Journal articles on the topic 'Java Server Pages (JSP)'

The purpose of the study is to demonstrate the diversity of solutions on the issue of connecting to a database, including a description of the developed connection controller class, as well as various ways to create connection pools on a web server and application servers. The article discusses the practical issues of using JDBC technology when building a Java web application. In the examples, the presentation and business layer of the application are developed using JSP-pages and servlets, the database operates on the MySQL platform. The described methods for creating and configuring a connection pool are shown on the example of the ApacheTomcat web server and the GlassFish application server. The question of optimizing database connections in Java applications remains open, despite the diversity of solutions. The study examines and proposes methods for constructing classes of connectors, various methods for creating pool connections, and describes the results of solving problems arising from the implementation of the described techniques. A detailed classification of ways to connect to the database is given.

Com o presente trabalho visou-se desenvolver um sistema de rastreabilidade aplicado à cadeia de produção do vinho. Foram utilizados a tecnologia de desenvolvimento JSP (Java Server Pages); o banco de dados MySQL; bem como o Tomcat, para servidor de JSP. O sistema para rastreabilidade do vinho desenvolvido é útil tanto para os produtores quanto para os consumidores por ser um indicador de segurança alimentar, visto que com ele é possível se rastrear a história da garrafa de um vinho desde o plantio da uva até o momento de seu consumo.

A multi-user remote transmission of CNC machining management system was developed based on B/S structure, which combines network management model with CNC machining technologies and replaces the traditional file-copy format. This system not only provides convenience for users to use CNC equipment but also greatly improves efficiency and safety. In this project, a JSP (Java Server Pages) dynamic web site was developed in the MyEclipse environment, which can carry out many functions, including management of users’ information and documents taking advantage of database technology, transmitting and operating NC code and source files which CAD/CAM software generated. This is an attempt of centralized CAD/CAM network manufacturing.

Project management is an important task in business although project is not just confined to business. Due to the uncertainty of the various variables involved in a project, over several past decades research is going on in the search for an efficient project management model. Although numerous crisp models are easily implementable, the potential of fuzzy models are huge. In the case of software development, the variables involved are highly dynamic. In this paper, we propose a ranking based fuzzy model that can prioritize various activities. We use a popular crisp model to test the effectiveness of the fuzzy model proposed. Simulation is done through Java Server Pages (JSP). There is considerable computational and managerial advantage in implementing the fuzzy model.

In order to promote the development of intelligent teaching system, artificial intelligence technology is combined with computer assisted instruction (CAI) system to produce intelligent CAI (ICAI), and the design of ICAI is studied in order to facilitate the application and implementation of intelligent teaching system. First, there is an introduction of the basic concepts, related theories, and implementation principles of ICAI. Then, the requirements of ICAI are analyzed in detail on the basis of studying the relevant technologies required by ICAI, including the functional and non-functional requirements. The subsystem is set based on the different needs of the target users (administrator, teacher, and student users). Finally, the general and functional structure of ICAI are designed, and there are tests for the system functions. The results show that the system takes Java Server Pages (JSP) as the development language, Struts2 as the technical framework, and SQL Server 2008 as the back-end database, which realizes a teaching platform mainly for teachers, students, and administrators. After testing, the overall operation of the system is good, and the functional test results of the login module, homework release, and learning resource upload meet the software design requirements. The response time of the system prolongs, the number of users who can’t successfully log in grows, and the utilization of server central procession unit (CPU) and memory utilization both increase, which are caused by the increasing number of concurrent users. The results indicate that the combination of CAI and artificial intelligence (AI) technology can meet students’ online teaching demands, break the time-space limitation of traditional teaching, and provide important reference value for the reform of teaching mode and the improvement of teaching quality

With the development of computer network technology, Java has a fairly extensive use of die circumference. Especially in recent years, the development of the smart phone system is also stimulated the use of the Java language. In this paper, Java server is mainly divided into two categories JSP server and Java EE servers. Java EE function which has more features than perfect JSP servers. Application server is a chief platform of Web-based application. J2EE is a standard of enterprise-scale application server. In this paper J2EE is analyzed from the point of view of software architecture and Java-based application development. Some defects of J2EE are pointed out, such as J2EE being unable to support version management and it having diverse concepts and notions due to its multi-tier architecture. Furthermore, a light weight application server—J Web Frame is developed, which overcomes some problems of J2EE.

This paper aims to set up the Web Server which can handle Flash streaming client, static HTTP requests, dynamic JSP requests and interact with the Database Server. The streaming media Server Red5 responses RTMP requests, Application Server Tomcat responses dynamic JSP requests, Web Server Apache responses static HTTP requests, Framework Spring achieves the dynamic equipment of each service object. The Object-Relational Mapping model Hibernate and the Java Database Connectivity JDBC do the persistence operation and realize data persistence layer. The Web Server can realize the Web Server of Web Video Conference based on B/W/D architecture.

The basic technology for creating a graphical user interface (GUI) for Java Enterprise Edition web applications is JavaServer Pages (JSP). However, the capabilities offered by JSP are not sufficient, which has resulted in many extensions that assist the programmer in quickly creating modern GUI. The paper presents the results of comparison JavaServer Faces, Rich Faces and Prime Faces libraries.

Web-based Code Management System (WCMS) is an essential tool for realizing information exchange in distant collaborative product design and manufacturing among global-based enterprises. A framework for WCMS is built up on a three-tier client/server system and the WCMS is developed utilizing JAVA and J2EE technologies. The developed WCMS mainly uses servlets and JSP to handle user inputs and manage and retrieve code data from the database through the JDBC driver, with the server components stored on a middleware program called Tomcat. The WCMS developed in this work has been successfully implemented in an enterprise.

This work proposes a Web-Based laboratory where researchers share the facilities of a simulation environment for parallel algorithms which solves scheduling problems known as Job Shop Problem (JSP). The environment supports multi-language platforms and uses a low cost, high performance Graphics Processing Unit (GPU) connected to a Java application server to help design more efficient solutions for JSP. Within a single web environment one can analyze and compare different methods and meta-heuristics. Each newly developed method is stored in an environment library and made available to all other users of the environment. This amassment of openly accessible solution methods will allow for the rapid convergence towards optimal solutions for JSP. The algorithm uses the parallel architecture of the system to handle threads. Each thread represents a job operation and the number of threads scales with the problem’s size. The threads exchange information in order to find the best solution. This cooperation decreases response times by one or two orders of magnitude.

