Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars

Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part. This concept provides a finer level of granularity than the traditional notion of the gene. However, a method of formally relating how a set of parts relates to a function has not yet emerged. Synthetic biology both demands such a formalism and provides an ideal setting for testing hypotheses about relationships between DNA sequences and phenotypes beyond the gene-centric methods used in genetics. Attribute grammars are used in computer science to translate the text of a program source code into the computational operations it represents. By associating attributes with parts, modifying the value of these attributes using rules that describe the structure of DNA sequences, and using a multi-pass compilation process, it is possible to translate DNA sequences into molecular interaction network models. These capabilities are illustrated by simple example grammars expressing how gene expression rates are dependent upon single or multiple parts. The translation process is validated by systematically generating, translating, and simulating the phenotype of all the sequences in the design space generated by a small library of genetic parts. Attribute grammars represent a flexible framework connecting parts with models of biological function. They will be instrumental for building mathematical models of libraries of genetic constructs synthesized to characterize the function of genetic parts. This formalism is also expected to provide a solid foundation for the development of computer assisted design applications for synthetic biology

CItyMaker:

Due to its complexity, the evolution of cities is something that is difficult to predict and planning new developments for cities is therefore a difficult task. This complexity can be identified on two levels: on a micro level, it emerges from the multiple relations between the many components and actors in cities, whereas on a macro level it stems from the geographical, social and economic relations between cities. However, many of these relations can be measured. The design of plans for cities can only be improved if designers are able to address measurements of some of the relationships between the components of cities during the design process. These measurements are called urban indicators. By calculating such measurements, designers can grasp the meaning of the changes being proposed, not just as simple alternative layouts, but also in terms of the changes in indicators adding a qualitative perception. This thesis presents a method and a set of tools to generate alternative solutions for an urban context. The method proposes the use of a combined set of design patterns encoding typical design moves used by urban designers. The combination of patterns generates different layouts which can be adjusted by manipulating several parameters in relation to updated urban indicators. The patterns were developed from observation of typical urban design procedures, first encoded as discursive grammars and later translated into parametric design patterns. The CItyMaker method and tools allows the designer to compose a design solution from a set of programmatic premises and fine-tune it by pulling parameters whilst checking the changes in urban indicators. These tools improve the designer’s awareness of the consequences of their design moves

SAGA: A project to automate the management of software production systems

The Software Automation, Generation and Administration (SAGA) project is investigating the design and construction of practical software engineering environments for developing and maintaining aerospace systems and applications software. The research includes the practical organization of the software lifecycle, configuration management, software requirements specifications, executable specifications, design methodologies, programming, verification, validation and testing, version control, maintenance, the reuse of software, software libraries, documentation, and automated management

Reorganization in Multi-Agent Architectures: An Active Graph Grammar Approach

Background: Organizational architecture is a holistic approach to design of humane organizations and studies an organization from five perspectives: structure, culture, processes, strategy and individuals. In this paper the concept of organizational architecture is firstly formalized using the fractal principle and then applied to multi-agent systems’ (MAS) organizations. Objectives: Providing a holistic framework for modelling all aspects of MASreorganization. Methods/Approach: MAS organizations are formalized using graph theory and a new active graph rewriting formalism inspired by the active database theory is introduced. Results: The newly developed framework is graphical, event-driven and applied in a distributed MAS environment. Conclusions: By defining organizational units, processes, strategies and cultural artefacts in a recursive way, it is shown that labelled graphs and hypergraphs can be used to model various levels of organizational architecture while active graph grammars allow one to model reorganization of each of the architectural perspectives