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Citing BioMASS
BioMASS
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Index
_
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
_
__post_init__() (biomass.result.OptimizationResults method)
_bind_and_dissociate() (biomass.construction.reaction_rules.ReactionRules method)
B
bind() (biomass.construction.reaction_rules.ReactionRules method)
biomass.construction.template.observable
module
biomass.construction.template.ode
module
biomass.construction.template.problem
module
biomass.construction.template.reaction_network
module
biomass.construction.template.search_param
module
biomass.construction.template.viz
module
biomass.core
module
biomass.models._copy
module
biomass.plotting
module
bounds (biomass.construction.template.problem.OptimizationProblem property)
C
cm (biomass.construction.template.viz.Visualization attribute)
cmap (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SensitivityOptions attribute)
(biomass.plotting.SingleObservable attribute)
condition (biomass.plotting.MultipleObservables attribute)
conditions (biomass.construction.template.observable.Observable attribute)
convert() (biomass.construction.text2model.Text2Model method)
convert_species_name() (biomass.construction.template.viz.Visualization static method)
copy_to_current() (in module biomass.models._copy)
create() (biomass.core.Model method)
create_model() (in module biomass.core)
D
degrade() (biomass.construction.reaction_rules.ReactionRules method)
dephosphorylate() (biomass.construction.reaction_rules.ReactionRules method)
diffeq() (biomass.construction.template.ode.DifferentialEquation method)
differential_equations (biomass.construction.reaction_rules.ReactionRules attribute)
DifferentialEquation (class in biomass.construction.template.ode)
dimerize() (biomass.construction.reaction_rules.ReactionRules method)
disp_here (biomass.estimation.Optimizer attribute)
divided_by (biomass.plotting.SingleObservable attribute)
dont_show (biomass.plotting.SingleObservable attribute)
double_arrows (biomass.construction.reaction_rules.ReactionRules attribute)
dynamic_assessment() (biomass.result.OptimizationResults method)
dynamic_plot() (biomass.construction.text2model.Text2Model method)
E
error_bars (biomass.construction.template.observable.Observable attribute)
exp_data (biomass.plotting.SingleObservable attribute)
experiments (biomass.construction.template.observable.Observable attribute)
F
figsize (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SensitivityOptions attribute)
(biomass.plotting.SingleObservable attribute)
find_cyclic_reaction_routes() (biomass.construction.thermodynamic_restrictions.ThermodynamicRestrictions method)
fixed_species (biomass.construction.reaction_rules.ReactionRules attribute)
flux() (biomass.construction.template.reaction_network.ReactionNetwork static method)
fname (biomass.plotting.MultipleObservables attribute)
fwd_arrows (biomass.construction.reaction_rules.ReactionRules attribute)
G
gene2val() (biomass.model_object.ModelObject method)
generate() (biomass.estimation.InitialPopulation method)
get_executable() (biomass.model_object.ModelObject method)
get_individual() (biomass.model_object.ModelObject method)
get_obj_val() (biomass.model_object.ModelObject method)
I
import_solution() (biomass.estimation.Optimizer method)
init_info (biomass.construction.reaction_rules.ReactionRules attribute)
initial_values() (in module biomass.construction.template.ode)
InitialPopulation (class in biomass.estimation)
input_txt (biomass.construction.reaction_rules.ReactionRules attribute)
(biomass.construction.text2model.Text2Model attribute)
is_degraded() (biomass.construction.reaction_rules.ReactionRules method)
is_dephosphorylated() (biomass.construction.reaction_rules.ReactionRules method)
is_phosphorylated() (biomass.construction.reaction_rules.ReactionRules method)
is_synthesized() (biomass.construction.reaction_rules.ReactionRules method)
L
lang (biomass.construction.text2model.Text2Model attribute)
legend_kws (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SensitivityOptions attribute)
(biomass.plotting.SingleObservable attribute)
load_param() (biomass.model_object.ModelObject method)
M
minimize() (biomass.estimation.Optimizer method)
model (biomass.estimation.InitialPopulation attribute)
(biomass.estimation.Optimizer attribute)
Model (class in biomass.core)
ModelObject (class in biomass.model_object)
module
biomass.construction.template.observable
biomass.construction.template.ode
biomass.construction.template.problem
biomass.construction.template.reaction_network
biomass.construction.template.search_param
