1
An Automated Translation from a Narrative Language
for Biological Modelling into Process Algebra
Maria Luisa Guerrriero1 , John K. Heath2 , Corrado Priami1,3
1 ICT Dept., University of Trento, Italy
2 School of Biosciences, University of Birmingham, UK
3 The Microsoft Research-University of Trento Centre for Computational and Systems Biology, Italy
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M.L. Guerriero
2
1 – Overview of the talk
2 – Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3
3 – The proposed framework
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
4 – The narrative language
5 – Beta-binders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
6 – Translation from the narrative language into Beta-binders . . . . . . . . . . . . . . . . . . . 12
7 – An example: enzymatic catalysed reaction . . . . . . . . . . . . . . . . . . . . . . . . . . 15
8 – Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
9 – Further work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
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2 – Introduction
☞ Tools for modelling, analysis and simulation (ODE, Petri nets, statecharts, process algebra, etc.)
☞ Standard exchange languages (SBML, CellML, etc.)
☞ Biological databases (Panther, KEGG, etc.)
☞ Desiderata of modelling languages:
➳ Intuitive for non computer scientists (i.e. graphical or similar to natural language)
➳ Unambiguous (i.e. computable)
➳ Translatable into standard languages (to exchange models)
➳ Compositional (to update models and build them incrementally)
➳ Insensitive to incomplete knowledge
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3 – The proposed framework
☞ High level textual modelling language ⇒ Intuitive description of biological systems
➳ Narrative-style language: sequence of basic events
➳ Basic events are biochemical reactions
☞ Automatic translation into formal language ⇒ Simulation and analysis of models
➳ Formal language hidden from the modeler
➳ Process algebra (Beta-binders)
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4 – The narrative language
☞ Models are composed of four sections:
➳ Compartments involved in the evolution of the system
➳ Components involved in the system
➳ Reactions occurring in the system
➳ Events sequence of the evolution of the system
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☞ A compartment is described by:
➳ identifier
➳ name
➳ size
➳ number of spatial dimensions
id
name
size (unit of measure)
1
exosol
9.95 · 10−12 (l)
3
2
cellMembrane
12.57 · 10−8 (dm2 )
2
3
cytosol
2.10 · 10−12 (l)
3
4
nucleus
0.25 · 10−12 (l)
3
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dimensions
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7
☞ A component is described by:
➳ name
➳ list of interaction sites (each site has a name and a state)
➳ list of states
➳ list of possible locations
➳ initial quantity/concentration (value and reliability)
name
site
site state
site active
LIF
gp130
STAT3
LIF
bound
false
Y767
phospho
false
Y814
phospho
false
Y705
phospho
false
gp130
bound
false
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state
state active
compart
compart active
initial quant
reliability
bound
false
1
true
3000
100%
dimer
false
2
true
1000
50%
dimer
false
3
true
5000
0%
4
false
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☞ A reaction is described by:
➳ identifier
➳ type
➳ rate (value and reliability)
id
type
rate (unit of measure)
1
binding
8 · 105 (M−1 s−1 )
100%
2
unbinding
6 · 10−4 (s−1 )
100%
3
dimerization
inf
(M−1 s−1 )
4
phosphorylation
0.2
(s−1 )
100%
5
homodimerization
inf
(s−1 )
20%
6
relocation
10
(min)
50%
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reliability
20%
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☞ The evolution of the system is described by a narrative of events, possibly grouped into processes
☞ An event is a textual description of a reaction, described by:
➳ identifier
➳ textual semiformal description
➳ identifier of the reaction
☞ The textual semiformal description can be prefixed by an optional condition
if condition then event description
➳ The condition can be on the state of a component (or site) or on its position (component.site is
state, component is in compartment, etc); negative and multiple conditions can be specified
➳ The event description points out the occurring reaction and the involved component(s) (component
reaction or component1 reaction component2, where reaction can be phosphorylates, binds,
activates, etc); interaction/modification site can be specified
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☞ Events can be concurrent (e.g. involving different proteins), sequential (e.g. phosphorylation allowed
after protein is bound), or alternative (e.g. competitive ligand/receptor binding); identifiers of alternative
events can be specified, and conditions can be used to enforce ordering of sequential events
id
description
react
alternative
LIF-gp130 binding
1
if gp130.LIF is not bound and LIF is not bound then LIF binds gp130 on LIF
1
2
if gp130.LIF is bound and LIF is bound then LIF unbinds gp130 on LIF
2
LIF pathway
3
if LIFR.LIF is bound then LIFR dimerises with gp130
3
4
if gp130 is dimer then gp130 phosphorylates on Y767;Y814
4
2
STAT3 pathway
5
if gp130.Y767 is phospho and STAT3 is in 3 then gp130 binds STAT3 on gp130