Publication refers to SQL Injection attacks whose are one of the most dangerous in a cyberspace. Based on a literature studies, classification of the SQL Injection attacks was prepared. The purpose of the work was to analyse of protections effectiveness against SQL Injection attacks. Research method has been based on author application, which was implemented in JSP (JavaServer Pages) technology using MySQL database server.

The network management system based on WEB has been becoming the current hot spots. The paper discusses the advantages and significance of WBM fully to discuss the possibility of a network management system based on JAVA implementation. Based on the SNMP protocol is proposed based on ARP protocol and network topology search found based on ICMP protocol and topology reconstruction. SNMP access to treatment and MIB information structure and based on the MIB information acquisition. Application server search and real time function and the realization of the corresponding technology such as network service monitoring method. And on the Linux platform, using TOMCAT as a JSP interpreter, information storage, publishing technology and by using XML and JAVA platform compatibility technology is verified to above ultimately proved: the network management system based on JAVA and XML can completely meet the requirements of network management has good feasibility and practical application value.

The flipped classroom (FC) is a novel teaching mode combining traditional class-room and computer network technology. This paper attempts to design a FC-based education system for college English teaching, which is critical to the quali-ty of English teaching in colleges. In our research, a college English education system is established based on SQL server and FC. The architecture and func-tional modules of the system were discussed in details. Specifically, the system architecture was created based on the browser/server (B/S) structure, the data management was realized by SQL server 2008, and the system functions were designed and achieved by JavaServer Pages (JSP). The proposed system was tested in an actual application. The results confirm that the system can meet the teaching demand, arouse the students’ interest in learning and improve the effect of English teaching.

The Internet and the World Wide Web are used for a wide variety of transportation applications. Most of these applications use static HTML documents. However, outside of transportation, considerably more attention is being given to dynamic content and XML. A way in which these technologies can be used to provide transit timetable information on the web is explored. Specifically, the transit timetable system, an online interactive transit timetable information exchange and administration system that uses Java server pages and the transit timetable markup language, is described.

Linear programming algorithms have been widely used in Decision Support Systems. These systems have incorporated linear programming algorithms for the solution of the given problems. Yet, the special structure of each linear problem may take advantage of different linear programming algorithms or different techniques used in these algorithms. This paper proposes a web-based DSS that assists decision makers in the solution of linear programming problems with a variety of linear programming algorithms and techniques. Two linear programming algorithms have been included in the DSS: (i) revised simplex algorithm and (ii) exterior primal simplex algorithm. Furthermore, ten scaling techniques, five basis update methods and eight pivoting rules have been incorporated in the DSS. All linear programming algorithms and methods have been implemented using MATLAB and converted to Java classes using MATLAB Builder JA, while the web interface of the DSS has been designed using Java Server Pages.

Real-time Seat Allocation System is a web application that assists employees and employers in handling modern-day seating issues at work. Currently, seats are assigned to employees manually, which is a time-consuming process. This might cause issues if seats were not assigned or if none were available for some employees. Furthermore, during pandemics, social distance rules must be followed, making it difficult to manage the workforce. The proportion of individuals allowed in the workplace must adhere properly. As the firm grows, so does the number of employees, which necessitates the expansion of infrastructure, which costs money and time. These issues can be addressed to some extent by a shared office concept, in which employees have access to a desk and can work as needed. This article presents a responsive web application through which company employees can registerusingtheircompanyIDandreserveaseatifoneisavailableonaspecified day and time. Admins can add or remove offices, floors, and seats with certain permissions. To implement the business logic, the application uses Java, Spring MVC web framework with Tomcat server, renders the views using Java Server Pages, and uses front-end technologies like HTML, CSS, and JavaScript for the front-end design of the User Interface. The web application built promotes the concept of using a shared workspace to maximize resource use. It also aids in increasing employee productivity by providing them with workplace seating and schedule flexibility.

The design of this application describes how to digitize the academic administration services of the Android-based Electronics Engineering department. The purpose of designing this application is to improve aspects of departmental administrative services and provide satisfaction to students in higher education, especially the Department of Electronics Engineering, Faculty of Engineering, Padang State University. Android-designed application that uses the Java programming language and developed using PHP and MySQL as database design and data management. The application is also designed based on client-server. The design stages in this application, namely system requirements analysis, system design, code making and testing. The method used in the design is the waterfall method which consists of needs analysis, design, implementation and testing. The interface design consists of the home page, login page, service input page, update and delete service pages and service pages received. Keywords: Administrative Services Department, Android

ABSTRACTTourism is one of the activities carried out by humans who have a purpose as entertainment. One of the objectives of designing this information system is to make tourist objects that have not been managed by the government to be managed and developed which makes it a source of income for the city of Padang. Padang City, the capital of West Sumatra Province, is one of the best tourism cities such as nature tourism, marine tourism and historical tourism. Natural attractions such as panoramas, waterfalls and natural baths, marine tourism such as beaches, while historical tourism such as monuments, and museums. However, due to lack of information, only a number of Padang City attractions are known by tourists. This system is built for two views, namely views for Web-based server pages, and views for android-based client pages using the android web view while system modeling uses UML (Unified Modeling Language). Then for the programming languages used are PHP, java and MySQL as Database..Keywords: Tourism, Tour Guide, UML, PHP, MySQL, Database, Tourism Objects, Padang City.

The article considers the features of the automated system of tenant service (ASOO) project building. It has been noted that the Vaadin is one of the platforms for creating web applications that provide convenient tools to support the interaction of software and hardware of the system and user interface. Among the main advantages of the framework, firstly, is the ability to create the user interface using only Java programming language, without JavaScript, HTML and CSS using. Vaadin programs run on the server and run automatically as well as securely. Building on a well-prepared Java ecosystem, the framework works with any development environment, tools and libraries. Secondly, it is a wide range of options for creating a user interface with minimal writing of program code: Form Inputs, Visualization & Interaction, Layouts, Pro Components. In addition, the framework API provides the ability to automatically and securely organize two-way communication between client and server, use Java Bean Validation, its own validators, and perform data conversions during data validation. The Apache Maven framework, which builds a project based on POM files, has been used as a means of automating work with software projects. A set of Spring Boot utilities has been used to automate the setup process, as well as speed up the process of creating and deploying the application. The use of Spring Boot is due to the following options: the ability to create a standalone application based on Spring; simplification of dependency management in the project through the use of starter-packages (for example, spring-boot-starter-data-jpa) and automatic configuration of the application based on the selected starter-package; built-in support for servlet container; no need to generate code and configure XML. MySQL relational database management system could be used as a database, as this open source technology has a wide range of functionality that can be used when developing dynamic web pages.