biomass.construction.template.viz
biomass.core
biomass.models._copy
biomass.plotting
multiple_observables_options (biomass.construction.template.viz.Visualization attribute)
MultipleObservables (class in biomass.plotting)
N
normalization (biomass.construction.template.observable.Observable attribute)
nothing (biomass.construction.reaction_rules.ReactionRules attribute)
O
objective() (biomass.construction.template.problem.OptimizationProblem method)
obs_desc (biomass.construction.reaction_rules.ReactionRules attribute)
obs_names (biomass.construction.template.observable.Observable attribute)
Observable (class in biomass.construction.template.observable)
observables (biomass.plotting.MultipleObservables attribute)
OptimizationProblem (class in biomass.construction.template.problem)
OptimizationResults (class in biomass.result)
optimize (biomass.estimation.Optimizer attribute)
optimize() (in module biomass.core)
Optimizer (class in biomass.estimation)
overwrite (biomass.estimation.Optimizer attribute)
P
param_constraints (biomass.construction.reaction_rules.ReactionRules attribute)
param_excluded (biomass.construction.reaction_rules.ReactionRules attribute)
param_info (biomass.construction.reaction_rules.ReactionRules attribute)
param_values() (in module biomass.construction.template.ode)
parameters (biomass.construction.reaction_rules.ReactionRules attribute)
phosphorylate() (biomass.construction.reaction_rules.ReactionRules method)
pkg_name (biomass.core.Model attribute)
popsize (biomass.estimation.InitialPopulation attribute)
R
ReactionNetwork (class in biomass.construction.template.reaction_network)
ReactionRules (class in biomass.construction.reaction_rules)
reactions (biomass.construction.reaction_rules.ReactionRules attribute)
register_word() (biomass.construction.text2model.Text2Model method)
rule_words (biomass.construction.reaction_rules.ReactionRules attribute)
run_analysis() (in module biomass.core)
run_simulation() (in module biomass.core)
S
savefig() (biomass.result.OptimizationResults method)
SearchParam (class in biomass.construction.template.search_param)
sensitivity_options (biomass.construction.template.viz.Visualization attribute)
SensitivityOptions (class in biomass.plotting)
set_sensitivity_rcParams() (biomass.construction.template.viz.Visualization static method)
set_timecourse_rcParams() (biomass.construction.template.viz.Visualization static method)
shape (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
sim_conditions (biomass.construction.reaction_rules.ReactionRules attribute)
sim_tspan (biomass.construction.reaction_rules.ReactionRules attribute)
sim_unperturbed (biomass.construction.reaction_rules.ReactionRules attribute)
similarity_threshold (biomass.construction.reaction_rules.ReactionRules attribute)
(biomass.construction.text2model.Text2Model attribute)
simulations (biomass.construction.template.observable.Observable attribute)
single_observable_options (biomass.construction.template.viz.Visualization attribute)
SingleObservable (class in biomass.plotting)
species (biomass.construction.reaction_rules.ReactionRules attribute)
state_transition() (biomass.construction.reaction_rules.ReactionRules method)
static_plot() (biomass.construction.text2model.Text2Model method)
synthesize() (biomass.construction.reaction_rules.ReactionRules method)
T
t (biomass.construction.template.observable.Observable attribute)
Text2Model (class in biomass.construction.text2model)
ThermodynamicRestrictions (class in biomass.construction.thermodynamic_restrictions)
threshold (biomass.estimation.InitialPopulation attribute)
to_csv() (biomass.result.OptimizationResults method)
to_markdown() (biomass.construction.text2model.Text2Model method)
trace_obj() (biomass.result.OptimizationResults method)
transcribe() (biomass.construction.reaction_rules.ReactionRules method)
translocate() (biomass.construction.reaction_rules.ReactionRules method)
U
user_defined() (biomass.construction.reaction_rules.ReactionRules method)
V
Visualization (class in biomass.construction.template.viz)
W
width (biomass.plotting.SensitivityOptions attribute)
X
x_id (biomass.estimation.Optimizer attribute)
xlabel (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
xlim (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
xticks (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
Y
ylabel (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
ylim (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
yticks (biomass.plotting.MultipleObservables attribute)
(biomass.plotting.SingleObservable attribute)
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