOMD0000000021.bc
BIOMD0000000071_curated.bc
BIOMD0000000071.bc
PreyPredator.bc
Switch.bc
Trypsin.bc
TrypsinQE.bc
TrypsinQSSA.bc
ode
MM_test.bc
MM.bc
small_cell_cycle
initial_state.bc
small_cell_cycle_test.bc
small_cell_cycle.bc
small
pepa.bc
pinv_test.bc
pinv1.bc
pinv2.bc
pinv3.bc
pinv4.bc
small_test.bc
small.bc
stoch
simple_test.bc
simple.bc
T7bacteriophage.bc
tyson_test.bc
transcriptional_cascade
cascade_analysis.bc
cascade.bc
Choose Theme
Afterdark
Afternoon
Afterwork
Aristo
Black-Tie
Blitzer
Bluesky
Bootstrap
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Deep-Purple
Delta
Dot-Luv
Eggplant
Excite-Bike
Flick
Glass-X
Home
Hot-Sneaks
Humanity
Le-Frog
Midnight
Mint-Choc
Overcast
Pepper-Grinder
Redmond
Rocket
Sam
Smoothness
South-Street
Start
Sunny
Swanky-Purse
Trontastic
UI-Darkness
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Vader
