Entwurf und Implementation einer auf Graph-Grammatiken beruhenden Sprache zur Funktions-Struktur-Modellierung von Pflanzen

Increasing biological knowledge requires more and more elaborate methods to translate the knowledge into executable model descriptions, and increasing computational power allows to actually execute these descriptions. Such a simulation helps to validate, extend and question the knowledge. For plant modelling, the well-established formal description language of Lindenmayer systems reaches its limits as a method to concisely represent current knowledge and to conveniently assist in current research. On one hand, it is well-suited to represent structural and geometric aspects of plant models - of which units is a plant composed, how are these connected, what is their location in 3D space -, but on the other hand, its usage to describe functional aspects - what internal processes take place in the plant structure, how does this interact with the structure - is not as convenient as desirable. This can be traced back to the underlying representation of structure as a linear chain of units, while the intrinsic nature of the structure is a tree or even a graph. Therefore, we propose to use graphs and graph grammars as a basis for plant modelling which combines structural and functional aspects. In the first part of this thesis, we develop the necessary theoretical framework. Starting with a presentation of the state of the art concerning Lindenmayer systems and graph grammars, we develop the formalism of relational growth grammars as a variant of graph grammars. We show that this formalism has a natural embedding of Lindenmayer systems which keeps all relevant properties, but represents branched structures directly as axial trees and not as linear chains with indirect encoding of branches. In the second part, we develop the main practical result, the XL programming language as an extension of the Java programming language by very general rule-based features. Short examples illustrate the application of the new language features. We describe the built-in pattern matching algorithm of the implemented run-time system for the XL programming language, and we sketch a possible implementation of an XL compiler. The third part is an application of relational growth grammars and the XL programming language. We show how the general XL interfaces can be customized for relational growth grammars. On top of this customization, several examples from a variety of disciplines demonstrate the usefulness of the developed formalism and language to describe plant growth, especially functional-structural plant models, but also artificial life, architecture or interactive games. Some examples operate on custom graphs like XML DOM trees or scene graphs of commercial 3D modellers, while the majority uses the 3D modelling platform GroIMP, a software developed in conjunction with this thesis. The appendix gives an overview of the GroIMP software. The practical usage of its plug-in for relational growth grammars is also illustrated.Das zunehmende Wissen über biologische Prozesse verlangt nach geeigneten Methoden, es in ausführbare Modelle zu übersetzen, und die zunehmende Rechenleistung der Computer ermöglicht es, diese Modelle auch tatsächlich auszuführen. Solche Simulationen dienen zur Validierung, Erweiterung und Hinterfragung des Wissens. Speziell für die Pflanzenmodellierung wurden Lindenmayer-Systeme mit Erfolg eingesetzt, jedoch stoßen diese bei aktuellen Modellierungsproblemen und Forschungsvorhaben an ihre Grenzen. Zwar sind sie gut geeignet, Pflanzenstruktur und Geometrie abzubilden - aus welchen Einheiten setzt sich eine Pflanze zusammen, wie sind diese verbunden, wie ist ihre räumliche Lage -, aber die lineare Datenstruktur erschwert die Integration von Funktionsmodellen, welche Prozesse innerhalb der verzweigten Struktur und des beanspruchten Raumes beschreiben. Daher wird in dieser Arbeit vorgeschlagen, anstelle der linearen Stuktur Graphen und Graph-Grammatiken als Grundlage für die kombinierte Funktions-Struktur-Modellierung von Pflanzen zu verwenden. Im ersten Teil der Dissertation wird der theoretische Unterbau entwickelt. Nach einer Vorstellung des aktuellen Wissensstandes auf dem Gebiet der Lindenmayer-Systeme und Graph-Grammatiken werden relationale Wachstumsgrammatiken eingeführt, die auf bekannten Mechanismen für parallele Graph-Grammatiken aufbauen und Lindenmayer-Systeme als Spezialfall enthalten, dabei jedoch verzweigte Strukturen direkt als axiale Bäume darstellen. Zur praktischen Anwendung wird im zweiten Teil die Programmiersprache XL entwickelt, die Java um allgemein gehaltene Sprachkonstrukte für Graph-Grammatiken erweitert. Kurze Beispiele zeigen die Anwendung der neuen Sprachmerkmale. Der Algorithmus zur Mustersuche wird erläutert, und die Implementation des XL-Compilers wird vorgestellt. Im dritten Teil werden mögliche Anwendungen relationaler Wachstumsgrammatiken aufgezeigt. Dazu werden zunächst die allgemeinen XL-Schnittstellen für relationale Wachstumsgrammatiken konkretisiert, um dieses System dann für Modelle aus verschiedenen Bereichen zu nutzen, darunter Funktions-Struktur-Modelle von Pflanzen, Künstliches Leben, Architektur und interaktive Spiele. Einige Beispiele nutzen spezifische Graphen wie XML-DOM-Bäume oder Szenengraphen kommerzieller 3D-Modellierprogramme, aber der überwiegende Teil baut auf der 3D-Plattform GroIMP auf, die zusammen mit dieser Dissertation entwickelt wurde. Im Anhang wird die Software GroIMP kurz vorgestellt und ihre praktische Anwendung für relationale Wachstumsgrammatiken erläutert

