WWW Interface Research Articles

Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases.

In spite of many efforts, the prediction of the location of proteins in eukaryotic cells (cytoplasm, mitochondrion or chloroplast) is still far from straightforward. In some cases (e.g. ribosomal proteins and aminoacyl-tRNA synthetases) both the cytoplasmic proteins and their organellar counterparts are encoded by the nuclear genome. A factorial correspondence analysis of the codon usage in yeast and Caenorhabditis elegans shows that the codon usage of those nuclear genes encoding ribosomal proteins or aminoacyl-tRNA synthetases is markedly different, depending on the final location of the proteins (cytoplasmic or mitochondrial). As a consequence, the location of such proteins-whose sequences are now frequently determined by systematic genomic sequencing-can be easily and quickly predicted. A WWW interface has been developed, aimed at providing a user-friendly tool for codon usage pattern analysis. It is available from http://www.genetique.uvsq.fr/afc.html

TransTerm, the translational signal database, extended to include full coding sequences and untranslated regions.

TransTerm is a database of mRNA sequences and parameters useful for detecting translational control signals in general. TransTerm-98 has been expanded beyond previous years to include full coding sequences and UTRs, while retaining the original small contexts about the coding sequence start- and stop-codons. The database contains more than 130 000 non-redundant coding sequences with associated untranslated regions (UTRs) from over 450 species. This includes the complete genomes of 12 prokaryotic and one eukaryotic organism. Several coding sequence parameters are available: coding sequence length, Nc, GC3 and, when it is computable, Codon Adaptation Index (CAI). Codon usage tables and summaries of start- and stop-codon contexts are also included. TransTerm-98 has both a relational database form with a WWW interface and a flatfile format, also available by Internet browser. TransTerm is available at: http://biochem.otago.ac.nz:800/Transterm/homepage.h tml

Thermodynamic Database for Protein-Nucleic Acid Interactions

Protein-nucleic acid interaction plays an essential role in the regulation of gene expression. Structural and binding information provides insight into the mechanism of protein-nucleic acid recognition. Although there are structural databases for protein-nucleic acid complexes, there exists no database for protein-nucleic acid binding. Thus, we have decided to develop the Thermodynamic Database for Protein-Nucleic Acid Interactions. It contains several important thermodynamic parameters, experimental conditions, structural information about proteins, nucleic acids and of the complex, and literature information. This database will be helpful for understanding the mechanism of proteinnucleic acid recognition. A WWW interface will help users to search the data based on various conditions with different sorting options for outputs.

ProTherm: Thermodynamic Database for Proteins and Mutants.

The first release of the Thermodynamic Database for Proteins and Mutants (ProTherm) contains more than 3300 data of several thermodynamic parameters for wild type and mutant proteins. Each entry includes numerical data for unfolding Gibbs free energy change, enthalpy change, heat capacity change, transition temperature, activity etc., which are important for understanding the mechanism of protein stability. ProTherm also includes structural information such as secondary structure and solvent accessibility of wild type residues, and experimental methods and other conditions. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm is cross-linked with NCBI PUBMED literature database, Protein Mutant Database, Enzyme Code and Protein Data Bank structural database. Moreover, all the mutation sites associated with each PDB structure are automatically mapped and can be directly viewed through 3DinSight developed in our laboratory. The database is available at the URL, http://www.rtc.riken.go.jp/protherm.htm l

Detection of Apoptotic Domains Against KEGG Database by the HMM Search

We have developed the knowledge base which consists of apoptotic molecular interactions [1], and provided the WWW interface for it. This database and user interfaces enabled us to find out entries containing different information about cell death. This information tells us that the apoptotic molecular interactions are supposed to be controlled under a series of specific conserved domains, like Bcl-2 homology domain, death domain or death effector domain. So the viewpoint of domain seems to be more effective, rather than the entire sequence, when analyzing pathways, molecules, genes and genomes, which are concerned with apoptosis. In this study, we collected a few hundred domain sequences of apoptotic interactions from our database, made 14 hidden Markov models for the domain groups, and searched against KEGG/GENES database [2] with those HMMs (hidden Markov models) to detect conserved domains.

Progress of ProTherm: Thermodynamic Database for Proteins and Mutants

Thermodynamic data for proteins are important for understanding the mechanism of protein stability. Pfeil [1] collected a set of thermodynamic data on protein folding and stability from experimental studies. Recently, we have developed an electronically accessible Thermodynamic Database for Proteins and Mutants (ProTherm) [2], which includes several thermodynamic data (unfolding Gibbs free energy change, enthalpy change, heat capacity change, transition temperature, activity, etc.), structural information (secondary structure, solvent accessibility, etc.), measuring methods, experimental conditions and literature information. We have developed a WWW interface to facilitate searching the database and sorting outputs. At present, the number of data has been increased to more than 5,500 covering the latest experimental data and several new features have been included in the database.

