Use of a secure Internet Web site for collaborative medical research.

PubMed

Marshall, W W; Haley, R W

2000-10-11

Researchers who collaborate on clinical research studies from diffuse locations need a convenient, inexpensive, secure way to record and manage data. The Internet, with its World Wide Web, provides a vast network that enables researchers with diverse types of computers and operating systems anywhere in the world to log data through a common interface. Development of a Web site for scientific data collection can be organized into 10 steps, including planning the scientific database, choosing a database management software system, setting up database tables for each collaborator's variables, developing the Web site's screen layout, choosing a middleware software system to tie the database software to the Web site interface, embedding data editing and calculation routines, setting up the database on the central server computer, obtaining a unique Internet address and name for the Web site, applying security measures to the site, and training staff who enter data. Ensuring the security of an Internet database requires limiting the number of people who have access to the server, setting up the server on a stand-alone computer, requiring user-name and password authentication for server and Web site access, installing a firewall computer to prevent break-ins and block bogus information from reaching the server, verifying the identity of the server and client computers with certification from a certificate authority, encrypting information sent between server and client computers to avoid eavesdropping, establishing audit trails to record all accesses into the Web site, and educating Web site users about security techniques. When these measures are carefully undertaken, in our experience, information for scientific studies can be collected and maintained on Internet databases more efficiently and securely than through conventional systems of paper records protected by filing cabinets and locked doors. JAMA. 2000;284:1843-1849.

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Multimedia data repository for the World Wide Web

NASA Astrophysics Data System (ADS)

Chen, Ken; Lu, Dajin; Xu, Duanyi

1998-08-01

This paper introduces the design and implementation of a Multimedia Data Repository served as a multimedia information system, which provides users a Web accessible, platform independent interface to query, browse, and retrieve multimedia data such as images, graphics, audio, video from a large multimedia data repository. By integrating the multimedia DBMS, in which the textual information and samples of the multimedia data is organized and stored, and Web server together into the Microsoft ActiveX Server Framework, users can access the DBMS and query the information by simply using a Web browser at the client-side. The original multimedia data can then be located and transmitted through the Internet from the tertiary storage device, a 400 CDROM optical jukebox at the server-side, to the client-side for further use.

Accessing NASA Technology with the World Wide Web

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Bianco, David J.

1995-01-01

NASA Langley Research Center (LaRC) began using the World Wide Web (WWW) in the summer of 1993, becoming the first NASA installation to provide a Center-wide home page. This coincided with a reorganization of LaRC to provide a more concentrated focus on technology transfer to both aerospace and non-aerospace industry. Use of WWW and NCSA Mosaic not only provides automated information dissemination, but also allows for the implementation, evolution and integration of many technology transfer and technology awareness applications. This paper describes several of these innovative applications, including the on-line presentation of the entire Technology OPportunities Showcase (TOPS), an industrial partnering showcase that exists on the Web long after the actual 3-day event ended. The NASA Technical Report Server (NTRS) provides uniform access to many logically similar, yet physically distributed NASA report servers. WWW is also the foundation of the Langley Software Server (LSS), an experimental software distribution system which will distribute LaRC-developed software. In addition to the more formal technology distribution projects, WWW has been successful in connecting people with technologies and people with other people.

GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide.

PubMed

Chande, Aroon T; Wang, Lu; Rishishwar, Lavanya; Conley, Andrew B; Norris, Emily T; Valderrama-Aguirre, Augusto; Jordan, I King

2018-05-18

Human populations from around the world show striking phenotypic variation across a wide variety of traits. Genome-wide association studies (GWAS) are used to uncover genetic variants that influence the expression of heritable human traits; accordingly, population-specific distributions of GWAS-implicated variants may shed light on the genetic basis of human phenotypic diversity. With this in mind, we developed the GlobAl Distribution of GEnetic Traits web server (GADGET http://gadget.biosci.gatech.edu). The GADGET web server provides users with a dynamic visual platform for exploring the relationship between worldwide genetic diversity and the genetic architecture underlying numerous human phenotypes. GADGET integrates trait-implicated single nucleotide polymorphisms (SNPs) from GWAS, with population genetic data from the 1000 Genomes Project, to calculate genome-wide polygenic trait scores (PTS) for 818 phenotypes in 2504 individual genomes. Population-specific distributions of PTS are shown for 26 human populations across 5 continental population groups, with traits ordered based on the extent of variation observed among populations. Users of GADGET can also upload custom trait SNP sets to visualize global PTS distributions for their own traits of interest.

Optimizing the NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Maa, Ming-Hokng

1996-01-01

The NASA Technical Report Server (NTRS), a World Wide Web report distribution NASA technical publications service, is modified for performance enhancement, greater protocol support, and human interface optimization. Results include: Parallel database queries, significantly decreasing user access times by an average factor of 2.3; access from clients behind firewalls and/ or proxies which truncate excessively long Uniform Resource Locators (URLs); access to non-Wide Area Information Server (WAIS) databases and compatibility with the 239-50.3 protocol; and a streamlined user interface.

ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.

PubMed

Chang, Darby Tien-Hau; Chen, Chien-Yu; Chung, Wen-Chin; Oyang, Yen-Jen; Juan, Hsueh-Fen; Huang, Hsuan-Cheng

2004-07-01

Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the alpha-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/.

Russian and CIS Library Internet Service: An Analysis of WWW-Server Development.

ERIC Educational Resources Information Center

Shraiberg, Yakov

This paper traces the expansion of the Internet into Russian and Commonwealth of Independent States (CIS) libraries from basic access to the development of World Wide Web (WWW) servers. An analysis of the most representative groups of library WWW-servers arranged by projects, by corporate library network, or by geographical characteristics is…

Securing the anonymity of content providers in the World Wide Web

NASA Astrophysics Data System (ADS)

Demuth, Thomas; Rieke, Andreas

1999-04-01

Nowadays the World Wide Web (WWW) is an established service used by people all over the world. Most of them do not recognize the fact that they reveal plenty of information about themselves or their affiliation and computer equipment to the providers of web pages they connect to. As a result, a lot of services offer users to access web pages unrecognized or without risk of being backtracked, respectively. This kind of anonymity is called user or client anonymity. But on the other hand, an equivalent protection for content providers does not exist, although this feature is desirable for many situations in which the identity of a publisher or content provider shall be hidden. We call this property server anonymity. We will introduce the first system with the primary target to offer anonymity for providers of information in the WWW. Beside this property, it provides also client anonymity. Based on David Chaum's idea of mixes and in relation to the context of the WWW, we explain the term 'server anonymity' motivating the system JANUS which offers both client and server anonymity.

HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

TRSkit: A Simple Digital Library Toolkit

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Esler, Sandra L.

1997-01-01

This paper introduces TRSkit, a simple and effective toolkit for building digital libraries on the World Wide Web. The toolkit was developed for the creation of the Langley Technical Report Server and the NASA Technical Report Server, but is applicable to most simple distribution paradigms. TRSkit contains a handful of freely available software components designed to be run under the UNIX operating system and served via the World Wide Web. The intended customer is the person that must continuously and synchronously distribute anywhere from 100 - 100,000's of information units and does not have extensive resources to devote to the problem.

Online characterization of planetary surfaces: PlanetServer, an open-source analysis and visualization tool

NASA Astrophysics Data System (ADS)

Marco Figuera, R.; Pham Huu, B.; Rossi, A. P.; Minin, M.; Flahaut, J.; Halder, A.

2018-01-01

The lack of open-source tools for hyperspectral data visualization and analysis creates a demand for new tools. In this paper we present the new PlanetServer, a set of tools comprising a web Geographic Information System (GIS) and a recently developed Python Application Programming Interface (API) capable of visualizing and analyzing a wide variety of hyperspectral data from different planetary bodies. Current WebGIS open-source tools are evaluated in order to give an overview and contextualize how PlanetServer can help in this matters. The web client is thoroughly described as well as the datasets available in PlanetServer. Also, the Python API is described and exposed the reason of its development. Two different examples of mineral characterization of different hydrosilicates such as chlorites, prehnites and kaolinites in the Nili Fossae area on Mars are presented. As the obtained results show positive outcome in hyperspectral analysis and visualization compared to previous literature, we suggest using the PlanetServer approach for such investigations.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows.

PubMed

Paraskevopoulou, Maria D; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A G

2013-07-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA-gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines.

DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows

PubMed Central

Paraskevopoulou, Maria D.; Georgakilas, Georgios; Kostoulas, Nikos; Vlachos, Ioannis S.; Vergoulis, Thanasis; Reczko, Martin; Filippidis, Christos; Dalamagas, Theodore; Hatzigeorgiou, A.G.

2013-01-01

MicroRNAs (miRNAs) are small endogenous RNA molecules that regulate gene expression through mRNA degradation and/or translation repression, affecting many biological processes. DIANA-microT web server (http://www.microrna.gr/webServer) is dedicated to miRNA target prediction/functional analysis, and it is being widely used from the scientific community, since its initial launch in 2009. DIANA-microT v5.0, the new version of the microT server, has been significantly enhanced with an improved target prediction algorithm, DIANA-microT-CDS. It has been updated to incorporate miRBase version 18 and Ensembl version 69. The in silico-predicted miRNA–gene interactions in Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans exceed 11 million in total. The web server was completely redesigned, to host a series of sophisticated workflows, which can be used directly from the on-line web interface, enabling users without the necessary bioinformatics infrastructure to perform advanced multi-step functional miRNA analyses. For instance, one available pipeline performs miRNA target prediction using different thresholds and meta-analysis statistics, followed by pathway enrichment analysis. DIANA-microT web server v5.0 also supports a complete integration with the Taverna Workflow Management System (WMS), using the in-house developed DIANA-Taverna Plug-in. This plug-in provides ready-to-use modules for miRNA target prediction and functional analysis, which can be used to form advanced high-throughput analysis pipelines. PMID:23680784

SPEER-SERVER: a web server for prediction of protein specificity determining sites

PubMed Central

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J.; Panchenko, Anna R.; Chakrabarti, Saikat

2012-01-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids’ Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/. PMID:22689646

SPEER-SERVER: a web server for prediction of protein specificity determining sites.

PubMed

Chakraborty, Abhijit; Mandloi, Sapan; Lanczycki, Christopher J; Panchenko, Anna R; Chakrabarti, Saikat

2012-07-01

Sites that show specific conservation patterns within subsets of proteins in a protein family are likely to be involved in the development of functional specificity. These sites, generally termed specificity determining sites (SDS), might play a crucial role in binding to a specific substrate or proteins. Identification of SDS through experimental techniques is a slow, difficult and tedious job. Hence, it is very important to develop efficient computational methods that can more expediently identify SDS. Herein, we present Specificity prediction using amino acids' Properties, Entropy and Evolution Rate (SPEER)-SERVER, a web server that predicts SDS by analyzing quantitative measures of the conservation patterns of protein sites based on their physico-chemical properties and the heterogeneity of evolutionary changes between and within the protein subfamilies. This web server provides an improved representation of results, adds useful input and output options and integrates a wide range of analysis and data visualization tools when compared with the original standalone version of the SPEER algorithm. Extensive benchmarking finds that SPEER-SERVER exhibits sensitivity and precision performance that, on average, meets or exceeds that of other currently available methods. SPEER-SERVER is available at http://www.hpppi.iicb.res.in/ss/.

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

USDA-ARS?s Scientific Manuscript database

Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

The World Wide Web and Technology Transfer at NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Bianco, David J.

1994-01-01

NASA Langley Research Center (LaRC) began using the World Wide Web (WWW) in the summer of 1993, becoming the first NASA installation to provide a Center-wide home page. This coincided with a reorganization of LaRC to provide a more concentrated focus on technology transfer to both aerospace and non-aerospace industry. Use of the WWW and NCSA Mosaic not only provides automated information dissemination, but also allows for the implementation, evolution and integration of many technology transfer applications. This paper describes several of these innovative applications, including the on-line presentation of the entire Technology Opportunities Showcase (TOPS), an industrial partnering showcase that exists on the Web long after the actual 3-day event ended. During its first year on the Web, LaRC also developed several WWW-based information repositories. The Langley Technical Report Server (LTRS), a technical paper delivery system with integrated searching and retrieval, has proved to be quite popular. The NASA Technical Report Server (NTRS), an outgrowth of LTRS, provides uniform access to many logically similar, yet physically distributed NASA report servers. WWW is also the foundation of the Langley Software Server (LSS), an experimental software distribution system which will distribute LaRC-developed software with the possible phase-out of NASA's COSMIC program. In addition to the more formal technology distribution projects, WWW has been successful in connecting people with technologies and people with other people. With the completion of the LaRC reorganization, the Technology Applications Group, charged with interfacing with non-aerospace companies, opened for business with a popular home page.

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

A web server for analysis, comparison and prediction of protein ligand binding sites.

PubMed

Singh, Harinder; Srivastava, Hemant Kumar; Raghava, Gajendra P S

2016-03-25

One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. In order to address this problem, we developed a web server named 'LPIcom' to facilitate users in understanding protein-ligand interaction. Analysis, comparison and prediction modules are available in the "LPIcom' server to predict protein-ligand interacting residues for 824 ligands. Each ligand must have at least 30 protein binding sites in PDB. Analysis module of the server can identify residues preferred in interaction and binding motif for a given ligand; for example residues glycine, lysine and arginine are preferred in ATP binding sites. Comparison module of the server allows comparing protein-binding sites of multiple ligands to understand the similarity between ligands based on their binding site. This module indicates that ATP, ADP and GTP ligands are in the same cluster and thus their binding sites or interacting residues exhibit a high level of similarity. Propensity-based prediction module has been developed for predicting ligand-interacting residues in a protein for more than 800 ligands. In addition, a number of web-based tools have been integrated to facilitate users in creating web logo and two-sample between ligand interacting and non-interacting residues. In summary, this manuscript presents a web-server for analysis of ligand interacting residue. This server is available for public use from URL http://crdd.osdd.net/raghava/lpicom .