Abstract:The performance of an agency is very dependent on the data and quality of information obtained, not least in the police agency. The Criminal Investigation Unit (SatResKrim) is one of the most important units in the police force. One form of handling SatResKrim is to manage crime data. Crime data is managed because it contains information to support the investigation process. The information used in the investigation process is included in the crime data, so it is necessary to search for documents of criminal data relevant to the investigation process. Currently, data on SatResKrim unit at East Sector Police Dept. of Yogyakarta Special Region still use Microsoft Excel application, so the process of searching data is still based on text not based on knowledge, consequently if the search keyword is not in accordance with the text contained in the data, then the data is not will appear, if the data does not appear it will slightly hamper the investigation process. From these problems raised the idea to represent police crime data into the form of knowledge as an effort in providing references to the police agencies against the form of development of data processing crime-based semantic ontology. Knowledge of crime data is limited to criminal data by category of theft. Knowledge related to theft criminal data is then stored or represented in an ontology-based semantic model. In representing knowledge using language Ontology Web Language (OWL) and SPARQL as its query. Software used to build systems in this study include protégé 3.5, NetBeans and Jena API as its library. The programming language used is Java Server Page (JSP). Based on the results of research that has been done, by representing crime data into the form of semantic ontology-based knowledge and tested into the form of search-based applications, can generate semantic-based search or search that is able to understand the meaning. It is also supported by test results using recall and precision methods, each of which results in a value of more than 90%. Abstrak:Kinerja suatu instansi sangat bergantung pada data dan mutu informasi yang diperoleh, tak terkecuali pada instansi kepolisian. Satuan Reserse Kriminal (SatResKrim) merupakan salah satu unit terpenting dalam kepolisian. Salah satu bentuk penanganan SatResKrim adalah dengan mengelola data kriminalitas. Data kriminalitas dikelola karena mengandung informasi guna menunjang proses investigasi. Informasi yang digunakan dalam proses investigasi diantaranya terdapat pada data kriminalitas, sehingga diperlukan adanya pencarian terhadap dokumen data kriminalitas yang relevan dengan proses investigasi. Saat ini data yang berada pada unit SatResKrim pada Kepolisian Sektor Depok Timur Daerah Istimewa Yogyakarta masih menggunakan aplikasi Microsoft Excel, sehingga proses pencarian data masih berdasarkan teks bukan berdasarkan pengetahuan, akibatnya apabila kata kunci pencarian tidak sesuai dengan teks yang terdapat pada data, maka data tidak akan muncul, jika data tidak muncul maka akan sedikit menghambat proses investigasi. Dari permasalahan tersebut memunculkan gagasan untuk merepresentasikan data kriminalitas kepolisian kedalam bentuk pengetahuan sebagai upaya dalam memberikan referensi kepada instansi kepolisian terhadap bentuk pengembangan pengolahan data kriminalitas berbasis semantik ontologi. Pengetahuan-pengetahuan mengenai data kriminalitas dibatasi pada data kriminalitas dengan kategori pencurian. Pengetahuan-pengetahuan terkait data kriminalitas pencurian kemudian disimpan atau di representasikan dalam model semantik berbasis ontologi. Dalam merepresentasikan pengetahuan menggunakan bahasa Ontology Web Language (OWL) serta SPARQL sebagai query-nya. Software yang digunakan untuk membangun sistem dalam penelitian ini meliputi protégé 3.5 ,NetBeans serta Jena API sebagai library-nya. Bahasa pemrograman yang digunakan adalah Java Server Page (JSP). Berdasarkan hasil penelitian yang telah dilakukan, dengan merepresentasikan data kriminalitas kedalam bentuk pengetahuan berbasis semantik ontologi dan di ujikan ke dalam bentuk aplikasi berbasis pencarian, dapat menghasilkan pencarian berbasis semantik atau pencarian yang mampu memahami makna. Hal tersebut juga didukung oleh hasil uji dengan menggunakan metode recall dan precision yang masing-masing hasilnya menunjukkan nilai lebih dari 90%.

This paper describes the design and development of a component-based object oriented Expert System's Integrated Development Environment (ExSIDE). It is integrated with (i) a user-friendly manual and automated knowledge acquisition and management tool (ExSIDE_KAMT);(ii) an independent and customizable runtime module (ExSIDE_RTM); (iii) an object-oriented in-process Component Object Model (COM)-based inference engine (ExSIDE_IE); (iv) an object-oriented out-of-process COM-based inference engine (ExSIDE_IESvr); (v) and a PHP based inference engine (ExSIDE_PHP). ExSIDE_RTM can function independently as an Expert System Shell (ESS) and helps user to develop Expert Systems rapidly. ExSIDE_IE and ExSIDE_IES can be integrated with COM-supporting general purpose and scientific application development tools such as variants of C/C++/C#, BASIC (Visual BASIC®, REALbasic®), Java, MATLAB®, LabVIEW®, and Mathematica® to develop more advanced Expert Systems. Finally, ExSIDE_IE and ExSIDE_PHP can be used with Active Server Pages (ASP) and PHP technologies to generate web based Expert Systems. The unique framework of the ExSIDE enables rapid development of Expert Systems' on PC and web for technical and non-technical users. The overall system was developed successfully, and its usability was demonstrated via five unique Expert Systems case studies discussed in this paper.

