- Methodology article
- Open Access
Lineage grammars: describing, simulating and analyzing population dynamics
- Adam Spiro^{1, 3},
- Luca Cardelli^{2} and
- Ehud Shapiro^{1, 3}Email author
https://doi.org/10.1186/1471-2105-15-249
© Spiro et al.; licensee BioMed Central Ltd. 2014
Received: 10 January 2014
Accepted: 7 July 2014
Published: 21 July 2014
Abstract
Background
Precise description of the dynamics of biological processes would enable the mathematical analysis and computational simulation of complex biological phenomena. Languages such as Chemical Reaction Networks and Process Algebras cater for the detailed description of interactions among individuals and for the simulation and analysis of ensuing behaviors of populations. However, often knowledge of such interactions is lacking or not available. Yet complete oblivion to the environment would make the description of any biological process vacuous. Here we present a language for describing population dynamics that abstracts away detailed interaction among individuals, yet captures in broad terms the effect of the changing environment, based on environment-dependent Stochastic Tree Grammars (eSTG). It is comprised of a set of stochastic tree grammar transition rules, which are context-free and as such abstract away specific interactions among individuals. Transition rule probabilities and rates, however, can depend on global parameters such as population size, generation count, and elapsed time.
Results
We show that eSTGs conveniently describe population dynamics at multiple levels including cellular dynamics, tissue development and niches of organisms. Notably, we show the utilization of eSTG for cases in which the dynamics is regulated by environmental factors, which affect the fate and rate of decisions of the different species. eSTGs are lineage grammars, in the sense that execution of an eSTG program generates the corresponding lineage trees, which can be used to analyze the evolutionary and developmental history of the biological system under investigation. These lineage trees contain a representation of the entire events history of the system, including the dynamics that led to the existing as well as to the extinct individuals.
Conclusions
We conclude that our suggested formalism can be used to easily specify, simulate and analyze complex biological systems, and supports modular description of local biological dynamics that can be later used as “black boxes” in a larger scope, thus enabling a gradual and hierarchical definition and simulation of complex biological systems. The simple, yet robust formalism enables to target a broad class of stochastic dynamic behaviors, especially those that can be modeled using global environmental feedback regulation rather than direct interaction between individuals.
Keywords
Background
In recent years there has been a great interest in modeling and simulating various aspects of population dynamics in biological and ecological systems [1–4]. The increasing computational resources along with a deeper understanding of biological and ecological phenomena have led to the development of many languages for describing, analyzing and simulating concurrent stochastic processes. Many such languages specify Markovian dynamics and differ by level of abstraction, ease and complexity of the description and execution efficiency [5]. Two widely used formalisms are based on Chemical Reaction Networks (CRN) [6] and stochastic Process Algebras (PA) [7].
CRNs were originally used to describe chemical systems. A CRN description consists of a finite set of reactions acting on a finite number of species. Each reaction specifies the identity and stoichiometry of the reactants and products along with a rate constant. Many processes can be described using CRNs, for example, Predator-Prey models [8], Cellular cascade pathways [9], Cancer progression [10], Epidemics dynamics [11], and many others [1]. Each of these processes consists of a continuous interaction between individual species (the reactants) that occurs at a certain rate and produces a group of other individuals (the products, which may be empty) that can be of the same (autocatalytic) or of different type. The description of dynamical systems using CRN is relatively simple and can be used both for analytical solving and simulations. However, this approach neglects biological aspects of the described systems by treating each object (reactant or product) as a simple entity, which ignores its environmental context and structure. For example, many molecular objects maintain their overall identity while changing in specific attributes, such as chemical modification or location. When using a CRN abstraction such molecules cannot retain identity while changing state.
PAs, on the other hand, are a family of mathematical formalisms that were originally developed to model concurrent computer systems. They enable the abstraction and specification of communication and synchronization between a collection of processes by passing messages between them. One of the most well studied PA is the π -calculus, which has been shown to be very useful in describing a range of biological systems [7, 12]. The language consists of processes that are mapped to real-world objects, and channels, which are mapped to communications and interactions between the different objects. A unique feature of the π -calculus allows to dynamically communicate new channels between the processes (this is termed mobility), which enables the objects to keep their identity while changing their internal states or interactions with other objects. This feature is more compatible with real biological and ecological scenarios and fits well to the way we think and observe these processes. It also allows one to abstract and specify the dynamics in a more accurate fashion. It has also been shown that this abstraction can be treated as an executable computer program, allowing to stochastically simulate any specified model [13].