A radiology department intranet: development and applications.

PubMed

Willing, S J; Berland, L L

1999-01-01

An intranet is a "private Internet" that uses the protocols of the World Wide Web to share information resources within a company or with the company's business partners and clients. The hardware requirements for an intranet begin with a dedicated Web server permanently connected to the departmental network. The heart of a Web server is the hypertext transfer protocol (HTTP) service, which receives a page request from a client's browser and transmits the page back to the client. Although knowledge of hypertext markup language (HTML) is not essential for authoring a Web page, a working familiarity with HTML is useful, as is knowledge of programming and database management. Security can be ensured by using scripts to write information in hidden fields or by means of "cookies." Interfacing databases and database management systems with the Web server and conforming the user interface to HTML syntax can be achieved by means of the common gateway interface (CGI), Active Server Pages (ASP), or other methods. An intranet in a radiology department could include the following types of content: on-call schedules, work schedules and a calendar, a personnel directory, resident resources, memorandums and discussion groups, software for a radiology information system, and databases.

mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications.

PubMed

Li, Zhongshan; Liu, Zhenwei; Jiang, Yi; Chen, Denghui; Ran, Xia; Sun, Zhong Sheng; Wu, Jinyu

2017-01-01

Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/. © 2016 WILEY PERIODICALS, INC.

CalFitter: a web server for analysis of protein thermal denaturation data.

PubMed

Mazurenko, Stanislav; Stourac, Jan; Kunka, Antonin; Nedeljkovic, Sava; Bednar, David; Prokop, Zbynek; Damborsky, Jiri

2018-05-14

Despite significant advances in the understanding of protein structure-function relationships, revealing protein folding pathways still poses a challenge due to a limited number of relevant experimental tools. Widely-used experimental techniques, such as calorimetry or spectroscopy, critically depend on a proper data analysis. Currently, there are only separate data analysis tools available for each type of experiment with a limited model selection. To address this problem, we have developed the CalFitter web server to be a unified platform for comprehensive data fitting and analysis of protein thermal denaturation data. The server allows simultaneous global data fitting using any combination of input data types and offers 12 protein unfolding pathway models for selection, including irreversible transitions often missing from other tools. The data fitting produces optimal parameter values, their confidence intervals, and statistical information to define unfolding pathways. The server provides an interactive and easy-to-use interface that allows users to directly analyse input datasets and simulate modelled output based on the model parameters. CalFitter web server is available free at https://loschmidt.chemi.muni.cz/calfitter/.

The Value of Web Log Data in Use-based Design and Testing.

ERIC Educational Resources Information Center

Burton, Mary C.; Walther, Joseph B.

2001-01-01

Suggests Web-based logs contain useful empirical data with which World Wide Web designers and design theorists can assess usability and effectiveness of design choices. Enumerates identification of types of Web server logs, client logs, types and uses of log data, and issues associated with the validity of these data. Presents an approach to…

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

PubMed Central

Tsirigos, Konstantinos D.; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-01-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. PMID:25969446

SEGEL: A Web Server for Visualization of Smoking Effects on Human Lung Gene Expression.

PubMed

Xu, Yan; Hu, Brian; Alnajm, Sammy S; Lu, Yin; Huang, Yangxin; Allen-Gipson, Diane; Cheng, Feng

2015-01-01

Cigarette smoking is a major cause of death worldwide resulting in over six million deaths per year. Cigarette smoke contains complex mixtures of chemicals that are harmful to nearly all organs of the human body, especially the lungs. Cigarette smoking is considered the major risk factor for many lung diseases, particularly chronic obstructive pulmonary diseases (COPD) and lung cancer. However, the underlying molecular mechanisms of smoking-induced lung injury associated with these lung diseases still remain largely unknown. Expression microarray techniques have been widely applied to detect the effects of smoking on gene expression in different human cells in the lungs. These projects have provided a lot of useful information for researchers to understand the potential molecular mechanism(s) of smoke-induced pathogenesis. However, a user-friendly web server that would allow scientists to fast query these data sets and compare the smoking effects on gene expression across different cells had not yet been established. For that reason, we have integrated eight public expression microarray data sets from trachea epithelial cells, large airway epithelial cells, small airway epithelial cells, and alveolar macrophage into an online web server called SEGEL (Smoking Effects on Gene Expression of Lung). Users can query gene expression patterns across these cells from smokers and nonsmokers by gene symbols, and find the effects of smoking on the gene expression of lungs from this web server. Sex difference in response to smoking is also shown. The relationship between the gene expression and cigarette smoking consumption were calculated and are shown in the server. The current version of SEGEL web server contains 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 Plus 2.0 platform. SEGEL will be an invaluable resource for researchers interested in the effects of smoking on gene expression in the lungs. The server also provides useful information for drug development against smoking-related diseases. The SEGEL web server is available online at http://www.chengfeng.info/smoking_database.html.

"WWW.MDTF.ORG": a World Wide Web forum for developing open-architecture, freely distributed, digital teaching file software by participant consensus.

PubMed

Katzman, G L; Morris, D; Lauman, J; Cochella, C; Goede, P; Harnsberger, H R

2001-06-01

To foster a community supported evaluation processes for open-source digital teaching file (DTF) development and maintenance. The mechanisms used to support this process will include standard web browsers, web servers, forum software, and custom additions to the forum software to potentially enable a mediated voting protocol. The web server will also serve as a focal point for beta and release software distribution, which is the desired end-goal of this process. We foresee that www.mdtf.org will provide for widespread distribution of open source DTF software that will include function and interface design decisions from community participation on the website forums.

sTeam--Providing Primary Media Functions for Web-Based Computer-Supported Cooperative Learning.

ERIC Educational Resources Information Center

Hampel, Thorsten

The World Wide Web has developed as the de facto standard for computer based learning. However, as a server-centered approach, it confines readers and learners to passive nonsequential reading. Authoring and Web-publishing systems aim at supporting the authors' design process. Consequently, learners' activities are confined to selecting and…

SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services.

PubMed

Basu, M K

2001-06-01

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser.

An Enhanced Z39.50 Gateway to the WorldWideWeb.

ERIC Educational Resources Information Center

Cunningham, David; Sloan, Stephen

1994-01-01

Describes how a university library uses the WorldWideWeb (WWW) to enable users to access resources mounted on a local Z39.50 server and to order prints from articles stored on a CD-ROM jukebox. The software used in the construction of the system, necessary modifications to the software, and software ordering information are covered. (KRN)

SIFTER search: a web server for accurate phylogeny-based protein function prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

An open source Java web application to build self-contained Web GIS sites

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Ahmed, A.; Chassignet, E.; Zavala-Hidalgo, J.

2014-12-01

This work describes OWGIS, an open source Java web application that creates Web GIS sites by automatically writing HTML and JavaScript code. OWGIS is configured by XML files that define which layers (geographic datasets) will be displayed on the websites. This project uses several Open Geospatial Consortium standards to request data from typical map servers, such as GeoServer, and is also able to request data from ncWMS servers. The latter allows for the displaying of 4D data stored using the NetCDF file format (widely used for storing environmental model datasets). Some of the features available on the sites built with OWGIS are: multiple languages, animations, vertical profiles and vertical transects, color palettes, color ranges, and the ability to download data. OWGIS main users are scientists, such as oceanographers or climate scientists, who store their data in NetCDF files and want to analyze, visualize, share, or compare their data using a website.

SIFTER search: a web server for accurate phylogeny-based protein function prediction

DOE PAGES

Sahraeian, Sayed M.; Luo, Kevin R.; Brenner, Steven E.

2015-05-15

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access tomore » precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.« less

Cyber-T web server: differential analysis of high-throughput data.

PubMed

Kayala, Matthew A; Baldi, Pierre

2012-07-01

The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is one of the most widely validated. Cyber-T implements a t-test using a Bayesian framework to compute a regularized variance of the measurements associated with each probe under each condition. This regularized estimate is derived by flexibly combining the empirical measurements with a prior, or background, derived from pooling measurements associated with probes in the same neighborhood. This approach flexibly addresses problems associated with low replication levels and technology biases, not only for DNA microarrays, but also for other technologies, such as protein arrays, quantitative mass spectrometry and next-generation sequencing (RNA-seq). Here we present an update to the Cyber-T web server, incorporating several useful new additions and improvements. Several preprocessing data normalization options including logarithmic and (Variance Stabilizing Normalization) VSN transforms are included. To augment two-sample t-tests, a one-way analysis of variance is implemented. Several methods for multiple tests correction, including standard frequentist methods and a probabilistic mixture model treatment, are available. Diagnostic plots allow visual assessment of the results. The web server provides comprehensive documentation and example data sets. The Cyber-T web server, with R source code and data sets, is publicly available at http://cybert.ics.uci.edu/.

E-Referencer: Transforming Boolean OPACs to Web Search Engines.

ERIC Educational Resources Information Center

Khoo, Christopher S. G.; Poo, Danny C. C.; Toh, Teck-Kang; Hong, Glenn

E-Referencer is an expert intermediary system for searching library online public access catalogs (OPACs) on the World Wide Web. It is implemented as a proxy server that mediates the interaction between the user and Boolean OPACs. It transforms a Boolean OPAC into a retrieval system with many of the search capabilities of Web search engines.…

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

PubMed

Tsirigos, Konstantinos D; Peters, Christoph; Shu, Nanjiang; Käll, Lukas; Elofsson, Arne

2015-07-01

TOPCONS (http://topcons.net/) is a widely used web server for consensus prediction of membrane protein topology. We hereby present a major update to the server, with some substantial improvements, including the following: (i) TOPCONS can now efficiently separate signal peptides from transmembrane regions. (ii) The server can now differentiate more successfully between globular and membrane proteins. (iii) The server now is even slightly faster, although a much larger database is used to generate the multiple sequence alignments. For most proteins, the final prediction is produced in a matter of seconds. (iv) The user-friendly interface is retained, with the additional feature of submitting batch files and accessing the server programmatically using standard interfaces, making it thus ideal for proteome-wide analyses. Indicatively, the user can now scan the entire human proteome in a few days. (v) For proteins with homology to a known 3D structure, the homology-inferred topology is also displayed. (vi) Finally, the combination of methods currently implemented achieves an overall increase in performance by 4% as compared to the currently available best-scoring methods and TOPCONS is the only method that can identify signal peptides and still maintain a state-of-the-art performance in topology predictions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The informatics superhighway: prototyping on the World Wide Web.

PubMed

Cimino, J J; Socratous, S A; Grewal, R

1995-01-01

We have experimented with developing a prototype Surgeon's Workstation which makes use of the World Wide Web client-server architecture. Although originally intended merely as a means for obtaining user feedback for use in designing a "real" system, the application has been adopted for use by our Department of Surgery. As they begin to use the application, they have suggested changes and we have responded. This paper illustrates some of the advantages we have found for prototyping with Web-based applications, including security aspects.

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana.

PubMed

Xiang, Shunian; Yan, Zhangming; Liu, Ke; Zhang, Yaou; Sun, Zhirong

2016-10-18

N 6 -Methyladenosine (m 6 A) is the most prevalent and abundant modification in mRNA that has been linked to many key biological processes. High-throughput experiments have generated m 6 A-peaks across the transcriptome of A. thaliana, but the specific methylated sites were not assigned, which impedes the understanding of m 6 A functions in plants. Therefore, computational prediction of mRNA m 6 A sites becomes emergently important. Here, we present a method to predict the m 6 A sites for A. thaliana mRNA sequence(s). To predict the m 6 A sites of an mRNA sequence, we employed the support vector machine to build a classifier using the features of the positional flanking nucleotide sequence and position-independent k-mer nucleotide spectrum. Our method achieved good performance and was applied to a web server to provide service for the prediction of A. thaliana m 6 A sites. The server also provides a comprehensive database of predicted transcriptome-wide m 6 A sites and curated m 6 A-seq peaks from the literature for query and visualization. The AthMethPre web server is the first web server that provides a user-friendly tool for the prediction and query of A. thaliana mRNA m 6 A sites, which is freely accessible for public use at .

TreeVector: scalable, interactive, phylogenetic trees for the web.

PubMed

Pethica, Ralph; Barker, Gary; Kovacs, Tim; Gough, Julian

2010-01-28

Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. We introduce TreeVector, a Scalable Vector Graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.

Lamprey: tracking users on the World Wide Web.

PubMed

Felciano, R M; Altman, R B

1996-01-01

Tracking individual web sessions provides valuable information about user behavior. This information can be used for general purpose evaluation of web-based user interfaces to biomedical information systems. To this end, we have developed Lamprey, a tool for doing quantitative and qualitative analysis of Web-based user interfaces. Lamprey can be used from any conforming browser, and does not require modification of server or client software. By rerouting WWW navigation through a centralized filter, Lamprey collects the sequence and timing of hyperlinks used by individual users to move through the web. Instead of providing marginal statistics, it retains the full information required to recreate a user session. We have built Lamprey as a standard Common Gateway Interface (CGI) that works with all standard WWW browsers and servers. In this paper, we describe Lamprey and provide a short demonstration of this approach for evaluating web usage patterns.

A web access script language to support clinical application development.

PubMed

O'Kane, K C; McColligan, E E

1998-02-01

This paper describes the development of a script language to support the implementation of decentralized, clinical information applications on the World Wide Web (Web). The goal of this work is to facilitate construction of low overhead, fully functional clinical information systems that can be accessed anywhere by low cost Web browsers to search, retrieve and analyze stored patient data. The Web provides a model of network access to data bases on a global scale. Although it was originally conceived as a means to exchange scientific documents, Web browsers and servers currently support access to a wide variety of audio, video, graphical and text based data to a rapidly growing community. Access to these services is via inexpensive client software browsers that connect to servers by means of the open architecture of the Internet. In this paper, the design and implementation of a script language that supports the development of low cost, Web-based, distributed clinical information systems for both Inter- and Intra-Net use is presented. The language is based on the Mumps language and, consequently, supports many legacy applications with few modifications. Several enhancements, however, have been made to support modern programming practices and the Web interface. The interpreter for the language also supports standalone program execution on Unix, MS-Windows, OS/2 and other operating systems.

