Edgars Celms

Model transformation language MOLA

The paper describes a new graphical model transformation language MOLA. The basic idea of MOLA is to merge traditional structured programming as a control structure with pattern-based transformation rules. The key language element is a graphical loop concept. The main goal of MOLA is to describe model transformations in a natural and easy readable way.

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

The incidence of renal cell carcinoma (RCC) is increasing worldwide, and its prevalence is particularly high in some parts of Central Europe. Here we undertake whole-genome and transcriptome sequencing of clear cell RCC (ccRCC), the most common form of the disease, in patients from four different European countries with contrasting disease incidence to explore the underlying genomic architecture of RCC. Our findings support previous reports on frequent aberrations in the epigenetic machinery and PI3K/mTOR signalling, and uncover novel pathways and genes affected by recurrent mutations and abnormal transcriptome patterns including focal adhesion, components of extracellular matrix (ECM) and genes encoding FAT cadherins. Furthermore, a large majority of patients from Romania have an unexpected high frequency of A:T>T:A transversions, consistent with exposure to aristolochic acid (AA). These results show that the processes underlying ccRCC tumorigenesis may vary in different populations and suggest that AA may be an important ccRCC carcinogen in Romania, a finding with major public health implications.

Graphical template language for transformation synthesis

Higher-Order Transformations (HOT) have become an important support for the development of model transformations in various transformation languages. Most frequently HOTs are used to synthesize transformations from different kinds of models, for example, mapping models. This means that model driven development (MDD) is being successfully applied to transformations themselves too. The standard HOT solution is to create the transformation as a model using the abstract syntax. However, for graphical transformation languages a significantly more efficient solution would be to create the transformation using its graphical (concrete) syntax. An analogy could be the textual template languages such as JET which directly create texts from a model in the concrete syntax of the target language. This paper introduces a new kind of language - a graphical template language for transformation synthesis, named Template MOLA. This language is used for creation of transformations in MOLA transformation language. Template MOLA is an adequate solution for many typical HOT applications.

Tool support for MOLA

The paper describes the MOLA Tool, which supports the model transformation language MOLA. MOLA Tool consists of two parts: MOLA definition environment and MOLA execution environment. MOLA definition environment is based on the GMF (Generic Modeling Framework) and contains graphical editors for metamodels and MOLA diagrams, as well as the MOLA compiler. The main component of MOLA execution environment is a MOLA virtual machine, which performs model transformations, using an SQL database as a repository. The execution environment may be used as a plug-in for Eclipse based modeling tools (e.g., IBM Rational RSA). The current status of the tool is truly academic.

From requirements to code in a model driven way

Though there is a lot of support for model driven development the support for complete model driven path from requirements to code is limited. The approach proposed in this paper offers such a path which is fully supported by model transformations. The starting point is semiformal requirements containing behaviour description in a controlled natural language. A chain of models is proposed including analysis, platform independent and platform specific models. A particular architecture style is chosen by means of selecting a set of appropriate design patterns for these models. It is shown how to define informally and then implement in model transformation language MOLA the required transformations. By executing these transformations a prototype of the system is obtained.

Tree based domain-specific mapping languages

Model transformation languages have been mainly used by researchers --- the software engineering industry has not yet widely accepted the model driven software development (MDSD). One of the main reasons is the complexity of metamodelling principles the developers are required to know to actually use model transformations in the way the OMG has stated. We offer the basic principles how to create domain-specific model transformation languages which can be used by developers relying only on familiar modelling concepts. We propose to use simple graphical mappings to specify the correspondence between source and target models which are represented using trees based on the concrete syntax of underlying modelling languages. If such principles were followed, then the range of potential users of model transformation languages would increase significantly.

Towards Self-explanatory Ontology Visualization with Contextual Verbalization

Ontologies are one of the core foundations of the Semantic Web. To participate in Semantic Web projects, domain experts need to be able to understand the ontologies involved. Visual notations can provide an overview of the ontology and help users to understand the connections among entities. However, the users first need to learn the visual notation before they can interpret it correctly. Controlled natural language representation would be readable right away and might be preferred in case of complex axioms, however, the structure of the ontology would remain less apparent. We propose to combine ontology visualizations with contextual ontology verbalizations of selected ontology (diagram) elements, displaying controlled natural language (CNL) explanations of OWL axioms corresponding to the selected visual notation elements. Thus, the domain experts will benefit from both the high-level overview provided by the graphical notation and the detailed textual explanations of particular elements in the diagram.

Editor Definition Language and Its Implementation

Universal graphical editor definition language based on logical metamodel extended by presentation classes is proposed. Implementation principles of this language, based on Graphical Diagramming Engine are described.

Behaviour modelling notation for information system design

Problems related to behaviour modelling within the platform independent model (PIM) during the model driven design are discussed in the paper. The emphasis is on design problems for information systems, especially on building a behaviour draft. At first issues in the traditional approach using sequence diagrams are discussed. Then a new approach based on activity diagrams is proposed. An extension of activity diagram notation specifically oriented towards comprehensive and readable behaviour design description is presented.

Application of Graph Clustering and Visualisation Methods to Analysis of Biomolecular Data

In this paper we present an approach based on integrated use of graph clustering and visualisation methods for semi-supervised discovery of biologically significant features in biomolecular data sets. We describe several clustering algorithms that have been custom designed for analysis of biomolecular data and feature an iterated two step approach involving initial computation of thresholds and other parameters used in clustering algorithms, which is followed by identification of connected graph components, and, if needed, by adjustment of clustering parameters for processing of individual subgraphs.