Modeling interactive memex-like applications based on self-modifiable petri nets

This paper introduces an interactive Memex-like application using a self-modifiable Petri Net model – Self-modifiable Color Petri Net (SCPN). The Memex (“memory extender”) device proposed by Vannevar Bush in 1945 focused on the problems of “locating relevant information in the published records and recording how that information is intellectually connected.” The important features of Memex include associative indexing and retrieval. In this paper, the self-modifiable functions of SCPN are used to achieve trail recording and retrieval. A place in SCPN represents a website and an arc indicates the trail direction. Each time when a new website is visited, a place corresponding to this website will be added. After a trail is built, users can use it to retrieve the websites they have visited. Besides, useful user interactions are supported by SCPN to achieve Memex functions. The types of user interactions include: forward, backward, history, search, etc. A simulator has been built to demonstrate that the SCPN model can realize Memex functions. Petri net instances can be designed to model trail record, back, and forward operations using this simulator. Furthermore, a client-server based application system has been built. Using this system, a user can surf online and record his surfing history on the server according to different topics and share them with other users

In-silico-Systemanalyse von Biopathways

Chen M. In silico systems analysis of biopathways. Bielefeld (Germany): Bielefeld University; 2004.In the past decade with the advent of high-throughput technologies, biology has migrated from a descriptive science to a predictive one. A vast amount of information on the metabolism have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis with an easy-to-use computational system. One major task is to implement molecular information systems that will allow to integrate different molecular database systems, and to design analysis tools (e.g. simulators of complex metabolic reactions). Three key problems are involved: 1) Modeling and simulation of biological processes; 2) Reconstruction of metabolic pathways, leading to predictions about the integrated function of the network; and 3) Comparison of metabolism, providing an important way to reveal the functional relationship between a set of metabolic pathways. This dissertation addresses these problems of in silico systems analysis of biopathways. We developed a software system to integrate the access to different databases, and exploited the Petri net methodology to model and simulate metabolic networks in cells. It develops a computer modeling and simulation technique based on Petri net methodology; investigates metabolic networks at a system level; proposes a markup language for biological data interchange among diverse biological simulators and Petri net tools; establishes a web-based information retrieval system for metabolic pathway prediction; presents an algorithm for metabolic pathway alignment; recommends a nomenclature of cellular signal transduction; and attempts to standardize the representation of biological pathways. Hybrid Petri net methodology is exploited to model metabolic networks. Kinetic modeling strategy and Petri net modeling algorithm are applied to perform the processes of elements functioning and model analysis. The proposed methodology can be used for all other metabolic networks or the virtual cell metabolism. Moreover, perspectives of Petri net modeling and simulation of metabolic networks are outlined. A proposal for the Biology Petri Net Markup Language (BioPNML) is presented. The concepts and terminology of the interchange format, as well as its syntax (which is based on XML) are introduced. BioPNML is designed to provide a starting point for the development of a standard interchange format for Bioinformatics and Petri nets. The language makes it possible to exchange biology Petri net diagrams between all supported hardware platforms and versions. It is also designed to associate Petri net models and other known metabolic simulators. A web-based metabolic information retrieval system, PathAligner, is developed in order to predict metabolic pathways from rudimentary elements of pathways. It extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. The system also provides a navigation platform to investigate metabolic related information, and transforms the output data into XML files for further modeling and simulation of the reconstructed pathway. An alignment algorithm to compare the similarity between metabolic pathways is presented. A new definition of the metabolic pathway is proposed. The pathway defined as a linear event sequence is practical for our alignment algorithm. The algorithm is based on strip scoring the similarity of 4-hierarchical EC numbers involved in the pathways. The algorithm described has been implemented and is in current use in the context of the PathAligner system. Furthermore, new methods for the classification and nomenclature of cellular signal transductions are recommended. For each type of characterized signal transduction, a unique ST number is provided. The Signal Transduction Classification Database (STCDB), based on the proposed classification and nomenclature, has been established. By merging the ST numbers with EC numbers, alignments of biopathways are possible. Finally, a detailed model of urea cycle that includes gene regulatory networks, metabolic pathways and signal transduction is demonstrated by using our approaches. A system biological interpretation of the observed behavior of the urea cycle and its related transcriptomics information is proposed to provide new insights for metabolic engineering and medical care

Analysing dependability and performance of a real-world Elastic Search application

—Increased complexity in IT, big data, and advanced analytical techniques are some of the trends driving demand for more sophisticated and scalable search technology. Despite Quality of Service (QoS) being a critical success factor in most enterprise software service offerings, it is often not a generic component of the enterprise search software stack. In this paper, we explore enterprise search engine dependability and performance using a real-world company architecture and associated data sourced from an ElasticSearch implementation on Linknovate.com. We propose a Fault Tree model to assess the availability and reliability of the Linknovate.com architecture. The results of the Fault Tree model are fed into a Stochastic Petri Net (SPN) model to analyze how failures and redundancy impact application performance of the use case system. Availability and MTTF were used to evaluate the reliability and throughput was used to evaluate the performance of the target system. The best results for all three metrics were returned in scenarios with high levels of redundancy

