World Wide Web Server Research Articles

Abnormal Web usage control by proxy strategies

The World Wide Web (WWW) has become an extremely popular information service. Large HTTP packets result in network congestion. Proxy cache servers are widely deployed on the Internet to overcome this obstacle. However, the approach yields an undesirable phenomenon – a small set of users misuse proxy servers to mirror the entire contents of Web sites. This behavior wastes network resources, increases WWW servers’ loads, increases users’ waiting time, and violates copyrights. Approaches to designing a proxy server with WWW usage control and to making the proxy server effective on local area networks are proposed to prevent such abnormal WWW access and to prioritize WWW usage. Finally, a system, ProxyBreaker, is implemented to demonstrate the approaches. The implementation reveals that the proposed approaches are effective, such that the abnormal Web access does not reoccur.

Performance issues in WWW servers

This paper evaluates techniques for improving operating system and network protocol software support for high-performance World Wide Web servers. We study approaches in three categories: i.e., new ...

NUREBASE: database of nuclear hormone receptors.

Nuclear hormone receptors are an abundant class of ligand activated transcriptional regulators, found in varying numbers in all animals. Based on our experience of managing the official nomenclature of nuclear receptors, we have developed NUREBASE, a database containing protein and DNA sequences, reviewed protein alignments and phylogenies, taxonomy and annotations for all nuclear receptors. The reviewed NUREBASE is completed by NUREBASE_DAILY, automatically updated every 24 h. Both databases are organized under a client/server architecture, with a client written in Java which runs on any platform. This client, named FamFetch, integrates a graphical interface allowing selection of families, and manipulation of phylogenies and alignments. NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html.

Performance issues in WWW servers

This paper evaluates techniques for improving operating system and network protocol software support for high-performance World Wide Web servers. We study approaches in three categories: i.e., new socket functions, per-byte optimizations, and per-connection optimizations. We examine two proposed socket functions, i.e., acceptex( ) and send-file( ), comparing send-file( )'s effectiveness with a combination of mmap( ) and writev( ). We show how send-file( ) provides the necessary semantic support to eliminate copies and checksums in the kernel, and quantify the benefit of the function's header and close options. We also present mechanisms to reduce the number of packets exchanged in an HTTP transaction, both increasing server performance and reducing network utilization, without compromising interoperability. Results using WebStone show that our combination of mechanisms can improve server throughput by up to 64%, and can eliminate up to 33% of the packets in an HTTP exchange. Results with SURGE show an aggregate increase in server throughput of 25%.

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) continues to provide genome-related information in a systematic way. MIPS supports both national and European sequencing and functional analysis projects, develops and maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences, and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the databases for the comprehensive set of genomes (PEDANT genomes), the database of annotated human EST clusters (HIB), the database of complete cDNAs from the DHGP (German Human Genome Project), as well as the project specific databases for the GABI (Genome Analysis in Plants) and HNB (Helmholtz-Netzwerk Bioinformatik) networks. The Arabidospsis thaliana database (MATDB), the database of mitochondrial proteins (MITOP) and our contribution to the PIR International Protein Sequence Database have been described elsewhere [Schoof et al. (2002) Nucleic Acids Res., 30, 91-93; Scharfe et al. (2000) Nucleic Acids Res., 28, 155-158; Barker et al. (2001) Nucleic Acids Res., 29, 29-32]. All databases described, the protein analysis tools provided and the detailed descriptions of our projects can be accessed through the MIPS World Wide Web server (http://mips.gsf.de).

RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database.

