WWW Server Research Articles

Sequence-dependent modelling of local DNA bending phenomena: curvature prediction and vibrational analysis.

Bending is a local conformational micropolymorphism of DNA in which the original B-DNA structure is only distorted but not extensively modified. Bending can be predicted by simple static geometry models as well as by a recently developed elastic model that incorporate sequence dependent anisotropic bendability (SDAB). The SDAB model qualitatively explains phenomena including affinity of protein binding, kinking, as well as sequence-dependent vibrational properties of DNA. The vibrational properties of DNA segments can be studied by finite element analysis of a model subjected to an initial bending moment. The frequency spectrum is obtained by applying Fourier analysis to the displacement values in the time domain. This analysis shows that the spectrum of the bending vibrations quite sensitively depends on the sequence, for example the spectrum of a curved sequence is characteristically different from the spectrum of straight sequence motifs of identical basepair composition. Curvature distributions are genome-specific, and pronounced differences are found between protein-coding and regulatory regions, respectively, that is, sites of extreme curvature and/or bendability are less frequent in protein-coding regions. A WWW server is set up for the prediction of curvature and generation of 3D models from DNA sequences (http:@www.icgeb.trieste.it/dna).

Object-oriented design for LHD data acquisition using client-server model

The LHD data acquisition system handles >600 MB data per shot. The fully distributed data processing and the object-oriented system design are the main principles of this system. Its wide flexibility has been realized by introducing the object-oriented method into the data processing, in which the object sharing and class libraries will provide the unified way of data handling for the network client-server programming. The object class libraries are described in C++, and the network object sharing is provided through the commercial software named HARNESS. As for the CAMAC setup, the Java script can use the C++ class libraries and thus establishes the relationship between the object-oriented database and the WWW server. In LHD experiments, the CAMAC system and the Windows NT operating system are applied for digitizing and acquiring data, respectively. For the purpose of the LHD data acquisition, the new CAMAC handling software on Windows NT have been developed to manipulate the SCSI-connected crate controllers. The CAMAC command lists and diagnostic data classes are shared between client and server computers. A lump of the diagnostic data can be treated as part of an object by the object-oriented programming.

MIPS: a database for genomes and protein sequences.

The Munich Information Center for Protein Sequences (MIPS-GSF), Martinsried near Munich, Germany, develops and maintains genome oriented databases. It is commonplace that the amount of sequence data available increases rapidly, but not the capacity of qualified manual annotation at the sequence databases. Therefore, our strategy aims to cope with the data stream by the comprehensive application of analysis tools to sequences of complete genomes, the systematic classification of protein sequences and the active support of sequence analysis and functional genomics projects. This report describes the systematic and up-to-date analysis of genomes (PEDANT), a comprehensive database of the yeast genome (MYGD), a database reflecting the progress in sequencing the Arabidopsis thaliana genome (MATD), the database of assembled, annotated human EST clusters (MEST), and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). MIPS provides access through its WWW server (http://www.mips.biochem.mpg.de) to a spectrum of generic databases, including the above mentioned as well as a database of protein families (PROTFAM), the MITOP database, and the all-against-all FASTA database.

Data-intensive Intra- and Internet applications based on Java, CORBA, and the World Wide Web

Intra/Internet technology has become a key issue in the development of modern systems. Nowadays it is no longer sufficient to present static information pages through the WWW, instead we need interactive applications that may even compute complex results or process large data sets. In this paper, we describe a prototype based on Java and CORBA. Both represent modern concepts that have been developed to fulfill these requirements. Their combination results in the kind of data processing we want to apply to the WWW: First, portable, powerful, modular and even reusable client programs instead of cryptic HTML scripts, second, well-defined interfaces, and, third, efficient server processes separated from the WWW server and its CGI extensions. Communication is controlled by a fault tolerant CORBA layer, which also enables server development using a different language than Java. In this paper, we focus on data-intensive applications, like, e.g., typical database applications and information systems, that are designed to run in Intra/Internet environments. Besides a discussion of CORBA and its data shipping capabilities, we take a closer look at Java and its runtime behavior. Finally, we report on the experiences gathered with our prototype system and its testbed application. Results measured within the last two years show that technology has already moved in the right direction, but performance is still a critical issue. The system described in this paper has also been used to gather experiences with and to influence the new language binding of the Standard Data Access Interface (SDAI) of the Standard for the Exchange of Product Data (STEP, ISO 10303) to Java. SDAI technology is extensively used in engineering applications and together with CORBA and WWW technology it provides the primitives to build on-line information systems, like catalogues or diagnostic systems. © 1999 John Wiley & Sons, Inc.

