WWW Server Research Articles

The effects of wide-area conditions on WWW server performance

WWW workload generators are used to evaluate web server performance, and thus have a large impact on what performance optimizations are applied to servers. However, current benchmarks ignore a crucial component: how these servers perform in the environment in which they are intended to be used, namely the wide-area Internet.This paper shows how WAN conditions can affect WWW server performance. We examine these effects using an experimental test-bed which emulates WAN characteristics in a live setting, by introducing factors such as delay and packet loss in a controlled and reproducible fashion. We study how these factors interact with the host TCP implementation and what influence they have on web server performance. We demonstrate that when more realistic wide-area conditions are introduced, servers exhibit very different performance properties and scaling behaviors, which are not exposed by existing benchmarks running on LANs. We show that observed throughputs can give misleading information about server performance, and thus find that maximum throughput, or capacity, is a more useful metric. We find that packet losses can reduce server capacity by as much as 50 percent and increase response time as seen by the client. We show that using TCP SACK can reduce client response time, without reducing server capacity.

DIDACTIC TOOLS ON THE WEB FOR STUDENTS AND TEACHERS: THE ISHTAR SERVER

A didactic project is being developed using multimedia techniques at the Physics Department of the University of Bologna to help both students and teachers. The ISHTAR WWW server comprises several courses on different chapters of physics and a set of tools for helping with the didactical activities. The level of the courses is adapted for students in their last years at high school and in their first years at university, and it is especially designed for students of the life sciences.

Analysis and measurement of the effect of kernel locks in SMP systems

AbstractThis article reports the use of case studies to evaluate the performance degradation caused by the kernel‐level lock. We define the lock ratio as a ratio of the execution time for critical sections to the total execution time of a parallel program. The kernel‐level lock ratio determines how effective programs work on symmetric multiprocessor (SMP) systems. We have measured the lock ratios and the performance of three types of parallel programs on SMP systems with Linux 2.0: matrix multiplication, parallel make, and WWW server programs. Experimental results show that the higher the lock ratio of parallel programs, the worse their performance becomes. Copyright © 2001 John Wiley & Sons, Ltd.

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB).

PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). The previous version of PDB-REPRDB provided 48 representative sets, whose similarity criteria were predetermined, on the WWW. The current version is designed 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. One can obtain a representative list and classification data of protein chains from the system. The current database includes 20 457 protein chains from PDB entries (August 6, 2000). The system for PDB-REPRDB is available at the Parallel Protein Information Analysis system (PAPIA) WWW server (http://www.rwcp.or.jp/papia/).

The SBASE protein domain library, release 8.0: a collection of annotated protein sequence segments.

SBASE 8.0 is the eighth release of the SBASE library of protein domain sequences that contains 294 898 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to most major sequence databases and sequence pattern collections. The entries are clustered into over 2005 statistically validated domain groups (SBASE-A) and 595 non-validated groups (SBASE-B), provided with several WWW-based search and browsing facilities for online use. A domain-search facility was developed, based on non-parametric pattern recognition methods, including artificial neural networks. SBASE 8.0 is freely available by anonymous 'ftp' file transfer from ftp.icgeb.trieste.it. Automated searching of SBASE can be carried out with the WWW servers http://www.icgeb.trieste.it/sbase/ and http://sbase.abc. hu/sbase/.

The European Large Subunit Ribosomal RNA Database.

The European Large Subunit Ribosomal RNA Database compiles all complete or nearly complete large subunit ribosomal RNA sequences available from public sequence databases. These are provided in aligned format and the secondary structure, as derived by comparative sequence analysis, is included. Additional information about the sequences such as literature references and taxonomic information is also included. The database is available from our WWW server at http://rrna.uia.ac.be/lsu/.

The RDP-II (Ribosomal Database Project).