Many tools have been developed in order to allow and simplify the use of mathematical modeling for the life-science community, and each one has its strengths and weaknesses [14–16]. There is no single formalism that has all the required features and choosing the appropriate one depends on the specific goals and resources of the modeler. Our goal in this work is to develop and formulate a simpler and practical tool for modeling and simulating the behavior and interaction of populations. We do so by extending the notion of Stochastic Tree Grammar (STG) [17] by incorporating both rates and probabilities to the transition rules. These can be dynamically updated by defining them as functions of the system’s state, which includes global values such as current population size, generation count or elapsed time. In addition, we extend the system by allowing each individual to hold its own internal states which can change through inheritance. We later discuss implementation of stochastic simulation and the relation to Ordinary Differential Equations (ODE).
A prominent feature of the language is that it enables to stochastically produce possible lineage trees corresponding to single executions. These lineage trees contain a representation of the entire events history of the process, including the dynamics that led to the existing as well as to the extinct individuals. As opposed to standard approaches that output only the population size dynamics, our implementation also outputs the corresponding lineage trees, which can be used to analyze the evolutionary and developmental history of the process.
Recently, Vaughan et al. [16] presented the usage of CRNs as lineage grammars and used them to simulate phylogenetic trees. Although they enable to sample possible genealogies based on the defined reaction rules, they do not allow the specification and analysis of more complex behaviors such as feedback onto the dynamic rates and general inherited properties.
Throughout the paper, we demonstrate the usability of the language by presenting a wide range of examples that can be modeled and simulated using this approach. The examples show that the language can provide simple descriptions of systems from various domains. Example parameter values were taken from the literature when available or chosen arbitrarily in order to simplify the presentation.
Results and discussion
eSTG programs
In this example, SC (stem cells) divide symmetrically 0.1 times per day, while self-renewing or differentiating with the same probability (50%), and Diff (differentiated cells) can once a day either proliferate (with probability 49%) or die (with probability 51%).
Internal states
This simulated data can be used for example to evaluate the relationship between n, the number of MS, and the accuracy of phylogenetic reconstruction based on MS lengths of the tree (see [22, 23] for details).
Other examples of internal states can be the counting of historical events (such as how many symmetric vs. asymmetric divisions a cell went through) or measuring the time since a certain event.
Probabilities and rates as functions
Population dynamics can change based on various conditions such as population size, internal or external changes, and elapsed time. A common phenomenon in population dynamics is the reaching of a homeostasis, meaning that at a certain point, the population size reaches a steady state.
where N is the population size, r is the growth rate and K is the target size (also termed carrying capacity). We can use the above parametric eSTG rule to model a logistic population growth by solving:
For simplicity, r in the eSTG rule is the same as the r in the logistic model.
Here, the rate is inversely dependent on the population size and the population is growing until reaching the steady state that is maintained by a feedback on p, which causes either a proliferation (p = 1) or death (p = 0). Figure 4D and Figure 4E show the resulting dynamics starting from a single A.
Lotka-Volterra unimolecular representation
Reaction | Global rate |
---|---|
Prey → 2Prey | c_{1} ⋅ Prey |
Prey → ϕ | c_{2} ⋅ Prey ⋅ Predator |
Predator → 2Predator | c_{2} ⋅ Prey ⋅ Predator |
Predator → ϕ | c_{3} ⋅ Predator |
The role of different feedback strategies on the control of organ and tissue growth can be investigated through the rates and probabilities of cellular decisions. Lander et al. [28] suggest two types of feedback strategies for the Olfactory Epithelium, one on the rate of division and the other on the probability of self-renewal (while keeping a constant division rate). They show that a feedback control onto the probability is a much more effective strategy for steady-state robustness and rapid regeneration.
and the two feedback strategies are implemented by updating the INP parameters.
Strategy 1: Feedback onto the probability
${p}_{1}=\frac{{p}_{1}}{1+g\cdot \left|\mathit{ORN}\right|}$ where g is a constant.