The ribosomal differentiation of medical micro-organisms (RIDOM) web server, first described by Harmsen et al. [Harmsden,D., Rothganger,J., Singer,C., Albert,J. and Frosch,M. (1999) Lancet, 353, 291], is an evolving electronic resource designed to provide micro-organism differentiation services for medical identification needs. The diagnostic procedure begins with a specimen partial small subunit ribosomal DNA (16S rDNA) sequence. Resulting from a similarity search, a species or genus name for the specimen in question will be returned. Where the first results are ambiguous or do not define to species level, hints for further molecular, i.e. internal transcribed spacer, and conventional phenotypic differentiation will be offered ('sequential and polyphasic approach'). Additionally, each entry in RIDOM contains detailed medical and taxonomic information linked, context-sensitive, to external World Wide Web services. Nearly all sequences are newly determined and the sequence chromatograms are available for intersubjective quality control. Similarity searches are now also possible by direct submission of trace files (ABI or SCF format). Based on the PHRED/PHRAP software, error probability measures are attached to each predicted nucleotide base and visualised with a new 'Trace Editor'. The RIDOM web site is directly accessible on the World Wide Web at http://www.ridom.de/. The email address for questions and comments is webmaster@ridom.de.

Introducing Computer-Based Telemedicine in Three Rural Missouri Counties

This study investigated predictors of utilization of the computer-based telemedicine in three rural Missouri counties. Participating health care agencies were given computers and access to an Internet-based workstation that provided e-mail and World Wide Web (WWW) services. Utilization data for e-mail messages sent and WWW pages accessed were collected through proxy servers. A survey was distributed to those employees who are enrolled in the Rural Telemedicine Evaluation Project (RTEP), which addressed perceptions of the Internet-based RTEP workstation. The results of the survey were analyzed to see how perceptions and demographic variables predicted actual utilization. The findings of the study revealed that for e-mail, behavioral intentions/attitude, age, organizational support, and time were the most significant predictors. For WWW, only the behavioral intentions/attitude subscale predicted utilization. The majority of respondents did not utilize the e-mail technology. Strategies need to be developed through training interventions and organizational policies to address non-utilization.

Experiences in engineering flexible Web services

The life-cycle of a World Wide Web service includes analysis, design, implementation and maintenance stages. Our experiences in building and maintaining the annual Vienna International Festival's Web site have led us to create engineering tools that cover all these phases.

QoS-based Architectures for Geographically Replicated Web Servers

In this paper, we discuss strategies for providing World Wide Web service users with adequate Quality of Service (i>QoS). We argue that QoS can be provided by distributing the service requests processing load among replicated Web servers (i>WSs), that can be geographically distributed across the Internet. In order to support our argument, we compare and contrast several load distribution strategies, and assess their effectivness when deployed within the context of a geographically replicated Web service; the principal figure of merit we use in this assessment is the response time experienced by the users of that service. As a result of this comparison, we propose a specific strategy, named i>QoS-based, that implements load distribution among WS replicas by binding a user to the replica that provides the shortest user response time. We examine several architectures that exploit our QoS-based strategy. Two of these architectures, named, respectively, i>Browser-based and i>Load Distribution-i>based, are described in detail as they are particularly appropriate for implementing our strategy.

PANAL: an integrated resource for Protein sequence ANALysis.

We present PANAL, an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the result as an intuitive graphical summary.

Internet by Proxy

This study investigated utilization of computer-based telemedicine in three rural Missouri counties. Participating health care agencies were given computers and access to an Internet-based workstation that provided e-mail and World Wide Web (WWW) services. Ten rural practices from three Missouri counties were profiled. Utilization data for e-mail messages sent and received, along with the number of WWW pages accessed, were collected through a proxy server. Results showed that most physicians received more messages than they sent and utilized the WWW more than they did e-mail. Moreover, physicians connected to a tertiary care center and who currently use extenders in their practice are more likely to use Internet technology, even if it is through a proxy user such as a nurse practitioner or office staff.