1
6
if STAT3.gp130 is bound then STAT3 phosphorylates on Y705
4
7
if STAT3.gp130 is bound and STAT3.Y705 is phospho then gp130 unbinds STAT3 on gp130
2
8
if STAT3.Y705 is phospho and STAT3.gp130 is not bound then STAT3 homodimerises
5
9
if STAT3 is in 3 and STAT3 is dimer then STAT3 relocates to 4
6
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5 – Beta-binders
☞ Bio-inspired language of concurrent interacting processes with typed interaction sites
Bio-process
Body: internal behaviour
P
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5 – Beta-binders
☞ Bio-inspired language of concurrent interacting processes with typed interaction sites
Bio-process
Body: internal behaviour
P
Interface: interactions
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5 – Beta-binders
☞ Bio-inspired language of concurrent interacting processes with typed interaction sites
Bio-process
Body: internal behaviour
P
x1 : ∆1
xh2 : ∆2
x3 : ∆3
P
Interface: interactions
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5 – Beta-binders
☞ Bio-inspired language of concurrent interacting processes with typed interaction sites
Bio-process
Body: internal behaviour
x1 : ∆1
P
xh2 : ∆2
x3 : ∆3
P
Interface: interactions
☞ System: parallel composition of interacting bio-processes
☞ Operations:
➳ Input/output communications (intra / inter)
➳ Operations on interfaces (expose / hide / unhide / chtype)
➳ Merging/splitting of processes (bind / unbind)
➳ Sequential/parallel/choice composition of processes
➳ Conditional expressions (on binders type/visibility)
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6 – Translation from the narrative language into Beta-binders
☞ Components ⇒ bio-processes
➳ Component interaction site ⇒ beta binder (active/inactive state ⇒ type)
➳ Component state ⇒ beta binder (active/inactive state ⇒ type)
➳ Component location ⇒ beta binder (current location ⇒ type)
☞ Events ⇒ pi-processes placed in parallel composition
➳ Monomolecular event ⇒ one pi-process
➳ Bimolecular event ⇒ pair of interacting pi-processes
➳ Site/state/location modification ⇒ chtype action
➳ Reaction rate ⇒ type affinity or action rate
➳ Condition/alternative event ⇒ condition on binder type
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☞ Empty bio-processes are added
☞ Beta binders for compartments are added (subject = “loc”, type = initial compartment name
concatenated with its identifier)
STAT3 located in compartment 3 (cytosol) ⇒ β(loc
: cytosol 3) added to ST AT 3 bio-process
☞ Beta binders for states are added (subject = state name, type = state name concatenated with
component name)
Gp130 can be a dimer ⇒ β(dimer : monomer gp130) added to gp130 bio-process.
☞ Beta binders for sites are added (subject = site name concatenated with state name, type = state
name concatenated with component name and site name)
Site Y705 of receptor STAT3 can be phosphorylated ⇒ β(Y 705 pho : depho ST AT 3 Y 705) added
to ST AT 3 bio-process
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☞ Pi-process for monomolecular event = sequence of chtype actions, possibly prefixed by conditions
Event 4 is phosphorylation of sites Y767 and Y814 on gp130 (phosphorylations can occur if gp130 is
dimer). Pi-process added to gp130:
P ho 4 = if (dimer, dimer gp130) then chtype(0.2, Y 767 pho, pho gp130 Y 767) .
chtype(inf, Y 814 pho, pho gp130 Y 814) . P ho 4
☞ Pi-processes for bimolecular event = communication action, followed by a sequence of chtype actions,
possibly prefixed by conditions
Event 6 is binding of gp130 to STAT3 (binding can occur if site Y767 on gp130 is phosphorylated and
STAT3 is in cytosol). Pi-processes added to gp130 and ST AT 3:
Bind 6A = if (Y 767 pho, pho gp130 Y 767) then gp130 binding 6hi . Bind 6A
Bind 6B = if (loc, cytosol 3) then gp130 bou() . chtype(inf, gp130 bou, bou ST AT 3 gp130) . Bind 6B
☞ Concurrent reactions = pi-processes placed in parallel composition
☞ Sequential reactions = the second one is prefixed by a condition on binder modified by the first one
☞ Mutually exclusive reactions = both prefixed by condition on binder modified at the end of the other one
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7 – An example: enzymatic catalysed reaction
E + S <--> ES --> EP --> E + P
id
1
name
E
S
descr
enzyme
substrate/product
site
site state
site act
product
active
false
id
id
1
2
3
4
name
cytosol
size
1.0
dimensions
3
state
bound
bound
state act
false
false
type
rate (unit of measure)
1
binding
2
unbinding
3
activation
4
unbinding
(M s )
−1
1 (s
)
−1 −1
1 (M
s )
−1
1 (s
)
1
−1 −1
compart
1
1
initial quant
100
1000
reliab
100%
100%
reliability
50%
50%
50%
50%
description
E-S binding/unbinding
if E is not bound and S is not bound and S.product is not active then E binds S
if E is bound and S is bound then E unbinds S
Product formation
if E is bound and S is bound and S.product is not active then E activates S on product
if E is bound and S is bound and S.product is active then E unbinds S
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compart act
true
true
reaction
alternative
1
2
3
4
2
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[steps = 100000]
<<
BASERATE:inf, s0:inf, s1:inf, s2:inf, s3:inf, s4:inf >>
let
let
let
let
let
Bind_1A : pproc = if (not(bou_E,Bound_E)) then bou_S_1<binding>.ch(inf,bou_E,Bound_E)...