Strategy 2: Feedback onto the rate:
Possible extensions
Compartments
In many cases the population moves stochastically between different compartments, where each compartment corresponds to a different environment and different resources. Extending the language to include compartments allows one to define the same transition rules for species from the same type but different rates and probabilities, depending on the physical location of the individual. The system’s state is then extended to include the population size in each compartment. In addition to the regular transition rules, one also needs to define rules for the migration of each species between each two compartments.
Individual’s probabilities and rates as functions
Defining probabilities and rates for each individual separately is not recommended due to heavy computational requirements when implementing such a scenario, however, an extension of the language can support such a definition. In this case we can allow the probabilities and rates of each individual to be also dependent on its internal states. This allows each individual to have a distinct stochastic value of its probabilities and transition rates. For example, we can define a more sophisticated predator/prey model where the probability of reproduction is dependent on the individual’s age (or weight) which is represented as an internal state, or define the proliferation dynamics of a cell based on its mutations (represented as internal states).
Conclusions
Stochastic simulation is a powerful tool to execute a complicated modeling system for which a closed form analytical solution is not possible. In addition, a simulation can generate a sample of representative scenarios that can be used for further analysis or as inputs to other programs. The complexity of natural phenomena requires a formal description framework which on one hand should be rich enough to capture the complexity and dynamics of the system and on the other hand will be compact and simple so it can be widely used by a broad community and could be implemented efficiently. There are many systems that are purely generative and derive their core results by ignoring interactions (e.g. L-Systems [29] and branching processes [24]). Although the assumption of independence enables certain analytical techniques, it precludes the ability to model processes and lineages that evolve through complex interactions between individuals and their environment. In order to allow both generativity and interaction, systems such as PA and CRN are more suitable. As described in [3], the trend towards individual-based stochastic models carries many advantages; they are easier to construct, more intuitive and can predict richer phenomena than population level models. In addition, it is possible to deduce population level conclusions (such as the underlined ODEs, see Methods) from the stochastic model. The presented formalism does not offer a new modeling approach in the sense that eSTG programs can be translated interchangeably into other languages (see Methods). Instead, the suggested eSTG language formalism allows a simpler description and specification of complex stochastic dynamics of individual entities. As demonstrated by the host of examples provided, these may include population level feedback from the current system’s state (either population size, internal or external factors) onto the rates and probabilities of the different species. In addition, eSTG, as a lineage grammar also enables the representation and analysis of historical events including those of extinct sub-lineages and transitional time points. Derivation trees produced by simulations can be examined for consistency with specific biological hypotheses [22, 30], so that eSTG models can be validated or falsified on the basis of the trees that they generate.
The language can also be used as a basis for inference and learning of the system’s governing rules, described in the eSTG formalism as the transition rules and the underlying rates and probabilities as functions of the system’s state. The question of parameter inference from biological data is an active area of study [31–34]. In our context, biological knowledge inferred from experimentally-obtained trees [22, 30, 35–43] could be used in order to infer the corresponding lineage grammars [17, 44, 45]. This will allow the use of computers and computing resources in order to gain new biological insights. This is a great challenge, especially given noise and hidden variables, and is a subject of our future work. We hope that the development of theoretical models and tools, such as the one presented here, will facilitate research in this important direction.
Methods
Stochastic simulation
eSTG programs can be naturally simulated by the well-known Gillespie stochastic simulation algorithm [6]. Gillespie's implementation uses the rates of all possible reactions and chooses stochastically the next reaction by assuming that the time to the next reaction is exponentially distributed with rate parameters corresponding to the reaction rates.
and thus existing implementations of the Gillespie algorithm can be used to determine the next reaction and the time interval. Applying these rules to build the lineage tree is described in the Operational semantics section.
The code that was used to generate the examples in this paper will be made available as an open source tool and is currently under preparation for publication.
Equivalence and conversion to other languages
- 1.
maODE: Ordinary Differential Equations arising from mass-action kinetics.
- 2.
maCRN: Chemical Reaction Networks with mass-action kinetics.
- 3.
gCRN: Chemical Reaction Networks with general rate kinetics.
- 4.
U-gCRN: Unimolecular Chemical Reaction Networks with general rate kinetics.