Automated generation of a World Wide Web-based data entry and check program for medical applications.

PubMed

Kiuchi, T; Kaihara, S

1997-02-01

The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch.

KoBaMIN: a knowledge-based minimization web server for protein structure refinement.

PubMed

Rodrigues, João P G L M; Levitt, Michael; Chopra, Gaurav

2012-07-01

The KoBaMIN web server provides an online interface to a simple, consistent and computationally efficient protein structure refinement protocol based on minimization of a knowledge-based potential of mean force. The server can be used to refine either a single protein structure or an ensemble of proteins starting from their unrefined coordinates in PDB format. The refinement method is particularly fast and accurate due to the underlying knowledge-based potential derived from structures deposited in the PDB; as such, the energy function implicitly includes the effects of solvent and the crystal environment. Our server allows for an optional but recommended step that optimizes stereochemistry using the MESHI software. The KoBaMIN server also allows comparison of the refined structures with a provided reference structure to assess the changes brought about by the refinement protocol. The performance of KoBaMIN has been benchmarked widely on a large set of decoys, all models generated at the seventh worldwide experiments on critical assessment of techniques for protein structure prediction (CASP7) and it was also shown to produce top-ranking predictions in the refinement category at both CASP8 and CASP9, yielding consistently good results across a broad range of model quality values. The web server is fully functional and freely available at http://csb.stanford.edu/kobamin.

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.« less

Turning Access into a web-enabled secure information system for clinical trials.

PubMed

Dongquan Chen; Chen, Wei-Bang; Soong, Mayhue; Soong, Seng-Jaw; Orthner, Helmuth F

2009-08-01

Organizations that have limited resources need to conduct clinical studies in a cost-effective, but secure way. Clinical data residing in various individual databases need to be easily accessed and secured. Although widely available, digital certification, encryption, and secure web server, have not been implemented as widely, partly due to a lack of understanding of needs and concerns over issues such as cost and difficulty in implementation. The objective of this study was to test the possibility of centralizing various databases and to demonstrate ways of offering an alternative to a large-scale comprehensive and costly commercial product, especially for simple phase I and II trials, with reasonable convenience and security. We report a working procedure to transform and develop a standalone Access database into a secure Web-based secure information system. For data collection and reporting purposes, we centralized several individual databases; developed, and tested a web-based secure server using self-issued digital certificates. The system lacks audit trails. The cost of development and maintenance may hinder its wide application. The clinical trial databases scattered in various departments of an institution could be centralized into a web-enabled secure information system. The limitations such as the lack of a calendar and audit trail can be partially addressed with additional programming. The centralized Web system may provide an alternative to a comprehensive clinical trial management system.

World wide web implementation of the Langley technical report server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.

1994-01-01

On January 14, 1993, NASA Langley Research Center (LaRC) made approximately 130 formal, 'unclassified, unlimited' technical reports available via the anonymous FTP Langley Technical Report Server (LTRS). LaRC was the first organization to provide a significant number of aerospace technical reports for open electronic dissemination. LTRS has been successful in its first 18 months of operation, with over 11,000 reports distributed and has helped lay the foundation for electronic document distribution for NASA. The availability of World Wide Web (WWW) technology has revolutionized the Internet-based information community. This paper describes the transition of LTRS from a centralized FTP site to a distributed data model using the WWW, and suggests how the general model for LTRS can be applied to other similar systems.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

EarthServer - 3D Visualization on the Web

NASA Astrophysics Data System (ADS)

Wagner, Sebastian; Herzig, Pasquale; Bockholt, Ulrich; Jung, Yvonne; Behr, Johannes

2013-04-01

EarthServer (www.earthserver.eu), funded by the European Commission under its Seventh Framework Program, is a project to enable the management, access and exploration of massive, multi-dimensional datasets using Open GeoSpatial Consortium (OGC) query and processing language standards like WCS 2.0 and WCPS. To this end, a server/client architecture designed to handle Petabyte/Exabyte volumes of multi-dimensional data is being developed and deployed. As an important part of the EarthServer project, six Lighthouse Applications, major scientific data exploitation initiatives, are being established to make cross-domain, Earth Sciences related data repositories available in an open and unified manner, as service endpoints based on solutions and infrastructure developed within the project. Clients technology developed and deployed in EarthServer ranges from mobile and web clients to immersive virtual reality systems, all designed to interact with a physically and logically distributed server infrastructure using exclusively OGC standards. In this contribution, we would like to present our work on a web-based 3D visualization and interaction client for Earth Sciences data using only technology found in standard web browsers without requiring the user to install plugins or addons. Additionally, we are able to run the earth data visualization client on a wide range of different platforms with very different soft- and hardware requirements such as smart phones (e.g. iOS, Android), different desktop systems etc. High-quality, hardware-accelerated visualization of 3D and 4D content in standard web browsers can be realized now and we believe it will become more and more common to use this fast, lightweight and ubiquitous platform to provide insights into big datasets without requiring the user to set up a specialized client first. With that in mind, we will also point out some of the limitations we encountered using current web technologies. Underlying the EarthServer web client and on top of HTML5, WebGL and JavaScript we have developed the X3DOM framework (www.x3dom.org), which makes possible to embed declarative X3D scenegraphs, an ISO standard XML-based file format for representing 3D computer graphics, directly within HTML, thus enabling developers to rapidly design 3D content that blends seamlessly into HTML interfaces using Javascript. This approach (commonly referred to as a polyfill layer) is used to mimic native web browser support for declarative 3D content and is an important component in our web client architecture.

Survey Software Evaluation

DTIC Science & Technology

2009-01-01

Oracle 9i, 10g  MySQL  MS SQL Server MS SQL Server Operating System Supported Windows 2003 Server  Windows 2000 Server (32 bit...WebStar (Mac OS X)  SunOne Internet Information Services (IIS) Database Server Supported MS SQL Server  MS SQL Server  Oracle 9i, 10g...challenges of Web-based surveys are: 1) identifying the best Commercial Off the Shelf (COTS) Web-based survey packages to serve the particular

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.

PubMed

Chong, Jasmine; Xia, Jianguo

2018-06-28

The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data. MetaboAnalystR is freely available from https://github.com/xia-lab/MetaboAnalystR. Supplementary data are available at Bioinformatics online.

CASTp 3.0: computed atlas of surface topography of proteins.

PubMed

Tian, Wei; Chen, Chang; Lei, Xue; Zhao, Jieling; Liang, Jie

2018-06-01

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a web server that provides online services for locating, delineating and measuring these geometric and topological properties of protein structures. It has been widely used since its inception in 2003. In this article, we present the latest version of the web server, CASTp 3.0. CASTp 3.0 continues to provide reliable and comprehensive identifications and quantifications of protein topography. In addition, it now provides: (i) imprints of the negative volumes of pockets, cavities and channels, (ii) topographic features of biological assemblies in the Protein Data Bank, (iii) improved visualization of protein structures and pockets, and (iv) more intuitive structural and annotated information, including information of secondary structure, functional sites, variant sites and other annotations of protein residues. The CASTp 3.0 web server is freely accessible at http://sts.bioe.uic.edu/castp/.

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

PubMed

Salvatore, M; Shu, N; Elofsson, A

2018-01-01

SubCons is a recently developed method that predicts the subcellular localization of a protein. It combines predictions from four predictors using a Random Forest classifier. Here, we present the user-friendly web-interface implementation of SubCons. Starting from a protein sequence, the server rapidly predicts the subcellular localizations of an individual protein. In addition, the server accepts the submission of sets of proteins either by uploading the files or programmatically by using command line WSDL API scripts. This makes SubCons ideal for proteome wide analyses allowing the user to scan a whole proteome in few days. From the web page, it is also possible to download precalculated predictions for several eukaryotic organisms. To evaluate the performance of SubCons we present a benchmark of LocTree3 and SubCons using two recent mass-spectrometry based datasets of mouse and drosophila proteins. The server is available at http://subcons.bioinfo.se/. © 2017 The Protein Society.

Using Web Server Logs in Evaluating Instructional Web Sites.

ERIC Educational Resources Information Center

Ingram, Albert L.

2000-01-01

Web server logs contain a great deal of information about who uses a Web site and how they use it. This article discusses the analysis of Web logs for instructional Web sites; reviews the data stored in most Web server logs; demonstrates what further information can be gleaned from the logs; and discusses analyzing that information for the…

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.

PubMed

Konc, Janez; Janezic, Dusanka

2012-07-01

The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si.

ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins

PubMed Central

Konc, Janez; Janežič, Dušanka

2012-01-01

The ProBiS web server is a web server for detection of structurally similar binding sites in the PDB and for local pairwise alignment of protein structures. In this article, we present a new version of the ProBiS web server that is 10 times faster than earlier versions, due to the efficient parallelization of the ProBiS algorithm, which now allows significantly faster comparison of a protein query against the PDB and reduces the calculation time for scanning the entire PDB from hours to minutes. It also features new web services, and an improved user interface. In addition, the new web server is united with the ProBiS-Database and thus provides instant access to pre-calculated protein similarity profiles for over 29 000 non-redundant protein structures. The ProBiS web server is particularly adept at detection of secondary binding sites in proteins. It is freely available at http://probis.cmm.ki.si/old-version, and the new ProBiS web server is at http://probis.cmm.ki.si. PMID:22600737

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web

NASA Astrophysics Data System (ADS)

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-03-01

We present here the design key concepts of WEBSLIDE, a software project whose objective is to provide a simple, cheap and efficient solution for showing slides during lessons in computer labs. In fact, WEBSLIDE allows the video monitors of several client machines (the "STUDENTS") to be synchronously updated by the actions of a particular client machine, called the "INSTRUCTOR." The system is based on the World Wide Web and the software components of WEBSLIDE mainly consists in a WWW server, browsers and small Cgi-Bill scripts. What makes WEBSLIDE particularly appealing for small educational institutions is that WEBSLIDE is built with "off the shelf" products: it does not involve using a specifically designed program but any Netscape browser, one of the most popular browsers available on the market, is sufficient. Another possible use is to use our system to implement "guided automatic tours" through several pages or Intranets internal news bulletins: the company Web server can broadcast to all employees relevant information on their browser.

Web-based home telemedicine system for orthopedics

NASA Astrophysics Data System (ADS)

Lau, Christopher; Churchill, Sean; Kim, Janice; Matsen, Frederick A., III; Kim, Yongmin

2001-05-01

Traditionally, telemedicine systems have been designed to improve access to care by allowing physicians to consult a specialist about a case without sending the patient to another location, which may be difficult or time-consuming to reach. The cost of the equipment and network bandwidth needed for this consultation has restricted telemedicine use to contact between physicians instead of between patients and physicians. Recently, however, the wide availability of Internet connectivity and client and server software for e- mail, world wide web, and conferencing has made low-cost telemedicine applications feasible. In this work, we present a web-based system for asynchronous multimedia messaging between shoulder replacement surgery patients at home and their surgeons. A web browser plug-in was developed to simplify the process of capturing video and transferring it to a web site. The video capture plug-in can be used as a template to construct a plug-in that captures and transfers any type of data to a web server. For example, readings from home biosensor instruments (e.g., blood glucose meters and spirometers) that can be connected to a computing platform can be transferred to a home telemedicine web site. Both patients and doctors can access this web site to monitor progress longitudinally. The system has been tested with 3 subjects for the past 7 weeks, and we plan to continue testing in the foreseeable future.

Dynamic Web Pages: Performance Impact on Web Servers.

ERIC Educational Resources Information Center

Kothari, Bhupesh; Claypool, Mark

2001-01-01

Discussion of Web servers and requests for dynamic pages focuses on experimentally measuring and analyzing the performance of the three dynamic Web page generation technologies: CGI, FastCGI, and Servlets. Develops a multivariate linear regression model and predicts Web server performance under some typical dynamic requests. (Author/LRW)

Design and evaluation of web-based image transmission and display with different protocols

NASA Astrophysics Data System (ADS)

Tan, Bin; Chen, Kuangyi; Zheng, Xichuan; Zhang, Jianguo

2011-03-01

There are many Web-based image accessing technologies used in medical imaging area, such as component-based (ActiveX Control) thick client Web display, Zerofootprint thin client Web viewer (or called server side processing Web viewer), Flash Rich Internet Application(RIA) ,or HTML5 based Web display. Different Web display methods have different peformance in different network environment. In this presenation, we give an evaluation on two developed Web based image display systems. The first one is used for thin client Web display. It works between a PACS Web server with WADO interface and thin client. The PACS Web server provides JPEG format images to HTML pages. The second one is for thick client Web display. It works between a PACS Web server with WADO interface and thick client running in browsers containing ActiveX control, Flash RIA program or HTML5 scripts. The PACS Web server provides native DICOM format images or JPIP stream for theses clients.

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

PubMed

Frank, M S; Dreyer, K

2001-06-01

We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

The NASA Technical Report Server

NASA Astrophysics Data System (ADS)

Nelson, M. L.; Gottlich, G. L.; Bianco, D. J.; Paulson, S. S.; Binkley, R. L.; Kellogg, Y. D.; Beaumont, C. J.; Schmunk, R. B.; Kurtz, M. J.; Accomazzi, A.; Syed, O.

The National Aeronautics and Space Act of 1958 established the National Aeronautics and Space Administration (NASA) and charged it to "provide for the widest practicable and appropriate dissemination of information concerning...its activities and the results thereof". The search for innovative methods to distribute NASA's information led a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems .

Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server

DTIC Science & Technology

2016-09-01

ARL-TR-7798 ● SEP 2016 US Army Research Laboratory Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server...for the Applied Anomaly Detection Tool (AADT) Web Server by Christian D Schlesiger Computational and Information Sciences Directorate, ARL...SUBTITLE Setup Instructions for the Applied Anomaly Detection Tool (AADT) Web Server 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

AsteriX: a Web server to automatically extract ligand coordinates from figures in PDF articles.

