Vitaliy Mezhuyev

Developing science gateways for drug discovery in a grid environment

BackgroundMethods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources.ResultsTo this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows.ConclusionsOur implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

Metamodelling Architecture for Modelling Domains with Different Mathematical Structure

The new metamodelling approach for domain specific modelling is proposed in the paper. The additional level of the metamodelling architecture is introduced, which gives the possibility of metamodels development in the different mathematical semantics. This allows to take into account the mathematical structure of modelled domains, and to use the mathematical operations for development of new effective methods for solving domain specific tasks. The applicability of the approach for development of metamodels for modelling different domains is shown.

Technology Acceptance Model in M-learning context: A systematic review

Abstract Various review studies were conducted to provide valuable insights into the current research trend of the Technology Acceptance Model (TAM). Nevertheless, this issue still needs to be investigated from further directions. It has been noticed that research overlooks the investigation of TAM with regard to Mobile learning (M-learning) studies from the standpoint of different perspectives. The present study systematically reviews and synthesizes the TAM studies related to M-learning aiming to provide a comprehensive analysis of 87 research articles from 2006 to 2018. The main findings include that most of the TAM studies involving M-learning focused on extending the TAM with external variables, followed by the studies that extended the model by factors from other theories/models. In addition, the main research problem that was frequently tackled among all the analyzed studies was to examine the acceptance of M-learning among students. Moreover, questionnaire surveys were the primarily relied research methods for data collection. Additionally, most of the analyzed studies were undertaken in Taiwan, this is followed by Spain, China, and Malaysia, respectively among the other countries. Besides, most of the analyzed studies were frequently conducted in humanities and educational context, followed by IT and computer science context, respectively among the other contexts. Most of the analyzed studies were carried out in the higher educational settings. To that end, the findings of this review study provide an insight into the current trend of TAM research involving M-learning studies and form an essential reference for scholars in the M-learning context.

An Industrial Case: Pitfalls and Benefits of Applying Formal Methods to the Development of a Network-Centric RTOS

This paper describes a project to develop a network-centric RTOS from scratch using formal methods. The (initial) purposes of the project was to get acquainted with the use of formal methods for software engineering and to obtain a trustworthy RTOS as a component for building networked embedded systems. The work was done by a small, distributed team that had no prior experience on using formal methods and with a small budget. The outcome is that the use of formal methods is most useful as an architectural design method, perhaps more than as a formal verification of software code. The resulting software has many properties that were not anticipated at the beginning and would likely not have been achieved without the use of Formal Methods.

Metamodeling Methodology for Modeling Cyber-Physical Systems

ABSTRACT Existing metamodeling approaches cannot effectively capture the properties of heterogeneous and multidimensional cyber-physical domains. To contribute to this area, a new metamodeling methodology for the development of metamodels with different mathematical semantics is proposed in this article. The new metamodeling architecture and the method for the development of metamodels as integrated formal systems are discussed. To prove the concept, a geometrical meta-metamodel, which allows linking physical properties of multidimensional domains with their spatial structures, is proposed.

Geometrical Meta-Metamodel for Cyber-Physical Modelling

Existing metamodels are not able to effectively capture the knowledge of multidimensional cyber-physical domains. In order to contribute to this area the approach for development of metamodels for modelling the multidimensional cyber-physical systems is considered in the paper. The geometrical meta-metamodel, allowing to link the physical properties of domains with its spatial structure, is proposed. The implementation of the metamodelling approach in the Visual Environment for Cyber-Physical Modelling is considered. The example of using the geometrical meta-metamodel for metamaterials design is given. Investigation, modeling, design and implementation of cyber-physical systems have to be considered as a new and essential part of cyber worlds.

Interacting Entities Modelling Methodology for Robust Systems Design

This paper describes the theoretical principles and the practical implementation of OpenCookbook, an environment for systems engineering. The environment guides and supports developers during requirements and specification capturing over architectural modelling and work plan development till validation and final release. It features a coherent and unified system engineering methodology based on the interacting entities paradigm. In order to implement it, a generic web portal was developed. Targeting embedded systems, it nevertheless was proven to be an effective tool for a wide range of other system domains. OpenCookbook can be tailored to the needs of a specific organisation as well as accommodate engineering standards like IEC61508.

PLS-SEM in Information Systems Research: A Comprehensive Methodological Reference

The partial least squares-structural equation modelling (PLS-SEM) has become a key approach for validating the conceptual models across many disciplines in general, and the Information Systems (IS) in specific. This is guided through the assessment of the measurement and structural models. Several research articles were carried out to provide an extensive coverage of the usage and application of PLS-SEM. These articles were mainly concentrated on providing guidelines of how to use PLS-SEM in terms of reflective and formative measures, measurement and structural models, and the steps for analysing a particular conceptual model. Nevertheless, there are several steps and procedures that precede the evaluation of the measurement and structural models. The understanding of these steps and procedures is very important for many IS scholars, Ph.D. and Master students who are always struggling to find a comprehensive reference that could guide them through their research journey. Hence, the main contribution of this study is to a build a comprehensive methodological guideline of how the PLS-SEM approach can be employed in the context of IS adoption and acceptance, starting from the research design stage till the assessment of the measurement and structural models. This study may serve as a comprehensive reference for formulating the methodology in the IS adoption and acceptance related studies in the case of PLS-SEM employment.

The method and algorithms to find essential attributes and objects of Subject Domains

The paper proposes a new model, method and algorithms for processing a Subject Domain (SD). It considers an SD as a tuple (E,V,T), where E is a set of all objects of this domain, V is a set of all connections between these objects, T is a set of mass problems that can be solved in this domain. Each object is represented by its essential attributes. This allows us to describe SD, to solve most of the mass problems from T, and to control a state of the domain. The goal of the paper is to develop a method and algorithms that allow us to find essential attributes of domains, described as relational databases or production systems. For a production system, we build a dependency graph with attributes as vertexes, and calculate for each of the vertexes a value that indicates how many other attributes can be found using a particular vertex. High-ranked vertexes are considered as essential. The method is based on considering as essential of the most frequently accessed attributes in a relational database. Having essential attributes of objects of a domain, it allows us to define essential attributes of the domain itself.

Architecture of software tools for Domain-Specific Mathematical Modelling

The paper discusses the methodology of Domain-Specific Mathematical Modelling, allowing development of metamodels and their application to modelling domains with different mathematical structure. The concepts of the metamodel, the metamodelling, the domain are considered, the stages of Domain-Specific Mathematical Modelling and the architecture of implementing this methodology software tools are defined.