World Wide Web Server Research Articles

A self-scaling and self-configuring benchmark for Web servers (extended abstract)

World Wide Web clients and servers have become some of the most important applications in our computing base, and we need realistic and meaningful ways of measuring their performance. Current server benchmarks do not capture the wide variation that we see in servers and are not accurate in their characterization of web traffic. In this paper, we present a self-configuring, scalable benchmark that generates a server benchmark load based on actual server loads. In contrast to other web benchmarks, our benchmark focuses on request latency instead of focusing exclusively on throughput sensitive metrics. We present our new benchmark hBench:Web, and demonstrate how it accurately models the load of an actual server. The benchmark can also be used to assess how continued growth or changes in the workload will affect future performance. Using existing log histories, we now that these predictions are sufficiently realistic to provide insight into tomorrow's Web performance.

Integrated medical informatics with small group teaching in medical education

National Taiwan University College of Medicine (NTUCM) introduced small groups of teaching and basic-clinical integrated courses for medical students in 1992. By using computer network and multimedia techniques, this study tried to overcome barriers to learning in small group teaching. The Department of Medical Informatics of NTUCM established campus networking and computer classrooms and provided Internet and intranet network services including mail, netnews, bulletin board systems (BBS), world wide web (WWW), gopher, ftp and local file servers. To implement an interactive learning environment, the authors first tried mail lists, newsgroups and BBS. Next an integrated learning system prototype on the WWW was developed to provide functions including online syllabus, discussion boards simulated to BBS, online talk, interactive case studies, virtual classroom with video on demand (VOD) and Internet medical resources. The results showed that after the medical students completed the required course of medical informatics and had good network access using a network to communicate with each other became a daily practice. In the future, the system will extend to the tutoring of clinical practice and continuing medical education. The authors expect a national medical education network and more international cooperation and exchange.

Developing a husbandry manual to facilitate the distribution and presentation of information: with special reference to Slender loris Loris tardigradus nordicus at Ruhr University, Bochum

Generally the practical information required for husbandry of wild species in captivity is not readily available in a single comprehensive source. This paper describes the sort of information which would be most useful for species management, using the Slender loris Loris tardigradus nordicus as an example, and provides a practical model of the possible form and content of a husbandry manual. A single, easily available source of husbandry data would be a valuable tool for all institutions and individuals which are willing to participate in coordinated breeding programmes, helping to maintain genetic diversity and increase the size of captive populations. It would be of particular interest to small institutions, such as zoos with limited staff, breeding colonies in scientific institutions, veterinarians and private breeders. Husbandry manuals which are updated at intervals using, for example, a subscription‐based amendment service or a database of husbandry information which can be accessed using a computer are both reasonable possibilities. Some existing sources of information for the management of Asian loris species and details about on‐line World Wide Web services, for accessing conservation information and species‐management data, which are in the development stages are described. This paper also presents some general information on minimum necessary requirements for successful husbandry of Slender lorises which, in captivity, are cautious but curious animals that become extremely familiar with their environment and react with excitement to novel stimuli. They are prone to both environmental and social stress, and stress‐related symptoms observed in the species, such as slow movements, freezing to motionless or apparent loss of fear in stressful situations, may be based on earlier learning and are sometimes difficult to gauge unless keepers are familiar with the habits of each individual. Enclosure design, lighting and temperature are all significant to the well‐being of the species. Slender lorises prefer to use the upper part of the enclosure, although they will use the lower area to avoid aggressive confrontations with conspecifics, and a system of branches and wiremesh which allows continuous locomotion with no ‘dead ends’ and furnishings that encourage locomotor activity should be provided. Because the species has a tendency towards adiposity and diabetes diet is a serious consideration. A comprehensive husbandry manual for Asian prosimians has been developed (Fitch‐Snyder et al., in press).

Superior performance in protein homology detection with the Blocks Database servers.

The Blocks Database World Wide Web (http://www.blocks.fhcrc.org ) and Email (blocks@blocks.fhcrc.org) servers provide tools for the detection and analysis of protein homology based on alignment blocks representing conserved regions of proteins. During the past year, searching has been augmented by supplementation of the Blocks Database with blocks from the Prints Database, for a total of 4754 blocks from 1163 families. Blocks from both the Blocks and Prints Databases and blocks that are constructed from sequences submitted to Block Maker can be used for blocks-versus-blocks searching of these databases with LAMA, and for viewing logos and bootstrap trees. Sensitive searches of up-to-date protein sequence databanks are carried out via direct links to the MAST server using position-specific scoring matrices and to the BLAST and PSI-BLAST servers using consensus-embedded sequence queries. Utilizing the trypsin family to evaluate performance, we illustrate the superiority of blocks-based tools over expert pairwise searching or Hidden Markov Models.