PubMed

Lounnas, V; Vriend, G

2012-02-27

Coordinates describing the chemical structures of small molecules that are potential ligands for pharmaceutical targets are used at many stages of the drug design process. The coordinates of the vast majority of ligands can be obtained from either publicly accessible or commercial databases. However, interesting ligands sometimes are only available from the scientific literature, in which case their coordinates need to be reconstructed manually--a process that consists of a series of time-consuming steps. We present a Web server that helps reconstruct the three-dimensional (3D) coordinates of ligands for which a two-dimensional (2D) picture is available in a PDF file. The software, called AsteriX, analyses every picture contained in the PDF file and attempts to determine automatically whether or not it contains ligands. Areas in pictures that may contain molecular structures are processed to extract connectivity and atom type information that allow coordinates to be subsequently reconstructed. The AsteriX Web server was tested on a series of articles containing a large diversity in graphical representations. In total, 88% of 3249 ligand structures present in the test set were identified as chemical diagrams. Of these, about half were interpreted correctly as 3D structures, and a further one-third required only minor manual corrections. It is principally impossible to always correctly reconstruct 3D coordinates from pictures because there are many different protocols for drawing a 2D image of a ligand, but more importantly a wide variety of semantic annotations are possible. The AsteriX Web server therefore includes facilities that allow the users to augment partial or partially correct 3D reconstructions. All 3D reconstructions are submitted, checked, and corrected by the users domain at the server and are freely available for everybody. The coordinates of the reconstructed ligands are made available in a series of formats commonly used in drug design research. The AsteriX Web server is freely available at http://swift.cmbi.ru.nl/bitmapb/.

eWaterCycle visualisation. combining the strength of NetCDF and Web Map Service: ncWMS

NASA Astrophysics Data System (ADS)

Hut, R.; van Meersbergen, M.; Drost, N.; Van De Giesen, N.

2016-12-01

As a result of the eWatercycle global hydrological forecast we have created Cesium-ncWMS, a web application based on ncWMS and Cesium. ncWMS is a server side application capable of reading any NetCDF file written using the Climate and Forecasting (CF) conventions, and making the data available as a Web Map Service(WMS). ncWMS automatically determines available variables in a file, and creates maps colored according to map data and a user selected color scale. Cesium is a Javascript 3D virtual Globe library. It uses WebGL for rendering, which makes it very fast, and it is capable of displaying a wide variety of data types such as vectors, 3D models, and 2D maps. The forecast results are automatically uploaded to our web server running ncWMS. In turn, the web application can be used to change the settings for color maps and displayed data. The server uses the settings provided by the web application, together with the data in NetCDF to provide WMS image tiles, time series data and legend graphics to the Cesium-NcWMS web application. The user can simultaneously zoom in to the very high resolution forecast results anywhere on the world, and get time series data for any point on the globe. The Cesium-ncWMS visualisation combines a global overview with local relevant information in any browser. See the visualisation live at forecast.ewatercycle.org

Accountable Information Flow for Java-Based Web Applications

DTIC Science & Technology

2010-01-01

runtime library Swift server runtime Java servlet framework HTTP Web server Web browser Figure 2: The Swift architecture introduced an open-ended...On the server, the Java application code links against Swift’s server-side run-time library, which in turn sits on top of the standard Java servlet ...AFRL-RI-RS-TR-2010-9 Final Technical Report January 2010 ACCOUNTABLE INFORMATION FLOW FOR JAVA -BASED WEB APPLICATIONS

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.

PubMed

Müller, Sören; Rycak, Lukas; Winter, Peter; Kahl, Günter; Koch, Ina; Rotter, Björn

2013-10-15

Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA-mRNA interaction databases. The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/.

Technical Considerations in Remote LIMS Access via the World Wide Web

PubMed Central

Schlabach, David M.

2005-01-01

The increased dependency on the World Wide Web by both laboratories and their customers has led LIMS developers to take advantage of thin-client web applications that provide both remote data entry and manipulation, along with remote reporting functionality. Use of an LIMS through a web browser allows a person to interact with a distant application, providing both remote administration and real-time analytical result delivery from virtually anywhere in the world. While there are many benefits of web-based LIMS applications, some concern must be given to these new methods of system architecture before justifying them as a suitable replacement for their traditional client-server systems. Developers and consumers alike must consider the security aspects of introducing a wide area network capable system into a production environment, as well as the concerns of data integrity and usability. PMID:18924736

Intranet technology in hospital information systems.

PubMed

Cimino, J J

1997-01-01

The clinical information system architecture at the Columbia-Presbyterian Medical Center in New York is being incorporated into an intranet using Internet and World Wide Web protocols. The result is an Enterprise-Wide Web which provides more flexibility for access to specific patient information and general medical knowledge. Critical aspects of the architecture include a central data repository and a vocabulary server. The new architecture provides ways of displaying patient information in summary, graphical, and multimedia forms. Using customized links called Infobuttons, we provide access to on-line information resources available on the World Wide Web. Our experience to date has raised a number of interesting issues about the use of this technology for health care systems.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.

PubMed

Wang, Yi; Coleman-Derr, Devin; Chen, Guoping; Gu, Yong Q

2015-07-01

Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that is useful for genome wide comparisons and visualization of orthologous clusters. OrthoVenn provides coverage of vertebrates, metazoa, protists, fungi, plants and bacteria for the comparison of orthologous clusters and also supports uploading of customized protein sequences from user-defined species. An interactive Venn diagram, summary counts, and functional summaries of the disjunction and intersection of clusters shared between species are displayed as part of the OrthoVenn result. OrthoVenn also includes in-depth views of the clusters using various sequence analysis tools. Furthermore, OrthoVenn identifies orthologous clusters of single copy genes and allows for a customized search of clusters of specific genes through key words or BLAST. OrthoVenn is an efficient and user-friendly web server freely accessible at http://probes.pw.usda.gov/OrthoVenn or http://aegilops.wheat.ucdavis.edu/OrthoVenn. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Biotool2Web: creating simple Web interfaces for bioinformatics applications.

PubMed

Shahid, Mohammad; Alam, Intikhab; Fuellen, Georg

2006-01-01

Currently there are many bioinformatics applications being developed, but there is no easy way to publish them on the World Wide Web. We have developed a Perl script, called Biotool2Web, which makes the task of creating web interfaces for simple ('home-made') bioinformatics applications quick and easy. Biotool2Web uses an XML document containing the parameters to run the tool on the Web, and generates the corresponding HTML and common gateway interface (CGI) files ready to be published on a web server. This tool is available for download at URL http://www.uni-muenster.de/Bioinformatics/services/biotool2web/ Georg Fuellen (fuellen@alum.mit.edu).

iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data.

PubMed

Yang, Chia-Chun; Andrews, Erik H; Chen, Min-Hsuan; Wang, Wan-Yu; Chen, Jeremy J W; Gerstein, Mark; Liu, Chun-Chi; Cheng, Chao

2016-08-12

Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired. To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF. The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

PubMed

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

2012-06-15

A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Arizona Libraries: Books to Bytes. Contributed Papers Presented at the AzLA Annual Conference (Phoenix, Arizona, November 17-18, 1995).

ERIC Educational Resources Information Center

Hammond, Carol, Ed.

This document contains three papers presented at the 1995 Arizona Library Association conference. Papers include: (1) "ERLs and URLs: ASU Libraries Database Delivery Through Web Technology" (Dennis Brunning & Philip Konomos), which illustrates how and why the libraries at Arizona State University developed a world wide web server and…

Standards-Based Open-Source Planetary Map Server: Lunaserv

NASA Astrophysics Data System (ADS)

Estes, N. M.; Silva, V. H.; Bowley, K. S.; Lanjewar, K. K.; Robinson, M. S.

2018-04-01

Lunaserv is a planetary capable Web Map Service developed by the LROC SOC. It enables researchers to serve their own planetary data to a wide variety of GIS clients without any additional processing or download steps.

Resource Management Scheme Based on Ubiquitous Data Analysis

PubMed Central

Lee, Heung Ki; Jung, Jaehee

2014-01-01

Resource management of the main memory and process handler is critical to enhancing the system performance of a web server. Owing to the transaction delay time that affects incoming requests from web clients, web server systems utilize several web processes to anticipate future requests. This procedure is able to decrease the web generation time because there are enough processes to handle the incoming requests from web browsers. However, inefficient process management results in low service quality for the web server system. Proper pregenerated process mechanisms are required for dealing with the clients' requests. Unfortunately, it is difficult to predict how many requests a web server system is going to receive. If a web server system builds too many web processes, it wastes a considerable amount of memory space, and thus performance is reduced. We propose an adaptive web process manager scheme based on the analysis of web log mining. In the proposed scheme, the number of web processes is controlled through prediction of incoming requests, and accordingly, the web process management scheme consumes the least possible web transaction resources. In experiments, real web trace data were used to prove the improved performance of the proposed scheme. PMID:25197692

A FPGA embedded web server for remote monitoring and control of smart sensors networks.

PubMed

Magdaleno, Eduardo; Rodríguez, Manuel; Pérez, Fernando; Hernández, David; García, Enrique

2013-12-27

This article describes the implementation of a web server using an embedded Altera NIOS II IP core, a general purpose and configurable RISC processor which is embedded in a Cyclone FPGA. The processor uses the μCLinux operating system to support a Boa web server of dynamic pages using Common Gateway Interface (CGI). The FPGA is configured to act like the master node of a network, and also to control and monitor a network of smart sensors or instruments. In order to develop a totally functional system, the FPGA also includes an implementation of the time-triggered protocol (TTP/A). Thus, the implemented master node has two interfaces, the webserver that acts as an Internet interface and the other to control the network. This protocol is widely used to connecting smart sensors and actuators and microsystems in embedded real-time systems in different application domains, e.g., industrial, automotive, domotic, etc., although this protocol can be easily replaced by any other because of the inherent characteristics of the FPGA-based technology.

A FPGA Embedded Web Server for Remote Monitoring and Control of Smart Sensors Networks

PubMed Central

Magdaleno, Eduardo; Rodríguez, Manuel; Pérez, Fernando; Hernández, David; García, Enrique

2014-01-01

This article describes the implementation of a web server using an embedded Altera NIOS II IP core, a general purpose and configurable RISC processor which is embedded in a Cyclone FPGA. The processor uses the μCLinux operating system to support a Boa web server of dynamic pages using Common Gateway Interface (CGI). The FPGA is configured to act like the master node of a network, and also to control and monitor a network of smart sensors or instruments. In order to develop a totally functional system, the FPGA also includes an implementation of the time-triggered protocol (TTP/A). Thus, the implemented master node has two interfaces, the webserver that acts as an Internet interface and the other to control the network. This protocol is widely used to connecting smart sensors and actuators and microsystems in embedded real-time systems in different application domains, e.g., industrial, automotive, domotic, etc., although this protocol can be easily replaced by any other because of the inherent characteristics of the FPGA-based technology. PMID:24379047

Chemistry on the world-wide-web: a ten year experiment.

PubMed

Goodman, Jonathan M

2004-11-21

The server logs for access to the Cambridge Chemistry webserver show how use of the server has increased over the last ten years, with access doubling every year and a half. This growth has started to slow, and extrapolation of the data suggests that the current rate of access is close to a plateau of ten million downloads a year. The transition for chemists from no internet access to saturation coverage, therefore, appears almost complete.

GenProBiS: web server for mapping of sequence variants to protein binding sites.

PubMed

Konc, Janez; Skrlj, Blaz; Erzen, Nika; Kunej, Tanja; Janezic, Dusanka

2017-07-03

Discovery of potentially deleterious sequence variants is important and has wide implications for research and generation of new hypotheses in human and veterinary medicine, and drug discovery. The GenProBiS web server maps sequence variants to protein structures from the Protein Data Bank (PDB), and further to protein-protein, protein-nucleic acid, protein-compound, and protein-metal ion binding sites. The concept of a protein-compound binding site is understood in the broadest sense, which includes glycosylation and other post-translational modification sites. Binding sites were defined by local structural comparisons of whole protein structures using the Protein Binding Sites (ProBiS) algorithm and transposition of ligands from the similar binding sites found to the query protein using the ProBiS-ligands approach with new improvements introduced in GenProBiS. Binding site surfaces were generated as three-dimensional grids encompassing the space occupied by predicted ligands. The server allows intuitive visual exploration of comprehensively mapped variants, such as human somatic mis-sense mutations related to cancer and non-synonymous single nucleotide polymorphisms from 21 species, within the predicted binding sites regions for about 80 000 PDB protein structures using fast WebGL graphics. The GenProBiS web server is open and free to all users at http://genprobis.insilab.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles.

PubMed

Dittmar, W James; McIver, Lauren; Michalak, Pawel; Garner, Harold R; Valdez, Gregorio

2014-07-01

The wealth of publicly available gene expression and genomic data provides unique opportunities for computational inference to discover groups of genes that function to control specific cellular processes. Such genes are likely to have co-evolved and be expressed in the same tissues and cells. Unfortunately, the expertise and computational resources required to compare tens of genomes and gene expression data sets make this type of analysis difficult for the average end-user. Here, we describe the implementation of a web server that predicts genes involved in affecting specific cellular processes together with a gene of interest. We termed the server 'EvoCor', to denote that it detects functional relationships among genes through evolutionary analysis and gene expression correlation. This web server integrates profiles of sequence divergence derived by a Hidden Markov Model (HMM) and tissue-wide gene expression patterns to determine putative functional linkages between pairs of genes. This server is easy to use and freely available at http://pilot-hmm.vbi.vt.edu/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Use of World Wide Web server and browser software to support a first-year medical physiology course.

