A Graph Grammar Approach to Artificial Life

2004 ◽  
Vol 10 (4) ◽  
pp. 413-431 ◽  
Author(s):  
Ole Kniemeyer ◽  
Gerhard H. Buck-Sorlin ◽  
Winfried Kurth
Keyword(s):  
Artificial Life ◽  
Regulatory Networks ◽  
Object Oriented ◽  
Graph Grammar ◽  
Lindenmayer Systems ◽  
Rewriting Systems ◽  
Flower Morphogenesis ◽  
Formal Framework ◽  
High Level ◽  
Rewriting Rules

We present the high-level language of relational growth grammars (RGGs) as a formalism designed for the specification of ALife models. RGGs can be seen as an extension of the well-known parametric Lindenmayer systems and contain rule-based, procedural, and object-oriented features. They are defined as rewriting systems operating on graphs with the edges coming from a set of user-defined relations, whereas the nodes can be associated with objects. We demonstrate their ability to represent genes, regulatory networks of metabolites, and morphologically structured organisms, as well as developmental aspects of these entities, in a common formal framework. Mutation, crossing over, selection, and the dynamics of a network of gene regulation can all be represented with simple graph rewriting rules. This is demonstrated in some detail on the classical example of Dawkins' biomorphs and the ABC model of flower morphogenesis: other applications are briefly sketched. An interactive program was implemented, enabling the execution of the formalism and the visualization of the results.

scholarly journals A High-Level Petri Net Framework for Genetic Regulatory Networks

2007 ◽  
Vol 4 (3) ◽  
pp. 1-14 ◽  
Author(s):  
Richard Banks ◽  
L. Jason Steggles
Keyword(s):  
Regulatory Networks ◽  
Formal Analysis ◽  
Boolean Model ◽  
Genetic Regulatory Networks ◽  
Cellular Systems ◽  
Logic Minimization ◽  
Formal Framework ◽  
The Individual ◽  
High Level ◽  
Compare And Contrast

Summary To understand the function of genetic regulatory networks in the development of cellular systems, we must not only realise the individual network entities, but also the manner by which they interact. Multi-valued networks are a promising qualitative approach for modelling such genetic regulatory networks, however, at present they have limited formal analysis techniques and tools. We present a flexible formal framework for modelling and analysing multi-valued genetic regulatory networks using high-level Petri nets and logic minimization techniques. We demonstrate our approach with a detailed case study in which part of the genetic regulatory network responsible for the carbon starvation stress response in Escherichia coli is modelled and analysed. We then compare and contrast this multivalued model to a corresponding Boolean model and consider their formal relationship.

scholarly journals Объектно-ориентированные данные как перезаписывающие системы

2015 ◽  
Author(s):  
A.E. Gutman
Keyword(s):  
Object Oriented ◽  
Conceptual Scheme ◽  
Data Systems ◽  
Rewriting Systems ◽  
Rewriting System ◽  
Rewriting Rules

A deterministic longest-prefix rewriting system is a rewriting system such that there are no rewriting rules X→Y, X→Z with Y≠Z, and only longest prefixes of words are subject to rewriting. Given such a system, analogs are defined and examined of some concepts related to object-oriented data systems: inheritance of classes and objects, instances of classes, class and instance attributes, conceptual dependence and consistency, conceptual scheme, types and subtypes, etc. A special attention is paid to the effective verification of various properties of the rewriting systems under consideration. In particular, algorithms are presented for answering the following questions: Are all words finitely rewritable? Do there exist recurrent words? Is the system conceptually consistent? Given two words X and Y, does X conceptually depend on Y? Does the type of X coincide with that of Y? Is the type of X a subtype of that of Y?

UML Based Design Approach for Storage System of Nano-Satellite

2014 ◽  
Vol 599-601 ◽  
pp. 530-533
Author(s):  
Hong Hao Wang ◽  
Hui Quan Wang ◽  
Zhong He Jin
Keyword(s):  
Storage System ◽  
Unified Modeling Language ◽  
Object Oriented ◽  
Modeling Language ◽  
Nand Flash ◽  
Unified Modeling ◽  
Object Oriented Design ◽  
High Level Modeling ◽  
High Level

Due to the complex timing sequence of NAND flash, a unified design process is urgently required to guarantee the reliability of storage system of nano-satellite. Unified Modeling Language (UML) is a widely used high level modeling language for object-oriented design. This paper adopts the UML as the design and modelling tool in the low level storage system design to elaborate the UML application in each phase of design in detail. The result shows taking UML as the modelling tool results in a clear and unambiguity design, which promotes the reliability and quality of software. At last, the feasibility of object-oriented implementation in C is presented.

scholarly journals A Fast and Effective Method to Identify Relevant Sets of Variables in Complex Systems

Mathematics ◽  
2021 ◽  
Vol 9 (9) ◽  
pp. 1022
Author(s):  
Gianluca D’Addese ◽  
Martina Casari ◽  
Roberto Serra ◽  
Marco Villani
Keyword(s):  
Complex Systems ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Computational Cost ◽  
Graph Analysis ◽  
The Past ◽  
Medium Level ◽  
Micro Level ◽  
Gene Regulatory ◽  
High Level

In many complex systems one observes the formation of medium-level structures, whose detection could allow a high-level description of the dynamical organization of the system itself, and thus to its better understanding. We have developed in the past a powerful method to achieve this goal, which however requires a heavy computational cost in several real-world cases. In this work we introduce a modified version of our approach, which reduces the computational burden. The design of the new algorithm allowed the realization of an original suite of methods able to work simultaneously at the micro level (that of the binary relationships of the single variables) and at meso level (the identification of dynamically relevant groups). We apply this suite to a particularly relevant case, in which we look for the dynamic organization of a gene regulatory network when it is subject to knock-outs. The approach combines information theory, graph analysis, and an iterated sieving algorithm in order to describe rather complex situations. Its application allowed to derive some general observations on the dynamical organization of gene regulatory networks, and to observe interesting characteristics in an experimental case.