The main objective of Medreonet is to share and exchange data, expertise, experiences and information on bluetongue (BT), African horse sickness (AHS) and epizootic haemorrhagic disease (EHD). In this context the web-based database and geographical information system (GIS) application is the most suitable tool to provide a friendly environment that is easy to use by the different actors involved in the project. The web-based database and GIS application has been developed using ESRI software (release 9.0) (ArcIMS, ArcGIS desktop, ArcSDE), Java and Active Server Pages (ASP). Users can access the public web-GIS through a generic Internet browser and the information required (maps and data) are published by ArcIMS using web server technology. ArcSDE and an Oracle relational database management system (release 8i) (RDBMS) are used to store and manage spatial and alphanumerical data. The authorized users can input new information and data on their geographical area of competence directly online, using ASP and a web interface. The accuracy of the data entered into the information system (e.g. missing values, duplicates, incorrect data format, etc.) is guaranteed by automatic check procedures that operate dur­ing the updating of the centralized database. The database was designed to store all the epidemiological data deemed relevant by the experts and all the scientific results, when available, pro­duced during the project. In particular, the data collected cover three main sets of information which are displayed and spread through an interactive, dynamic mapping system: – outbreak distribution, i.e. the geographical distribution of the disease by year and serotype at the regional level in the European Union (EU) and Mediterranean countries for BT, AHS, and EHD, respectively; – serological surveillance results, i.e. geographical distribution of the true and apparent prevalence of infection based on the analyses of BT serological surveillance data; – entomological distribution, i.e. geographical distribution of nine vector species by year and month, number of catch sites, number of catches, vector and maximum number of midges at the regional level in the EU and Mediterranean countries. Medreonet database and GIS application fulfill all the require­ments stipulated in the project; moreover the system is fully scalable and may adapt to future demands.

Monitoring siswa merupakan bentuk proses pengawasan sekolah terhadap kegiatan belajar mengajar siswa, salah satunya di tingkat Sekolah Menengah Atas Negeri atau SMAN Mojoagung, Jombang, Jawa Timur, Indonesia. Monitoring siswa tersebut meliputi jurnal kelas, presensi siswa dan capaian kompetensi dasar siswa. Proses pengolahan monitoring yang berjalan selama ini memiliki beberapa kendala, diantaranya 1) Belum tersedianya rekapitulasi absensi per mata pelajaran, sehingga guru mata pelajaran kesulitan memonitor kehadiran siswa ketika mata pelajaran sedang berlangsung; dan 2) Tidak terdokumentasi dengan baik capaian kompetensi dasar yang telah diajarkan pada tiap mata pelajaran, yang akhirnya mempengaruhi kualitas proses belajar mengajar. Berdasarkan kendala yang dialami, perlu dibangun sebuah sistem informasi yang mampu mengakomodasi pengelolaan proses aktivitas belajar mengajar meliputi pelaporan jurnal kelas, rekapitulasi absesi kehadiran siswa per mata pelajaran, dan laporan capaian kompetensi dasar. Pengembangan sistem informasi pada penelitian ini menggunakan Waterfall. Sistem monitoring ini menggunakan tiga aspek pengujian, diantaranya efficiency, reliability, dan usability berdasarkan Web Quality Evaluation Method (WebQEM). Hasilnya menunjukkan rata-rata loadtime 2,78 detik dan rata-rata pagesize 190,52 KB pada kecepatan internet 20,98 Mbps, serta persentase session, pages dan hits dengan nilai 99% dengan 25 data pada pengujian efficiency. Pengujian reliability menunjukkan performa yang baik karena mampu mengakomodasi 600 user yang menangani 1.085 request dan throughput 227,098/menit dengan 0% error dari total 5.322 data yang tersimpan. Sedangkan pengujian usability yang melibatkan 322 responden memiliki persentase 76,72% yang masuk kategori baik. Dari hasil pengujian tersebut aplikasi mampu menangani permintaan data dalam jumlah besar dan memastikan kehandalan server mengakomodasi akses seluruh siswa SMAN Mojoagung. Student monitoring is the form of school's supervision process on the teaching and learning activities at SMAN Mojoagung, Jombang, East Java, Indonesia, which includes the class journals, student's attendance, and students' achievement of basic competencies. However, the recent monitoring process has had some obstacles, including 1) The absence of recapitulation of students' attendance in each lesson which makes it difficult for the teacher to monitor the students' attendance in the teaching and learning process; and 2) poor documentation of the students' achievements of basic competencies in each lesson, which ultimately affects the quality of the teaching and learning process. Based on the obstacles, it is crucial to build a web-based information system which is capable to accommodate the supervision process of the teaching and learning activity involving class journal report, recapitulation of the students' attendance in each lesson and the report of basic-competence achievement. The approach of this current research in this information system development used Waterfall method. The approach of this current research in this information system development used Waterfall method. The developed monitoring system used three aspects of testing, including efficiency, reliability, and usability based on the Web Quality Evaluation Method (WebQEM). The results showed an average loadtime of 2.78 seconds and an average pagesize of 190.52 KB at 20.98 Mbps internet speed as well as a percentage of sessions, pages, and hits of 99% in the efficiency testing on 25 data. The reliability testing showed proper performance since it could accommodate 600 users which handle 1,085 Request and 227.098/minute Throughput with 0% Error from the total of 5,322 saved data. Meanwhile, the usability testing involving 322 respondents showed a percentage of 76.72% and were categorized as good. Based the test results, the application was able to handle a large amount of data demand and ensured the reliability of the server in accommodating the access to all students of SMAN Mojoagung.

