WWW Interface Research Articles

Stellar parameters for the central star of the planetary nebula PRTM 1 using the German Astrophysical Virtual Observatory service TheoSSA

The German Astrophysical Virtual Observatory (GAVO) developed the registered service TheoSSA (theoretical stellar spectra access) and the supporting registered VO tool TMAW (Tuebingen Model-Atmosphere WWW interface). These allow individual spectral analyses of hot, compact stars with state-of-the-art non-local thermodynamical equilibrium (NLTE) stellar-atmosphere models that presently consider opacities of the elements H, He, C, N, O, Ne, Na, and Mg, without requiring detailed knowledge about the involved background codes and procedures. Presently, TheoSSA provides easy access to about 150000 pre-calculated stellar SEDs and is intended to ingest SEDs calculated by any model-atmosphere code. In the case of the exciting star of PRTM 1, we demonstrate the easy way to calculate individual NLTE stellar model-atmospheres to reproduce an observed optical spectrum. We measured Teff = 98000 +/- 5000 K, log (g / cm/s**2) = 5.0 (+0.3/-0.2) and photospheric mass fractions of H = 7.5 x 10**-1 (1.02 times solar), He = 2.4 x 10**-1 (0.96), C = 2.0 x 10**-3 (0.84), N = 3.2 x 10**-4 (0.46), O = 8.5 x 10**-3 (1.48) with uncertainties of +/- 0.2 dex. We determined the stellar mass and luminosity of 0.73 (+0.16/-0.15) Msun and log (L / Lsun) = 4.2 +/- 0.4, respectively.

Teaching High Performance Computing Using BeesyCluster and Relevant Usage Statistics*

The paper presents motivations and experiences from using the BeesyCluster middleware for teaching high performance computing at the Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology. Features of BeesyCluster well suited for conducting courses are discussed including: easy-to-use WWW interface for application development and running hiding queuing systems, publishing applications as services and running in a sandbox by novice users, team work and workflow management environments. Additionally, practical experiences are discussed from courses: High Performance Computing Systems and Architectures of Internet Services. For the former, activities such as the number of team work activities, numbers of applications run on clusters and the number of WWW user sessions are shown over the period of one semester. Results of survey from a general course on BeesyCluster for HPC conducted for the university staff and students are also presented.

Biomat _dBase: A Database on Biomaterials

Biomaterial science provides a platform for the development of bio-artificial implants. Growth or development of engineered tissues for the purpose of repairing, restoring and enhancing the function of a damaged tissue or organ needs designed biomaterials. The most studied tissue engineering strategy consists on using cells growth factors and temporary three-dimensional (3D) porous scaffolds. 3D scaffolds play a very important role in the success of tissue engineering and regenerative medicine. They provide structural support for cells to proliferate and maintain their differentiated phenotype and permit the convenient delivery of cells into the patients. Several features of scaffold can influence the cell growth and its functions. The artificial extracellular matrices can be produced from different biomaterials including ceramics, natural or synthetic polymers and composites. Recent discoveries and innovations in this emerging field adopt varieties of techniques ranging from biotechnology to material science and nanotechnology. The result is a huge amount of data. To maintain and keep updated, this would not be an easy task. New advances in computers and information technology help to create and organize the databases quite easy. Their contents can easily be accessed, managed and updated. A WWW interface benefits the users to search the different types of data based on the types of biomaterials, their abundance, structure and applications. This provides the scope and archive of information on this emerging field of biomaterials to the global scientific community. The database is freely accessible through http://dbbiomat.iitkgp.ernet.in.

EuHCVdb: the European hepatitis C virus database

The hepatitis C virus (HCV) genome shows remarkable sequence variability, leading to the classification of at least six major genotypes, numerous subtypes and a myriad of quasispecies within a given host. A database allowing researchers to investigate the genetic and structural variability of all available HCV sequences is an essential tool for studies on the molecular virology and pathogenesis of hepatitis C as well as drug design and vaccine development. We describe here the European Hepatitis C Virus Database (euHCVdb, ), a collection of computer-annotated sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as well as three-dimensional (3D) molecular models of proteins. A WWW interface has been developed to facilitate database searches and the export of data for sequence and structure analyses. As part of an international collaborative effort with the US and Japanese databases, the European HCV Database (euHCVdb) is mainly dedicated to HCV protein sequences, 3D structures and functional analyses.