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [Nucleic Acids Res. (2000), 28, 173-174], continued during the past year to add new rRNA sequences to the aligned data and to improve the analysis commands. Release 8.0 (June 1, 2000) consisted of 16 277 aligned prokaryotic small subunit (SSU) rRNA sequences while the number of eukaryotic and mitochondrial SSU rRNA sequences in aligned form remained at 2055 and 1503, respectively. The number of prokaryotic SSU rRNA sequences more than doubled from the previous release 14 months earlier, and approximately 75% are longer than 899 bp. An RDP-II mirror site in Japan is now available (http://wdcm.nig.ac.jp/RDP/html/index.h tml). RDP-II provides aligned and annotated rRNA sequences, derived phylogenetic trees and taxonomic hierarchies, and analysis services through its WWW server (http://rdp.cme.msu.edu/). Analysis services include rRNA probe checking, approximate phylogenetic placement of user sequences, screening user sequences for possible chimeric rRNA sequences, automated alignment, production of similarity matrices and services to plan and analyze terminal restriction fragment polymorphism experiments. The RDP-II email address for questions and comments has been changed from curator@cme.msu.edu to rdpstaff@msu.edu.

Toward Chromosome-Level Comparative Analysis of Vertebrate Genomes

Since the publication of the human draft genome sequence, steady progress around the world is made to analyze the genome. In addition, mouse genome project and other vertebrate genome projects of model organisms are rapidly producing much genomic sequences. Comparative analysis is becoming increasingly important as a tool for genome sequence analysis [3]. In this study, we focus on vertebrate genome sequences of various species, such as human, mouse and rat. The evolutionary conserved regions in human genome sequences are identified effectively by the comparison with those vertebrate genome sequences. The main goal of this research is to identify novel genes and regulatory regions and to elucidate genome-level events in evolution from genome sequences. We have developed a comparative genome system which collects data, compares them, visualizes the results, and produces primer sets using primer3 [6] for the PCR experiments for confirmation of the exon prediction. Users can submit syntenic genomic sequences or select a publicly available syntenic region. The system allow the users to analyze and convert data easily, so that users can browse the various analysis results using PipMaker [4] (WWW server for genome comparison and java application laj), and Alfresco [2] (java application), without producing annotation files on their own.

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Model.it: building three dimensional DNA models from sequence data.

A WWW server is described for creating 3D models of canonical or bent DNA starting from sequence data. Predicted DNA trajectory is first computed based on a choice of di- and tri-nucleotide models (M.G. Munteanu et al., Trends Biochem. Sci. 23, 341-347, 1998); an atomic model is then constructed and optionally energy-minimized with constrained molecular dynamics. The data are presented as a standard PDB file, directly viewable on the user's PC using any molecule manipulation program. The model.it server is freely available at http://www.icgeb.trieste.it/dna/ kristian@icgeb.trieste.it; pongor@icgeb.trieste.it a series of help files is available at the above address.

Application of the distributed database (Data-Free-Way) on the analysis of mechanical properties in neutron irradiated 316 stainless steel

A distributed database system named ‘Data-Free-Way’ for advanced nuclear materials has been developed by the National Research Institute for Metals (NRIM), the Japan Atomic Energy Research Institute (JAERI), the Japan Nuclear Cycle Development Institute (JNC), and the Japan Science and Technology Corporation (JST) under a cooperative agreement. In this paper, features and functions of the system including input data, are described together with a method to share the database among the four organizations as well as examples of the easy accessible search of material properties provided by the system. Results of an analysis of tensile and fatigue properties data on type 316 stainless steel collected by the different organizations and stored in the present system are introduced as an example of attractive utilization of the system. In addition to show the capability of the system some WWW server sites of the Data-Free-Way are introduced with respect to information supply on nuclear materials.

PASS: prediction of activity spectra for biologically active substances.

The concept of the biological activity spectrum was introduced to describe the properties of biologically active substances. The PASS (prediction of activity spectra for substances) software product, which predicts more than 300 pharmacological effects and biochemical mechanisms on the basis of the structural formula of a substance, may be efficiently used to find new targets (mechanisms) for some ligands and, conversely, to reveal new ligands for some biological targets. We have developed a WWW interface for the PASS software. A WWW server for the on-line prediction of the biological activity spectra of substances has been constructed.