To date, discrete event stochastic simulations of large scale biological reaction systems are extremely compute-intensive and time-consuming. Besides, it has been widely accepted that spatial factor plays a critical role in the dynamics of most biological reaction systems. The NSM (the Next Sub-Volume Method), a spatial variation of the Gillespie’s stochastic simulation algorithm (SSA), has been proposed for spatially stochastic simulation of those systems. While being able to explore high degree of parallelism in systems, NSM is inherently sequential, which still suffers from the problem of low simulation speed. Fine-grained parallel execution is an elegant way to speed up sequential simulations. Thus, based on the discrete event simulation framework JAMES II, we design and implement a PDES (Parallel Discrete Event Simulation) TW (time warp) simulator to enable the fine-grained parallel execution of spatial stochastic simulations of biological reaction systems using the ANSM (the Abstract NSM), a parallel variation of the NSM. The simulation results of classical Lotka-Volterra biological reaction system show that our time warp simulator obtains remarkable parallel speed-up against sequential execution of the NSM.I.IntroductionThe goal of Systems biology is to obtain system-level investigations of the structure and behavior of biological reaction systems by integrating biology with system theory, mathematics and computer science [1][3], since the isolated knowledge of parts can not explain the dynamics of a whole system. As the complement of “wet-lab” experiments, stochastic simulation, being called the “dry-computational” experiment, plays a more and more important role in computing systems biology [2]. Among many methods explored in systems biology, discrete event stochastic simulation is of greatly importance [4][5][6], since a great number of researches have present that stochasticity or “noise” have a crucial effect on the dynamics of small population biological reaction systems [4][7]. Furthermore, recent research shows that the stochasticity is not only important in biological reaction systems with small population but also in some moderate/large population systems [7].To date, Gillespie’s SSA [8] is widely considered to be the most accurate way to capture the dynamics of biological reaction systems instead of traditional mathematical method [5][9]. However, SSA-based stochastic simulation is confronted with two main challenges: Firstly, this type of simulation is extremely time-consuming, since when the types of species and the number of reactions in the biological system are large, SSA requires a huge amount of steps to sample these reactions; Secondly, the assumption that the systems are spatially homogeneous or well-stirred is hardly met in most real biological systems and spatial factors play a key role in the behaviors of most real biological systems [19][20][21][22][23][24]. The next sub-volume method (NSM) [18], presents us an elegant way to access the special problem via domain partition. To our disappointment, sequential stochastic simulation with the NSM is still very time-consuming, and additionally introduced diffusion among neighbor sub-volumes makes things worse. Whereas, the NSM explores a very high degree of parallelism among sub-volumes, and parallelization has been widely accepted as the most meaningful way to tackle the performance bottleneck of sequential simulations [26][27]. Thus, adapting parallel discrete event simulation (PDES) techniques to discrete event stochastic simulation would be particularly promising. Although there are a few attempts have been conducted [29][30][31], research in this filed is still in its infancy and many issues are in need of further discussion. The next section of the paper presents the background and related work in this domain. In section III, we give the details of design and implementation of model interfaces of LP paradigm and the time warp simulator based on the discrete event simulation framework JAMES II; the benchmark model and experiment results are shown in Section IV; in the last section, we conclude the paper with some future work.II. Background and Related WorkA. Parallel Discrete Event Simulation (PDES)The notion Logical Process (LP) is introduced to PDES as the abstract of the physical process [26], where a system consisting of many physical processes is usually modeled by a set of LP. LP is regarded as the smallest unit that can be executed in PDES and each LP holds a sub-partition of the whole system’s state variables as its private ones. When a LP processes an event, it can only modify the state variables of its own. If one LP needs to modify one of its neighbors’ state variables, it has to schedule an event to the target neighbor. That is to say event message exchanging is the only way that LPs interact with each other. Because of the data dependences or interactions among LPs, synchronization protocols have to be introduced to PDES to guarantee the so-called local causality constraint (LCC) [26]. By now, there are a larger number of synchronization algorithms have been proposed, e.g. the null-message [26], the time warp (TW) [32], breath time warp (BTW) [33] and etc. According to whether can events of LPs be processed optimistically, they are generally divided into two types: conservative algorithms and optimistic algorithms. However, Dematté and Mazza have theoretically pointed out the disadvantages of pure conservative parallel simulation for biochemical reaction systems [31]. B. NSM and ANSM The NSM is a spatial variation of Gillespie’ SSA, which integrates the direct method (DM) [8] with the next reaction method (NRM) [25]. The NSM presents us a pretty good way to tackle the aspect of space in biological systems by partitioning a spatially inhomogeneous system into many much more smaller “homogeneous” ones, which can be simulated by SSA separately. However, the NSM is inherently combined with the sequential semantics, and all sub-volumes share one common data structure for events or messages. Thus, directly parallelization of the NSM may be confronted with the so-called boundary problem and high costs of synchronously accessing the common data structure [29]. In order to obtain higher efficiency of parallel simulation, parallelization of NSM has to firstly free the NSM from the sequential semantics and secondly partition the shared data structure into many “parallel” ones. One of these is the abstract next sub-volume method (ANSM) [30]. In the ANSM, each sub-volume is modeled by a logical process (LP) based on the LP paradigm of PDES, where each LP held its own event queue and state variables (see Fig. 1). In addition, the so-called retraction mechanism was introduced in the ANSM too (see algorithm 1). Besides, based on the ANSM, Wang etc. [30] have experimentally tested the performance of several PDES algorithms in the platform called YH-SUPE [27]. However, their platform is designed for general simulation applications, thus it would sacrifice some performance for being not able to take into account the characteristics of biological reaction systems. Using the similar ideas of the ANSM, Dematté and Mazza have designed and realized an optimistic simulator. However, they processed events in time-stepped manner, which would lose a specific degree of precisions compared with the discrete event manner, and it is very hard to transfer a time-stepped simulation to a discrete event one. In addition, Jeschke etc.[29] have designed and implemented a dynamic time-window simulator to execution the NSM in parallel on the grid computing environment, however, they paid main attention on the analysis of communication costs and determining a better size of the time-window.Fig. 1: the variations from SSA to NSM and from NSM to ANSMC. JAMES II JAMES II is an open source discrete event simulation experiment framework developed by the University of Rostock in Germany. It focuses on high flexibility and scalability [11][13]. Based on the plug-in scheme [12], each function of JAMES II is defined as a specific plug-in type, and all plug-in types and plug-ins are declared in XML-files [13]. Combined with the factory method pattern JAMES II innovatively split up the model and simulator, which makes JAMES II is very flexible to add and reuse both of models and simulators. In addition, JAMES II supports various types of modelling formalisms, e.g. cellular automata, discrete event system specification (DEVS), SpacePi, StochasticPi and etc.[14]. Besides, a well-defined simulator selection mechanism is designed and developed in JAMES II, which can not only automatically choose the proper simulators according to the modeling formalism but also pick out a specific simulator from a serious of simulators supporting the same modeling formalism according to the user settings [15].III. The Model Interface and SimulatorAs we have mentioned in section II (part C), model and simulator are split up into two separate parts. Thus, in this section, we introduce the designation and implementation of model interface of LP paradigm and more importantly the time warp simulator.A. The Mod Interface of LP ParadigmJAMES II provides abstract model interfaces for different modeling formalism, based on which Wang etc. have designed and implemented model interface of LP paradigm[16]. However, this interface is not scalable well for parallel and distributed simulation of larger scale systems. In our implementation, we accommodate the interface to the situation of parallel and distributed situations. Firstly, the neighbor LP’s reference is replaced by its name in LP’s neighbor queue, because it is improper even dangerous that a local LP hold the references of other LPs in remote memory space. In addition, (pseudo-)random number plays a crucial role to obtain valid and meaningful results in stochastic simulations. However, it is still a very challenge work to find a good random number generator (RNG) [34]. Thus, in order to focus on our problems, we introduce one of the uniform RNGs of JAMES II to this model interface, where each LP holds a private RNG so that random number streams of different LPs can be independent stochastically. B. The Time Warp SimulatorBased on the simulator