The PRINTS protein fingerprint database in its fifth year.

PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 800 fingerprints have been constructed and stored in PRINTS. The current version, 17.0, encodes approximately 4500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via the UCL Bioinformatics World Wide Web (WWW) Server at http://www. biochem.ucl.ac.uk/bsm/dbbrowser/ . We have recently enhanced the usefulness of PRINTS by making available new, intuitive search software. This allows both individual query sequence and bulk data submission, permitting easy analysis of single sequences or complete genomes. Preliminary results indicate that use of the PRINTS system is able to assign additional functions not found by other methods, and hence offers a useful adjunct to current genome analysis protocols.

Dynamic adaptation in an image transcoding proxy for mobile Web browsing

Transcoding proxies are used as intermediaries between generic World Wide Web servers and a variety of client devices in order to adapt to the greatly varying bandwidths of different client communication links and to handle the heterogeneity of possibly small-screened client devices. Such transcoding proxies can adaptively adjust the amount by which a data stream is reduced, using an aggressive lossy compression method (e.g., an image becomes less clear, text is summarized). We present an analytical framework for determining whether to transcode and how much to transcode an image for the two cases of store-and-forward transcoding as well as streamed transcoding. These methods require prediction of transcoding delay, prediction of transcoded image size (in bytes), and estimation of network bandwidth. We discuss methods of adaptation based on fixed quality as well as fixed delay (automated/dynamic transcoding). We conclude with a description of the practical adaptation policies that have been implemented in our adaptive image transcoding proxy.

The non-redundant Bacillus subtilis (NRSub) database: update 1998

The non-redundant Bacillus subtilis database (NRSub) has been developed in the context of the sequencing project devoted to this bacterium. As this project has reached completion, the whole genome is now available as a single contig. Thanks to the ACNUC database management system and its associated retrieval system Query_win, each functional region of the genome can be accessed individually. Extra annotations have been added such as accession numbers for the genes, locations on the genetic map, codon adaptation index values, as well as cross-references with other collections. NRSub is distributed through anonymous FTP as a text file in EMBL format and as an ACNUC database. It is also possible to access NRSub through two dedicated World Wide Web servers located in France (http://acnuc. univ-lyon1.fr/nrsub/nrsub.html ) and in Japan (http://ddbjs4h.genes. nig.ac.jp/ ).

Applying military grade security to the Internet

The explosive growth witnessed in the Internet over the last few years has encouraged companies to connect to it and to offer services to their customers over it. Concerns about security are holding them back from all but the most restrictive connectivity. This paper explores the use of a military development, the Compartmented Mode Workstation in a commercial setting, as a platform that is secure enough to implement services that are accessed over the Internet. Two applications have been investigated in detail, a firewalled Domain Name System and a World Wide Web service with enhanced authentication. Finally, there is discussion of how other Internet-based services might benefit from the application of CMW technology.

Using the Internet as a pharmacokinetic resource.

The Internet is an growing resource for scientific information, and includes information which can be useful to the pharmacokineticist. Once connected to the Internet there is a wide variety of information sources available. Collaboration with colleagues, research groups, discussion lists or news groups can be a valuable use of the Internet. Interactive discussions are possible using Internet Relay Chat or other conferencing software. There are a multitude of data, software and other information available via FTP, gopher or World Wide Web servers. This information may be exclusively research-oriented or more useful for instructional use, or suitable for both.

Improving the performance of CGI compliant database gateways

The phenomenal growth that the World Wide Web (WWW) service currently experiences, necessitates the adaptation of legacy information systems like RDBMSs or full-text search systems to HTTP servers. Existing standards for performing this adaptation (i.e. CGI), although well-established, prove highly inefficient throughout periods of heavy load (multiple hits per unit time). In this paper, after reviewing all the relevant mechanisms, we propose a generic architecture which adheres to the existing standards and client/server model and alleviates the performance handicap of classical database gateways. The performance evaluation which was realised as part of this research effort revealed a noteworthy superiority of the proposed architecture with respect to monolithic (non-client/server) CGI based approaches.

WebGALAXY: beyond point and click — a conversational interface to a browser

This paper presents WebGALAXY, a flexible multi-modal user interface system that allows wide access to selected information on the World Wide Web (WWW) by integrating spoken and typed natural language queries and hypertext navigation. WebALAXY extends our GALAXY spoken language system, a distributed client-server system for retrieving information from online sources through speech and natural language. WebGALAXY supports a spoken user interface via a standard telephone line as well as a graphical user interface via a standard Web browser using either Java/JavaScript or a cgi-bin/forms front end. Natural language understanding is performed by the system and information servers retrieve the requested information from various online resources including WWW servers, Gopher servers and CompuServe. Currently, queries about three domains are supported: weather, air travel, and points of interest around Boston.

