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Cardelli L, Tribastone M, Tschaikowski M, Vandin A. Maximal aggregation of polynomial dynamical systems. Proc Natl Acad Sci U S A 2017; 114:10029-10034. [PMID: 28878023 PMCID: PMC5617256 DOI: 10.1073/pnas.1702697114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ordinary differential equations (ODEs) with polynomial derivatives are a fundamental tool for understanding the dynamics of systems across many branches of science, but our ability to gain mechanistic insight and effectively conduct numerical evaluations is critically hindered when dealing with large models. Here we propose an aggregation technique that rests on two notions of equivalence relating ODE variables whenever they have the same solution (backward criterion) or if a self-consistent system can be written for describing the evolution of sums of variables in the same equivalence class (forward criterion). A key feature of our proposal is to encode a polynomial ODE system into a finitary structure akin to a formal chemical reaction network. This enables the development of a discrete algorithm to efficiently compute the largest equivalence, building on approaches rooted in computer science to minimize basic models of computation through iterative partition refinements. The physical interpretability of the aggregation is shown on polynomial ODE systems for biochemical reaction networks, gene regulatory networks, and evolutionary game theory.
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Affiliation(s)
- Luca Cardelli
- Microsoft Research, Cambridge CB1 2FB, United Kingdom
- Department of Computing, University of Oxford, Oxford OX1 3QD, United Kingdom
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Cardelli L, Tribastone M, Tschaikowski M, Vandin A. Efficient Syntax-Driven Lumping of Differential Equations. TOOLS AND ALGORITHMS FOR THE CONSTRUCTION AND ANALYSIS OF SYSTEMS 2016. [DOI: 10.1007/978-3-662-49674-9_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Chylek LA, Wilson BS, Hlavacek WS. Modeling biomolecular site dynamics in immunoreceptor signaling systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 844:245-62. [PMID: 25480645 DOI: 10.1007/978-1-4939-2095-2_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The immune system plays a central role in human health. The activities of immune cells, whether defending an organism from disease or triggering a pathological condition such as autoimmunity, are driven by the molecular machinery of cellular signaling systems. Decades of experimentation have elucidated many of the biomolecules and interactions involved in immune signaling and regulation, and recently developed technologies have led to new types of quantitative, systems-level data. To integrate such information and develop nontrivial insights into the immune system, computational modeling is needed, and it is essential for modeling methods to keep pace with experimental advances. In this chapter, we focus on the dynamic, site-specific, and context-dependent nature of interactions in immunoreceptor signaling (i.e., the biomolecular site dynamics of immunoreceptor signaling), the challenges associated with capturing these details in computational models, and how these challenges have been met through use of rule-based modeling approaches.
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Affiliation(s)
- Lily A Chylek
- Department of Chemistry and Chemical Biology, Cornell University, 14853, Ithaca, NY, USA,
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Bouhaddou M, Birtwistle MR. Dimerization-based control of cooperativity. MOLECULAR BIOSYSTEMS 2014; 10:1824-32. [PMID: 24736836 PMCID: PMC4060435 DOI: 10.1039/c4mb00022f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cooperativity of ligand-receptor binding influences the input-output behavior of a biochemical system and thus is an important determinant of its physiological function. Canonically, such cooperativity is understood in terms of ligand-receptor binding affinity, where an initial binding event changes the affinity for subsequent binding events. Here, we demonstrate that dimerization-a simple yet pervasive signaling motif across biology-can have significant control over cooperativity and even dominate over the canonical mechanism. Through an exhaustive parameter sensitivity analysis of a general kinetic model for signal-mediated dimerization, we show that quantitative modulation of dimerization processes can reinforce, eliminate, and even reverse cooperativity imposed by the canonical allosteric ligand-receptor binding affinity mechanism. The favored accumulation of stoichiometrically asymmetric dimers (those with ligand-receptor stoichiometry of 1 : 2) is a major determinant of dimerization-based cooperativity control. However, simulations demonstrate that favoring accumulation of such stoichiometrically asymmetric dimers can either increase or decrease cooperativity, and thus the quantitative relationship between stoichiometrically asymmetric dimers and cooperativity is highly dependent on the parameter values of the particular system of interest. These results suggest that the dimerization motif provides a novel mechanism for both generating and quantitatively tuning cooperativity that, due to the ubiquity of dimerization motifs in biochemical systems, may play a major role in a host of biological functions. Thus, the canonical, allosteric view of cooperativity is incomplete without considering dimerization effects, which is of particular importance as dimerization is often a necessary feature of the allosteric mechanism.