INFOGENE: a database of known gene structures and predicted genes and proteins in sequences of genome sequencing projects.

INFOGENE is a database of known and predicted gene structures with descriptions of basic functional signals and gene components. It provides a possibility to create compilations of sequences with a given gene feature as well as to accumulate and analyze predicted genes in finished and unfinished sequences from genome sequencing projects. Protein sequence similarity searches in the database of predicted proteins is offered through the BLASTP program. INFOGENE is realized under the Sequence Retrieval System that provides useful links with the other informational databases. The database is available through the WWW server of the Computational Genomics Group at http://genomic.sanger.ac.uk/db.html

A keyword search system for medical doctors to introduce their patients to specialists.

We developed an online keyword search system on a WWW server to help medical doctors to introduce their patients to specialists. The system stores special knowledge and advanced techniques of 287 medical specialists in Kyushu University Hospital. The data set was presented by the medical specialists themselves. Specialists can rewrite their data set using the browser anytime to keep their data set up to date. In addition, the specialists are reminded to keep their data set up to date by direct mail once a year. The system does not use any database management systems. We used only two text files and the "grep" command, one of the basic commands of the UNIX system. Then, it takes less than 1 sec to search one medical specialist's data set from 200 specialists' data sets. The system is useful not only inside the hospital but also for practitioners in the local area.

Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program.

G Protein-Coupled Receptors (GPCRs) constitute a superfamily of receptors that forms an important therapeutic target. The number of known GPCR sequences and related information increases rapidly. For these reasons, we are developing the Viseur program to integrate the available information related to GPCRs. The Viseur program allows one to interactively visualise and/or modify the sequences, transmembrane areas, alignments, models and results of mutagenesis experiments in an integrated environment. This integration increases the ease of modelling GPCRs: visualisation and manipulation improvements enable easier databank interrogation and interpretation. Unique program features include: (i) automatic construction of 'Snake-like' diagrams or hyperlinked GPCR molecular models to HTML or VRML and (ii) automatic access to a mutagenesis data server through the Internet. The novel algorithms or methods involved are presented, followed by the overall complementary features of the program. Finally, we present two applications of the program: (i) an automatic construction of GPCR snake-like diagrams for the GPCRDB WWW server, and (ii) a preparation of the modelling of the 5HT receptor subtypes. The interest of the direct access to mutagenesis results through an alignment and a molecular model are discussed. The Viseur program, which runs on SGI workstations, is freely available and can be used for preparing the modelling of integral membrane proteins or as an alignment editor tool.

Database on the structure of large subunit ribosomal RNA.

The Antwerp database on large subunit ribosomal RNA now contains 607 complete or nearly complete aligned sequences. The alignment incorporates secondary structure information for each sequence. Other information about the sequences, such as literature references, accession numbers and taxonomic information is also available. Information from the database can be downloaded or searched on the rRNA WWW Server at URL http://rrna.uia.ac.be/

The PIR-International Protein Sequence Database.

The Protein Information Resource (PIR; http://www-nbrf.georgetown. edu/pir/) supports research on molecular evolution, functional genomics, and computational biology by maintaining a comprehensive, non-redundant, well-organized and freely available protein sequence database. Since 1988 the database has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new sequence data and new computer technologies. The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available. Full-scale family classification supports comparative genomics research, aids sequence annotation, assists database organization and improves database integrity. The PIR WWW server supports direct on-line sequence similarity searches, information retrieval, and knowledge discovery by providing the Protein Sequence Database and other supplementary databases. Sequence entries are extensively cross-referenced and hypertext-linked to major nucleic acid, literature, genome, structure, sequence alignment and family databases. The weekly release of the Protein Sequence Database can be accessed through the PIR Web site. The quarterly release of the database is freely available from our anonymous FTP server and is also available on CD-ROM with the accompanying ATLAS database search program.