PubMed

Davis, M J; Wythe, J; Rozum, J S; Gore, R W

1997-06-01

We describe the use of a World Wide Web (Web) server to support a team-taught physiology course for first-year medical students. Our objectives were to reduce the number of formal lecture hours and enhance student enthusiasm by using more multimedia materials and creating opportunities for interactive learning. On-line course materials, consisting of administrative documents, lecture notes, animations, digital movies, practice tests, and grade reports, were placed on a departmental computer with an Internet connection. Students used Web browsers to access on-line materials from a variety of computing platforms on campus, at home, and at remote sites. To assess use of the materials and their effectiveness, we analyzed 1) log files from the server, and 2) the results of a written course evaluation completed by all students. Lecture notes and practice tests were the most-used documents. The students' evaluations indicated that computer use in class made the lecture material more interesting, while the on-line documents helped reinforce lecture materials and the textbook. We conclude that the effectiveness of on-line materials depends on several different factors, including 1) the number of instructors that provide materials; 2) the quantity of other materials handed out; 3) the degree to which computer use is demonstrated in class and integrated into lectures; and 4) the ease with which students can access the materials. Finally, we propose that additional implementation of Internet-based resources beyond what we have described would further enhance a physiology course for first-year medical students.

GRAMM-X public web server for protein–protein docking

PubMed Central

Tovchigrechko, Andrey; Vakser, Ilya A.

2006-01-01

Protein docking software GRAMM-X and its web interface () extend the original GRAMM Fast Fourier Transformation methodology by employing smoothed potentials, refinement stage, and knowledge-based scoring. The web server frees users from complex installation of database-dependent parallel software and maintaining large hardware resources needed for protein docking simulations. Docking problems submitted to GRAMM-X server are processed by a 320 processor Linux cluster. The server was extensively tested by benchmarking, several months of public use, and participation in the CAPRI server track. PMID:16845016

Implementation of Sensor Twitter Feed Web Service Server and Client

DTIC Science & Technology

2016-12-01

ARL-TN-0807 ● DEC 2016 US Army Research Laboratory Implementation of Sensor Twitter Feed Web Service Server and Client by...Implementation of Sensor Twitter Feed Web Service Server and Client by Bhagyashree V Kulkarni University of Maryland Michael H Lee Computational...

[The database server for the medical bibliography database at Charles University].

PubMed

Vejvalka, J; Rojíková, V; Ulrych, O; Vorísek, M

1998-01-01

In the medical community, bibliographic databases are widely accepted as a most important source of information both for theoretical and clinical disciplines. To improve access to medical bibliographic databases at Charles University, a database server (ERL by Silver Platter) was set up at the 2nd Faculty of Medicine in Prague. The server, accessible by Internet 24 hours/7 days, hosts now 14 years' MEDLINE and 10 years' EMBASE Paediatrics. Two different strategies are available for connecting to the server: a specialized client program that communicates over the Internet (suitable for professional searching) and a web-based access that requires no specialized software (except the WWW browser) on the client side. The server is now offered to academic community to host further databases, possibly subscribed by consortia whose individual members would not subscribe them by themselves.

NOBAI: a web server for character coding of geometrical and statistical features in RNA structure

PubMed Central

Knudsen, Vegeir; Caetano-Anollés, Gustavo

2008-01-01

The Numeration of Objects in Biology: Alignment Inferences (NOBAI) web server provides a web interface to the applications in the NOBAI software package. This software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly in NEXUS format and provides sequence randomization options. The web server is an effective tool that facilitates the search for evolutionary history embedded in the structure of functional RNA molecules. The NOBAI web server is accessible at ‘http://www.manet.uiuc.edu/nobai/nobai.php’. This web site is free and open to all users and there is no login requirement. PMID:18448469

Radiology teaching file cases on the World Wide Web.

PubMed

Scalzetti, E M

1997-08-01

The presentation of a radiographic teaching file on the World Wide Web can be enhanced by attending to principles of web design. Chief among these are appropriate control of page layout, minimization of the time required to download a page from the remote server, and provision for navigation within and among the web pages that constitute the site. Page layout is easily accomplished by the use of tables; column widths can be fixed to maintain an acceptable line length for text. Downloading time is minimized by rigorous editing and by optimal compression of image files; beyond this, techniques like preloading of images and specification of image width and height are also helpful. Navigation controls should be clear, consistent, and readily available.

The research and implementation of coalfield spontaneous combustion of carbon emission WebGIS based on Silverlight and ArcGIS server

NASA Astrophysics Data System (ADS)

Zhu, Z.; Bi, J.; Wang, X.; Zhu, W.

2014-02-01

As an important sub-topic of the natural process of carbon emission data public information platform construction, coalfield spontaneous combustion of carbon emission WebGIS system has become an important study object. In connection with data features of coalfield spontaneous combustion carbon emissions (i.e. a wide range of data, which is rich and complex) and the geospatial characteristics, data is divided into attribute data and spatial data. Based on full analysis of the data, completed the detailed design of the Oracle database and stored on the Oracle database. Through Silverlight rich client technology and the expansion of WCF services, achieved the attribute data of web dynamic query, retrieval, statistical, analysis and other functions. For spatial data, we take advantage of ArcGIS Server and Silverlight-based API to invoke GIS server background published map services, GP services, Image services and other services, implemented coalfield spontaneous combustion of remote sensing image data and web map data display, data analysis, thematic map production. The study found that the Silverlight technology, based on rich client and object-oriented framework for WCF service, can efficiently constructed a WebGIS system. And then, combined with ArcGIS Silverlight API to achieve interactive query attribute data and spatial data of coalfield spontaneous emmission, can greatly improve the performance of WebGIS system. At the same time, it provided a strong guarantee for the construction of public information on China's carbon emission data.

Data Driven Device Failure Prediction

DTIC Science & Technology

2016-09-15

Microsoft enterprise authentication service and Apache web server in an effort to increase up-time and improve mission effectiveness. These new fault loads...54 4.2.2 Web Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59...predictor. Finally, the implementation is validated by running the same experiment on a web server. 1.1 Problem Statement According to the operational

3Drefine: an interactive web server for efficient protein structure refinement

PubMed Central

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-01-01

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. PMID:27131371

DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs.

PubMed

Wang, Lin; Zhang, Min; Alexov, Emil

2016-02-15

A new pKa prediction web server is released, which implements DelPhi Gaussian dielectric function to calculate electrostatic potentials generated by charges of biomolecules. Topology parameters are extended to include atomic information of nucleotides of RNA and DNA, which extends the capability of pKa calculations beyond proteins. The web server allows the end-user to protonate the biomolecule at particular pH based on calculated pKa values and provides the downloadable file in PQR format. Several tests are performed to benchmark the accuracy and speed of the protocol. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhiPKa program. The computation is performed on the Palmetto supercomputer cluster and results/download links are given back to the end-user via http protocol. The web server takes advantage of MPI parallel implementation in DelPhiPKa and can run a single job on up to 24 CPUs. The DelPhiPKa web server is available at http://compbio.clemson.edu/pka_webserver. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automated grading of homework assignments and tests in introductory and intermediate statistics courses using active server pages.

PubMed

Stockburger, D W

1999-05-01

Active server pages permit a software developer to customize the Web experience for users by inserting server-side script and database access into Web pages. This paper describes applications of these techniques and provides a primer on the use of these methods. Applications include a system that generates and grades individualized homework assignments and tests for statistics students. The student accesses the system as a Web page, prints out the assignment, does the assignment, and enters the answers on the Web page. The server, running on NT Server 4.0, grades the assignment, updates the grade book (on a database), and returns the answer key to the student.

GFFview: A Web Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome.

PubMed

Deng, Feilong; Chen, Shi-Yi; Wu, Zhou-Lin; Hu, Yongsong; Jia, Xianbo; Lai, Song-Jia

2017-10-01

Owing to wide application of RNA sequencing (RNA-seq) technology, more and more eukaryotic genomes have been extensively annotated, such as the gene structure, alternative splicing, and noncoding loci. Annotation information of genome is prevalently stored as plain text in General Feature Format (GFF), which could be hundreds or thousands Mb in size. Therefore, it is a challenge for manipulating GFF file for biologists who have no bioinformatic skill. In this study, we provide a web server (GFFview) for parsing the annotation information of eukaryotic genome and then generating statistical description of six indices for visualization. GFFview is very useful for investigating quality and difference of the de novo assembled transcriptome in RNA-seq studies.

Parallel Computing Using Web Servers and "Servlets".

ERIC Educational Resources Information Center

Lo, Alfred; Bloor, Chris; Choi, Y. K.

2000-01-01

Describes parallel computing and presents inexpensive ways to implement a virtual parallel computer with multiple Web servers. Highlights include performance measurement of parallel systems; models for using Java and intranet technology including single server, multiple clients and multiple servers, single client; and a comparison of CGI (common…

R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures.

PubMed

Rahrig, Ryan R; Petrov, Anton I; Leontis, Neocles B; Zirbel, Craig L

2013-07-01

The R3D Align web server provides online access to 'RNA 3D Align' (R3D Align), a method for producing accurate nucleotide-level structural alignments of RNA 3D structures. The web server provides a streamlined and intuitive interface, input data validation and output that is more extensive and easier to read and interpret than related servers. The R3D Align web server offers a unique Gallery of Featured Alignments, providing immediate access to pre-computed alignments of large RNA 3D structures, including all ribosomal RNAs, as well as guidance on effective use of the server and interpretation of the output. By accessing the non-redundant lists of RNA 3D structures provided by the Bowling Green State University RNA group, R3D Align connects users to structure files in the same equivalence class and the best-modeled representative structure from each group. The R3D Align web server is freely accessible at http://rna.bgsu.edu/r3dalign/.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Unni, Samir; Huang, Yong; Hanson, Robert M.

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in currentmore » distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.« less

Web servers and services for electrostatics calculations with APBS and PDB2PQR

PubMed Central

Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

2011-01-01

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

w4CSeq: software and web application to analyze 4C-seq data.

PubMed

Cai, Mingyang; Gao, Fan; Lu, Wange; Wang, Kai

2016-11-01

Circularized Chromosome Conformation Capture followed by deep sequencing (4C-Seq) is a powerful technique to identify genome-wide partners interacting with a pre-specified genomic locus. Here, we present a computational and statistical approach to analyze 4C-Seq data generated from both enzyme digestion and sonication fragmentation-based methods. We implemented a command line software tool and a web interface called w4CSeq, which takes in the raw 4C sequencing data (FASTQ files) as input, performs automated statistical analysis and presents results in a user-friendly manner. Besides providing users with the list of candidate interacting sites/regions, w4CSeq generates figures showing genome-wide distribution of interacting regions, and sketches the enrichment of key features such as TSSs, TTSs, CpG sites and DNA replication timing around 4C sites. Users can establish their own web server by downloading source codes at https://github.com/WGLab/w4CSeq Additionally, a demo web server is available at http://w4cseq.wglab.org CONTACT: kaiwang@usc.edu or wangelu@usc.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Using Web Server Logs to Track Users through the Electronic Forest

ERIC Educational Resources Information Center

Coombs, Karen A.

2005-01-01

This article analyzes server logs, providing helpful information in making decisions about Web-based services. The author indicates, as a result of analyzing server logs, several interesting things about the users' behavior were learned. The resulting findings are discussed in this article. Certain pages of the author's Web site, for instance, are…

Server-Side Includes Made Simple.

ERIC Educational Resources Information Center

Fagan, Jody Condit

2002-01-01

Describes server-side include (SSI) codes which allow Webmasters to insert content into Web pages without programming knowledge. Explains how to enable the codes on a Web server, provides a step-by-step process for implementing them, discusses tags and syntax errors, and includes examples of their use on the Web site for Southern Illinois…

WEB-server for search of a periodicity in amino acid and nucleotide sequences

NASA Astrophysics Data System (ADS)

E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

2017-12-01

A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

The HydroServer Platform for Sharing Hydrologic Data

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Horsburgh, J. S.; Schreuders, K.; Maidment, D. R.; Zaslavsky, I.; Valentine, D. W.

2010-12-01

The CUAHSI Hydrologic Information System (HIS) is an internet based system that supports sharing of hydrologic data. HIS consists of databases connected using the Internet through Web services, as well as software for data discovery, access, and publication. The HIS system architecture is comprised of servers for publishing and sharing data, a centralized catalog to support cross server data discovery and a desktop client to access and analyze data. This paper focuses on HydroServer, the component developed for sharing and publishing space-time hydrologic datasets. A HydroServer is a computer server that contains a collection of databases, web services, tools, and software applications that allow data producers to store, publish, and manage the data from an experimental watershed or project site. HydroServer is designed to permit publication of data as part of a distributed national/international system, while still locally managing access to the data. We describe the HydroServer architecture and software stack, including tools for managing and publishing time series data for fixed point monitoring sites as well as spatially distributed, GIS datasets that describe a particular study area, watershed, or region. HydroServer adopts a standards based approach to data publication, relying on accepted and emerging standards for data storage and transfer. CUAHSI developed HydroServer code is free with community code development managed through the codeplex open source code repository and development system. There is some reliance on widely used commercial software for general purpose and standard data publication capability. The sharing of data in a common format is one way to stimulate interdisciplinary research and collaboration. It is anticipated that the growing, distributed network of HydroServers will facilitate cross-site comparisons and large scale studies that synthesize information from diverse settings, making the network as a whole greater than the sum of its parts in advancing hydrologic research. Details of the CUAHSI HIS can be found at http://his.cuahsi.org, and HydroServer codeplex site http://hydroserver.codeplex.com.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

Worldwide telemedicine services based on distributed multimedia electronic patient records by using the second generation Web server hyperwave.

PubMed

Quade, G; Novotny, J; Burde, B; May, F; Beck, L E; Goldschmidt, A

1999-01-01

A distributed multimedia electronic patient record (EPR) is a central component of a medicine-telematics application that supports physicians working in rural areas of South America, and offers medical services to scientists in Antarctica. A Hyperwave server is used to maintain the patient record. As opposed to common web servers--and as a second generation web server--Hyperwave provides the capability of holding documents in a distributed web space without the problem of broken links. This enables physicians to browse through a patient's record by using a standard browser even if the patient's record is distributed over several servers. The patient record is basically implemented on the "Good European Health Record" (GEHR) architecture.