Phylogenetic Analyses of the Fungi Based on Large rDNA Data Sets

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Da- tabase Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group sup- port and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequences. The analyses were conducted by us- ing a parsimony jackknifing computer program to search rapidly for supported groups in combination with branch swapping and random addition sequenc- es. The results show that gross topology is very simi- lar. The major differences were with the Ascomycetes, which were not recovered in the RDP tree, and with the Holobasidiomycetes, which were not recovered in the RNA-S tree. Both data sets identify and support many well known fungal groups such as the Gloma- les, Saccharomycetes, Dikaryomycetes, Basidiomy- cetes, Uredinomycetes, Ustilaginomycetes, Euasco- mycetes, Leotiomyceta, Sordariomycetes and the Chaetothyriomycetes. No support was found for some previously proposed groups, including the Chy- tridiomycetes, Taphrinomycotina, Pezizomycotina through Pezizales, Hymenomycetes, Tremellomyce- tes, Leotiomycetes and the Dothideomycetes. The analysis contradicted some other previously proposed groups, among them the Zygomycota, Zygomycetes, Lecanoromycetes and the Sordariomycetidae. Trans- version parsimony performed on the same data sets

Phylogenetic analyses of the fungi based on large rDNA data sets

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Database Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group support and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequences. The analyses were conducted by using a parsimony jackknifing computer program to search rapidly for supported groups in combination with branch swapping and random addition sequences. The results show that gross topology is very similar. The major differences were with the Ascomycetes, which were not recovered in the RDP tree, and with the Holobasidiomycetes, which were not recovered in the RNA-S tree. Both data sets identify and support many well known fungal groups such as the Glomales, Saccharomycetes, Dikaryomycetes, Basidiomycetes, Uredinomycetes, Ustilaginomycetes, Euascomycetes, Leotiomyceta, Sordariomycetes and the Chaetothyriomycetes. No support was found for some previously proposed groups, including the Chytridiomycetes, Taphrinomycotina, Pezizomycotina through Pezizales, Hymenomycetes, Tremellomycetes, Leotiomycetes and the Dothideomycetes. The analysis contradicted some other previously proposed groups, among them the Zygomycota, Zygomycetes, Lecanoromycetes and the Sordariomycetidae. Transversion parsimony performed on the same data sets resulted in extremely poor resolution in both trees and evidently transitional mutations are important contributors to the structure of the trees.

Ab initio Gene Finding in Drosophila Genomic DNA

Ab initio gene identification in the genomic sequence of Drosophila melanogaster was obtained using (human gene predictor) and Fgenesh programs that have organism-specific parameters for human, Drosophila, plants, yeast, and nematode. We did not use information about cDNA/EST in most predictions to model a real situation for finding new genes because information about complete cDNA is often absent or based on very small partial fragments. We investigated the accuracy of gene prediction on different levels and designed several schemes to predict an unambiguous set of genes (annotation CGG1), a set of reliable exons (annotation CGG2), and the most complete set of exons (annotation CGG3). For 49 genes, protein products of which have clear homologs in protein databases, predictions were recomputed by Fgenesh+ program. The first annotation serves as the optimal computational description of new sequence to be presented in a database. Reliable exons from the second annotation serve as good candidates for selecting the PCR primers for experimental work for gene structure verification. Our results shows that we can identify approximately 90% of coding nucleotides with 20% false positives. At the exon level we accurately predicted 65% of exons and 89% including overlapping exons with 49% false positives. Optimizing accuracy of prediction, we designed a gene identification scheme using Fgenesh, which provided sensitivity (Sn) = 98% and specificity (Sp) = 86% at the base level, Sn = 81% (97% including overlapping exons) and Sp = 58% at the exon level and Sn = 72% and Sp = 39% at the gene level (estimating sensitivity on std1 set and specificity on std3 set). In general, these results showed that computational gene prediction can be a reliable tool for annotating new genomic sequences, giving accurate information on 90% of coding sequences with 14% false positives. However, exact gene prediction (especially at the gene level) needs additional improvement using gene prediction algorithms. The program was also tested for predicting genes of human Chromosome 22 (the last variant of Fgenesh can analyze the whole chromosome sequence). This analysis has demonstrated that the 88% of manually annotated exons in Chromosome 22 were among the ab initio predicted exons. The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html.