The ENZYME data bank in 1999.

The ENZYME data bank is a repository of information related to the nomenclature of enzymes. In recent years it has become an indispensable resource for the development of metabolic databases. The current version contains information on 3704 enzymes. It is available through the ExPASy WWW server (http://www.expasy.ch/).

New tools and resources for analysing protein structures and their interactions.

The determination of protein structures has furthered our understanding of how various proteins perform their functions. With the large number of structures currently available in the PDB, it is necessary to be able to easily study these proteins in detail. Here new software tools are presented which aim to facilitate this analysis; these include the PDBsum WWW site which provides a summary description of all PDB entries, the programs TOPS and NUCPLOT to plot schematic diagrams representing protein topology and DNA-binding interactions, SAS a WWW-based sequence-analysis tool incorporating structural data, and WWW servers for the analysis of protein-protein interfaces and analyses of over 300 haem-binding proteins.

Modeling Distance Decay Effects in Web Server Information Flows

Previous studies have shown that there is a direct correlation between the popularity of a medium and the cost in transmitting information through that medium. On this basis the World Wide Web may become more important as a mass medium than radio and television. Yet despite the enormous growth in Internet information and Internet‐supported businesses, there has been, as yet, little in the way of quantitative spatial analysis of information flows on the WWW. One major issue is whether or not distance influences the web sites that a user may visit. If distance is a factor, then the location of servers delivering content becomes important. In this paper an analysis of information flows from U.K. academic web servers to the rest of the world is carried out. Using a UNIX utility called ping, the average time taken for a defined amount of information to travel between the United Kingdom and sixty‐six other countries across the Internet was measured. This time measurement known as latency is used as a measure of distance on the Internet. The latency measurements are combined with counts of visitors from each of these countries to approximately one hundred U. K. academic WWW servers and used to build a simple gravity model of WWW information flows. The latency measurements between the United Kingdom and the other countries were gathered over a week in 1996. The counts of visitors relate to the total number of visits to the web servers over various time‐scales for the years 1995 and 1996. We make the assumption that the distance measurements used are relevant to the visit counts. We also assume that all visitors from the .edu domain are geographically located in the United States. The gravity model is used to determine the effect of Internet distance on the number of expected visits to a web server. The study shows that latency values are a useful metric for measuring Internet distance. The results also demonstrate that the number of visitors to a web site falls off with distance on the Internet, as measured by latency values.

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr

Using a WWW-based Mail User Agent for Secure Electronic Mail Service for Health Care Users

WWW-based user interface is presented for secure electronic mail service for healthcare users. Using this method, communications between an electronic mail (WWW) server and users (WWW browsers) can be performed securely using Secure Socket Layer protocol-based Hypertext Transfer Protocol (SSL-HTTP). The mail can be encrypted, signed, and sent to the recipients and vice versa on the remote WWW server. The merit of this method is that many healthcare users can use a secure electronic mail system easily and immediately, because SSL-compatible WWW browsers are widely used and this system can be made available simply by installing a WWW-based mail user agent on a mail server. We implemented a WWW-based mail user agent which is compatible with PEM-based secure mail and made it available to about 16,000 healthcare users. We believe this approach is effective in facilitating secure network-based information exchange among medical professionals.

SharedWeb—a shared virtual environment over the World Wide Web

The design, implementation and experimental results of a multiple-user 3D web-browsing system, called the SharedWeb system, are described in this paper. The system is based on the request–response method of the WWW server. The key features of this system include the ability of the WWW server to remember all the browsers connected to it in order to transmit the messages required to maintain consistent states among browsers. The dead-reckoning technique of distributive interactive simulation (DIS) is used by browsers in order to reduce the number of messages sent onto the network and to satisfy the timing requirement demanded by the virtual environment. The protocol data unit (PDU) defined in DIS is also adapted by the SharedWeb system not only to communicate information among browsers but also to integrate with the DIS environment in the near future. © 1998 John Wiley & Sons, Ltd.

