Event-driven grammars: Relating abstract and concrete levels of visual languages

The final publication is available at Springer via http://dx.doi.org/10.1007/s10270-007-0051-2In this work we introduce event-driven grammars, a kind of graph grammars that are especially suited for visual modelling environments generated by meta-modelling. Rules in these grammars may be triggered by user actions (such as creating, editing or connecting elements) and in their turn may trigger other user-interface events. Their combination with triple graph transformation systems allows constructing and checking the consistency of the abstract syntax graph while the user is building the concrete syntax model, as well as managing the layout of the concrete syntax representation. As an example of these concepts, we show the definition of a modelling environment for UML sequence diagrams. A discussion is also presented of methodological aspects for the generation of environments for visual languages with multiple views, its connection with triple graph grammars, the formalization of the latter in the double pushout approach and its extension with an inheritance concept.This work has been partially sponsored by the Spanish Ministry of Education and Science with projects MOSAIC (TSI2005-08225-C07-06) and MODUWEB (TIN 2006-09678)

Ten virtues of structured graphs

This paper extends the invited talk by the first author about the virtues of structured graphs. The motivation behind the talk and this paper relies on our experience on the development of ADR, a formal approach for the design of styleconformant, reconfigurable software systems. ADR is based on hierarchical graphs with interfaces and it has been conceived in the attempt of reconciling software architectures and process calculi by means of graphical methods. We have tried to write an ADR agnostic paper where we raise some drawbacks of flat, unstructured graphs for the design and analysis of software systems and we argue that hierarchical, structured graphs can alleviate such drawbacks

Metamodel Instance Generation: A systematic literature review

Modelling and thus metamodelling have become increasingly important in Software Engineering through the use of Model Driven Engineering. In this paper we present a systematic literature review of instance generation techniques for metamodels, i.e. the process of automatically generating models from a given metamodel. We start by presenting a set of research questions that our review is intended to answer. We then identify the main topics that are related to metamodel instance generation techniques, and use these to initiate our literature search. This search resulted in the identification of 34 key papers in the area, and each of these is reviewed here and discussed in detail. The outcome is that we are able to identify a knowledge gap in this field, and we offer suggestions as to some potential directions for future research.Comment: 25 page

Systems Biology Graphical Notation: Process Diagram Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps

Systems Biology Graphical Notation: Activity Flow language Level 1

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps

Development of a client interface for a methodology independent object-oriented CASE tool : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Computer Science at Massey University

The overall aim of the research presented in this thesis is the development of a prototype CASE Tool user interface that supports the use of arbitrary methodology notations for the construction of small-scale diagrams. This research is part of the larger CASE Tool project, MOOT (Massey's Object Oriented Tool). MOOT is a meta-system with a client-server architecture that provides a framework within which the semantics and syntax of methodologies can be described. The CASE Tool user interface is implemented in Java so it is as portable as possible and has a consistent look and feel. It has been designed as a client to the rest of the MOOT system (which acts as a server). A communications protocol has been designed to support the interaction between the CASE Tool client and a MOOT server. The user interface design of MOOT must support all possible graphical notations. No assumptions about the types of notations that a software engineer may use can be made. MOOT therefore provides a specification language called NDL for the definition of a methodology's syntax. Hence, the MOOT CASE Tool client described in this thesis is a shell that is parameterised by NDL specifications. The flexibility provided by such a high level of abstraction presents significant challenges in terms of designing effective human-computer interaction mechanisms for the MOOT user interface. Functional and non-functional requirements of the client user interface have been identified and applied during the construction of the prototype. A notation specification that defines the syntax for Coad and Yourdon OOA/OOD has been written in NDL and used as a test case. The thesis includes the iterative evaluation and extension of NDL resulting from the prototype development. The prototype has shown that the current approach to NDL is efficacious, and that the syntax and semantics of a methodology description can successfully be separated. The developed prototype has shown that it is possible to build a simple, non-intrusive, and efficient, yet flexible, useable, and helpful interface for meta-CASE tools. The development of the CASE Tool client, through its generic, methodology independent design, has provided a pilot with which future ideas may be explored