interface provided by JAMES II, we design and implement the time warp simulator, which contains the (master-)simulator, (LP-)simulator. The simulator works strictly as master/worker(s) paradigm for fine-grained parallel and distributed stochastic simulations. Communication costs are crucial to the performance of a fine-grained parallel and distributed simulation. Based on the Java remote method invocation (RMI) mechanism, P2P (peer-to-peer) communication is implemented among all (master-and LP-)simulators, where a simulator holds all the proxies of targeted ones that work on remote workers. One of the advantages of this communication approach is that PDES codes can be transferred to various hardwire environment, such as Clusters, Grids and distributed computing environment, with only a little modification; The other is that RMI mechanism is easy to realized and independent to any other non-Java libraries. Since the straggler event problem, states have to be saved to rollback events that are pre-processed optimistically. Each time being modified, the state is cloned to a queue by Java clone mechanism. Problem of this copy state saving approach is that it would cause loads of memory space. However, the problem can be made up by a condign GVT calculating mechanism. GVT reduction scheme also has a significant impact on the performance of parallel simulators, since it marks the highest time boundary of events that can be committed so that memories of fossils (processed events and states) less than GVT can be reallocated. GVT calculating is a very knotty for the notorious simultaneous reporting problem and transient messages problem. According to our problem, another GVT algorithm, called Twice Notification (TN-GVT) (see algorithm 2), is contributed to this already rich repository instead of implementing one of GVT algorithms in reference [26] and [28].This algorithm looks like the synchronous algorithm described in reference [26] (pp. 114), however, they are essentially different from each other. This algorithm has never stopped the simulators from processing events when GVT reduction, while algorithm in reference [26] blocks all simulators for GVT calculating. As for the transient message problem, it can be neglect in our implementation, because RMI based remote communication approach is synchronized, that means a simulator will not go on its processing until the remote the massage get to its destination. And because of this, the high-costs message acknowledgement, prevalent over many classical asynchronous GVT algorithms, is not needed anymore too, which should be constructive to the whole performance of the time warp simulator.IV. Benchmark Model and Experiment ResultsA. The Lotka-Volterra Predator-prey SystemIn our experiment, the spatial version of Lotka-Volterra predator-prey system is introduced as the benchmark model (see Fig. 2). We choose the system for two considerations: 1) this system is a classical experimental model that has been used in many related researches [8][30][31], so it is credible and the simulation results are comparable; 2) it is simple but helpful enough to test the issues we are interested in. The space of predator-prey System is partitioned into a2D NXNgrid, whereNdenotes the edge size of the grid. Initially the population of the Grass, Preys and Predators are set to 1000 in each single sub-volume (LP). In Fig. 2,r1,r2,r3stand for the reaction constants of the reaction 1, 2 and 3 respectively. We usedGrass,dPreyanddPredatorto stand for the diffusion rate of Grass, Prey and Predator separately. Being similar to reference [8], we also take the assumption that the population of the grass remains stable, and thusdGrassis set to zero.R1:Grass + Prey ->2Prey(1)R2:Predator +Prey -> 2Predator(2)R3:Predator -> NULL(3)r1=0.01; r2=0.01; r3=10(4)dGrass=0.0;dPrey=2.5;dPredato=5.0(5)Fig. 2: predator-prey systemB. Experiment ResultsThe simulation runs have been executed on a Linux Cluster with 40 computing nodes. Each computing node is equipped with two 64bit 2.53 GHz Intel Xeon QuadCore Processors with 24GB RAM, and nodes are interconnected with Gigabit Ethernet connection. The operating system is Kylin Server 3.5, with kernel 2.6.18. Experiments have been conducted on the benchmark model of different size of mode to investigate the execution time and speedup of the time warp simulator. As shown in Fig. 3, the execution time of simulation on single processor with 8 cores is compared. The result shows that it will take more wall clock time to simulate much larger scale systems for the same simulation time. This testifies the fact that larger scale systems will leads to more events in the same time interval. More importantly, the blue line shows that the sequential simulation performance declines very fast when the mode scale becomes large. The bottleneck of sequential simulator is due to the costs of accessing a long event queue to choose the next events. Besides, from the comparison between group 1 and group 2 in this experiment, we could also conclude that high diffusion rate increased the simulation time greatly both in sequential and parallel simulations. This is because LP paradigm has to split diffusion into two processes (diffusion (in) and diffusion (out) event) for two interactive LPs involved in diffusion and high diffusion rate will lead to high proportional of diffusion to reaction. In the second step shown in Fig. 4, the relationship between the speedups from time warp of two different model sizes and the number of work cores involved are demonstrated. The speedup is calculated against the sequential execution of the spatial reaction-diffusion systems model with the same model size and parameters using NSM.Fig. 4 shows the comparison of speedup of time warp on a64X64grid and a100X100grid. In the case of a64X64grid, under the condition that only one node is used, the lowest speedup (a little bigger than 1) is achieved when two cores involved, and the highest speedup (about 6) is achieved when 8 cores involved. The influence of the number of cores used in parallel simulation is investigated. In most cases, large number of cores could bring in considerable improvements in the performance of parallel simulation. Also, compared with the two results in Fig. 4, the simulation of larger model achieves better speedup. Combined with time tests (Fig. 3), we find that sequential simulator’s performance declines sharply when the model scale becomes very large, which makes the time warp simulator get better speed-up correspondingly.Fig. 3: Execution time (wall clock time) of Seq. and time warp with respect to different model sizes (N=32, 64, 100, and 128) and model parameters based on single computing node with 8 cores. Results of the test are grouped by the diffusion rates (Group 1: Sequential 1 and Time Warp 1. dPrey=2.5, dPredator=5.0; Group 2: dPrey=0.25, dPredator=0.5, Sequential 2 and Time Warp 2).Fig. 4: Speedup of time warp with respect to the number of work cores and the model size (N=64 and 100). Work cores are chose from one computing node. Diffusion rates are dPrey=2.5, dPredator=5.0 and dGrass=0.0.V. Conclusion and Future WorkIn this paper, a time warp simulator based on the discrete event simulation framework JAMES II is designed and implemented for fine-grained parallel and distributed discrete event spatial stochastic simulation of biological reaction systems. Several challenges have been overcome, such as state saving, roll back and especially GVT reduction in parallel execution of simulations. The Lotka-Volterra Predator-Prey system is chosen as the benchmark model to test the performance of our time warp simulator and the best experiment results show that it can obtain about 6 times of speed-up against the sequential simulation. The domain this paper concerns with is in the infancy, many interesting issues are worthy of further investigated, e.g. there are many excellent PDES optimistic synchronization algorithms (e.g. the BTW) as well. Next step, we would like to fill some of them into JAMES II. In addition, Gillespie approximation methods (tau-leap[10] etc.) sacrifice some degree of precision for higher simulation speed, but still could not address the aspect of space of biological reaction systems. The combination of spatial element and approximation methods would be very interesting and promising; however, the parallel execution of tau-leap methods should have to overcome many obstacles on the road ahead.AcknowledgmentThis work is supported by the National Natural Science Foundation of China (NSF) Grant (No.60773019) and the Ph.D. Programs Foundation of Ministry of Education of China (No. 200899980004). The authors would like to show their great gratitude to Dr. Jan Himmelspach and Dr. Roland Ewald at the University of Rostock, Germany for their invaluable advice and kindly help with JAMES II.ReferencesH. Kitano, "Computational systems biology." Nature, vol. 420, no. 6912, pp. 206-210, November 2002.H. Kitano, "Systems biology: a brief overview." 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Elastic search is a way to organize the data and make it easily accessible. It is a server based search on Lucene. It is a highly scalable, distributed and full-text search engine. Elastic search is developed in Java. It is published as open source under the terms of the Apache License. Elastic search is the most popular enterprise search engine. Elastic search includes all advances in speed, security, scalability, and hardware efficiency. Elastic search is a tool for querying written words. It can perform some other smart tasks, but its principal is returning text similar to a given query and statistical analyses of a quantity of text. Elasticsearch is a standalone database server, which is written in Java and using HTTP/JSON protocol,it’s takes data and optimized the data according to language based searches and stores it in a sophisticated format. Elastic search is very convenient, supporting clustering and leader selection out of the box. Whether it’s searching a database of trade products by description, finding similar text in a body of crawled web pages. In this manuscript elastic search capability of copied data identification and its removing techniques performance are analyzed