Unbind_2A : pproc = if (bou_E,Bound_E) then bou_S_2<unbinding>.ch(inf,bou_E,Unbound_E)...
Act_3A : pproc = if (bou_E,Bound_E) then act_S_3<activation>.s3<s0>.nil endif;
Unbind_4A : pproc = if (bou_E,Bound_E) then bou_S_4<unbinding>.ch(inf,bou_E,Unbound_E)...
P_E : pproc = !s1{}.Bind_1A | !s2{}.Unbind_2A | !s3{}.Act_3A | !s4{}.Unbind_4A;
let E : bproc = #(bou_S_4:0,Unbinding_S_4), #(act_S_3:0,Activation_S_3),
#(bou_S_2:0,Unbinding_S_2), #(bou_S_1:0,Binding_S_1), #(bou_E:0,Unbound_E), #(loc_E:0,Cyto_1)
[ Bind_1A | Unbind_2A | Act_3A | Unbind_4A | P_E ];
let
let
let
let
let
Bind_1B : pproc = if ((not(bou_S,Bound_S)) and (not(product_act_S,Active_S_product)))...
Unbind_2B : pproc = if (not(product_act_S,Active_S_product)) then if (bou_S,Bound_S)...
Act_3B : pproc = if (not(bou_S,Unbound_S)) then if ((bou_S,Bound_S) and (not...
Unbind_4B : pproc = if ((bou_S,Bound_S) and (product_act_S,Active_S_product)) then.
P_S : pproc = !s1{}.Bind_1B | !s2{}.Unbind_2B | !s3{}.Act_3B | !s4{}.Unbind_4B;
let S : bproc = #(product_act_S:0,Inactive_S_product), #(bou_S:0,Unbound_S), #(loc_S:0,Cyto_1)
[ Bind_1B | Unbind_2B | Act_3B | Unbind_4B | P_S ];
run 100 E || 1000 S
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☞ Beta-binders model was simulated with BetaWBa
a
See
http://www.cosbi.eu/Rpty Soft BetaWB.php
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8 – Conclusions
☞ Positive feedback from biologists!
☞ The proposed language is simple, and nevertheless it is unambiguous and automatically translatable
into formal languages
☞ Modelers can describe biological systems in simple words, simulate models, and obtain results,
without the need to know the target formal language
☞ Main differences with SBML:
➳ System evolution is given in terms of a narrative of events
➳ It is easy to represent details about components and reactions
➳ Components can have multiple states
➳ Reliability values to represent uncertainty of biological knowledge
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9 – Further work
☞ Additional primitives and features can be added to the language, and new features of the target
language can be exploited ⇒ compactness, efficiency, representation of other types of events
☞ The translator can be extended to other languages ⇒ SBML for exchange of models, other formal
languages to use and compare different tools for simulation and analysis
☞ Integration with biological databases ⇒ automatic extraction of data and parameters
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Thank you!