Using the World Wide Web—a new approach to risk identification of diabetes mellitus

Diabetes mellitus is a major health problem with a rising tendency world-wide. A new strategy for risk evaluation and data collection of undiagnosed non-insulin-dependent diabetes mellitus (NIDDM) using the World Wide Web (WWW) is presented. An easy-to-handle questionnaire on typical risk factors was converted into an interactive WWW document. The Internet provides the suitable platform for the net-based distribution of the questionnaire form as well as the computer-assisted entering and interpretation of the data (http://www.uni-leipzig.de/∼diabetes). The analysis program, installed on our WWW server, interprets the information and sends the assessment on-line back to the inquiring user PC. The data are also collected anonymously in a database for epidemiological studies. In the test period, 744 world-wide accesses were registered: 433 men, mean age 39.8±14.4 years (range 10–83) and 311 women, mean age 36.7±12.7 years (range 11–77). An increased risk for undiagnosed diabetes was identified to 43.6%. The risk profile of male and female users showed no significant gender-related differences. Using the WWW technology can support early detection and adequate treatment of undiagnosed diabetes. This innovative strategy to screen for a high risk profile is an useful, cost-effective and up-to-date tool for broad community health education and epidemiological studies world-wide.

CALAT: An intelligent CAI system using the World Wide Web

This paper describes an intelligent CAI system, called CALAT, which provides an individual adaptation capability on the World Wide Web (WWW). CALAT consists of an intelligent tutoring system (ITS) on a WWW server. A newly developed user identification mechanism makes the system capable of adapting to individuals over the stateless protocol of the WWW. A viewer control mechanism using control script has also been developed in order to improve response speed and to implement viewer control capability from the server. An evaluation experiment shows that the individual adaptation capability works well and that the response speed is sufficient for practical use. CALAT is now in operation on the Internet. © 1997 Scripta Technica, Inc. Syst Comp Jpn, 28(9): 17–25, 1997

WebMonitor: a Tool for Measuring World-Wide Web Server Performance

Server performance has become a crucial issue for improving the overall performance of the World-Wide Web. This paper describes WebMonitor, a tool for evaluating and understanding server performance, and presents new results for realistic workloads. WebMonitor measures activity and resource consumption, both within the kernel and in HTTP processes running in user space. WebMonitor is implemented using an efficient combination of sampling and event-driven techniques that exhibit low overhead. Our initial implementation is for the Apache World-Wide Web server running on the Linux operating system. We demonstrate the utility of WebMonitor by measuring and understanding the performance of a Pentium-based PC acting as a dedicated WWW server. Our workloads use file size distributions with a heavy tail. This captures the fact that Web servers must concurrently handle some requests for large audio and video files, and a large number of requests for small documents, containing text or images. Our results show that in a Web server saturated by client requests, up to 90% of the time spent handling HTTP requests is spent in the kernel. These results emphasize the important role of operating system implementation in determining Web server performance. It also suggests the need for new operating system implementations that are designed to perform well when running on Web servers.

HOSEpipe--a WWW-hosted data management and analysis system for STS content mapping projects.

We have developed a data management system, 'HOSEpipe' (High Output STS Evaluation pipeline) to aid sample tracking and data analysis in STS content mapping projects. The system is based around a World Wide Web (WWW) server that provides a number of pages including forms for sample processing and data entry accessible via a standard WWW browser application. The system is split into two main modules: firstly, a sequence evaluation and annotation module that takes de novo sequence for a potential STS, screens it against existing STSs and DNA sequence databases, followed by appropriate primer sequence design; secondly, a module that handles YAC library STS screening and includes facilities for both sample tracking and experimental data analysis. We present the design and rationale of the HOSEpipe system and its development to support a whole chromosomal physical mapping project. This software and design approach is potentially applicable to physical mapping projects of varying sizes and resolution and to similar projects, such as sample sequencing and the construction of sequence-ready maps.

Computer analysis of phytochrome sequences and reevaluation of the phytochrome secondary structure by Fourier transform infrared spectroscopy