A web server's view of the transport layer

This paper presents observations of traffic to and from a particular World-Wide Web server over the course a year and a half. This paper presents a longitudinal look at various network path properties, as well as the implementation status of various protocol options and mechanisms. In particular, this paper considers how World-Wide Web clients utilize TCP connections to transfer web data; the deployment of various TCP and HTTP options; the range of round-trip times observed in the network; packet sizes used for WWW transfers; the implications of the measured advertised window sizes; and the impact of using larger initial congestion window sizes. These properties/mechanisms and their implications are explored. An additional goal of this paper is to provide information to help researchers better simulate and emulate realistic networks.

Providing a differentiated quality of service in a World Wide Web server

This paper presents a strategy of extending a Web server to be able to differentiate between requests in different classes. This is required because most Web servers are unable to do this by themselves. We present our strategy and its design along with some initial performance results.

The UICC Telepathology Consultation Center. International Union Against Cancer. A global approach to improving consultation for pathologists in cancer diagnosis.

The morphologic diagnosis of tumor specimens with precise tumor typing, staging, and grading remains the basis of almost all cancer treatments. Thus, in each tumor case, a histologic diagnosis of the highest quality should be the physician's priority. In approximately 10-20% of tumor cases, diagnostic uncertainty remains to some degree, requiring a second opinion in determining the biologic behavior, the histogenesis, the grade of dedifferentiation, or any other parameter. Facilitating the communication between pathologists and the exchange of cases, telepathology gains more and more importance. To benefit from this technical development, the International Union Against Cancer (UICC) has decided to establish a Telepathology Consultation Center (UICC-TPCC) for interested pathologists around the world. The communication and exchange of histologic images works via the Internet. To ensure constant documentation, a case-based data base and image archive is used. Special TPCC software handles all requests to the TPCC and controls the interaction among requesting pathologists, TPCC, and UICC experts (transferring, reading, answering, logging, storing, etc.). All necessary data for controlling the telepathology service are stored in a customized SQL data base. The necessary equipment for the requesting pathologist is a personal computer; a digital or television camera/frame grabber, which is attached to a microscope; and access to the Internet. The requesting party contacts the TPCC's World Wide Web server and uploads the images and the clinical data of their case. To ensure uninterrupted functioning, the hardware will be part of a high-level communication center, which is connected via ATM (asynchronous transfer mode, 155 megabits per second) to the Internet. The UICC has decided to establish the TPCC at the Institute of Pathology at the Charité, Humboldt-University, Berlin, Germany. The TPCC will not make the diagnoses itself but will involve an affiliated specialized expert pathologist. He or she will be on the panel of UICC experts who will constitute the "diagnostic backbone" of the TPCC. The center will function as follows: If a pathologist anywhere on the globe is confronted with the diagnosis of a difficult tumor case, he takes digitized histologic images (5-40 in number) and sends them along with sufficient clinical data to the server of the UICC-TPCC, asking for a second opinion. The center checks the case and transfers it to one of the UICC experts. This expert makes his or her diagnostic suggestion, which is then transferred back to the requesting pathologist via the UICC-TPCC. The UICC-TPCC will be able to provide rapid and inexpensive diagnostic aid to pathologists all over the world, offering the possibility of a second opinion in accordance with the UICC-TNM and World Health Organization (WHO) standards. During the first and second year, the UICC-TPCC will be financed by sponsors. Telepathology makes the distribution of new developments of diagnostic standards, e.g., of the TNM system, WHO terminology, new tumor classifications, and updated information on actual technologies, globally accessible in a direct and rapid way. It also enables a high quality of education and teaching.

Quick selection of representative protein chain sets based on customizable requirements.

Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification have been proposed, and several databases have been constructed using these methods. Since some proteins with very similar sequences may exhibit structural diversities, we have proposed PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), which strategy of selection is based not only on sequence similarity but also on structural similarity. Forty-eight representative sets whose similarity criteria were predetermined were made available over the World Wide Web (WWW). However, the sets were insufficient in number to satisfy users researching protein structures by various methods. We have improved the system for PDB-REPRDB so that the user may obtain a quick selection of representative chains from PDB. The selection of representative chains can be dynamically configured according to the user's requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. This paper describes the method we use to classify chains and select the representatives in the system. We also describe the interface used to set the parameters.