ON-LINE DELTA ADAPTIVE TOOLBOX FOR THE SECOND ORDER SYSTEMS

The MATLAB® Web Server enables to create MATLAB applications that use the capabilities of the World Wide Web to send data to MATLAB for computation and to display the results in a Web browser. The developed Delta Adaptive Toolbox is accessible via WWW interface. Toolbox demonstrates properties of delta adaptive controllers and recursive least square methods for the second order systems. There are described one of more than ten controllers and one of three modifications of recursive least square methods in the contribution.

PINT: Protein-protein Interactions Thermodynamic Database

The first release of Protein–protein Interactions Thermodynamic Database (PINT) contains >1500 data of several thermodynamic parameters along with sequence and structural information, experimental conditions and literature information. Each entry contains numerical data for the free energy change, dissociation constant, association constant, enthalpy change, heat capacity change and so on of the interacting proteins upon binding, which are important for understanding the mechanism of protein–protein interactions. PINT also includes the name and source of the proteins involved in binding, their Protein Information Resource, SWISS-PROT and Protein Data Bank (PDB) codes, secondary structure and solvent accessibility of residues at mutant positions, measuring methods, experimental conditions, such as buffers, ions and additives, and literature information. A WWW interface facilitates users to search data based on various conditions, feasibility to select the terms for output and different sorting options. Further, PINT is cross-linked with other related databases, PIR, SWISS-PROT, PDB and NCBI PUBMED literature database. The database is freely available at

Debris disk radiative transfer simulation tool (DDS)

A WWW interface for the simulation of spectral energy distributions of optically thin dust configurations with an embedded radiative source is presented. The density distribution, radiative source, and dust parameters can be selected either from an internal database or defined by the user. This tool is optimized for studying circumstellar debris disks where large grains ( a grain ≫ 1 μ m ) are expected to determine the far-infrared through millimeter dust reemission spectral energy distribution. The tool is available at http://aida28.mpia-hd.mpg.de/~swolf/dds. Program summary Title of program:Debris Disk Radiative Transfer Simulator (DDS) Catalogue identifier:ADVV Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVV Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:none Computers:PC with Intel(R) XEON(TM) 2.80 GHz processor Operating systems or monitors under which the program has been tested:SUSE Linux 9.1 Programming language used:Fortran 90 (for the main program; furthermore Perl, CGI and HTML) Memory required to execute with typical data:10 8 words No. of bits in a word:8 No. of lines in distributed program, including test data, etc.:44 636 No. of bytes in distributed program, including test data, etc.: 4 806 280 Distribution format:tar.gz Nature of the physical problem:Simulation of scattered light and thermal reemission in arbitrary optically dust distributions with spherical, homogeneous grains where the dust parameters (optical properties, sublimation temperature, grain size) and SED of the illuminating/heating radiative source can be arbitrarily defined (example application: [S. Wolf, L.A. Hillenbrand, Astrophys. J. 596 (2003) 603]). The program is optimized for studying circumstellar debris disks where large grains (i.e. with large size parameters) are expected to determine the far-infrared through millimeter dust reemission spectral energy distribution. Method of solution:Calculation of the dust temperature distribution and dust reemission and scattering spectrum in the optically thin limit. Restrictions on the complexity of the problem:(1) The approach to calculate dust temperatures and dust reemission spectra is only valid in the optically thin regime. The validity of this constraint is verified for each model during the runtime of the code. (2) The relative abundances of different grains can be arbitrarily chosen, but must be constant outside the dust sublimation region, i.e. the shape of the (arbitrary) radial dust density distribution outside the dust sublimation region is the same for all grain sizes and chemistries. (3) The size of upload files (such as the dust density distribution, optical data of the dust grains, stellar spectral energy distribution, etc.) is limited (see http://aida28.mpia-hd.mpg.de/~swolf/dds/ for current file size limits). However, the resulting limitation to the complexity of possible model definitions is marginal only. Typical running time:3 sec–30 min (depending on the complexity of the model). Unusual features of the program:The program as provided through the CPC Program Library is equipped with an HTML user interface. It is installed and available at http://aida28.mpia-hd.mpg.de/~swolf/dds.

The Inorganic Crystal Structure Database (ICSD)—Present and Future

The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of crystal structure entries for inorganic materials. ICSD is produced by Fachinformationszentrum Karlsruhe, Germany, and the National Institute of Standards and Technology, US. The WWW interface is developed in cooperation with the Institut Laue-Langevin, Grenoble. The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. ICSD includes records of all inorganic crystal structures with atomic coordinates published since 1913. The data base contains 70 102 records as of July 2003. All data are recorded by experts and are checked several times. Apart from updating, data integrity and completeness are important objectives. Incorporation of missing structures, evaluation and correction of data, with the help of authors, users and experts are ongoing activities. This review article gives an overview of the product portfolio and the current activities.

PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification.

We have developed a bioinformatics tool named PAINT that automates the promoter analysis of a given set of genes for the presence of transcription factor binding sites. Based on coincidence of regulatory sites, this tool produces an interaction matrix that represents a candidate transcriptional regulatory network. This tool currently consists of (1) a database of promoter sequences of known or predicted genes in the Ensembl annotated mouse genome database, (2) various modules that can retrieve and process the promoter sequences for binding sites of known transcription factors, and (3) modules for visualization and analysis of the resulting set of candidate network connections. This information provides a substantially pruned list of genes and transcription factors that can be examined in detail in further experimental studies on gene regulation. Also, the candidate network can be incorporated into network identification methods in the form of constraints on feasible structures in order to render the algorithms tractable for large-scale systems. The tool can also produce output in various formats suitable for use in external visualization and analysis software. In this manuscript, PAINT is demonstrated in two case studies involving analysis of differentially regulated genes chosen from two microarray data sets. The first set is from a neuroblastoma N1E-115 cell differentiation experiment, and the second set is from neuroblastoma N1E-115 cells at different time intervals following exposure to neuropeptide angiotensin II. PAINT is available for use as an agent in BioSPICE simulation and analysis framework (www.biospice.org), and can also be accessed via a WWW interface at www.dbi.tju.edu/dbi/tools/paint/.

Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription.

We have generated a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of analysis tools that allow de novo discovery of regulatory motifs, along with refinement and in-depth investigation of fully or partially characterized motifs. The presented discovery and analysis tools are fundamentally different from existing tools in their basic rational, statistical background and specificity and sensitivity towards true regulatory elements. We thus anticipate that the service will be of great importance to the experimental and computational biology communities alike. The motif discovery and diagnosis workbench is available at http://longitude.weizmann.ac.il/rMotif/.

JetWeb: A WWW interface and database for Monte Carlo tuning and validation

A World Wide Web interface to a Monte Carlo tuning facility is described. The aim of the package is to allow rapid and reproducible comparisons to be made between detailed measurements at high-energy physics colliders and general physics simulation packages. The package includes a relational database, a Java servlet query and display facility, and clean interfaces to simulation packages and their parameters.

A Web-based Database System for Providing Technical Information on ATM Networking Platforms

This paper presents a Web-based database hosting technical information about pioneering ATM networking platforms, associated research activities engaging these platforms, and related important trials conducted in the framework of these research activities. The paper outlines the organisation and structure of the information content in the database and discusses methods of access through the WWW interface. Besides the “static” information offered by the database, other Java-based tools provide for the on-line monitoring of the status of the ATM platforms and for manipulating data arising from technological trials on these platforms. The integration of these tools with the database, under a common WWW interface is discussed.

New Trends in Distance Learning Utilising Next Generation Multimedia Networks

Bandwidth capabilities of next generation networks have turned interactive multimedia services to a cost effective reality, targeting not only large companies, but SMEs and individual users as well. An application with direct social impact is tele-teaching and in the broader sense distance learning. A large numbers of colleges, universities, and other higher education institutions already offer online courses to their local and remote students, via new methods of education. In this paper, combining the WWW, the H.323/MPEG-4 protocol family and the CORBA model, we specify an open system and network architecture towards the Virtual Classroom realisation. Over this architecture an educational process is described using formal Object Modelling Technique (OMT) rules, while educational services are provided as methods of distributed objects. In this way, a framework is proposed in order to allow educational institutes to publish content in an abstract object-oriented manner, so as to become widely available via the well-known WWW interface.

Recent Developments in ProTherm: Thermodynamic Database for Proteins and Mutants

Due to the rapid progress in genome analysis, complete genome sequences of many organisms become available. Now proteins are the next target for intensive study, as evidenced by the emerging fields such as structural genomics and proteome analysis. In order to elucidate molecular function of proteins, we need to have knowledge of their amino acid sequence and structure. The sequence and structural information, however, is not enough to infer the protein function, because protein is a microscopic entity and its behavior obeys the law of thermodynamics. Thus, the information of thermodynamic quantities of proteins and their interactions is as fundamental as sequence and structural information. Although the databases for sequence and structure are well established and available, databases for thermodynamic quantities on protein stability and interactions are few. Thermodynamic data for proteins are essential not only for understanding the mechanism of protein folding and stability, but also for designing stable mutants. The compilation of thermodynamic data along with the sequence, structural, functional and literature information would be a valuable resource for such studies [2, 4]. Thus, we have designed an electronically accessible database, ProTherm [3], including several thermodynamic parameters, along with sequence and structural information, experimental methods and conditions, and literature information. Further, we have provided a WWW interface to facilitate searching the database, sorting and visualizing the results. Currently ProTherm contains about 12,000 entries.