Recent Trends in Software Engineering Research As Seen Through Its Publications

This study provides some insight into the field of software engineering through analysis of its recent research publications. Data for this study are taken from the ACM\u27s Guide to Computing Literature (GUIDE) They include both the professionally assigned Computing Classification System (CCS) descriptors and the title text of each software engineering publication reviewed by the GUIDE from 1998 through 2001. The first part of this study provides a snapshot of software engineering by applying co-word analysis techniques to the data. This snapshot indicates recent themes or areas of interest, which, when compared with the results from earlier studies, reveal current trends in software engineering. Software engineering continues to have no central focus. Concepts like software development, process improvement, applications, parallelism, and user interfaces are persistent and, thus, help define the field, but they provide little guidance for researchers or developers of academic curricula. Of more interest and use are the specific themes illuminated by this study, which provide a clearer indication of the current interests of the field. Two prominent themes are the related issues of programming-in-the-large and best practices. Programming-in-the-large is the term often applied to large-scale and long-term software development, where project and people management, code reusability, performance measures, documentation, and software maintenance issues take on special importance. These issues began emerging in earlier periods, but seem to have risen to prominence during the current period. Another important discovery is the trend in software development toward using networking and the Internet. Many network- and Internet-related descriptors were added to the CCS in 1998. The prominent appearance and immediate use of these descriptors during this period indicate that this is a real trend and not just an aberration caused by their recent addition. The titles of the period reflect the prominent themes and trends. In addition to corroborating the keyword analysis, the title text confirms the relevance of the CCS and its most recent revision. By revealing current themes and trends in software engineering, this study provides some guidance to the developers of academic curricula and indicates directions for further research and study

An Evaluation Framework for Comparative Analysis of Generalized Stochastic Petri Net Simulation Techniques

Availability of a common, shared benchmark to provide repeatable, quantifiable, and comparable results is an added value for any scientific community. International consortia provide benchmarks in a wide range of domains, being normally used by industry, vendors, and researchers for evaluating their software products. In this regard, a benchmark of untimed Petri net models was developed to be used in a yearly software competition driven by the Petri net community. However, to the best of our knowledge there is not a similar benchmark to evaluate solution techniques for Petri nets with timing extensions. In this paper, we propose an evaluation framework for the comparative analysis of generalized stochastic Petri nets (GSPNs) simulation techniques. Although we focus on simulation techniques, our framework provides a baseline for a comparative analysis of different GSPN solvers (e.g., simulators, numerical solvers, or other techniques). The evaluation framework encompasses a set of 50 GSPN models including test cases and case studies from the literature, and a set of evaluation guidelines for the comparative analysis. In order to show the applicability of the proposed framework, we carry out a comparative analysis of steady-state simulators implemented in three academic software tools, namely, GreatSPN, PeabraiN, and TimeNET. The results allow us to validate the trustfulness of these academic software tools, as well as to point out potential problems and algorithmic optimization opportunities

Universal access in digital libraries

Digital libraries are concerned with the creation and management of information sources, the movement of information across global networks and the effective use of this information by a wide range of users. A digital library is a vast collection of obj ects that are of multimedia nature, e.g., text, video, images, and audio. Users wishing to access the digital library objects may possess varying capabilities, preferences, domain expertise, and may use different information appliances. With the phenomenal growth of the Internet, the number of different information appliances will, if not already, increase substantially in the near future. Facilitating access to complex multimedia digital library obj ects that suits to the users\u27 requirements is known as universal access. The main objective of this thesis is to present our research work in the area of Universal Access within digital library environment. In this thesis, we will first present the current and future trend in information appliances, followed by discussion on the scope of our work. We propose an object manifestation approach in which digital library objects automatically manifest themselves to cater to the users\u27 capabilities and characteristics. We provide a formal framework, based on Petri nets, to represent the various components of the digital library objects, their modality and fidelity and the playback synchronization relationships among them. We develop methodologies for object delivery without any deadtime under network delays. We have implemented a working system prototype to realize our approach

Exploratory study to explore the role of ICT in the process of knowledge management in an Indian business environment

In the 21st century and the emergence of a digital economy, knowledge and the knowledge base economy are rapidly growing. To effectively be able to understand the processes involved in the creating, managing and sharing of knowledge management in the business environment is critical to the success of an organization. This study builds on the previous research of the authors on the enablers of knowledge management by identifying the relationship between the enablers of knowledge management and the role played by information communication technologies (ICT) and ICT infrastructure in a business setting. This paper provides the findings of a survey collected from the four major Indian cities (Chennai, Coimbatore, Madurai and Villupuram) regarding their views and opinions about the enablers of knowledge management in business setting. A total of 80 organizations participated in the study with 100 participants in each city. The results show that ICT and ICT infrastructure can play a critical role in the creating, managing and sharing of knowledge in an Indian business environment