IR Spectra Simulation and Information Processing on the WWW

Substance identification by IR-spectroscopic methods generally is performed by comparing the measured spectrum with a reference spectrum from a database. If the desired spectrum is not contained in the database, another method of substance identification has to be found.Based on neural network techniques, we have developed a method which provides rapid access to simulated reference spectra. Within the scope of the 'TeleSpec-Telecooperation in Spectroscopy'-Project, this algorithm has been made available through a WWW interface. With a JAVA-enabled Web browser, interactive spectra prediction experiments can be performed.

W2H: WWW interface to the GCG sequence analysis package.

The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due to the lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearly the same functionality as the X-windows interface WPI. The new WWW interface (W2H) to the GCG Sequence Analysis Software Package (Wisconsin Package) supports modern Web technologies, like client-pull method, or embedded scripting language, and provides a reasonable platform independence. The interface is quite comprehensive with advanced features like sequence selector, search set builder, enzyme chooser, access to sequence databases, uploading client files to the GCG server or displaying and manipulating graphical outputs in addition to GCG analysis programs. W2H also manages secure access to both GCG server and user data. For special environments, like workshops, conferences and company intranets, there is a special mode (Intranet mode) with less security constraints. The behaviour of W2H is mostly controlled by meta-data files describing the applications and giving a base for dynamic creation of HTML documents. This paper presents mainly the development approaches used, and architectural design aspects of W2H. W2H is available by ftp://ftp.ebi.ac. uk/pub/software/unix/w2h or ftp://genome.dkfz-heidelberg.de/pub/w2h m.senger@ebi.ac.uk

Hypermedia learning environments limit access to information

Audit trails and questionnaires were used to evaluate students' use of a highly interactive hypermedia learning environment. The learning material under investigation had similar functionality to a WWW interface and was composed of images and text combined with rollover and clickable maps, hypertext links and interactive questions. Every interaction a student made was logged in the audit trail, and a method of analysing the audit trails was applied to measure the amount of information accessed by each student. The most successful student accessed only 32% of the available information in 93 minutes, and each student studied different material to the others. Students overestimated how much information they had accessed from the total available, with those accessing the least overestimating comparatively more. The interactive strategy adopted by learners affected the amount of information accessed, and it was concluded that the increasing use of interactive hypermedia in teaching highlights the need for further research in order to ensure that some students are not systematically disadvantaged.

A WWW-assisted fax system for Internet fax-to-fax communication

This paper describes a WWW-assisted fax system (WAX) that is developed to provide reliable and enhanced Internet fax-to-fax communication. It integrates the easy-to-use WWW interface with conventional faxing procedures, resulting in an Internet fax system which not only circumvents the cost of long distance fax charges but also adds enhanced functionality not otherwise possible. The WAX system comprises two gateways, namely, the Fax-In and the Fax-Out Gateways. The Fax-In Gateway accepts fax messages over Public Switched Telephone Network (PSTN) and stores them in a transit database. The system interfaces with the user over the WWW to provide access to his stored faxes, with the basic ability to send them out over the Internet to recipients. The Fax-Out Gateway receives fax files from the Fax-In Gateway through the Internet and transmits them out to the intended recipients via the local PSTN. WAX users do not require any additional hardware except for a fax machine and a personal computer with Internet connectivity to gain access to WAX via any WWW browser. In addition, WAX provides a host of other enhanced features such as the ability to construct mini-faxes from a single incoming fax as well as dynamically attach cover notes to outgoing faxes.

IXDB, an X chromosome integrated database.

The integrated X chromosome database (IXDB) is a repository for physical mapping data of the human X chromosome. Its current content is the result of a strict integration of data stemming from many different sources. The main features of IXDB include a flexible and extendible schema, a comfortable and fully cross-referenced WWW interface (http://ixdb.mpimg-berlin-dahlem.mpg.de ) and a graphical map viewer implemented in JAVA. The database stores objects used in physical mapping as well as the maps resulting from this work, but a strong emphasis is placed on recording experiments that connect objects together. This should greatly contribute to fulfilling one of the major goals of the database: to support the construction of an integrated physical, genetic, transcript and sequence map of the human X chromosome.

