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web-based applications for building, managing and analysing kinetic models of biological systems

BRIEFINGS IN BIOINFORMATICS 2009年第1期10卷 65-74页

作者： Lee, Dong-Yup Saha, Rajib KhanYusufi, Faraaz Noor Park, Wonjun Karimi, Iftekhar A. Natl Univ Singapore Dept Chem & Biomol Engn Singapore 117576 Singapore

Mathematical modelling and computational analysis play an essential role in improving our capability to elucidate the functions and characteristics of complex biological systems such as metabolic, regulatory and cell signalling pathways. The modelling and concomitant simulation render it possible to predict the cellular behaviour of systems under various genetically and/or environmentally perturbed conditions. This motivates systems biologists/bioengineers/bioinformaticians to develop new tools and applications, allowing non-experts to easily conduct such modelling and analysis. However, among a multitude of systems biology tools developed to date, only a handful of projects have adopted a web-based approach to kinetic modelling. In this report, we evaluate the capabilities and characteristics of current web-based tools in systems biology and identify desirable features, limitations and bottlenecks for further improvements in terms of usability and functionality. A short discussion on software architecture issues involved in web-based applications and the approaches taken by existing tools is included for those interested in developing their own simulation applications.

关键词： systems biology web-based applications kinetic modelling dynamic simulation

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On the Use of XML in Medical Imaging web-based applications

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IRBM 2017年第1期38卷 3-12页

作者： Mata, C. Oliver, A. Lalande, A. Walker, P. Marti, J. Univ Girona Comp Vision & Robot Inst Campus MontiliviEd P IV Girona 17071 Spain Univ Bourgogne CNRS UMR Lab Elect Informat & Image Le21 F-6306 Dijon France

The rapid growth of digital technology in medical fields over recent years has increased the need for applications able to manage patient medical records, imaging data, and chart information. web-based applications are implemented with the purpose to link digital databases, storage and transmission protocols, management of large volumes of data and security concepts, allowing the possibility to read, analyze, and even diagnose remotely from the medical center where the information was acquired. The objective of this paper is to analyze the use of the Extensible Markup Language (XML) language in web-based applications that aid in diagnosis or treatment of patients, considering how this protocol allows indexing and exchanging the huge amount of information associated with each medical case. The purpose of this paper is to point out the main advantages and drawbacks of the XML technology in order to provide key ideas for future web-based applications. (C) 2016 AGBM. Published by Elsevier Masson SAS. All rights reserved.

关键词： XML language web-based applications Computational medicine Digital databases Security

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A study of security and performance issues in designing web-based applications

A study of security and performance issues in designing Web-...

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IEEE International Conference on e-Business Engineering

作者： Yang, Shin-Jer Chen, Jia-Shin Soochow Univ Dept Comp & Informat Sci Taipei Taiwan

ISBN: (纸本)9780769530031

Due to the evolution of Internet technology and application popularization, security and performance have become key issues for implementing web-based applications. Presently, most of the web-based applications design only consider security issue, but ignore performance problem. According to these two issues, we propose a new approach to integrate security and performance aspects for web-based applications, called ISPWAD, which combines SWAP and RBAC frameworks. The purposes of proposed ISPWAD are to fix the security holes and improve the processing performance during in designing web-based applications. In this paper we propose the ISPWAD framework and design its algorithm, and also illustrate how to implement the secure web-based applications with tuning performance. Then, we will utilize the ISPWAD to set up a practical EIP system and perform simulations for security solutions and performance improvements. Finally, our experimental results indicate that the proposed ISPWAD can solve related security holes, obtain better processing performance, and reduce development time and cost. In addition, the ISPWAD can attain a good balance-point between security and performance. In the future, the ISPWAD framework can provide a reference model for implementing e-Commerce, ERP II, or EIP systems.