A real-time hydrological model for flood prediction using GIS and the WWW

The purpose of this paper is to examine the current status of real time hydrological models used for flood nowcasting and hazard mitigation and indicate how WWW-based systems can overcome some of the limitations of existing systems. Whilst hydrologically innovative and robust models are available, they are poorly suited to real time application, are often not well integrated with spatial datasets such as GIS. Current systems also lack flexibility, customisability and accessibility by a range of end users. We describe the development of a Web-based hydrological modelling system that permits integrated handling of real-time rainfall data from a wireless monitoring network. A spatially distributed GIS-based model is integrated on the basis of this incoming data, approximating real-time to produce data on catchment hydrology and runoff. The data can be accessed from any WWW interface, and they can be analysed online using a number of GIS and numerical functions. We discuss the potential users of such a system and the requirements for interfacing model output with these users for hydrological nowcasting and spatial real-time, emergency decision support. Rather than discuss developments in the modelling of hydrology for flood hazard mitigation, this paper focuses on developments in interfacing these models with end users.

Towards a comprehensive collection of diagnostic patterns for protein sequence classification

The PROSITE collection of patterns for family classification of protein sequences requires much manual labour for motif finding and pattern updating, and yet has only moderate classification accuracy . Out of 1026 families with patterns in PROSITE release 16.0, there was only 523 (51%) with a diagnostic pattern, i.e., a pattern which discriminates perfectly between family and non-family sequences in the training set. Therefore, there is a need to find reliable methods for automating the processes of motif-finding and pattern construction, so that improved speed can be combined with greater classification accuracy. In this paper we present our approach to automating the construction of a collection of patterns, and we announce release 1.0 of the pattern collection built by motif-finding by analysis of multiple alignments (MAMA). MAMA is found to improve the classification accuracy over PROSITE by finding many more diagnostic patterns. On 926 tested families, MAMA finds such patterns for 771 (83%). Furthermore, both the average specificity and sensitivity of MAMA patterns are found to be higher than for PROSITE. A WWW interface that allows users to submit sequences and scan for matches in the MAMA pattern collection is available, 1 Located at http://www.his.se/ida/mama . 1 together with a listing of all the patterns in MAMA release 1.0.

The MONS Sky

AbstractThe MONS project on the Rømer satellite aims at studying properties of stellar interiors through observations of oscillations in stellar luminosity and surface temperature. The main targets are stars exhibiting oscillations similar to those observed in the Sun, with very low amplitudes. During the planned two-year lifetime of the mission, around 20 such stars will be observed with the MONS Main Telescope. Additional data on variability of a large number of stars of a broad range of types may be obtained from the Star Trackers. In order to assist in planning of both ground-based science as well as mission science itself, various tools and databases have been or are being developed. These tools are/will be accessible through the MONS Information System (MIS) which can be queried through a WWW interface. One such tool is a clickable map of the full sky with on it the various fields around the designated main targets of MONS. A click on a field leads to information on the stars within those fields which can be of interest for asteroseismic studies.

3DinSight: Integrated Database for Structure, Property and Function of Biomolecules.

3DinSight is an integrated database and search tool for the structure, property and function of biomolecules. 3DinSight consists of an integrated database, a set of search programs, a WWW interface and visualization tools. It has been open to public through the Internet. 3DinSight would help researchers to get insight into the relationship among the structure, property and function of biomolecules.

ProNIT: Thermodynamic Database for Protein-Nucleic Acid Interactions.

Quantitative data of protein-nucleic acid interactions are important for understanding the molecular mechanisms of their recognition and gene regulation. We have developed the database, ProNIT:Thermodynamic Database for Protein-Nucleic Acid Interactions, which contains numerical data for several experimental binding data, structural information of proteins, nucleic acids and the complex, experimental methods and conditions, and functional and literature information. A WWW interface allows users to search for data based on various conditions, and to visualize molecular structures, properties and their interactions. ProNIT is freely available at above URL.

SeqHound: biological sequence and structure database as a platform for bioinformatics research

BackgroundSeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment.ResultsSeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries.ConclusionsThe system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.