Abstract Since 2012, the Center for Genome Science of the Korea National Institute of Health (KNIH) has been sequencing complete genomes of 1722 Korean individuals. As a result, more than 32 million variant sites have been identified, and a large proportion of the variant sites have been detected for the first time. In this article, we describe the Korean Reference Genome Database (KRGDB) and its genome browser. The current version of our database contains both single nucleotide and short insertion/deletion variants. The DNA samples were obtained from four different origins and sequenced in different sequencing depths (10× coverage of 63 individuals, 20× coverage of 194 individuals, combined 10× and 20× coverage of 135 individuals, 30× coverage of 230 individuals and 30× coverage of 1100 individuals). The major features of the KRGDB are that it contains information on the Korean genomic variant frequency, frequency difference between the Korean and other populations and the variant functional annotation (such as regulatory elements in ENCODE regions and coding variant functions) of the variant sites. Additionally, we performed the genome-wide association study (GWAS) between Korean genome variant sites for the 30×230 individuals and three major common diseases (diabetes, hypertension and metabolic syndrome). The association results are displayed on our browser. The KRGDB uses the MySQL database and Apache-Tomcat web server adopted with Java Server Page (JSP) and is freely available at http://coda.nih.go.kr/coda/KRGDB/index.jsp. Availability: http://coda.nih.go.kr/coda/KRGDB/index.jsp