An maCRN is a chemical reaction network where each reaction has an associated rate constant, and where the instantaneous rate of a reaction is determined by the product of the rate constant with the instantaneous concentrations of the reagents. It is known that an maCRN under that mass-action law produces a system of ODEs with a special structure, here called an maODE system. In an maODE system each right-hand-side of each differential equation for species s has the form of a polynomial over the set of species, where each monomial with a negative sign has s as a factor (raised to some non-zero power). Conversely each maODE determines a canonical maCRN that has that maODE as its kinetics. Therefore there are canonical translations back and forth between maODEs and maCRNs [46].
A gCRN is instead a Chemical Reaction Network where each reaction has an associated rate function from current or past system states to changes of concentrations. The instantaneous rate of a reaction is then given immediately by its rate function without further considerations; the class of ODEs that a gCRN may generate depends on the class of rate functions that are available.
A U-gCRN is a special case of a gCRN where all the reactions are unimolecular. For sufficiently powerful rate functions it is possible to have a (nominally) unimolecular reaction depend on the concentrations of other species, so that U-gCRN is in fact as expressive as gCRN. For example, an maCRN reaction $A\stackrel{r}{\to}B$ can be translated to the gCRN reaction $A\stackrel{r\xb7\left[A\right]}{\to}B$ where [A] is the instantaneous concentration of A, and an maCRN reaction $A+B\stackrel{r}{\to}C$ can be translated to a gCRN reaction $A+B\stackrel{r\xb7\left[A\right]\xb7\left[B\right]}{\to}C$ or to two U-gCRN reactions $A\stackrel{r\cdot \left[A\right]\cdot \left[B\right]}{\to}\mathit{C}$ and $B\stackrel{r\xb7\left[A\right]\xb7\left[B\right]}{\to}0$.
The family of population dynamics specifications that can be described using basic eSTG is equivalent to U-gCRN. A U-gCRN reaction $A\stackrel{r}{\to}{B}_{1}+\dots +{B}_{n}$ can be translated into an eSTG reaction $A\stackrel{r}{\to}{\left\{{B}_{1},\dots ,{B}_{n}\right\}}_{1.0}$, and conversely an eSTG reaction $A\stackrel{r\phantom{\rule{0.25em}{0ex}}}{\to}{\left\{{B}_{1,1},\dots \right\}}_{{\mathrm{p}}_{1}}|\dots |{\left\{{B}_{n,1},\dots \right\}}_{{\mathrm{p}}_{n}}$ can be translated into a set of U-gCRN reactions $A\stackrel{r\cdot {p}_{1}}{\to}{B}_{1,1}+\cdots ,\dots ,A\stackrel{r\cdot {p}_{n}}{\to}{B}_{n,1}+\cdots $.
The U-gCRN form of eSTGs implies that one must make choices in modelling: the main species that are the focus of a model, and occur in the left-hand side of productions, will be reflected in the generated lineage trees, but auxiliary species that appear only in the rate laws will not, even when those would be considered as equal in a model based on bimolecular interactions.
Operational semantics
We will start with basic definitions for the semantics of Lineage Trees. Paths in a tree are represented as finite sequences of natural numbers π = n_{1}, …, n_{ m } ∈ ℕ* (star means finite sequence, with nil as the empty sequence, and ", " as sequence concatenation). Each number n in a path represents the n^{ th } child of a node, starting from the root. Nodes in a tree are labeled by an alphabet S_{0} = S ∪ {0} consisting of species in S and a distinguished symbol 0 ∉ S (the "dead" leaf).
Definition: a tree L is a partial function in ℕ* → S_{0}, from paths in ℕ* to label nodes in S_{0}, whose domain is non-empty and prefix-closed (that is, L(π_{1}, π_{2}) defined ⇒ L(π_{1}) defined).
Definition: A leaf in a tree L is a maximal path π - one such that L(π) is defined and there is no π ' ≠ nil where L(π , π') is defined. We also say that π, B is a (B -labeled) leaf in L if π is a leaf in L and L(π) = B.
Definition: A lineage tree L is a tree where each path π such that L(π) = 0 is a leaf. $\mathbb{L}\subseteq {\mathrm{\mathbb{N}}}^{*}\to {S}_{0}$ is the set of such trees.
By these definitions, a tree is a non-empty set of paths and each node has a "unique label" which is the path π that leads to it. A root-only tree is a function from nil to some species A.