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hmodeli
hcomparts decli
hcompons decli
hreacts decli
hprocs decli
::=
::=
::=
::=
::=
hcomparts declihcompons declihreacts declihprocs decli
Compartments hcomparts listi
Components hcompons listi
Reactions hreacts listi
Narrative hprocs listi
hcomparts listi
::=
|
::=
|
::=
|
::=
|
hcompartmenti
hcompartmentihcomparts listi
hcomponenti
hcomponentihcompons listi
hreactioni
hreactionihreacts listi
hproci
hprocihprocs listi
hcompartmenti
hcomponenti
::=
::=
hreactioni
::=
(hidi, hcompart namei, hopt sizei, hopt uniti, hopt dimi)
(hnamei, hopt inf orm descri, hopt sites def i,
hopt states def i, hopt comparts def i, hinitial quantityi)
(hidi, hreact typei, hrate consti)
hcompons listi
hreacts listi
hprocs listi
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hproci
hevents listi
heventi
hopt sites def i
hsites def i
hsite def i
hopt states def i
hstates def i
hstate def i
hopt comparts def i
hcomparts def i
hcompart def i
::=
::=
|
::=
::=
|
::=
|
::=
Process hopt
inf orm descrihevents listi
heventi
heventihevents listi
(hidi, hf orm descri, hreact idi, hopt altern eventi)
hsites def i
hsite def i
hsite def i; hsites def i
hnamei : hstate namei : his activei
::=
|
::=
|
::=
hstates def i
hstate def i
hstate def i; hstates def i
hstate namei : his activei
::=
|
::=
|
::=
hcomparts def i
hcompart def i
hcompart def i; hcomparts def i
hidi : his activei
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hinitial quantityi
hrate consti
::=
::=
(hquantityi, hopt reliabilityi)
(hratei, hopt uniti, hopt reliabilityi)
hf orm descri
::=
|
hevent descri
if hcondsi then hevent descri
hcondsi
::=
|
::=
|
|
|
hcondi
hcondi and hcondsi
hnamesi is hstate namei
hnamesi is not hstate namei
hnamesi is in hidi
hnamesi is not in hidi
::=
|
|
|
::=
|
hnamei
hnamei.hnamei
hnamei; hnamesi
hnamei.hnamei; hnamesi
hnamei
hnamei; hsitesi
hcondi
hnamesi
hsitesi
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hevent descri
hcomplex namei
hidi
::=
|
|
|
|
|
|
|
|
|
|
|
::=
|
hcomplex nameihbimol reactihcomplex namei on hsitesi
hcomplex nameihbimol reactihcomplex namei
hcomplex nameihmonomol reacti on hsitesi
hcomplex nameihmonomol reacti
hcomplex namei relocates to hidi
hcomplex namei degrades
hcomplex namei degrades hcomplex namei
hcomplex namei synthesises hcomplex namei
hcomplex namei homodimerises
hcomplex namei dehomodimerises
hcomplex namei dimerises with hcomplex namei
hcomplex namei dedimerises from hcomplex namei
hnamei
hnamei : hcomplex namei
::=
Int
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hopt sizei
hopt uniti
hopt dimi
hnamei
hopt inf orm descri
hquantityi
hopt reliabilityi
hratei
hreact idi
hopt altern eventi
his activei
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::=
|
::=
|
::=
|
::=
::=
|
::=
::=
|
::=
::=
::=
|
::=
Int
Str
Int
Ide
Str
Int | Real
Int
Int | Real | inf
Int
alternative to hidi
Bool
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hcompart namei
hreact typei
::=
|
nucleus | cytosol | exosol
cellMembrane | nucleusMembrane | Ide
::=
|
|
|
|
|
|
phosphorylation | dephosphorylation
hstate namei
::=
phosphorylated | bound | active | hydrolysed | dimer
hbimol reacti
::=
|
phosphorylates | dephosphorylates | binds | unbinds
activates | deactivates | hydrolyses | dehydrolyses
::=
phosphorylates | dephosphorylates | hydrolyses | dehydrolyses
hmonomol reacti
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binding | unbinding
homodimerization | dehomodimerization
dimerization | dedimerization
activation | deactivation
hydrolysis | dehydrolysis
degradation | synthesis | relocation
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☞ Bio-processes are initially empty, and then beta binders are added
1: for all component ∈ Components do
2:
component.bioprocess ← new empty bio-process
3:
CompartsToBetaBinders (component)
4:
StatesToBetaBinders (component)
5:
SitesToBetaBinders (component)
6: end for
☞ Type of a beta binder representing a compartment = compartment name concatenated with
compartment identifier
STAT3 located in compartment 3 (cytosol) ⇒ β(loc
: cytosol 3) added to ST AT 3 bio-process
1: binder ← new beta binder in component.bioprocess
2: binder.name ←“loc”
3: if component is in compartment at initial state then
4:
binder.type
5: end if
← compartment.name∧ compartment.id
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☞ Type of a binder representing a state = state name concatenated with component name
Gp130 can be a dimer ⇒ β(dimer : monomer gp130) added to gp130 bio-process.
