MetaPlab Virtual Laboratory

Category Cross-Omics>Agent-Based Modeling/Simulation/Tools

Abstract MetaPlab is a virtual laboratory which aims at assisting modelers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes.

The MetaPlab framework is based on a core module which enables you to design and manage biological models, and an extensible set of plug-ins (see below...) by which MP models can be generated, optimized, simulated and analyzed.

MP Systems modeling framework --

Metabolic P systems, (MP systems), are a special class of deterministic P systems (introduced in 1998 by Gheorghe Paun), proposed as models for biological metabolism.

Their dynamics are computed by a molar multiset rewriting regulated by functions, where reactions act on object populations, rather than on single objects (as P system rules do).

The dynamics is deterministic at a population level, whereas nothing can be said about the dynamical evolution of single objects. This situation resembles what happens in the macroscopic gas laws, which specify deterministic relationships among pressure, volume and temperature measures, but do Not cope with the mechanical behavior of single molecules.

Two (2) main features of MP systems are relevant for their application in modeling real complex phenomena. Their dynamics is easily computed by suitable recurrent equations, also called metabolic algorithms, and moreover, these equations can be stated by suitable algebraic manipulations of data coming from macroscopic observation of the system under investigation.

The essence of the metabolic algorithm is the following: compute reaction units, which give a matter partition, apply reactions to the matter assigned to them, and finally collect their products, after removing the matter they consume.

MP systems are essentially multiset grammars where rules are regulated by functions. This means that, if the state of a system is the multiset of objects inside it, for each reaction, a state dependent function provides the value of the reaction unit which has to be moved by the reaction in that state.

In other words, an MP system can be identified with a multiset grammar regulated by maps.

For this reason, the manufacturer adopts two (2) different ways for representing MP systems: ‘MP graphs’ (where the manufacturer can distinguish a reaction level from a regulation level), and a set of rewriting rules, where each rule is equipped with an (algebraic) formula expressing the regulation map of the rule.

Regulation function, also called flux maps, are usually polynomials with variables denoting the quantities of different types of objects, expressed with respect to some conventional population unit, called conventional mole.

The principles of functioning of MP systems are related to some generalization of chemical laws of Avogadro (molarity principle: any reaction involves integer multiples of the same molar amount of any kind of its reactants or products);

Dalton (additivity principle: substance variations are the sums of substance variations due to all reactions); and Lavoisier (conservation principle: in any reaction the mass consumed equates the mass produced) which is generalized by the mass conservativeness.

MP Plug-ins --

MP plug-ins is processing tools by which MP models can be generated, simulated and analyzed. Due to their specific Java structure, these modules can be automatically recognized and loaded by the MetaPlab plug-in manager.

MetaPlab users may launch MP plug-ins by selecting them from a list. The outputs are shown by suitable graphical interfaces.

1) CHART PLOTTING - A tool which allows the visualization of experiment data by plotting the related charts.

2) DYNAMICS COMPUTATION - A simulator which computes the dynamics of MP systems.

3) EMPTYPLUGIN - The EmptyPlugin is a toy MP plug-in created as a template for MP plug-in developers.

4) FLUX INTEGRATOR - A tool which computes macro-fluxes for large time intervals from micro-fluxes having small time intervals.

5) FLUX_DISCOVERY (LOG-GAIN) - The FluxDiscovery (Log-gain) permits you to generate flux time-series from substance and parameter time-series by means of the Log-gain theory.

6) HTMLPLUGIN - The HTMLPlugin permits you to export to an HTML file, the specification of an MP experiment modeled with MetaPlab.

7) LINEAR REGRESSION - The Linear regression plug-in generates flux regulation functions from the observed time-series of substances, parameters and fluxes by means of linear regression.

8) NEURALSYNTH - A tool for generating MP flux regulation functions from data of substance and parameter time evolutions by using Neural Networks (NN).

Four (4) kinds of learning algorithms are implemented: Backpropagation, Genetic Algorithms (GA), Particle Swarm Optimization (PSO) and a Memetic algorithm.

9) SBML PLUG-IN - A tool for importing Systems Biology Markup Language (SBML) models into the MetaPlab environment and transforming them into MP models.

Examples of phenomena already modeled --

1) MITOTICUS - An MP model of the mitotic oscillator in early amphibian embryos.

2) SIRIUS CREATIVUS - An MP model which provides a simple ‘metabolic oscillator’ with only three substances and No parameters.

3) SIRIUS BINARIUS - An MP model which provides a simple metabolic oscillator with only two substances and No parameters.

4) MIZAR ERRATICUS - An MP model which provides a very interesting behavior.

5) VEGA ARCUATUS - An MP model which provides a very interesting behavior.

6) BRUSSELATUS - An MP model of the well-known Brusselator system from the Nicolis and Prygogine's formulation.

7) VOLTERANUS - An MP model of the predator-prey LotkaVolterra system.

8) PHOTOSYNTHETICUS - An MP model of the ‘Non Photochemical Quenching’ phenomenon. This phenomenon determines the plant accommodation to the environmental light.

9) SINUS - An MP sinusoidal oscillator.

10) SYRAKUS - A solver of the 3x+1 problem which uses an MP formulation of the Collatz dynamical system.

System Requirements

Contact manufacturer.


Manufacturer Web Site MetaPlab Virtual Laboratory

Price Contact manufacturer.

G6G Abstract Number 20599

G6G Manufacturer Number 104201