ProtEST: protein multiple sequence alignments from expressed sequence tags.

An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed. A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for > 58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe. The average family size of the resulting alignments of translated EST sequences contained > 10 sequences. In a cross-validated test of protein secondary structure prediction, alignments from the new procedure led to an improvement of 3.4% average Q3 prediction accuracy over single sequences. The ProtEST method is available as an Internet World Wide Web service http://barton.ebi.ac.uk/servers/protest.html+ ++ The Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at http://www.sanger.ac.uk/Software/Wise2 geoff@ebi.ac.uk

Accessing endoscopic images for remote conference and diagnosis using WWW server with a secure socket layer.

Out of 137 hospitals in Niigata prefecture, 13 are connected to the Internet. The number of private clinics using the Internet has also increased. It is thought that an endoscopic information exchange over the Internet connection is useful for the cooperation between hospitals, clinics and organizations in related fields. A conventional World Wide Web (WWW) server of endoscopic images has been built around a compressed JPEG (Joint Panel Expert Group) format, for remote conferences and diagnoses. It has been made secure using a proxy server, a firewall server and a Secure Socket Layer (SSL). It is easy to access the server and view these endoscopic images using the usual homepage browsing method. Ordinarily, gastroenterologists would diagnose lesions with endoscopy in most cases. It is suggested that this conventional WWW server will be effective for remote conferences in some cases, even consultation will be possible.

Bioinformatics in protein analysis.

The chapter gives an overview of bioinformatic techniques of importance in protein analysis. These include database searches, sequence comparisons and structural predictions. Links to useful World Wide Web (WWW) pages are given in relation to each topic. Databases with biological information are reviewed with emphasis on databases for nucleotide sequences (EMBL, GenBank, DDBJ), genomes, amino acid sequences (Swissprot, PIR, TrEMBL, GenePept), and three-dimensional structures (PDB). Integrated user interfaces for databases (SRS and Entrez) are described. An introduction to databases of sequence patterns and protein families is also given (Prosite, Pfam, Blocks). Furthermore, the chapter describes the widespread methods for sequence comparisons, FASTA and BLAST, and the corresponding WWW services. The techniques involving multiple sequence alignments are also reviewed: alignment creation with the Clustal programs, phylogenetic tree calculation with the Clustal or Phylip packages and tree display using Drawtree, njplot or phylo_win. Finally, the chapter also treats the issue of structural prediction. Different methods for secondary structure predictions are described (Chou-Fasman, Garnier-Osguthorpe-Robson, Predator, PHD). Techniques for predicting membrane proteins, antigenic sites and postranslational modifications are also reviewed.

The promise of a voice-enabled Web

Many computing professionals have heard of XML, and some use it to describe text, images and other data with rich structure. The author discusses an innovative use of XML, called VoiceXML, to support human-computer dialogs via spoken input and audio output. VoiceXML defines dialogs between humans and machines in terms of audio files to be played, text-to-speech synthesis and speech recognition capabilities, and touch-tone input. The author reviews the existing architectures for World Wide Web and telephone services, describes how VoiceXML enables consolidation of service logic for Web and phone, and summarizes the features of the VoiceXML 1.0 specification. Implementation of VoiceXML clients and VoiceXML services has begun in many of the VoiceXML Forum's member companies and will soon be available in the marketplace. The World Wide Web Voice Browser working group has adopted VoiceXML 1.0 as the basis for the dialog markup language that is part of its speech user interface framework.

Using a Firewall Product to Improve the security of a World Wide Web Server

Servers that connect to the World Wide Web (WWW) need to be protected from potential attack. A firewall product can make it more difficult for would-be intruders to compromise an organization's information assets. However, installing a firewall does not guarantee that no compromise will occur. Reasonable precautions need to be taken when installing and operating a firewall product.