1: for all state ∈ component.states do
2:
binder ← new beta binder in component.bioprocess
3:
binder.name ← state.name
4:
if component is in state at initial state then
5:
binder.type ← state.name∧ component.name
6:
else
7:
binder.type ← state.opposite name∧ component.name
8:
end if
9: end for
☞ Type of a binder representing a site = state name concatenated with component name and site name
Site Y705 of receptor STAT3 can be phosphorylated ⇒ β(Y 705 pho : depho ST AT 3 Y 705) added
to ST AT 3 bio-process
1: for all site ∈ component.sites do
2:
binder ← new beta binder in component.bioprocess
3:
binder.name ← site.name∧ site.state.name
4:
if site is in state at initial state then
5:
binder.type ← site.state.name∧ component.name∧ site.name
6:
else
7:
binder.type ← site.state.opposite name∧ component.name∧ site.name
8:
end if
9: end for
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☞ Pi-process representing a monomolecular event = sequence of chtype actions, possibly prefixed by
conditions; reaction rates are based on input definitions
Event 4 is phosphorylation of sites Y767 and Y814 on gp130 (phosphorylations can occur if gp130 is
dimer). The pi-process added to gp130 is a sequence of two chtype actions, prefixed by a condition:
P ho 4 = if (dimer, dimer gp130) then chtype(0.2, Y 767 pho, pho gp130 Y 767) .
chtype(inf, Y 814 pho, pho gp130 Y 814) . P ho 4
1:
2:
3:
4:
5:
6:
7:
8:
9:
10:
11:
if event.reaction is relocation then
piproc ← chtype(“loc”, new location type)
else if event.reaction is phosphorylation then
piproc ← chtype(binder site pho, site phosphorylated type)
else if event.reaction is dephosphorylation then
piproc ← chtype(binder site pho, site dephosphorylated type)
else if ... then
end if
if event.condition is specified then
piproc ← if (binder cond, cond state type) then piproc
end if
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☞ Pi-processes representing a bimolecular event = communication action, followed by a sequence of
chtype actions, possibly prefixed by conditions; types affinities are based on input definitions
Event 6 is binding of gp130 to STAT3 (binding can occur if site Y767 on gp130 is phosphorylated and
STAT3 is in cytosol). The pi-process added to gp130 is an output action, prefixed by a condition:
Bind 6A = if (Y 767 pho, pho gp130 Y 767) then gp130 binding 6hi . Bind 6A
The pi-process added to ST AT 3 is a chtype action, prefixed by an input action, and by a condition:
Bind 6B = if (loc, cytosol 3) then gp130 bou() . chtype(inf, gp130 bou, bou ST AT 3 gp130) . Bind 6B
event.reaction is phosphorylation then
piproc1 ← binder event idhi
piproc2 ← binder site pho().chtype(binder site pho, site phosphorylated type)
AddAffinity (binder event id type, site dephosphorylated type)
1: if
2:
3:
4:
5:
6:
7:
8:
9:
10:
11:
12:
else if ... then
end if
if event.condition is specified on event.component1 then
piproc1 ← if (binder cond, cond state type) then piproc1
end if
if event.condition is specified on event.component2 then
piproc2 ← if (binder cond, cond state type) then piproc2
end if
21/09/2007 – CMSB 2007, Edinburgh, UK
M.L. Guerriero
32
☞ Concurrent reactions = pi-processes placed in parallel composition. Sequential reactions = the
second one is prefixed by a condition on binder modified by the first on. Mutually exclusive reactions =
both are prefixed by a condition on binder modified at the end of the other one
1: for all ev ∈ Events do
2:
if ev is monomolecular then
3:
pproc ← EventToPiProcess (ev )
4:
if ev is alternative to prev ev then
5:
pproc ← if not(prev ev.mod binder, prev ev.mod type) then pproc
6:
prev ev.pproc ← if not(ev.mod binder, ev.mod type) then prev ev.pproc
7:
end if
8:
AddPiprocessInParallel (ev.component.bioproc, pproc)
9:
else if ev is bimolecular then
10:
h pproc1, pproc2 i ← EventToPiProcesses (ev )
11:
if ev is alternative to prev ev then
12:
if both ev and prev ev involve ev.component1 then
13:
pproc1 ← if not(prev ev.mod binder, prev ev.mod type) then pproc1
14:
prev ev.pproc ← if not(ev.mod binder, ev.mod type) then prev ev.pproc
15:
end if
16:
if both ev and prev ev involve ev.component2 then ...
17:
end if
18:
end if
19:
AddPiprocessInParallel (ev.component1.bioproc, pproc1)
20:
AddPiprocessInParallel (ev.component2.bioproc, pproc2)
21:
end if
22: end for
21/09/2007 – CMSB 2007, Edinburgh, UK
M.L. Guerriero