关键词： ISPWAD web-based applications SWAP RBAC EIP

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web-based applications to Simulate Drinking Water Inorganic Chloramine Chemistry

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JOURNAL AMERICAN WATER WORKS ASSOCIATION 2018年第11期110卷 E43-E61页

作者： Wahman, David G. US EPA Off Res & Dev Cincinnati OH 45268 USA

Two web-based applications (WBAs) relevant to drinking water practice are presented to simulate (1) inorganic chloramine formation and stability, including an example inorganic chloramine demand reaction for organic matter, and (2) breakpoint curves. The model underlying both WBAs is a well-established inorganic chloramine formation-and-decay model. The WBAs were developed to be freely accessible over the Internet as web pages (https://***/Unified-Combo/ and https://***/Breakpoint-Curve/), providing drinking water practitioners (e.g., operators, regulators, engineers, professors, students) with learning tools to explore inorganic chloramine chemistry in an interactive manner without requiring proprietary software or user modeling expertise. The WBAs allow the user to specify two side-byside simulations, providing a direct comparison of impacts associated with changing simulation conditions (e.g., free chlorine, free ammonia, and total organic carbon concentrations;pH;total alkalinity;and temperature). Once completed, the user may download simulation data to use offline. The WBAs' implementation, validation, and example simulations are described.

关键词： breakpoint chloramines formation and decay web-based applications

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Automatic Physical Database Tuning Middleware for web-based applications

Automatic Physical Database Tuning Middleware for Web-Based ...

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15th International Conference on Advances in Databases and Information Systems

作者： Patvarczki, Jozsef Heffernan, Neil T. Worcester Polytech Inst Dept Comp Sci Worcester MA 01609 USA

ISBN: (纸本)9783642237362;9783642237379

In this paper we conceptualize the database layout problem as a. state space search problem. A state is a given assignment of tables to computer servers. We begin with a database and collect, for use as a workload input, a sequence of queries that were executed during normal usage of the database. The operators in the search are to fully replicate, horizontally partition, vertically partition, and de-normalize a table. We do a time intensive search over different table layouts, and at each iteration, physically create the configurations, and evaluate the total throughput of the system. We report our empirical results of two forms. First, we empirically validate as facts the heuristics that Database Administrators (DBAs) currently use as in doing this task manually: for tables that have a high ratio of update, delete, and insert to retrieval queries one should horizontally partition, but for a small ratio one should fully replicate a table. Such rules of thumb are reasonable, however we want to parameterize some common guidelines that DBAs can use. Our second empirical result is that we applied this search to our existing data test case and found a reliable increase in total system throughput. The search over layouts is very expensive, but we argue that our method is practical and useful, as entities trying to scale up their web-based applications would be perfectly happy to spend a few weeks of CPU time to increase their system throughput (and potentially reduce the investment in hardware). To make this search more practical, we want to learn reasonable rules to guide the search to eliminate many layout configurations that are not very likely to succeed. The second aspect of our project (not reported here) is to use the created configurations as input into a machine learning system, to create general rules about when to use the different layout operators.

关键词： Database tuning partitioning layout search web-based applications

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Effort Estimation of web-based applications using Machine Learning Techniques 5

Effort Estimation of Web-based Applications using Machine Le...

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International Conference on Advances in Computing, Communications and Informatics (ICACCI)

作者： Satapathy, Shashank Mouli Rath, Santanu Kumar Manipal Univ Jaipur Sch Comp & Informat Technol Jaipur 303007 Rajasthan India Natl Inst Technol Dept Comp Sci & Engn Rourkela 769008 Odisha India

ISBN: (纸本)9781509020287

Effort estimation techniques play a crucial role in planning of the development of web-based applications. web based software projects, considered in the present-day scenario are different from conventional object oriented projects, and hence the task of effort estimation is a complex one. It is observed that the literature do not provide a guidance to the analysts to use a particular model as being the most suitable one, for effort estimation of web-based applications. A number of models like IFPUG Function Point Model, NESMA, MARK-II, etc. are being considered for web effort estimation purpose. The efficiency of these models can be improved by employing certain intelligent techniques on them. Keeping in mind the end goal to enhance the efficiency of evaluating the effort required to develop web based application, certain machine learning techniques such as Stochastic Gradient Boosting and Support Vector Regression Kernels are considered in this study for effort estimation of web based applications using IFPUG Function Point approach. The ISBSG dataset, Release 12 has been considered in this study for obtaining the IFPUG Function Point data. The performance effort estimation models based on various machine learning techniques is assessed with the help of certain metrics, in order to examine them critically.

关键词： Stochastic Gradient Boosting Support Vector Regression Software Effort Estimation web-based applications

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Security methods for web-based applications on embedded system

Security methods for web-based applications on embedded syst...