Foundations of Software Science and Computation Structures

This open access book constitutes the proceedings of the 22nd International Conference on Foundations of Software Science and Computational Structures, FOSSACS 2019, which took place in Prague, Czech Republic, in April 2019, held as part of the European Joint Conference on Theory and Practice of Software, ETAPS 2019. The 29 papers presented in this volume were carefully reviewed and selected from 85 submissions. They deal with foundational research with a clear significance for software science

Components as coalgebras

In the tradition of mathematical modelling in physics and chemistry, constructive formal specification methods are based on the notion of a software model, understood as a state-based abstract machine which persists and evolves in time, according to a behavioural model capturing, for example, partiality or (different degrees of) nondeterminism. This can be identified with the more prosaic notion of a software component advocated by the software industry as ‘building block’ of large, often distributed, systems. Such a component typically encapsulates a number of services through a public interface which provides a limited access to a private state space, paying tribute to the nowadays widespread object-oriented programming principles. The tradition of communicating systems formal design, by contrast, has developed the notion of a process as an abstraction of the behavioural patterns of a computing system, deliberately ignoring the data and state aspects of software systems. Both processes and components are among the broad group of computing phenomena which are hardly definable (or simply not definable) algebraically, i.e., in terms of a complete set of constructors. Their semantics is essentially observational, in the sense that all that can be traced of their evolution is their interaction with the environment. Therefore, coalgebras, whose theory has recently witnessed remarkable developments, appear as a suitable modelling tool. The basic observation of category theory that universal constructions always come in pairs, has motivated research on the duality between algebras and coalgebras, which provides a bridge between models of static (constructive, data-oriented) and dynamical (observational, behaviour-oriented) systems. At the programming level, the intuitive symmetry between data and behaviour provides evidence of such a duality, in its canonical initial-final specialisation. This line of thought entails both definitional and proof principles, i.e., a basis for the development of program calculi directly based on (actually driven by) type specifications. Moreover, such properties can be expressed in terms of generic programming combinators which are used, not only to calculate programs, but also to program with. Framed in this context, this thesis addresses the following main themes: The investigation of a semantic model for (state-based) software components. These are regarded as concrete coalgebras for some Set endofunctors, with specified initial conditions, and organise themselves in a bicategorical setting. The model is able to capture both behavioural issues, which are usually left implicit in state-based specification methods, and interaction through structured data, which is usually a minor concern on process calculi. Two basic cases are considered entailing, respectively, a ‘functional’ and an ‘object-oriented’ shape for components. Both cases are parametrized by a model of behaviour, introduced as a strong (usually commutative) monad. The development of corresponding component calculi, also parametric on the behaviour model, which adds to the genericity of the approach. The study of processes and the ‘reconstruction’ of classical (CCS-like) process calculi on top of their representation as inhabitants of (the carriers of) final coalgebras, in an essentially pointfree, calculational style. An overall concern for genericity, in the sense that models and calculi for both components and processes are parametric on the behaviour model and the interaction discipline, respectively. The animation of both processes and components in CHARITY, a functional programming language entirely based on inductive and coinductive categorical data types. In particular this leads to the development of a process calculi interpreter parametric on the interaction discipline.PRAXIS XXI - Projecto LOGCAMP; POO11/IC-PME/II/S -Projecto KARMA; Fundação para a Ciência e Tecnologia; ALGORITMI Research Center