We present the results of the <tt>&lt;bigwig&gt;</tt> project, which aims to design and implement a high-level domain-specific language for programming interactive Web services.<br /> <br />A fundamental aspect of the development of the World Wide Web during the last decade is the gradual change from static to dynamic generation of Web pages. Generating Web pages dynamically in dialogue with the client has the advantage of providing up-to-date and tailor-made information. The development of systems for constructing such dynamic Web services has emerged as a whole new research area.<br /> <br />The <tt>&lt;bigwig&gt;</tt> language is designed by analyzing its application domain and identifying fundamental aspects of Web services inspired by problems and solutions in existing Web service development languages. The core of the design consists of a session-centered service model together with a flexible template-based mechanism for dynamic Web page construction. Using specialized program analyses, certain Web specific properties are verified at compile-time, for instance that only valid HTML 4.01 is ever shown to the clients. In addition, the design provides high-level solutions to form field validation, caching of dynamic pages, and temporal-logic based concurrency control, and it proposes syntax macros for making highly domain-specific languages. The language is implemented via widely available Web technologies, such as Apache on the server-side and JavaScript and Java Applets on the client-side. We conclude with experience and evaluation of the project.

In "Speed and Information: Cyberspace Alarm!", Paul Virilio claims that telecommunications are ushering in the "invention of a perspective of real time" which results in "some kind of choking of the senses, a loss of control over reason". As users of this new technology, as the receptors of the stream of computer-mediated information, we need to figure out the terms and conditions of our acceptance of cyberspace as a space and realtime as a form of time, to understand the implications of this new mode of communication, for "no information exists without dis-information". In "Speed and Information: Cyberspace Alarm!", Paul Virilio claims that telecommunications are ushering in the "invention of a perspective of real time" which results in "some kind of choking of the senses, a loss of control over reason". As users of this new technology, as the receptors of the stream of computer-mediated information, we need to figure out the terms and conditions of our acceptance of cyberspace as a space and realtime as a form of time, to understand the implications of this new mode of communication, for "no information exists without dis-information". Even Virilio proclaims apocalyptically that "our history will happen in universal time, itself the outcome of instantaneity -- and there only". In fact, time also governs narrative choices: their availability, viability, desirability, relevance. Despite the hype surrounding the instantaneity of virtual travel, narrative in cyberspace is inherently subordinate to connection speed and loadtime. This is why the "loading screen" has become the standard welcome on Shockwave-heavy sites, developing into a kind of mini-genre of low-bandwidth animation. The possiblity of using temporality as a narrative catalyst has been exploited in cinema, as in classic Hollywood dissolves and fades. Metaphors of the passing of time are a familiar cliche: the pages of a daily calendar fluttering away, the changing of the seasons. Stanley Kubrick's bold cut from a spinning bone to a space station in orbit in 2001: A Space Odyssey is an extreme and unusual example of this sort of metaphor. These all function as temporal ellipses. The passage of time can also function as plot, as in Warhol's Blow Job and Richard Linklater's Slacker, both of which are ostensibly about merely the passage of time. Slacker lacks a traditional narrative and instead progresses through a series of vignettes, each one following seemingly random characters through seemingly random events (an idea developed further by the recent Magnolia). The change from one vignette to the next is motivated simply by the camera's movement from one character or event to another. The camera is like a nosy passerby, a voyeur, showing noncommittal interest in one thing, then another, and the viewer must give up interest in each vignette without the satisfaction of narrative closure. As the filmmaker tells the cabdriver in the beginning, each turn of events, each decision made, results in all possibilities going on to live out their potential realities. We, the viewers, in turn, follow the camera's gaze with the frustrating knowledge that other, unresolved realities are continuing without that gaze. The recent Timecode uses the same hypertext-type approach with four simultaneous screens, each a single shot capturing one part of an interlocked world. These are all extreme, overt examples of Deleuze's time-image. Online, similar moves have been made in Mark Napier's Shredder and Maciej Wisniewski's Netomat interfaces. Both function as alternatives to conventional browsing, Netomat even labelled an "anti-browser" that engages "an Internet that is an intelligent application and not simply a large database of static files". The above-mentioned devices for manipulating the perception and understanding of time as represented in film (fade, dissolve, et al.) exploited an inherently filmic problem: simply put, that there is a serious discrepancy between time as it happens and its perception, much like the time it takes to enjoy a Website's multimedia content and the length of its download. In the case of the fade, for instance, an inherent problem of the medium has been internalised in a non-transparent way and used overtly to further the narrative meaning. Likewise, the "loading screen" offers a morsel of content typically focussed on its function ("loading... 5 seconds to go..."). The existence of these filmic conventions makes us aware of when they are broken, as in the "realtime" films Nick of Time, Blow Job, and Timecode, and also in instances of extended time, as in the classic shower scene in Hitchcock's Psycho. Think, too, of the last time you had to wait before you saw any of a Website's content. Just as filmic time is typically compressed for the sake of appearing real, navigational movement on the Web is in fact constrained while seeming free, and delayed while seeming instantaneous. The promise of instant access has instead been fulfilled by erratic connection speeds and server problems. Because Web time ostensibly passes almost in an instant (this is, after all, the industry in which a product might become passé while still at the beta phase), information ages just as quickly: "404 File not found" is a familiar sight, telling us that the link we followed may have been coded, not last year, but maybe even last week, or yesterday. Information loses relevance, even disappears, often in no time at all. These problems have been exploited by JODI, whose experimental online work foregrounds the nuts and bolts (and kinks) of the Web, instead of hiding it beneath a clean "other" design. The desirability of information over time is also the focus of Rhizome's Starry Night interface which, utilizing Java, shifts over time to emphasise popular links, eventually eradicating unpopular ones. In The Work of Art in the Age of Mechanical Reproduction, Walter Benjamin writes that "even the most perfect reproduction of a work of art is lacking in one element: its presence in time and space, its unique existence at the place where it happens to be" (220). But what of the Web art project, whose existence on a server somewhere does not need to be known for the work to be understood, whose duplication yields a copy that is indistinguishable from the original? What of the work that is both static and temporal, which is inherently mediated through time, including time (as in server and connection speed) which cannot be completely accounted for by the author? He goes on to say that technical reproduction "enables the original to meet the beholder halfway" (220), but what is the Website's point of departure? Its creator's computer? The server on which it lives? The end user's computer? How can we map the path from the "original" to its "reproduction" when the two are indistinguishable, when, in fact, there is no confirmable original? As if in response to Benjamin, Paul Virilio writes in "Speed and Information: Cyberspace Alarm!" that "the specific negative aspect of these information superhighways is precisely this loss of orientation regarding alterity (the other), this disturbance in the relationship with the other and with the world". Virilio is concerned with the problem of orientation, that is, of the lack of geographical, historical, and temporal specificity and point of reference when experiencing a Web-based narrative. Compare that to Deleuze's claim that, in the time-image, "the brain has lost its Euclidean co-ordinates, and now emits other signs" (278), a notion similar to the "loading screen", a bit of content which exists merely to inform that content is forthcoming. Virilio sees this as a crucial problem facing us today and adds that "there is talk of substituting the term 'global' by 'glocal,' a concatenation of the words local and global". The Internet yields both seeming temporal instantaneity and spatial compression. We can be everywhere all at once, all the time; but what of the inevitable slippage of time involved? The World Wide Web has created a life of dead moments, of moments spent waiting for the instantaneous to happen. References Baudrillard, Jean. "Radical Thought." Trans. Francois Debrix in CTheory. Collection Morsure. Eds. Sens and Tonka. Paris: 1994. Benjamin, Walter. Illuminations. New York: Shocken Books, 1968. Debord, Guy. The Society of the Spectacle. London: Rebel Press, 1992. Deleuze, Gilles. Cinema 2: The Time-Image. Minneapolis: U of Minnesota P, 1989. Napier, Mark. Shredder. 27 June 2000 <http://www.potatoland.org/shredder/>. Rhizome. 27. June 2000 <http://www.rhizome.org/>. Virilio, Paul. "Speed and Information: Cyberspace Alarm!" Le Monde Diplomatique Aug. 1995. Trans. Patrice Riemens in CTheory. Wisniewski, Maciej. Netomat. 27 June 2000 <http://www.netomat.net/>. Citation reference for this article MLA style: Maya Drozdz. "Waiting for Instantaneity." M/C: A Journal of Media and Culture 3.3 (2000). [your date of access] <http://www.api-network.com/mc/0006/instantaneity.php>. Chicago style: Maya Drozdz, "Waiting for Instantaneity," M/C: A Journal of Media and Culture 3, no. 3 (2000), <http://www.api-network.com/mc/0006/instantaneity.php> ([your date of access]). APA style: Maya Drozdz. (2000) Waiting for instantaneity. M/C: A Journal of Media and Culture 3(3). <http://www.api-network.com/mc/0006/instantaneity.php> ([your date of access]).