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IEEE Region 10 Conference on Analog and Digital Techniques in Electrical Engineering

作者： Maharak, C Sowanwanichakul, B Chulalongkorn Univ Dept Comp Engn Bangkok 10330 Thailand

ISBN: (纸本)0780385608

Currently, embedded system is becoming a main solution to most specific tasks because of its high stability, economic power consumption, portability, and numerous useful. As a result, embedded system was used as. a tiny computer to process many applications. Nowadays, many new applications are developed using web-based technologies, which users can access from anywhere through the Internet. However data communicated between users and web-based applications may be revealed by anyone in the Internet, so secured communication is needed for web-based applications. SSL standard was developed to handle this situation, nevertheless SSL is not appropriated with embedded system due to limited resources of the embedded system. This paper proposes the design and implementation of security methods that suitable with web-based application on embedded system. By applied these methods with web-based applications, the embedded system is be able to communicate with users more confidently. These security methods use the advantage of digest authentication based on HTTP/1.1 and conceals data by using symmetric cryptography. The results indicate that using these methods expend more resources and time consuming. However, security is also necessary with sensitive data.

关键词： embedded systems telecommunication security cryptography authorisation Internet hypermedia transport protocols data communication security methods web-based applications embedded system economic power consumption authentication HTTP symmetric cryptography

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Experience using formal methods for capturing requirements of web-based applications 1

Experience using formal methods for capturing requirements o...

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1st IEEE International Conference on Cognitive Informatics (ICCI 2002)

作者： Redouane, A High-Tech Consultant Canada

ISBN: (纸本)0769517242

The current practice in capturing requirements of web-based applications is accomplished by an ad-hoc and informal manner. In this paper we investigate the use of formal methods to formalize the requirements of a web-based application. We have used a simple yet powerful Definitional Specification Language (DSL) for this task. DSL is based on first order predicate calculus, and has three main concepts: a resource, a transitional, and a state type. These concepts help in specifying dynamic behaviors and the resultant specification is clear with no cumbersome manipulation of time variables. A brief description of DSL is given before we provide the informal requirements of our web-based application. We formalize the requirements using DSL and describe how this is done. We conclude that the benefits gained with such formalization have made the development clear and minimized the cycle of fix-and-test.

关键词： web-based applications formal methods predicate calculus dynamic behavior modularity and parameterization

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web Engineering Process Matrix for Sustainable Deployment of web-based applications

Web Engineering Process Matrix for Sustainable Deployment of...

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7th International Conference on Cooperative Design, Visualization, and Engineering

作者： Tumin, Sharil Encheva, Sylvia Univ Bergen IT Dept POB 7800 N-5020 Bergen Norway Stord Haugesund Univ Coll N-5528 Haugesund Norway

ISBN: (纸本)9783642160653

Sustainable deployment needs a clear cooperative model of actors during different phases of planning, design, implementation and maintenance for a web-based application project. Solving web engineering problems involves multifaceted working stages, multi-domains expertise and multidisciplinary workers. The key to success is effective communication among actors. Actors can be both active and passive, either humans or non-human entities. Cooperative models can ensure effective flow of information between actors at all stages.

关键词： cooperative model process matrix sustainable deployment web-based applications effective communication

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Fault-Tolerant Bi-Directional Communications in web-based applications 20

Fault-Tolerant Bi-Directional Communications in Web-Based Ap...

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20th IEEE International Conference on Parallel and Distributed Systems (ICPADS)

作者： Ivaki, Naghmeh Araujo, Filipe Univ Coimbra Dept Informat Engn CISUC P-3000 Coimbra Portugal

ISBN: (纸本)9781479976157

The Hypertext Transfer Protocol (HTTP) and the Transmission Control Protocol (TCP) are the most popular protocols used in the development of web-based applications. Despite their popularity, the use of these protocols brings two limitations to applications and systems that require reliable interactive real-time communications: 1) HTTP forces applications to work in a request-response paradigm, even if a reply is not necessary, not allowing the server to send anything to a client without the client explicitly requesting it;2) TCP provides no recovery options for network outages, thus forcing developers to write their own error-prone, complex, and ad hoc solutions. In this paper we introduce a solution that offers both bi-directional and reliable communication to web-based applications, even in presence of connection failures. To make this possible, we combine the idea behind webSockets and a Session-based Fault-Tolerant design pattern.

关键词： Fault-Tolerance Bi-Directional Communication Connection Failure webSocket web-based applications

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