A repertoire of various methods of computer sequence analysis was applied to phytochromes in order to gain new insights into their structure and function. A statistical analysis of 23 complete phytochrome sequences revealed regions of non-random amino acid composition, which are supposed to be of particular structural or functional importance. All phytochromes other than phyD and phyE from Arabidopsis have at least one such region at the N-terminus between residues 2 and 35. A sequence similarity search of current databases indicated striking homologies between all phytochromes and a hypothetical 84.2-kDa protein from the cyanobacterium Synechocystis. Furthermore, scanning the phytochrome sequences for the occurrence of patterns defined in the prosite database detected the signature of the WD repeats of the β-transducin family within the functionally important 623–779 region (sequence numbering of phyA from Avena) in a number of phytochromes. A multiple sequence alignment performed with 23 complete phytochrome sequences is made available via the IMB Jena World-Wide Web server (http://www.imb-jena.de/PHYTO.html). It can be used as a working tool for future theoretical and experimental studies. Based on the multiple alignment striking sequence differences between phytochromes A and B were detected directly at the N-terminal end, where all phytochromes B have an additional stretch of 15–42 amino acids. There is also a variety of positions with totally conserved but different amino acids in phytochromes A and B. Most of these changes are found in the sequence segment 150–200. It is, therefore, suggested that this region might be of importance in determining the photosensory specificity of the two phytochromes. The secondary structure prediction based on the multiple alignment resulted in a small but significant β-sheet content. This finding is confirmed by a reevaluation of the secondary structure using FTIR spectroscopy.

Use of World Wide Web server and browser software to support a first-year medical physiology course.

We describe the use of a World Wide Web (Web) server to support a team-taught physiology course for first-year medical students. Our objectives were to reduce the number of formal lecture hours and enhance student enthusiasm by using more multimedia materials and creating opportunities for interactive learning. On-line course materials, consisting of administrative documents, lecture notes, animations, digital movies, practice tests, and grade reports, were placed on a departmental computer with an Internet connection. Students used Web browsers to access on-line materials from a variety of computing platforms on campus, at home, and at remote sites. To assess use of the materials and their effectiveness, we analyzed 1) log files from the server, and 2) the results of a written course evaluation completed by all students. Lecture notes and practice tests were the most-used documents. The students' evaluations indicated that computer use in class made the lecture material more interesting, while the on-line documents helped reinforce lecture materials and the textbook. We conclude that the effectiveness of on-line materials depends on several different factors, including 1) the number of instructors that provide materials; 2) the quantity of other materials handed out; 3) the degree to which computer use is demonstrated in class and integrated into lectures; and 4) the ease with which students can access the materials. Finally, we propose that additional implementation of Internet-based resources beyond what we have described would further enhance a physiology course for first-year medical students.

Visualization and interaction tools for aerial photograph mosaics

This paper describes the development of a digital spatial library based on mosaics of digital orthophotos, called Interactive Portugal, that will enable users both to retrieve geospatial information existing in the Portuguese National System for Geographic Information World Wide Web server, and to develop local databases connected to the main system. A set of navigation, interaction, and visualization tools are proposed and discussed. They include sketching, dynamic sketching, and navigation capabilities over the digital orthophotos mosaics. Main applications of this digital spatial library are pointed out and discussed, namely for education, professional, and tourism markets. Future developments are considered. These developments are related to user reactions, technological advancements, and projects that also aim at delivering and exploring digital imagery on the World Wide Web. Future capabilities for site selection and change detection are also considered.

Toward a Scalable Distributed WWW Server on Workstation Clusters

In this paper, we investigate the issues involved in developing a scalable World Wide Web (WWW) server called SWEB on a cluster of workstations. The objective is to strengthen the processing capabilities of such a server in order to match huge demands in simultaneous access requests from the Internet, especially when these requests involve delivery of large digitized documents. The scheduling component of the system actively monitors the usages of CPU, disk I/O channels and the interconnection network to effectively distribute HTTP requests across processing units to exploit task and I/O parallelism. We analyze the maximum number of requests that can be handled by the system and present several experiments to examine the performance of this system.

Protein secondary structure prediction using local alignments

The accuracy of secondary structure prediction methods has been improved significantly by the use of aligned protein sequences. The PHD method and the NNSSP method reach 71 to 72% of sustained overall three-state accuracy when multiple sequence alignments are with neural networks and nearest-neighbor algorithms, respectively. We introduce a variant of the nearest-neighbor approach that can achieve similar accuracy using a single sequence as the query input. We compute the 50 best non-intersecting local alignments of the query sequence with each sequence from a set of proteins with known 3D structures. Each position of the query sequence is aligned with the database amino acids in α-helical, β-strand or coil states. The prediction type of secondary structure is selected as the type of aligned position with the maximal total score. On the dataset of 124 non-membrane non-homologous proteins, used earlier as a benchmark for secondary structure predictions, our method reaches an overall three-state accuracy of 71.2%. The performance accuracy is verified by an additional test on 461 non-homologous proteins giving an accuracy of 71.0%. The main strength of the method is the high level of prediction accuracy for proteins without any known homolog. Using multiple sequence alignments as input the method has a prediction accuracy of 73.5%. Prediction of secondary structure by the SSPAL method is available via Baylor College of Medicine World Wide Web server.