A price and performance comparison of three different storage architectures for data in cloud-based systems

NASA Astrophysics Data System (ADS)

Gallagher, J. H. R.; Jelenak, A.; Potter, N.; Fulker, D. W.; Habermann, T.

2017-12-01

Providing data services based on cloud computing technology that is equivalent to those developed for traditional computing and storage systems is critical for successful migration to cloud-based architectures for data production, scientific analysis and storage. OPeNDAP Web-service capabilities (comprising the Data Access Protocol (DAP) specification plus open-source software for realizing DAP in servers and clients) are among the most widely deployed means for achieving data-as-service functionality in the Earth sciences. OPeNDAP services are especially common in traditional data center environments where servers offer access to datasets stored in (very large) file systems, and a preponderance of the source data for these services is being stored in the Hierarchical Data Format Version 5 (HDF5). Three candidate architectures for serving NASA satellite Earth Science HDF5 data via Hyrax running on Amazon Web Services (AWS) were developed and their performance examined for a set of representative use cases. The performance was based both on runtime and incurred cost. The three architectures differ in how HDF5 files are stored in the Amazon Simple Storage Service (S3) and how the Hyrax server (as an EC2 instance) retrieves their data. The results for both the serial and parallel access to HDF5 data in the S3 will be presented. While the study focused on HDF5 data, OPeNDAP and the Hyrax data server, the architectures are generic and the analysis can be extrapolated to many different data formats, web APIs, and data servers.

AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.

PubMed

Labbé, Céline M; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O; Pajeva, Ilza; Miteva, Maria A

2017-07-03

AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

3Drefine: an interactive web server for efficient protein structure refinement.

PubMed

Bhattacharya, Debswapna; Nowotny, Jackson; Cao, Renzhi; Cheng, Jianlin

2016-07-08

3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

AMMOS2: a web server for protein–ligand–water complexes refinement via molecular mechanics

PubMed Central

Labbé, Céline M.; Pencheva, Tania; Jereva, Dessislava; Desvillechabrol, Dimitri; Becot, Jérôme; Villoutreix, Bruno O.; Pajeva, Ilza

2017-01-01

Abstract AMMOS2 is an interactive web server for efficient computational refinement of protein–small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein–ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein–ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein–ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein–ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein–ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein–ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php. PMID:28486703

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

PubMed

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

PubMed Central

Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-01-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

Implementation of an Enterprise Information Portal (EIP) in the Loyola University Health System

PubMed Central

Price, Ronald N.; Hernandez, Kim

2001-01-01

Loyola University Chicago Stritch School of Medicine and Loyola University Medical Center have long histories in the development of applications to support the institutions' missions of education, research and clinical care. In late 1998, the institutions' application development group undertook an ambitious program to re-architecture more than 10 years of legacy application development (30+ core applications) into a unified World Wide Web (WWW) environment. The primary project objectives were to construct an environment that would support the rapid development of n-tier, web-based applications while providing standard methods for user authentication/validation, security/access control and definition of a user's organizational context. The project's efforts resulted in Loyola's Enterprise Information Portal (EIP), which meets the aforementioned objectives. This environment: 1) allows access to other vertical Intranet portals (e.g., electronic medical record, patient satisfaction information and faculty effort); 2) supports end-user desktop customization; and 3) provides a means for standardized application “look and feel.” The portal was constructed utilizing readily available hardware and software. Server hardware consists of multiprocessor (Intel Pentium 500Mhz) Compaq 6500 servers with one gigabyte of random access memory and 75 gigabytes of hard disk storage. Microsoft SQL Server was selected to house the portal's internal or security data structures. Netscape Enterprise Server was selected for the web server component of the environment and Allaire's ColdFusion was chosen for access and application tiers. Total costs for the portal environment was less than $40,000. User data storage is accomplished through two Microsoft SQL Servers and an existing SUN Microsystems enterprise server with eight processors, 750 gigabytes of disk storage operating Sybase relational database manager. Total storage capacity for all system exceeds one terabyte. In the past 12 months, the EIP has supported development of more than 88 applications and is utilized by more than 2,200 users.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

Web scraping technologies in an API world.

PubMed

Glez-Peña, Daniel; Lourenço, Anália; López-Fernández, Hugo; Reboiro-Jato, Miguel; Fdez-Riverola, Florentino

2014-09-01

Web services are the de facto standard in biomedical data integration. However, there are data integration scenarios that cannot be fully covered by Web services. A number of Web databases and tools do not support Web services, and existing Web services do not cover for all possible user data demands. As a consequence, Web data scraping, one of the oldest techniques for extracting Web contents, is still in position to offer a valid and valuable service to a wide range of bioinformatics applications, ranging from simple extraction robots to online meta-servers. This article reviews existing scraping frameworks and tools, identifying their strengths and limitations in terms of extraction capabilities. The main focus is set on showing how straightforward it is today to set up a data scraping pipeline, with minimal programming effort, and answer a number of practical needs. For exemplification purposes, we introduce a biomedical data extraction scenario where the desired data sources, well-known in clinical microbiology and similar domains, do not offer programmatic interfaces yet. Moreover, we describe the operation of WhichGenes and PathJam, two bioinformatics meta-servers that use scraping as means to cope with gene set enrichment analysis. © The Author 2013. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Surfing for Data: A Gathering Trend in Data Storage Is the Use of Web-Based Applications that Make It Easy for Authorized Users to Access Hosted Server Content with Just a Computing Device and Browser

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

In recent years, the widespread availability of networks and the flexibility of Web browsers have shifted the industry from a client-server model to a Web-based one. In the client-server model of computing, clients run applications locally, with the servers managing storage, printing functions, and network traffic. Because every client is…

The anatomy of a World Wide Web library service: the BONES demonstration project. Biomedically Oriented Navigator of Electronic Services.

PubMed Central

Schnell, E H

1995-01-01

In 1994, the John A. Prior Health Sciences Library at Ohio State University began to develop a World Wide Web demonstration project, the Biomedically Oriented Navigator of Electronic Services (BONES). The initial intent of BONES was to facilitate the health professional's access to Internet resources by organizing them in a systematic manner. The project not only met this goal but also helped identify the resources needed to launch a full-scale Web library service. This paper discusses the tasks performed and resources used in the development of BONES and describes the creation and organization of documents on the BONES Web server. The paper also discusses the outcomes of the project and the impact on the library's staff and services. PMID:8547903

Integrated databanks access and sequence/structure analysis services at the PBIL.

PubMed

Perrière, Guy; Combet, Christophe; Penel, Simon; Blanchet, Christophe; Thioulouse, Jean; Geourjon, Christophe; Grassot, Julien; Charavay, Céline; Gouy, Manolo; Duret, Laurent; Deléage, Gilbert

2003-07-01

The World Wide Web server of the PBIL (Pôle Bioinformatique Lyonnais) provides on-line access to sequence databanks and to many tools of nucleic acid and protein sequence analyses. This server allows to query nucleotide sequence banks in the EMBL and GenBank formats and protein sequence banks in the SWISS-PROT and PIR formats. The query engine on which our data bank access is based is the ACNUC system. It allows the possibility to build complex queries to access functional zones of biological interest and to retrieve large sequence sets. Of special interest are the unique features provided by this system to query the data banks of gene families developed at the PBIL. The server also provides access to a wide range of sequence analysis methods: similarity search programs, multiple alignments, protein structure prediction and multivariate statistics. An originality of this server is the integration of these two aspects: sequence retrieval and sequence analysis. Indeed, thanks to the introduction of re-usable lists, it is possible to perform treatments on large sets of data. The PBIL server can be reached at: http://pbil.univ-lyon1.fr.

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

Creation of a Web-Based GIS Server and Custom Geoprocessing Tools for Enhanced Hydrologic Applications

NASA Astrophysics Data System (ADS)

Welton, B.; Chouinard, K.; Sultan, M.; Becker, D.; Milewski, A.; Becker, R.

2010-12-01

Rising populations in the arid and semi arid parts of the World are increasing the demand for fresh water supplies worldwide. Many data sets needed for assessment of hydrologic applications across vast regions of the world are expensive, unpublished, difficult to obtain, or at varying scales which complicates their use. Fortunately, this situation is changing with the development of global remote sensing datasets and web-based platforms such as GIS Server. GIS provides a cost effective vehicle for comparing, analyzing, and querying a variety of spatial datasets as geographically referenced layers. We have recently constructed a web-based GIS, that incorporates all relevant geological, geochemical, geophysical, and remote sensing data sets that were readily used to identify reservoir types and potential well locations on local and regional scales in various tectonic settings including: (1) extensional environment (Red Sea rift), (2) transcurrent fault system (Najd Fault in the Arabian-Nubian Shield), and (3) compressional environments (Himalayas). The web-based GIS could also be used to detect spatial and temporal trends in precipitation, recharge, and runoff in large watersheds on local, regional, and continental scales. These applications were enabled through the construction of a web-based ArcGIS Server with Google Map’s interface and the development of customized geoprocessing tools. ArcGIS Server provides out-of-the-box setups that are generic in nature. This platform includes all of the standard web based GIS tools (e.g. pan, zoom, identify, search, data querying, and measurement). In addition to the standard suite of tools provided by ArcGIS Server an additional set of advanced data manipulation and display tools was also developed to allow for a more complete and customizable view of the area of interest. The most notable addition to the standard GIS Server tools is the custom on-demand geoprocessing tools (e.g., graph, statistical functions, custom raster creation, profile, TRMM). The generation of a wide range of derivative maps (e.g., buffer zone, contour map, graphs, temporal rainfall distribution maps) from various map layers (e.g., geologic maps, geophysics, satellite images) allows for more user flexibility. The use of these tools along with Google Map’s API which enables the website user to utilize high quality GeoEye 2 images provide by Google in conjunction with our data, creates a more complete image of the area being observed and allows for custom derivative maps to be created in the field and viewed immediately on the web, processes that were restricted to offline databases.

RSRE: RNA structural robustness evaluator

PubMed Central

Shu, Wenjie; Zheng, Zhiqiang; Wang, Shengqi

2007-01-01

Biological robustness, defined as the ability to maintain stable functioning in the face of various perturbations, is an important and fundamental topic in current biology, and has become a focus of numerous studies in recent years. Although structural robustness has been explored in several types of RNA molecules, the origins of robustness are still controversial. Computational analysis results are needed to make up for the lack of evidence of robustness in natural biological systems. The RNA structural robustness evaluator (RSRE) web server presented here provides a freely available online tool to quantitatively evaluate the structural robustness of RNA based on the widely accepted definition of neutrality. Several classical structure comparison methods are employed; five randomization methods are implemented to generate control sequences; sub-optimal predicted structures can be optionally utilized to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate analysis. The RSRE will be helpful in the wide exploration of RNA structural robustness and will catalyze our understanding of RNA evolution. The RSRE web server is freely available at http://biosrv1.bmi.ac.cn/RSRE/ or http://biotech.bmi.ac.cn/RSRE/. PMID:17567615

The Role of the Web Server in a Capstone Web Application Course

ERIC Educational Resources Information Center

Umapathy, Karthikeyan; Wallace, F. Layne

2010-01-01

Web applications have become commonplace in the Information Systems curriculum. Much of the discussion about Web development for capstone courses has centered on the scripting tools. Very little has been discussed about different ways to incorporate the Web server into Web application development courses. In this paper, three different ways of…

Experimental evaluation of the impact of packet capturing tools for web services.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choe, Yung Ryn; Mohapatra, Prasant; Chuah, Chen-Nee

Network measurement is a discipline that provides the techniques to collect data that are fundamental to many branches of computer science. While many capturing tools and comparisons have made available in the literature and elsewhere, the impact of these packet capturing tools on existing processes have not been thoroughly studied. While not a concern for collection methods in which dedicated servers are used, many usage scenarios of packet capturing now requires the packet capturing tool to run concurrently with operational processes. In this work we perform experimental evaluations of the performance impact that packet capturing process have on web-based services;more » in particular, we observe the impact on web servers. We find that packet capturing processes indeed impact the performance of web servers, but on a multi-core system the impact varies depending on whether the packet capturing and web hosting processes are co-located or not. In addition, the architecture and behavior of the web server and process scheduling is coupled with the behavior of the packet capturing process, which in turn also affect the web server's performance.« less

MCTBI: a web server for predicting metal ion effects in RNA structures.