On implicit program constructs

Session types are a well-established approach to ensuring protocol conformance and the absence of communication errors such as deadlocks in message passing systems. Implicit parameters, introduced by Haskell and popularised in Scala, are a mechanism to improve program readability and conciseness by allowing the programmer to omit function call arguments, and have the compiler insert them in a principled manner at compile-time. Scala recently gave implicit types first-class status (implicit functions), yielding an expressive tool for handling context dependency in a type-safe manner. DOT (Dependent Object Types) is an object calculus with path-dependent types and abstract type members, developed to serve as a theoretical foundation for the Scala programming language. As yet, DOT does not model all of Scala’s features, but a small subset. Among those features of Scala not yet modelled by DOT are implicit functions. We ask: can type-safe implicit functions be generalised from Scala’s sequential setting to message passing computation, to improve readability and conciseness of message passing programs? We answer this question in the affirmative by generalising the concept of an implicit function to an implicit message, its concurrent analogue, a programming language construct for session-typed concurrent computation. We explore new applications for implicit program constructs by integrating theminto four novel calculi, each demonstrating a new use case or theoretical result for implicits. Firstly, we integrate implicit functions and messages into the concurrent functional language LAST, Gay and Vasconcelos’s calculus of linear types for asynchronous sessions. We demonstrate their utility by example, and explore use cases for both implicit functions and implicit messages. We integrate implicit messages into two pi calculi, further demonstrating the robustness of our approach to extending calculi with implicits. We show that implicit messages are possible in the absence of lambda calculus, in languages with concurrency primitives only, and that they are sound not only in binary session-typed computation, but also in multi-party context. Finally we extend DOT to include implicit functions. We show type safety of the resulting calculus by translation to DOT, lending a higher degree of confidence to the correctness of implicit functions in Scala. We demonstrate that typical use cases for implicit functions in Scala are typably expressible in DOT when extended with implicit functions

Kiel Declarative Programming Days 2013

This report contains the papers presented at the Kiel Declarative Programming Days 2013, held in Kiel (Germany) during September 11-13, 2013. The Kiel Declarative Programming Days 2013 unified the following events: * 20th International Conference on Applications of Declarative Programming and Knowledge Management (INAP 2013) * 22nd International Workshop on Functional and (Constraint) Logic Programming (WFLP 2013) * 27th Workshop on Logic Programming (WLP 2013) All these events are centered around declarative programming, an advanced paradigm for the modeling and solving of complex problems. These specification and implementation methods attracted increasing attention over the last decades, e.g., in the domains of databases and natural language processing, for modeling and processing combinatorial problems, and for high-level programming of complex, in particular, knowledge-based systems

Foundations of Software Science and Computation Structures

This open access book constitutes the proceedings of the 23rd International Conference on Foundations of Software Science and Computational Structures, FOSSACS 2020, which took place in Dublin, Ireland, in April 2020, and was held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020. The 31 regular papers presented in this volume were carefully reviewed and selected from 98 submissions. The papers cover topics such as categorical models and logics; language theory, automata, and games; modal, spatial, and temporal logics; type theory and proof theory; concurrency theory and process calculi; rewriting theory; semantics of programming languages; program analysis, correctness, transformation, and verification; logics of programming; software specification and refinement; models of concurrent, reactive, stochastic, distributed, hybrid, and mobile systems; emerging models of computation; logical aspects of computational complexity; models of software security; and logical foundations of data bases.

Programming Languages and Systems

This open access book constitutes the proceedings of the 29th European Symposium on Programming, ESOP 2020, which was planned to take place in Dublin, Ireland, in April 2020, as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2020. The actual ETAPS 2020 meeting was postponed due to the Corona pandemic. The papers deal with fundamental issues in the specification, design, analysis, and implementation of programming languages and systems

LIPIcs, Volume 261, ICALP 2023, Complete Volume

LIPIcs, Volume 261, ICALP 2023, Complete Volum