- 1.The lineage tree with just one dead leaf:$0=\mathit{\lambda x}.\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x=\mathit{nil}\phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}0\phantom{\rule{0.25em}{0ex}}\mathit{else}\phantom{\rule{0.25em}{0ex}}\mathit{undef}$
- 2.The lineage tree with root A ∈ S and children L _{ i }, for A ≠ 0 and n > = 0:$\begin{array}{c}\hfill A\left({L}_{1},\dots ,{L}_{n}\right)\phantom{\rule{0.25em}{0ex}}=\hfill \\ \hfill \mathit{\lambda x}.\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x=\mathit{nil}\phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}A\phantom{\rule{0.25em}{0ex}}\mathit{else}\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x=1,\pi \phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}{L}_{1}\left(\pi \right)\dots \phantom{\rule{0.25em}{0ex}}\mathit{else}\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x\hfill \\ \hfill =n,\pi \phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}{L}_{n}\left(\pi \right)\phantom{\rule{0.25em}{0ex}}\mathit{else}\phantom{\rule{0.25em}{0ex}}\mathit{undef}\hfill \end{array}$
where for n = 0, A = A() is a "live" leaf.
- 3.The leaf-extension operator L, π, A ⊲ (B _{1}, … B _{ n }), which is defined if π is an A -labeled live leaf in L(L(π) = A ≠ 0), and n > 0, and B _{1} … B _{ n } ∈ S _{0}:$\begin{array}{l}L,\pi ,A\u22b2\left(B1,\dots \mathit{Bn}\right)\phantom{\rule{0.25em}{0ex}}=\mathit{\lambda x}.\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x=\pi ,1\phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}{B}_{1},\phantom{\rule{0.25em}{0ex}}\dots ,\mathit{else}\phantom{\rule{0.25em}{0ex}}\mathit{if}\phantom{\rule{0.25em}{0ex}}x\hfill \\ \phantom{\rule{7em}{0ex}}=\pi ,n\phantom{\rule{0.25em}{0ex}}\mathit{then}\phantom{\rule{0.25em}{0ex}}{B}_{n},\phantom{\rule{0.25em}{0ex}}\mathit{else}\phantom{\rule{0.25em}{0ex}}L\left(x\right)\hfill \end{array}$
For example, by the above definitions a tree with root C and with n children B_{1}, …, B_{ n } which are all leaves can be written as the expression C(B_{1}(), …, B_{ n }()), representing a function that given the sequence nil returns the label C, given the sequence i, nil returns the label B_{ i }, and is otherwise undefined. Similarly, the expression C(), nil, C ⊲ (B_{1}, …, B_{ n }) represents the tree C() where the leaf C is extended into a node with children B_{1}, …, B_{ n }; this is then the same as the tree C(B_{1}(), …, B_{ n }()).
A collection of eSTG reactions describes a way of generating and transforming lineage trees. We now describe how each eSTG reaction transforms a lineage tree into new lineage trees. More precisely, since eSTG reactions are stochastic/probabilistic, how each reaction produces a measure of new lineage trees, where each new lineage tree is associated with its rate of occurrence.
the leaf-extension measure, where π, B is a leaf in L; this is a function in ${\mathbb{L}}^{1}\to {\mathrm{\mathbb{R}}}^{+}$. This is the measure such that any extended tree of the form L, π, B ⊲ (L_{1,} …, L_{ n }) for some L_{1}, …, L_{ n } receives the measure M(L_{1}, …, L_{ n }).
For example, C(), nil, C ⊲ (d(r, (D(), E())) + d(s, F())) = d(r, C(D(), E())) + d(s, C(F())) because C(D(), E()) has the shape C(), nil, C ⊲ (D(), E()) and so it receives measure r, and C(F()) has shape C(), nil, C ⊲ (F()) and so it receives measure s.
This rule prescribes, for example, how to carry out a simulation of a set of eSTG reactions given an initial lineage tree: at each step apply the rule above to all applicable reactions and tree leaves, sum all the measures so obtained, and sample a new lineage tree according to the resulting measure.
Declarations
Acknowledgements
This research was supported by The European Union FP7-ERC-AdG Foundation and by the Kenneth and Sally Leafman Appelbaum Discovery Fund. Ehud Shapiro is the Incumbent of The Harry Weinrebe Professorial Chair of Computer Science and Biology.
Authors’ Affiliations
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