PubMed

Sun, Li-Zhen; Zhang, Jing-Xiang; Chen, Shi-Jie

2017-08-01

Metal ions play critical roles in RNA structure and function. However, web servers and software packages for predicting ion effects in RNA structures are notably scarce. Furthermore, the existing web servers and software packages mainly neglect ion correlation and fluctuation effects, which are potentially important for RNAs. We here report a new web server, the MCTBI server (http://rna.physics.missouri.edu/MCTBI), for the prediction of ion effects for RNA structures. This server is based on the recently developed MCTBI, a model that can account for ion correlation and fluctuation effects for nucleic acid structures and can provide improved predictions for the effects of metal ions, especially for multivalent ions such as Mg 2+ effects, as shown by extensive theory-experiment test results. The MCTBI web server predicts metal ion binding fractions, the most probable bound ion distribution, the electrostatic free energy of the system, and the free energy components. The results provide mechanistic insights into the role of metal ions in RNA structure formation and folding stability, which is important for understanding RNA functions and the rational design of RNA structures. © 2017 Sun et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Jenner-predict server: prediction of protein vaccine candidates (PVCs) in bacteria based on host-pathogen interactions

PubMed Central

2013-01-01

Background Subunit vaccines based on recombinant proteins have been effective in preventing infectious diseases and are expected to meet the demands of future vaccine development. Computational approach, especially reverse vaccinology (RV) method has enormous potential for identification of protein vaccine candidates (PVCs) from a proteome. The existing protective antigen prediction software and web servers have low prediction accuracy leading to limited applications for vaccine development. Besides machine learning techniques, those software and web servers have considered only protein’s adhesin-likeliness as criterion for identification of PVCs. Several non-adhesin functional classes of proteins involved in host-pathogen interactions and pathogenesis are known to provide protection against bacterial infections. Therefore, knowledge of bacterial pathogenesis has potential to identify PVCs. Results A web server, Jenner-Predict, has been developed for prediction of PVCs from proteomes of bacterial pathogens. The web server targets host-pathogen interactions and pathogenesis by considering known functional domains from protein classes such as adhesin, virulence, invasin, porin, flagellin, colonization, toxin, choline-binding, penicillin-binding, transferring-binding, fibronectin-binding and solute-binding. It predicts non-cytosolic proteins containing above domains as PVCs. It also provides vaccine potential of PVCs in terms of their possible immunogenicity by comparing with experimentally known IEDB epitopes, absence of autoimmunity and conservation in different strains. Predicted PVCs are prioritized so that only few prospective PVCs could be validated experimentally. The performance of web server was evaluated against known protective antigens from diverse classes of bacteria reported in Protegen database and datasets used for VaxiJen server development. The web server efficiently predicted known vaccine candidates reported from Streptococcus pneumoniae and Escherichia coli proteomes. The Jenner-Predict server outperformed NERVE, Vaxign and VaxiJen methods. It has sensitivity of 0.774 and 0.711 for Protegen and VaxiJen dataset, respectively while specificity of 0.940 has been obtained for the latter dataset. Conclusions Better prediction accuracy of Jenner-Predict web server signifies that domains involved in host-pathogen interactions and pathogenesis are better criteria for prediction of PVCs. The web server has successfully predicted maximum known PVCs belonging to different functional classes. Jenner-Predict server is freely accessible at http://117.211.115.67/vaccine/home.html PMID:23815072

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites.

PubMed

Konc, Janez; Janežič, Dušanka

2014-07-01

The ProBiS-ligands web server predicts binding of ligands to a protein structure. Starting with a protein structure or binding site, ProBiS-ligands first identifies template proteins in the Protein Data Bank that share similar binding sites. Based on the superimpositions of the query protein and the similar binding sites found, the server then transposes the ligand structures from those sites to the query protein. Such ligand prediction supports many activities, e.g. drug repurposing. The ProBiS-ligands web server, an extension of the ProBiS web server, is open and free to all users at http://probis.cmm.ki.si/ligands. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

PubMed Central

Drory Retwitzer, Matan; Polishchuk, Maya; Churkin, Elena; Kifer, Ilona; Yakhini, Zohar; Barash, Danny

2015-01-01

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular—no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence. Here, we introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods. RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site. PMID:25940619

The design and implementation of web mining in web sites security

NASA Astrophysics Data System (ADS)

Li, Jian; Zhang, Guo-Yin; Gu, Guo-Chang; Li, Jian-Li

2003-06-01

The backdoor or information leak of Web servers can be detected by using Web Mining techniques on some abnormal Web log and Web application log data. The security of Web servers can be enhanced and the damage of illegal access can be avoided. Firstly, the system for discovering the patterns of information leakages in CGI scripts from Web log data was proposed. Secondly, those patterns for system administrators to modify their codes and enhance their Web site security were provided. The following aspects were described: one is to combine web application log with web log to extract more information, so web data mining could be used to mine web log for discovering the information that firewall and Information Detection System cannot find. Another approach is to propose an operation module of web site to enhance Web site security. In cluster server session, Density-Based Clustering technique is used to reduce resource cost and obtain better efficiency.

Engineering Proteins for Thermostability with iRDP Web Server

PubMed Central

Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C. G.

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements. PMID:26436543

Engineering Proteins for Thermostability with iRDP Web Server.

PubMed

Panigrahi, Priyabrata; Sule, Manas; Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C G

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.

Server-Based and Server-Less Byod Solutions to Support Electronic Learning

DTIC Science & Technology

2016-06-01

Knowledge Online NSD National Security Directive OS operating system OWA Outlook Web Access PC personal computer PED personal electronic device PDA...mobile devices, institute mobile device policies and standards, and promote the development and use of DOD mobile and web -enabled applications” (DOD...with an isolated BYOD web server, properly educated system administrators must carry out and execute the necessary, pre-defined network security

CovalentDock Cloud: a web server for automated covalent docking.

PubMed

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-07-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/.

CovalentDock Cloud: a web server for automated covalent docking

PubMed Central

Ouyang, Xuchang; Zhou, Shuo; Ge, Zemei; Li, Runtao; Kwoh, Chee Keong

2013-01-01

Covalent binding is an important mechanism for many drugs to gain its function. We developed a computational algorithm to model this chemical event and extended it to a web server, the CovalentDock Cloud, to make it accessible directly online without any local installation and configuration. It provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. This web server is free and open to all users at http://docking.sce.ntu.edu.sg/. PMID:23677616

deFUME: Dynamic exploration of functional metagenomic sequencing data.

PubMed

van der Helm, Eric; Geertz-Hansen, Henrik Marcus; Genee, Hans Jasper; Malla, Sailesh; Sommer, Morten Otto Alexander

2015-07-31

Functional metagenomic selections represent a powerful technique that is widely applied for identification of novel genes from complex metagenomic sources. However, whereas hundreds to thousands of clones can be easily generated and sequenced over a few days of experiments, analyzing the data is time consuming and constitutes a major bottleneck for experimental researchers in the field. Here we present the deFUME web server, an easy-to-use web-based interface for processing, annotation and visualization of functional metagenomics sequencing data, tailored to meet the requirements of non-bioinformaticians. The web-server integrates multiple analysis steps into one single workflow: read assembly, open reading frame prediction, and annotation with BLAST, InterPro and GO classifiers. Analysis results are visualized in an online dynamic web-interface. The deFUME webserver provides a fast track from raw sequence to a comprehensive visual data overview that facilitates effortless inspection of gene function, clustering and distribution. The webserver is available at cbs.dtu.dk/services/deFUME/and the source code is distributed at github.com/EvdH0/deFUME.

Computational algorithm to evaluate product disassembly cost index

NASA Astrophysics Data System (ADS)

Zeid, Ibrahim; Gupta, Surendra M.

2002-02-01

Environmentally conscious manufacturing is an important paradigm in today's engineering practice. Disassembly is a crucial factor in implementing this paradigm. Disassembly allows the reuse and recycling of parts and products that reach their death after their life cycle ends. There are many questions that must be answered before a disassembly decision can be reached. The most important question is economical. The cost of disassembly versus the cost of scrapping a product is always considered. This paper develops a computational tool that allows decision-makers to calculate the disassembly cost of a product. The tool makes it simple to perform 'what if' scenarios fairly quickly. The tool is Web based and has two main parts. The front-end part is a Web page and runs on the client side in a Web browser, while the back-end part is a disassembly engine (servlet) that has disassembly knowledge and costing algorithms and runs on the server side. The tool is based on the client/server model that is pervasively utilized throughout the World Wide Web. An example is used to demonstrate the implementation and capabilities of the tool.

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra.

PubMed

Micsonai, András; Wien, Frank; Bulyáki, Éva; Kun, Judit; Moussong, Éva; Lee, Young-Ho; Goto, Yuji; Réfrégiers, Matthieu; Kardos, József

2018-06-11

Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

HOED: Hypermedia Online Educational Database.

ERIC Educational Resources Information Center

Duval, E.; Olivie, H.

This paper presents HOED, a distributed hypermedia client-server system for educational resources. The aim of HOED is to provide a library facility for hyperdocuments that is accessible via the world wide web. Its main application domain is education. The HOED database not only holds the educational resources themselves, but also data describing…

A General Purpose Connections type CTI Server Based on SIP Protocol and Its Implementation

NASA Astrophysics Data System (ADS)

Watanabe, Toru; Koizumi, Hisao

In this paper, we propose a general purpose connections type CTI (Computer Telephony Integration) server that provides various CTI services such as voice logging where the CTI server communicates with IP-PBX using the SIP (Session Initiation Protocol), and accumulates voice packets of external line telephone call flowing between an IP telephone for extension and a VoIP gateway connected to outside line networks. The CTI server realizes CTI services such as voice logging, telephone conference, or IVR (interactive voice response) with accumulating and processing voice packets sampled. Furthermore, the CTI server incorporates a web server function which can provide various CTI services such as a Web telephone directory via a Web browser to PCs, cellular telephones or smart-phones in mobile environments.

cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets.

PubMed

Xu, Huayong; Yu, Hui; Tu, Kang; Shi, Qianqian; Wei, Chaochun; Li, Yuan-Yuan; Li, Yi-Xue

2013-01-01

We are witnessing rapid progress in the development of methodologies for building the combinatorial gene regulatory networks involving both TFs (Transcription Factors) and miRNAs (microRNAs). There are a few tools available to do these jobs but most of them are not easy to use and not accessible online. A web server is especially needed in order to allow users to upload experimental expression datasets and build combinatorial regulatory networks corresponding to their particular contexts. In this work, we compiled putative TF-gene, miRNA-gene and TF-miRNA regulatory relationships from forward-engineering pipelines and curated them as built-in data libraries. We streamlined the R codes of our two separate forward-and-reverse engineering algorithms for combinatorial gene regulatory network construction and formalized them as two major functional modules. As a result, we released the cGRNB (combinatorial Gene Regulatory Networks Builder): a web server for constructing combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. The cGRNB enables two major network-building modules, one for MPGE (miRNA-perturbed gene expression) datasets and the other for parallel miRNA/mRNA expression datasets. A miRNA-centered two-layer combinatorial regulatory cascade is the output of the first module and a comprehensive genome-wide network involving all three types of combinatorial regulations (TF-gene, TF-miRNA, and miRNA-gene) are the output of the second module. In this article we propose cGRNB, a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets. Since parallel miRNA/mRNA expression datasets are rapidly accumulated by the advance of next-generation sequencing techniques, cGRNB will be very useful tool for researchers to build combinatorial gene regulatory networks based on expression datasets. The cGRNB web-server is free and available online at http://www.scbit.org/cgrnb.

Distributing medical images with internet technologies: a DICOM web server and a DICOM java viewer.

PubMed

Fernàndez-Bayó, J; Barbero, O; Rubies, C; Sentís, M; Donoso, L

2000-01-01

With the advent of filmless radiology, it becomes important to be able to distribute radiologic images digitally throughout an entire hospital. A new approach based on World Wide Web technologies was developed to accomplish this objective. This approach involves a Web server that allows the query and retrieval of images stored in a Digital Imaging and Communications in Medicine (DICOM) archive. The images can be viewed inside a Web browser with use of a small Java program known as the DICOM Java Viewer, which is executed inside the browser. The system offers several advantages over more traditional picture archiving and communication systems (PACS): It is easy to install and maintain, is platform independent, allows images to be manipulated and displayed efficiently, and is easy to integrate with existing systems that are already making use of Web technologies. The system is user-friendly and can easily be used from outside the hospital if a security policy is in place. The simplicity and flexibility of Internet technologies makes them highly preferable to the more complex PACS workstations. The system works well, especially with magnetic resonance and computed tomographic images, and can help improve and simplify interdepartmental relationships in a filmless hospital environment.

Cloud Computing Trace Characterization and Synthetic Workload Generation

DTIC Science & Technology

2013-03-01

measurements [44]. Olio is primarily for learning Web 2.0 technologies, evaluating the three implementations (PHP, Java EE, and RubyOnRails (ROR...Add Event 17 Olio is well documented, but assumes prerequisite knowledge with setup and operation of apache web servers and MySQL databases. Olio...Faban supports numerous servers such as Apache httpd, Sun Java System Web, Portal and Mail Servers, Oracle RDBMS, memcached, and others [18]. Perhaps

How Public Is the Web?: Robots, Access, and Scholarly Communication.

ERIC Educational Resources Information Center

Snyder, Herbert; Rosenbaum, Howard

1998-01-01

Examines the use of Robot Exclusion Protocol (REP) to restrict the access of search engine robots to 10 major United States university Web sites. An analysis of Web site searching and interviews with Web server administrators shows that the decision to use this procedure is largely technical and is typically made by the Web server administrator.…

New Web Server - the Java Version of Tempest - Produced

NASA Technical Reports Server (NTRS)

York, David W.; Ponyik, Joseph G.

2000-01-01

A new software design and development effort has produced a Java (Sun Microsystems, Inc.) version of the award-winning Tempest software (refs. 1 and 2). In 1999, the Embedded Web Technology (EWT) team received a prestigious R&D 100 Award for Tempest, Java Version. In this article, "Tempest" will refer to the Java version of Tempest, a World Wide Web server for desktop or embedded systems. Tempest was designed at the NASA Glenn Research Center at Lewis Field to run on any platform for which a Java Virtual Machine (JVM, Sun Microsystems, Inc.) exists. The JVM acts as a translator between the native code of the platform and the byte code of Tempest, which is compiled in Java. These byte code files are Java executables with a ".class" extension. Multiple byte code files can be zipped together as a "*.jar" file for more efficient transmission over the Internet. Today's popular browsers, such as Netscape (Netscape Communications Corporation) and Internet Explorer (Microsoft Corporation) have built-in Virtual Machines to display Java applets.

Filmless PACS in a multiple facility environment

NASA Astrophysics Data System (ADS)

Wilson, Dennis L.; Glicksman, Robert A.; Prior, Fred W.; Siu, Kai-Yeung; Goldburgh, Mitchell M.