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Affiliation(s)
- Mehdi Bouhaddou
- Icahn School of Medicine at Mount Sinai, Department of Pharmacology and Systems Therapeutics, New York, NY 10029, USA.
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Machado D, Costa RS, Rocha M, Ferreira EC, Tidor B, Rocha I. Modeling formalisms in Systems Biology. AMB Express 2011; 1:45. [PMID: 22141422 PMCID: PMC3285092 DOI: 10.1186/2191-0855-1-45] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/05/2011] [Indexed: 12/18/2022] Open
Abstract
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.
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Affiliation(s)
- Daniel Machado
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Rafael S Costa
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Miguel Rocha
- Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Eugénio C Ferreira
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Bruce Tidor
- Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isabel Rocha
- IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Maus C, Rybacki S, Uhrmacher AM. Rule-based multi-level modeling of cell biological systems. BMC SYSTEMS BIOLOGY 2011; 5:166. [PMID: 22005019 PMCID: PMC3306009 DOI: 10.1186/1752-0509-5-166] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 10/17/2011] [Indexed: 11/10/2022]
Abstract
BACKGROUND Proteins, individual cells, and cell populations denote different levels of an organizational hierarchy, each of which with its own dynamics. Multi-level modeling is concerned with describing a system at these different levels and relating their dynamics. Rule-based modeling has increasingly attracted attention due to enabling a concise and compact description of biochemical systems. In addition, it allows different methods for model analysis, since more than one semantics can be defined for the same syntax. RESULTS Multi-level modeling implies the hierarchical nesting of model entities and explicit support for downward and upward causation between different levels. Concepts to support multi-level modeling in a rule-based language are identified. To those belong rule schemata, hierarchical nesting of species, assigning attributes and solutions to species at each level and preserving content of nested species while applying rules. Further necessities are the ability to apply rules and flexibly define reaction rate kinetics and constraints on nested species as well as species that are nested within others. An example model is presented that analyses the interplay of an intracellular control circuit with states at cell level, its relation to cell division, and connections to intercellular communication within a population of cells. The example is described in ML-Rules - a rule-based multi-level approach that has been realized within the plug-in-based modeling and simulation framework JAMES II. CONCLUSIONS Rule-based languages are a suitable starting point for developing a concise and compact language for multi-level modeling of cell biological systems. The combination of nesting species, assigning attributes, and constraining reactions according to these attributes is crucial in achieving the desired expressiveness. Rule schemata allow a concise and compact description of complex models. As a result, the presented approach facilitates developing and maintaining multi-level models that, for instance, interrelate intracellular and intercellular dynamics.
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Affiliation(s)
- Carsten Maus
- University of Rostock, Institute of Computer Science, Albert-Einstein-Str. 22, 18059 Rostock, Germany
| | - Stefan Rybacki
- University of Rostock, Institute of Computer Science, Albert-Einstein-Str. 22, 18059 Rostock, Germany
| | - Adelinde M Uhrmacher
- University of Rostock, Institute of Computer Science, Albert-Einstein-Str. 22, 18059 Rostock, Germany
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Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Guidelines for visualizing and annotating rule-based models. MOLECULAR BIOSYSTEMS 2011; 7:2779-95. [PMID: 21647530 PMCID: PMC3168731 DOI: 10.1039/c1mb05077j] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Rule-based modeling provides a means to represent cell signaling systems in a way that captures site-specific details of molecular interactions. For rule-based models to be more widely understood and (re)used, conventions for model visualization and annotation are needed. We have developed the concepts of an extended contact map and a model guide for illustrating and annotating rule-based models. An extended contact map represents the scope of a model by providing an illustration of each molecule, molecular component, direct physical interaction, post-translational modification, and enzyme-substrate relationship considered in a model. A map can also illustrate allosteric effects, structural relationships among molecular components, and compartmental locations of molecules. A model guide associates elements of a contact map with annotation and elements of an underlying model, which may be fully or partially specified. A guide can also serve to document the biological knowledge upon which a model is based. We provide examples of a map and guide for a published rule-based model that characterizes early events in IgE receptor (FcεRI) signaling. We also provide examples of how to visualize a variety of processes that are common in cell signaling systems but not considered in the example model, such as ubiquitination. An extended contact map and an associated guide can document knowledge of a cell signaling system in a form that is visual as well as executable. As a tool for model annotation, a map and guide can communicate the content of a model clearly and with precision, even for large models.