The implementation of an integrated on-line health education system at RMIT

The Faculty of Biomedical and Health Sciences at RMIT has been developing an on-line health education system using a systems thinking approach, to create a learning environment whose basis is supported by Information Technology (IT). The centre-piece of this system is the Faculty Learning Centre, which has been created, both in space and layout, to promote collaborative learning between the students, so that the educator is physically assimilated with the student body. This facility is supplemented by the Faculty WWW server, which has been the main vehicle for course material dissemination to students. To ensure an effective on-line teaching environment, the position of an on-line facilitator has been created, whose responsibilities include both the continual evaluation of the system and the implementation of appropriate system changes. Aspects have included the production of a staff development training program and extensive user documentation. This paper discusses the systems thinking approach used to implement this integrated on-line system, and the establishment of explicit educational rationales in the use of IT to support learning strategies. Some examples of the on-line educational programs are also presented.

WCP—a tool for consistent on-line update of documents in a WWW server

With the growing use of the Web infrastructure as an information provider, it has become necessary to consider the problem of accessing documents from a WWW server in a consistent fashion. When a group of related documents that are very frequently updated are accessed, it is desirable to provide a access semantics in which either only old copies of all the documents in the group are provided or only new copies of the documents are provided. As Web servers are stateless, they do not maintain information about the sequence of documents that are retrieved. Hence, this type of semantics is not provided for a group of documents, and special measures need to be taken to support such semantics. We describe a tool WCP (Web-Copy) that facilitates the on-line update of documents such that the above document access semantics is ensured within a persistent HTTP connection without making any changes to the WWW server program.

Throughput analysis method for TCP/IP communication using monitor-based data

In TCP/IP communication, the effective throughput as seen from the user end is decreased when the load is increased. When such a service is offered by the network provider, there must be management to realize and maintain effective throughput so as to satisfy the user, while considering the cost. This study proposes a method of analysis for the effective throughput based on the packet monitoring technique, in order to reflect the results of management of the network services. In the proposed method of analysis, several metrics for evaluation are prepared, such as the round-trip time (RTT) and the IP datagram loss ratio, in addition to the effective throughput. The effective throughput performance is analyzed as closely related to those metrics. As an example of evaluation by the proposed method, a TCP/IP network is considered, where multiple WWW clients and a WWW server are connected through low-speed links. The relation between the load and the effective throughput is derived, and the effectiveness of the proposed evaluation method is clearly demonstrated. © 1998 Scripta Technica. Electron Comm Jpn Pt 1, 81(4): 20–30, 1998

Version augmented URIs for reference permanencevia an apache module design

The World Wide Web is perhaps the most convenient library resource ever to exist. Yet it also suffers from a critical flaw: WWW document citations existing as clickable links and as standard references in printed documents are quite unreliable. This arises from the ease with which these documents may be altered. Alteration of cited WWW documents may lead to the citations themselves becoming invalid or inaccurate. Printed documents are less prone to such problems due to the greater difficulty in altering or eradicating them. As a consequence of the alterability of WWW documents, the whole traditional system of new work building upon an archive of unchangeable previous work ceases to be valid. For the first time in history, documents are being built upon a shifting foundation to an extent of ever increasing and serious proportions. This work investigates a system aimed at encouraging the stability of WWW documents. In doing so it helps to preserve the accuracy of citations over time. The system presented extends a document's URI (Universal Resource Identifier) to include date or revision information thus allowing document providers to permit users to refer accurately to a particular document version. This paper both describes the system and demonstrates its use. The system is implemented as an Apache WWW server module. The module processes and retrieves documents referenced with extended URIs. It provides a model public domain system for alleviating the problem of content stable WWW documents.

Evaluating electronic journals services and monitoring their usage by means of WWW server log file analysis

Most electronic journals are now Web‐based. This paper introduces the method of WWW server log file analysis and its application to evaluating electronic journals services and in monitoring their usage. Following a short description on the method and its possible application, the main results of a study of WWW server log file analysis of the electronic journal “Review of Information Science” will be presented and discussed. Finally, several concluding remarks will be given.