FEMLIB: An Object-Oriented Framework for Optimization and Simulation

1995 ◽  
Author(s):  
Michael M. Tiller ◽  
Jonathan A. Dantzig
Keyword(s):  
Material Properties ◽  
Object Oriented ◽  
The Finite Element Method ◽  
Simulation And Optimization ◽  
Gradient Based ◽  
Level Problem ◽  
Simulation Results ◽  
Optimization And Simulation ◽  
High Level ◽  
Simulation Parameters

Abstract In this paper we discuss the design of an object-oriented framework for simulation and optimization. Although oriented around high-level problem solving, the framework defines several classes of problems and includes concrete implementations of common algorithms for solving these problems. Simulations are run by combining these algorithms, as needed, for a particular problem. Included in this framework is the capability to compute the sensitivity of simulation results to the different simulation parameters (e.g. material properties, boundary conditions, etc). This sensitivity information is valuable in performing optimization because it allows the use of gradient-based optimization algorithms. Also included in the system are many useful abstractions and implementations related to the finite element method.

scholarly journals An Open-Source Cloud-FPGA Gene Regulatory Accelerator

2021 ◽  
Author(s):  
Lucas Bragança ◽  
Jeronimo Penha ◽  
Michael Canesche ◽  
Dener Ribeiro ◽  
José Augusto M. Nacif ◽  
...  
Keyword(s):  
Open Source ◽  
Gene Regulatory Networks ◽  
High Performance ◽  
Regulatory Networks ◽  
Cloud Services ◽  
On Demand ◽  
Speed Up ◽  
Gene Regulatory ◽  
High Level ◽  
Better Than

FPGAs are suitable to speed up gene regulatory network (GRN) algorithms with high throughput and energy efficiency. In addition, virtualizing FPGA using hardware generators and cloud resources increases the computing ability to achieve on-demand accelerations across multiple users. Recently, Amazon AWS provides high-performance Cloud's FPGAs. This work proposes an open source accelerator generator for Boolean gene regulatory networks. The generator automatically creates all hardware and software pieces from a high-level GRN description. We evaluate the accelerator performance and cost for CPU, GPU, and Cloud FPGA implementations by considering six GRN models proposed in the literature. As a result, the FPGA accelerator is at least 12x faster than the best GPU accelerator. Furthermore, the FPGA reaches the best performance per dollar in cloud services, at least 5x better than the best GPU accelerator.

A Survey of Object-Oriented Design Quality Improvement

2009 ◽  
pp. 2646-2664
Author(s):  
Juan José Olmedilla
Keyword(s):  
Quality Improvement ◽  
Evaluation Model ◽  
Object Oriented ◽  
Measurement Model ◽  
Design Quality ◽  
Quality Properties ◽  
Object Oriented Design ◽  
Design Improvement ◽  
High Level

The use of object-oriented (OO) architecture knowledge such as patterns, heuristics, principles, refactorings and bad smells improve the quality of designs, as Garzás and Piattini (2005) state in their study; according to it, the application of those elements impact on the quality of an OO design and can serve as basis to establish some kind of software design improvement (SDI) method. But how can we measure the level of improvement? Is there a set of accepted internal attributes to measure the quality of a design? Furthermore, if such a set exists will it be possible to use a measurement model to guide the SDI in the same way software processimprovement models (Humphrey, 1989; Paulk, Curtis, Chrissis, & Weber, 1993) are guided by process metrics (Fenton & Pfleeger, 1998)? Since (Chidamber & Kemerer, 1991) several OO metrics suites have been proposed to measure OO properties, such as encapsulation, cohesion, coupling and abstraction, both in designs and in code, in this chapter we review the literature to find out to which high level quality properties are mapped and if an OO design evaluation model has been formally proposed or even is possible.

scholarly journals Emergence of Organisms

Entropy ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1163
Author(s):  
Andrea Roli ◽  
Stuart A. Kauffman
Keyword(s):  
Artificial Intelligence ◽  
Adaptive Behavior ◽  
Artificial Life ◽  
Living Systems ◽  
Self Sufficiency ◽  
Evolution Of Life ◽  
High Level ◽  
Hostile Environments

Since early cybernetics studies by Wiener, Pask, and Ashby, the properties of living systems are subject to deep investigations. The goals of this endeavour are both understanding and building: abstract models and general principles are sought for describing organisms, their dynamics and their ability to produce adaptive behavior. This research has achieved prominent results in fields such as artificial intelligence and artificial life. For example, today we have robots capable of exploring hostile environments with high level of self-sufficiency, planning capabilities and able to learn. Nevertheless, the discrepancy between the emergence and evolution of life and artificial systems is still huge. In this paper, we identify the fundamental elements that characterize the evolution of the biosphere and open-ended evolution, and we illustrate their implications for the evolution of artificial systems. Subsequently, we discuss the most relevant issues and questions that this viewpoint poses both for biological and artificial systems.

Sign in / Sign up

Export Citation Format

Share Document