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Affiliation(s)
- Lily A Chylek
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Szopa P, Lipniacki T, Kazmierczak B. Exact solutions to a spatially extended model of kinase-receptor interaction. Phys Biol 2011; 8:055005. [PMID: 21832804 DOI: 10.1088/1478-3975/8/5/055005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
B and Mast cells are activated by the aggregation of the immune receptors. Motivated by this phenomena we consider a simple spatially extended model of mutual interaction of kinases and membrane receptors. It is assumed that kinase activates membrane receptors and in turn the kinase molecules bound to the active receptors are activated by transphosphorylation. Such a type of interaction implies positive feedback and may lead to bistability. In this study we apply the Steklov eigenproblem theory to analyze the linearized model and find exact solutions in the case of non-uniformly distributed membrane receptors. This approach allows us to determine the critical value of receptor dephosphorylation rate at which cell activation (by arbitrary small perturbation of the inactive state) is possible. We found that cell sensitivity grows with decreasing kinase diffusion and increasing anisotropy of the receptor distribution. Moreover, these two effects are cooperating. We showed that the cell activity can be abruptly triggered by the formation of the receptor aggregate. Since the considered activation mechanism is not based on receptor crosslinking by polyvalent antigens, the proposed model can also explain B cell activation due to receptor aggregation following binding of monovalent antigens presented on the antigen presenting cell.
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Affiliation(s)
- Piotr Szopa
- Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
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Lemons NW, Hu B, Hlavacek WS. Hierarchical graphs for rule-based modeling of biochemical systems. BMC Bioinformatics 2011; 12:45. [PMID: 21288338 PMCID: PMC3152790 DOI: 10.1186/1471-2105-12-45] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 02/02/2011] [Indexed: 11/23/2022] Open
Abstract
Background In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system. Results For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm. Conclusions Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models.
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Affiliation(s)
- Nathan W Lemons
- Department of Mathematics and its Applications, Central European University, H-1051 Budapest, Hungary
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Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG. RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics 2010; 11:404. [PMID: 20673321 PMCID: PMC2921409 DOI: 10.1186/1471-2105-11-404] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 07/30/2010] [Indexed: 12/31/2022] Open
Abstract
Background The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be specified using model-specification languages, such as the BioNetGen language (BNGL). A set of rules implicitly defines a (bio)chemical reaction network. The reaction network implied by a set of rules is often very large, and as a result, generation of the network implied by rules tends to be computationally expensive. Moreover, the cost of many commonly used methods for simulating network dynamics is a function of network size. Together these factors have limited application of the rule-based modeling approach. Recently, several methods for simulating rule-based models have been developed that avoid the expensive step of network generation. The cost of these "network-free" simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is now needed for the simulation and analysis of rule-based models of biochemical systems. Results Here, we present a software tool called RuleMonkey, which implements a network-free method for simulation of rule-based models that is similar to Gillespie's method. The method is suitable for rule-based models that can be encoded in BNGL, including models with rules that have global application conditions, such as rules for intramolecular association reactions. In addition, the method is rejection free, unlike other network-free methods that introduce null events, i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant tool for network-free simulation of rule-based models. We also compare RuleMonkey against problem-specific codes implementing network-free simulation methods. Conclusions RuleMonkey enables the simulation of rule-based models for which the underlying reaction networks are large. It is typically faster than DYNSTOC for benchmark problems that we have examined. RuleMonkey is freely available as a stand-alone application http://public.tgen.org/rulemonkey. It is also available as a simulation engine within GetBonNie, a web-based environment for building, analyzing and sharing rule-based models.
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Affiliation(s)
- Joshua Colvin
- Clinical Translational Research Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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