Tracing and reexecuting operating system calls for reproducible performance experiments

This paper shows how system call traces can be obtained with minimal interference to the system being characterized, and used as realistic, repeatable workloads for experiments to evaluate operating system and file system designs and configuration alternatives. Our system call trace mechanism, called ULTra, captures a complete trace of each UNIX process’s calls to the operating system. The performance impact is normally small, and it runs in user mode without special privileges. Traces can be rerun in two ways: the operating system activity can be reproduced by simply replaying the system calls interspersed with appropriate delays. More interestingly, we also show how the resulting traces can be used to drive full, repeatable reexecution of the captured behaviour. The paper concludes with an evaluation and comparison of the usefulness and accuracy of these techniques for predicting the performance impact of system configuration alternatives. We present two case studies, examining the effect of file system caching on a WWW server’s performance, and the performance benefit of using a local disk instead of an NFS fileserver.

Markov regenerative stochastic Petri nets with general execution policies: supplementary variable analysis and a prototype tool

Stochastic Petri nets (SPNs) with general firing time distributions are considered. Generally timed transitions can have general execution policies: the preemption policy may be preemptive repeat different (prd) or preemptive resume (prs) and the firing time distribution can be marking-dependent. A stationary analysis method covering all possible combinations is presented by means of supplementary variables. The method is implemented in a prototype tool SPNica which is based on Mathematica. The use of the general execution policies is illustrated by a WWW server model.

EMGLib: the enhanced microbial genomes library (update 2000).

As the number of complete microbial genomes publicly available is still growing, the problem of annotation quality in these very large sequences remains unsolved. Indeed, the number of annotations associated with complete genomes is usually lower than those of the shorter entries encountered in the repository collections. Moreover, classical sequence database management systems have difficulties in handling entries of such size. In this context, the Enhanced Microbial Genomes Library (EMGLib) was developed to try to alleviate these problems. This library contains all the complete genomes from prokaryotes (bacteria and archaea) already sequenced and the yeast genome in GenBank format. The annotations are improved by the introduction of data on codon usage, gene orientation on the chromosome and gene families. It is possible to access EMGLib through two database systems set up on WWW servers: the PBIL server at http://pbil.univ-lyon1.fr/emglib.html and the MICADO server at http://locus.jouy.inra.fr/micado

The SBASE protein domain library, release 7.0: a collection of annotated protein sequence segments.

SBASE 7.0 is the seventh release of the SBASE protein domain library sequences that contains 237 937 annotated structural, functional, ligand-binding and topogenic segments of proteins, cross-referenced to all major sequence databases and sequence pattern collections. The entries are clustered into over 1811 groups and are provided with two WWW-based search facilities for on-line use. SBASE 7.0 is freely available by anonymous 'ftp' file transfer from ftp.icgeb. trieste.it. Automated searching of SBASE with BLAST can be carried out with the WWW servers http://www.icgeb.trieste.it/sbase/and http://sbase.abc.hu/sbase/

ProClass protein family database.

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of >155 000 sequence entries retrieved from both PIR-International and SWISS-PROT databases. Approximately 92 000 or 60% of the ProClass entries are classified into approximately 6000 families, including a large number of new members detected by our GeneFIND family identification system. The ProClass motif collection contains approximately 72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including >21 000 matches not listed in PROSITE and mostly detected from unique PIR sequences. To maximize family information retrieval, the database provides links to various protein family, domain, alignment and structural class databases. With its high classification rate and comprehensive family relationships, ProClass can be used to support full-scale genomic annotation. The database, now being implemented in an object-relational database management system, is available for online sequence search and record retrieval from our WWW server at http://pir.georgetown.edu/gfserver/proclass.html