ProTherm: Thermodynamic Database for Proteins and Mutants

The first release of the Thermodynamic Database for Proteins and Mutants (ProTherm) contains more than 3300 data of several thermodynamic parameters for wild type and mutant proteins. Each entry includes numerical data for unfolding Gibbs free energy change, enthalpy change, heat capacity change, transition temperature, activity etc., which are important for understanding the mechanism of protein stability. ProTherm also includes structural information such as secondary structure and solvent accessibility of wild type residues, and experimental methods and other conditions. A WWW interface enables users to search data based on various conditions with different sorting options for outputs. Further, ProTherm is cross-linked with NCBI PUBMED literature database, Protein Mutant Database, Enzyme Code and Protein Data Bank structural database. Moreover, all the mutation sites associated with each PDB structure are automatically mapped and can be directly viewed through 3DinSight developed in our laboratory. The database is available at the URL, http://www.rtc.riken.go.jp/protherm.htm l

World Wide Web interface for advanced SPECT reconstruction algorithms implemented on a remote massively parallel computer

Data from Single Photon Emission Computed Tomography (SPECT) studies are blurred by inevitable physical phenomena occurring during data acquisition. These errors may be compensated by means of reconstruction algorithms which take into account accurate physical models of the data acquisition procedure. Unfortunately, this approach involves high memory requirements as well as a high computational burden which cannot be afforded by the computer systems of SPECT acquisition devices. In this work the possibility of accessing High Performance Computing and Networking (HPCN) resources through a World Wide Web interface for the advanced reconstruction of SPECT data in a clinical environment was investigated. An iterative algorithm with an accurate model of the variable system response was ported on the Multiple Instruction Multiple Data (MIMD) parallel architecture of a Cray T3D massively parallel computer. The system was accessible even from low cost PC-based workstations through standard TCP/IP networking. A speedup factor of 148 was predicted by the benchmarks run on the Cray T3D. A complete brain study of 30 (64×64) slices was reconstructed from a set of 90 (64×64) projections with ten iterations of the conjugate gradients algorithm in 9 s which corresponds to an actual speed-up factor of 135. The technique was extended to a more accurate 3D modeling of the system response for a true 3D reconstruction of SPECT data; the reconstruction time of the same data set with this more accurate model was 5 min. This work demonstrates the possibility of exploiting remote HPCN resources from hospital sites by means of low cost workstations using standard communication protocols and an user-friendly WWW interface without particular problems for routine use.

The Sequence Alerting Server--a new WEB server.

A Sequence Alerting Server with a WWW interface is described which informs users with query sequences in database searches about new entries in protein databases related to their query. The server address is http://www.bork.embl-heidelberg.de/alerting/.

A simple WWW interface and quick response system-information query system for cross-sectional body dimensions.

We developed a query and analysis system for normal growth measurement of Japanese children on our WWW server using CGI. It has two subsystems. The first shows standard height and standard weight calculated by height. This subsystem can calculate the difference between measured height and the standard along with deviation and the ratio of measured weight to the standard weight. The second shows standard height, weight, head circumference, and chest circumference. This subsystem can calculate differences between the measurements and the standard as well as deviation. Because of the low amount of output required, very short turn-around time was required. This system also allows use of the same interface no matter which brand terminal is used and has wide reusability. This system will save doctors and nurses the difficulty of looking up a child's data, then having to make the calculation. We also compare the merits of CGI and Java.

A WWW Interface for Viewing and Searching Sets of Digital Images

As microscope images are increasingly being created and stored digitally, researchers are in need of tools to help them organize and quickly search these collections. Because of the large amount of storage taken up by digital images they are frequently kept on bulk storage systems remote from the microscopist’s PC or workstation. The interface to these mass storage systems may be awkward and viewing large, remotely stored images can be very slow, making it difficult for the user to find a desired image.The LBNL Image Library was designed and implemented to provide a system to help researchers organize, browse and search through digital image collections, especially collections where the original images are stored off-line in a mass storage system. We also wanted to facilitate co-operative research by allowing access to the images by specified users at local and remote sites.

A WWW interface to the OMNIS/Myriad literature retrieval engine

Cataloguing and searching procedures in traditional library systems are expensive, time-consuming and often incomplete. OMNIS is a novel multimedia information retrieval system for the administration of documents in libraries and offices. Using the fulltext database system Myriad combined with scanning and OCR technologies it offers the disclosing, archiving and searching functions at drastically reduced costs with much more precision. Documents may contain page images, full-length PostScript or other medial information and offer the user a much better insight into documents. At Technische Universität München a considerable number of computer science documents have been made searchable by a simple fulltext query language. To make this document retrieval system available to WWW clients the OMNIS document access function was implemented as OMNIS-WWW server which is already in operation. This paper contains the substantial features of OMNIS (especially its searching function) and discusses the concepts and the implementation of its WWW server. The development of OMNIS is promoted by DFG (Deutsche Forschungsgemeinschaft) and DFN-Verein (Deutsches Forschungsnetz) [6].

WWW interface to the ESIS services at ESRIN and CDS

WWW interface to the ESIS services at ESRIN and CDS