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 [2]
Chapter 1.
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Chapter 2.

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[5] [6

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Chapter 3.

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Chapter 4.
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[9] [10

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Chapter 5.

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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 a->b\EU1/lmtt/b/sl/10 biocham: 
.\EU1/lmtt/m/it/10 a-<a\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 present(a)
\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 numerical_simulation(5,method:msb
df)\EU1/lmtt/b/sl/10 biocham:
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\EU1/lmr/m/n/10 contained in the file are executed (with the file directory as 
current directory).[]\EU1/lmtt/m/n/10 export_biocham(output_file). 
 []


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\EU1/lmtt/m/n/10 …, []ref$[]$[]}). \EU1/lmr/m/n/10 selects some models.[]\EU1
/lmtt/m/n/10 set_model_name(name). \EU1/lmr/m/n/10 changes the current model na
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[11]
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[] []\EU1/lmtt/m/n/10 new_ode_system. \EU1/lmr/m/n/10 creates an ODE system.[]\
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\EU1/lmr/m/n/10 an ODE system.[]\EU1/lmtt/m/n/10 set_ode_system_name(name). \EU
1/lmr/m/n/10 sets the name of the current ODE system.[]\EU1/lmtt/m/n/10 list_od
e_systems.
 []


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\EU1/lmr/m/n/10 system, imports the reactions inferred from the given set of OD
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[]\EU1/lmr/m/n/10 builds the set of ODES corresponding to the reactions of the 
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[]\EU1/lmr/m/n/10 acts as []load_biocham/1[] but importing a model from an ODE 
system. []\EU1/lmtt/m/n/10 add_ode_system(input_file). 
 []


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[]\EU1/lmr/m/n/10 acts as []add_biocham/1[] but importing a model from an ODE s
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 []


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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 present(x,1)\EU1/lmtt/b/sl/10 b
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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 compile_wgpac(a::integral integ
ral-1*a,100)\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 present(a)\EU1/lmtt/b
/sl/10 biocham:
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[12]

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[] [][] []\EU1/lmtt/m/n/10 enable_plus_minus_mode.
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\EU1/lmr/m/n/10 part.[]\EU1/lmtt/m/n/10 disable_plus_minus_mode. \EU1/lmr/m/n/1
0 Each variable corresponds to one species.[]\EU1/lmtt/m/n/10 which_plus_minus_
mode.
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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 set_kinetics_rate(1000)\EU1/lmt
t/b/sl/10 biocham: .\EU1/lmtt/m/it/10 compile_transfer_function([22,51,47,19,3]
,[30,66,67,36,10,1],a,b)\EU1/lmtt/b/sl/10 biocham:
 []


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\EU1/lmtt/m/n/10 add_event(condition, []parameter$[]$[] = []arithmetic_expressi
on$[]$[], …, []parameter$[]$[] = []arithmetic_expression$[]$[]). 
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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 'MA'(k)for a=>b\EU1/lmtt/b/sl/1
0 biocham: .\EU1/lmtt/m/it/10 set_parameter(k=1)\EU1/lmtt/b/sl/10 biocham: .\EU
1/lmtt/m/it/10 add_event(b>0.5,k=0)\EU1/lmtt/b/sl/10 biocham:
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\EU1/lmtt/b/sl/10 .\EU1/lmtt/m/it/10 present(a)\EU1/lmtt/b/sl/10 biocham: .\EU1
/lmtt/m/it/10 numerical_simulation(2,maximum_step_size:0.001)\EU1/lmtt/b/sl/10 
biocham: .\EU1/lmtt/m/it/10 plot 
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[13]
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[]\EU1/lmr/m/n/10 Every object in \EU1/lmtt/m/n/10 [[]object$[]$[], …, []obje
ct$[]$[]] \EU1/lmr/m/n/10 is made present in the initial state.[]\EU1/lmtt/m/n/
10 present({[]object$[]$[],
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[]\EU1/lmr/m/n/10 Every object in \EU1/lmtt/m/n/10 [[]object$[]$[], …, []obje
ct$[]$[]] \EU1/lmr/m/n/10 is made absent in the initial state.[]\EU1/lmtt/m/n/1
0 undefined({[]object$[]$[],
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[]\EU1/lmr/bx/n/14.4 Listing and declaring parameters, functions, aliases and
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\EU1/lmtt/m/n/10 set_parameter([]parameter$[]$[] = []arithmetic_expression$[]$[
], …, []parameter$[]$[] = []arithmetic_expression$[]$[]).
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\EU1/lmr/m/n/10 sets the value of parameters.[]\EU1/lmtt/m/n/10 show_parameter(
parameter). \EU1/lmr/m/n/10 shows the value of \EU1/lmtt/m/n/10 parameter\EU1/l
mr/m/n/10 .[]\EU1/lmtt/m/n/10 list_parameters.
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[14]
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\EU1/lmr/m/n/10 checks all conservation laws against reactions, and if necessar
y kinetics (see also []add_conservation/1[]).[]\EU1/lmtt/m/n/10 search_conserva
tions.
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\EU1/lmr/m/n/10 The page []$[][][][] [] [] [] [][][] [] [][][] [] [][][] [] [][
][][][][][][] [] [][][] [] [][][][][][] [] [][][][] [] [][][][] [] [][][][][][]
[][][][][][][][][][][][][] [] [][][][][][][][][][][][][][][][][][][][][][][][]$
[]
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\EU1/lmr/m/n/10 gives a detailed description of all the numerical methods liste
d below. [][]
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[]\EU1/lmr/m/n/10 exports the current table into a \EU1/lmtt/m/n/10 .csv \EU1/l
mr/m/n/10 file.[]\EU1/lmtt/m/n/10 list_tables. \EU1/lmr/m/n/10 lists the curren
t set of tables.[]\EU1/lmtt/m/n/10 select_table(table).
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\EU1/lmr/m/n/10 selects \EU1/lmtt/m/n/10 table \EU1/lmr/m/n/10 to be the curren
t table.[]\EU1/lmtt/m/n/10 rename_table(name). \EU1/lmr/m/n/10 renames the curr
ent table.[]\EU1/lmtt/m/n/10 delete_table({table$[]$,
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[15]
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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 load(library:examples/mapk/mapk
)\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 numerical_simulation(20,method:m
sbdf)\EU1/lmtt/b/sl/10 biocham:
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[]\EU1/lmr/m/n/10 saves the current trace into two files: \EU1/lmtt/m/it/10 Fil
eTemplate\EU1/lmtt/m/n/10 .csv \EU1/lmr/m/n/10 and \EU1/lmtt/m/n/10 .plot\EU1/l
mr/m/n/10 . []\EU1/lmtt/m/n/10 export_plot_to_png(output_file).
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\EU1/lmtt/m/n/10 reaction_graph. \EU1/lmr/m/n/10 Builds the reaction graph of t
he current model.[]\EU1/lmtt/m/n/10 import_reactions_from_graph. 
 []


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[]\EU1/lmr/m/n/10 Draws the reaction graph of the current model. Equivalent to 
\EU1/lmtt/m/n/10 reaction_graph. draw_graph.
 []


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[][] [][] [][] []\EU1/lmtt/m/n/10 new_graph. \EU1/lmr/m/n/10 Creates a new grap
h.[]\EU1/lmtt/m/n/10 delete_graph(name).
 []


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[]\EU1/lmr/m/n/10 Adds the given set of edges to the current graph. The vertice
s are added if needed. []\EU1/lmtt/m/n/10 delete_edge([]edgeref$[]$[],
 []


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\EU1/lmr/m/n/10 current graph.[]\EU1/lmtt/m/n/10 list_isolated_vertices. \EU1/l
mr/m/n/10 Lists the isolated vertices of the current graph.[]\EU1/lmtt/m/n/10 l
ist_graph_objects. 
 []


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[][] []\EU1/lmtt/m/n/10 set_attribute({[]graph_object$[]$[], …, []graph_objec
t$[]$[]}, attribute). 
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[]\EU1/lmr/m/n/10 Sets that the vertices \EU1/lmtt/m/n/10 [[]name$[]$[], …, [
]name$[]$[]] \EU1/lmr/m/n/10 are transitions. []\EU1/lmtt/m/n/10 delete_attribu
te(graph_object,
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\EU1/lmtt/m/it/10 Attribute\EU1/lmtt/m/n/10 : []name[]). \EU1/lmr/m/n/10 Remove
s an attribute from \EU1/lmtt/m/n/10 graph_object\EU1/lmr/m/n/10 .[]\EU1/lmtt/m
/n/10 list_attributes(graph_object).
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\EU1/lmr/m/n/10 List the attributes of \EU1/lmtt/m/n/10 graph_object\EU1/lmr/m/
n/10 .[]\EU1/lmtt/m/n/10 draw_graph. \EU1/lmr/m/n/10 Draws the current graph.[]
\EU1/lmtt/m/n/10 export_graph(output_file). 
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[16]
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[] [][] [][]
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[] [][] [][]
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[]\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 present(a)\EU1/lmtt/b/sl/10 bio
cham: .\EU1/lmtt/m/it/10 absent(b)\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10
 a=>b\EU1/lmtt/b/sl/10 biocham: .\EU1/lmtt/m/it/10 a+b=>a\EU1/lmtt/b/sl/10 bioc
ham:
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\EU1/lmtt/b/sl/10 .\EU1/lmtt/m/it/10 check_ctl('EX'(not a$\OMS/cmsy/m/n/10 n$\E
U1/lmtt/m/it/10 /'EG'(not b)),nusmv_counter_example:yes)\EU1/lmtt/b/sl/10 bioch
am: .\EU1/lmtt/m/it/10 check_ctl('EG'(not
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\EU1/lmtt/m/it/10 b),nusmv_counter_example:yes)\EU1/lmtt/b/sl/10 biocham: .\EU1
/lmtt/m/it/10 check_ctl(reachable(b),nusmv_counter_example:yes) 
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[17] [18

]
Chapter 6.
[19] [20

]
Chapter 7.
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