1996-05-01

A Picture Archiving and Communication System centered on a shared image file server can support a filmless hospital. Systems based on this architecture have proven themselves in over four years of clinical operation. Changes in healthcare delivery are causing radiology groups to support multiple facilities for remote clinic support and consolidation of services. There will be a corresponding need for communicating over a standardized wide area network (WAN). Interactive workflow, a natural extension to the single facility case, requires a means to work effectively and seamlessly across moderate to low speed communication networks. Several schemes for supporting a consortium of medical treatment facilities over a WAN are explored. Both centralized and distributed database approaches are evaluated against several WAN scenarios. Likewise, several architectures for distributing image file servers or buffers over a WAN are explored, along with the caching and distribution strategies that support them. An open system implementation is critical to the success of a wide area system. The role of the Digital Imaging and Communications in Medicine (DICOM) standard in supporting multi- facility and multi-vendor open systems is also addressed. An open system can be achieved by using a DICOM server to provide a view of the system-wide distributed database. The DICOM server interface to a local version of the global database lets a local workstation treat the multiple, distributed data servers as though they were one local server for purposes of examination queries. The query will recover information about the examination that will permit retrieval over the network from the server on which the examination resides. For efficiency reasons, the ability to build cross-facility radiologist worklists and clinician-oriented patient folders is essential. The technologies of the World-Wide-Web can be used to generate worklists and patient folders across facilities. A reliable broadcast protocol may be a convenient way to notify many different users and many image servers about new activities in the network of image servers. In addition to ensuring reliability of message delivery and global serialization of each broadcast message in the network, the broadcast protocol should not introduce significant communication overhead.

DiseaseConnect: a comprehensive web server for mechanism-based disease–disease connections

PubMed Central

Liu, Chun-Chi; Tseng, Yu-Ting; Li, Wenyuan; Wu, Chia-Yu; Mayzus, Ilya; Rzhetsky, Andrey; Sun, Fengzhu; Waterman, Michael; Chen, Jeremy J. W.; Chaudhary, Preet M.; Loscalzo, Joseph; Crandall, Edward; Zhou, Xianghong Jasmine

2014-01-01

The DiseaseConnect (http://disease-connect.org) is a web server for analysis and visualization of a comprehensive knowledge on mechanism-based disease connectivity. The traditional disease classification system groups diseases with similar clinical symptoms and phenotypic traits. Thus, diseases with entirely different pathologies could be grouped together, leading to a similar treatment design. Such problems could be avoided if diseases were classified based on their molecular mechanisms. Connecting diseases with similar pathological mechanisms could inspire novel strategies on the effective repositioning of existing drugs and therapies. Although there have been several studies attempting to generate disease connectivity networks, they have not yet utilized the enormous and rapidly growing public repositories of disease-related omics data and literature, two primary resources capable of providing insights into disease connections at an unprecedented level of detail. Our DiseaseConnect, the first public web server, integrates comprehensive omics and literature data, including a large amount of gene expression data, Genome-Wide Association Studies catalog, and text-mined knowledge, to discover disease–disease connectivity via common molecular mechanisms. Moreover, the clinical comorbidity data and a comprehensive compilation of known drug–disease relationships are additionally utilized for advancing the understanding of the disease landscape and for facilitating the mechanism-based development of new drug treatments. PMID:24895436

BRepertoire: a user-friendly web server for analysing antibody repertoire data.

PubMed

Margreitter, Christian; Lu, Hui-Chun; Townsend, Catherine; Stewart, Alexander; Dunn-Walters, Deborah K; Fraternali, Franca

2018-04-14

Antibody repertoire analysis by high throughput sequencing is now widely used, but a persisting challenge is enabling immunologists to explore their data to discover discriminating repertoire features for their own particular investigations. Computational methods are necessary for large-scale evaluation of antibody properties. We have developed BRepertoire, a suite of user-friendly web-based software tools for large-scale statistical analyses of repertoire data. The software is able to use data preprocessed by IMGT, and performs statistical and comparative analyses with versatile plotting options. BRepertoire has been designed to operate in various modes, for example analysing sequence-specific V(D)J gene usage, discerning physico-chemical properties of the CDR regions and clustering of clonotypes. Those analyses are performed on the fly by a number of R packages and are deployed by a shiny web platform. The user can download the analysed data in different table formats and save the generated plots as image files ready for publication. We believe BRepertoire to be a versatile analytical tool that complements experimental studies of immune repertoires. To illustrate the server's functionality, we show use cases including differential gene usage in a vaccination dataset and analysis of CDR3H properties in old and young individuals. The server is accessible under http://mabra.biomed.kcl.ac.uk/BRepertoire.

Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Seelus, Christoph; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; King, Todd; Hughes, John; Fung, Shing; Galkin, Ivan; Hapgood, Michael; Belehaki, Anna

2015-04-01

Opportunities for the Mashup of Heterogenous Data Server via Semantic Web Technology European Union ESPAS, Japanese IUGONET and GFZ ISDC data server are developed for the ingestion, archiving and distributing of geo and space science domain data. Main parts of the data -managed by the mentioned data server- are related to near earth-space and geomagnetic field data. A smart mashup of the data server would allow a seamless browse and access to data and related context information. However the achievement of a high level of interoperability is a challenge because the data server are based on different data models and software frameworks. This paper is focused on the latest experiments and results for the mashup of the data server using the semantic Web approach. Besides the mashup of domain and terminological ontologies, especially the options to connect data managed by relational databases using D2R server and SPARQL technology will be addressed. A successful realization of the data server mashup will not only have a positive impact to the data users of the specific scientific domain but also to related projects, such as e.g. the development of a new interoperable version of NASA's Planetary Data System (PDS) or ICUS's World Data System alliance. ESPAS data server: https://www.espas-fp7.eu/portal/ IUGONET data server: http://search.iugonet.org/iugonet/ GFZ ISDC data server (semantic Web based prototype): http://rz-vm30.gfz-potsdam.de/drupal-7.9/ NASA PDS: http://pds.nasa.gov ICSU-WDS: https://www.icsu-wds.org

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

PubMed

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

2017-11-15

Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Studying the co-evolution of protein families with the Mirrortree web server.

PubMed

Ochoa, David; Pazos, Florencio

2010-05-15

The Mirrortree server allows to graphically and interactively study the co-evolution of two protein families, and investigate their possible interactions and functional relationships in a taxonomic context. The server includes the possibility of starting from single sequences and hence it can be used by non-expert users. The web server is freely available at http://csbg.cnb.csic.es/mtserver. It was tested in the main web browsers. Adobe Flash Player is required at the client side to perform the interactive assessment of co-evolution. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

PubMed

Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

2015-11-23

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

MovieMaker: a web server for rapid rendering of protein motions and interactions

PubMed Central

Maiti, Rajarshi; Van Domselaar, Gary H.; Wishart, David S.

2005-01-01

MovieMaker is a web server that allows short (∼10 s), downloadable movies of protein motions to be generated. It accepts PDB files or PDB accession numbers as input and automatically calculates, renders and merges the necessary image files to create colourful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating (i) simple rotation, (ii) morphing between two end-state conformers, (iii) short-scale, picosecond vibrations, (iv) ligand docking, (v) protein oligomerization, (vi) mid-scale nanosecond (ensemble) motions and (vii) protein folding/unfolding. MovieMaker does not perform molecular dynamics calculations. Instead it is an animation tool that uses a sophisticated superpositioning algorithm in conjunction with Cartesian coordinate interpolation to rapidly and automatically calculate the intermediate structures needed for many of its animations. Users have extensive control over the rendering style, structure colour, animation quality, background and other image features. MovieMaker is intended to be a general-purpose server that allows both experts and non-experts to easily generate useful, informative protein animations for educational and illustrative purposes. MovieMaker is accessible at . PMID:15980488

CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

PubMed

Kuriata, Aleksander; Gierut, Aleksandra Maria; Oleniecki, Tymoteusz; Ciemny, Maciej Pawel; Kolinski, Andrzej; Kurcinski, Mateusz; Kmiecik, Sebastian

2018-05-14

Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

A Two-Tiered Model for Analyzing Library Web Site Usage Statistics, Part 1: Web Server Logs.

ERIC Educational Resources Information Center

Cohen, Laura B.

2003-01-01

Proposes a two-tiered model for analyzing web site usage statistics for academic libraries: one tier for library administrators that analyzes measures indicating library use, and a second tier for web site managers that analyzes measures aiding in server maintenance and site design. Discusses the technology of web site usage statistics, and…

Integrating DXplain into a clinical information system using the World Wide Web.

PubMed

Elhanan, G; Socratous, S A; Cimino, J J

1996-01-01

The World Wide Web(WWW) offers a cross-platform environment and standard protocols that enable integration of various applications available on the Internet. The authors use the Web to facilitate interaction between their Web-based Clinical Information System and a decision-support system-DXplain, at the Massachusetts General Hospital-using local architecture and Common Gateway Interface programs. The current application translates patients laboratory test results into DXplain's terms to generate diagnostic hypotheses. Two different access methods are utilized for this model; Hypertext Transfer Protocol (HTTP) and TCP/IP function calls. While clinical aspects cannot be evaluated as yet, the model demonstrates the potential of Web-based applications for interaction and integration and how local architecture, with a controlled vocabulary server, can further facilitate such integration. This model serves to demonstrate some of the limitations of the current WWW technology and identifies issues such as control over Web resources and their utilization and liability issues as possible obstacles for further integration.

WebPresent: a World Wide Web-based telepresentation tool for physicians

NASA Astrophysics Data System (ADS)

Sampath-Kumar, Srihari; Banerjea, Anindo; Moshfeghi, Mehran

1997-05-01

In this paper, we present the design architecture and the implementation status of WebPresent - a world wide web based tele-presentation tool. This tool allows a physician to use a conference server workstation and make a presentation of patient cases to a geographically distributed audience. The audience consists of other physicians collaborating on patients' health care management and physicians participating in continuing medical education. These physicians are at several locations with networks of different bandwidth and capabilities connecting them. Audiences also receive the patient case information on different computers ranging form high-end display workstations to laptops with low-resolution displays. WebPresent is a scalable networked multimedia tool which supports the presentation of hypertext, images, audio, video, and a white-board to remote physicians with hospital Intranet access. WebPresent allows the audience to receive customized information. The data received can differ in resolution and bandwidth, depending on the availability of resources such as display resolution and network bandwidth.

Abnormal Web Usage Control by Proxy Strategies.

ERIC Educational Resources Information Center

Yu, Hsiang-Fu; Tseng, Li-Ming

2002-01-01

Approaches to designing a proxy server with Web usage control and to making the proxy server effective on local area networks are proposed to prevent abnormal Web access and to prioritize Web usage. A system is implemented to demonstrate the approaches. The implementation reveals that the proposed approaches are effective, such that the abnormal…

Web Platform for Sharing Modeling Software in the Field of Nonlinear Optics

NASA Astrophysics Data System (ADS)

Dubenskaya, Julia; Kryukov, Alexander; Demichev, Andrey

2018-02-01

We describe the prototype of a Web platform intended for sharing software programs for computer modeling in the rapidly developing field of the nonlinear optics phenomena. The suggested platform is built on the top of the HUBZero open-source middleware. In addition to the basic HUBZero installation we added to our platform the capability to run Docker containers via an external application server and to send calculation programs to those containers for execution. The presented web platform provides a wide range of features and might be of benefit to nonlinear optics researchers.

RNAiFold: a web server for RNA inverse folding and molecular design.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

2013-07-01

Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

Sirepo - Warp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

SIRW: A web server for the Simple Indexing and Retrieval System that combines sequence motif searches with keyword searches.

PubMed

Ramu, Chenna

2003-07-01

SIRW (http://sirw.embl.de/) is a World Wide Web interface to the Simple Indexing and Retrieval System (SIR) that is capable of parsing and indexing various flat file databases. In addition it provides a framework for doing sequence analysis (e.g. motif pattern searches) for selected biological sequences through keyword search. SIRW is an ideal tool for the bioinformatics community for searching as well as analyzing biological sequences of interest.

Graph and Network for Model Elicitation (GNOME Phase 2)

DTIC Science & Technology

2013-02-01

10 3.3 GNOME UI Components for NOEM Web Client...20 Figure 17: Sampling in Web -client...the web -client). The server-side service can run and generate data asynchronously, allowing a cluster of servers to run the sampling. Also, a

WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

ERIC Educational Resources Information Center

Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

Tao of Gateway: Providing Internet Access to Licensed Databases.

ERIC Educational Resources Information Center

McClellan, Gregory A.; Garrison, William V.

1997-01-01

Illustrates an approach for providing networked access to licensed databases over the Internet by positioning the library between patron and vendor. Describes how the gateway systems and database connection servers work and discusses how treatment of security has evolved with the introduction of the World Wide Web. Outlines plans to reimplement…

Content Consumption and Hierarchical Structures of Web-Supported Courses

ERIC Educational Resources Information Center

Hershkovitz, Arnon; Hardof-Jaffe, Sharon; Nachmias, Rafi

2014-01-01

This study presents an empirical investigation of the relationship between the hierarchical structure of content delivered to students within a Learning Management System (LMS) and its actual consumption. To this end, campus-wide data relating to 1,203 courses were collected from the LMS' servers and were subsequently analyzed using data mining…

Rclick: a web server for comparison of RNA 3D structures.

PubMed

Nguyen, Minh N; Verma, Chandra

2015-03-15

RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least-squares fitting. Our server Rclick has been benchmarked and compared with other popular servers and methods for RNA structural alignments. In most cases, Rclick alignments were better in terms of structure overlap. Our server also recognizes conformational changes between structures. For this purpose, the server produces complementary alignments to maximize the extent of detectable similarity. Various examples showcase the utility of our web server for comparison of RNA, RNA-protein complexes and RNA-ligand structures. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.

PubMed

Bonnet, Eric; He, Ying; Billiau, Kenny; Van de Peer, Yves

2010-06-15

We present a new web server called TAPIR, designed for the prediction of plant microRNA targets. The server offers the possibility to search for plant miRNA targets using a fast and a precise algorithm. The precise option is much slower but guarantees to find less perfectly paired miRNA-target duplexes. Furthermore, the precise option allows the prediction of target mimics, which are characterized by a miRNA-target duplex having a large loop, making them undetectable by traditional tools. The TAPIR web server can be accessed at: http://bioinformatics.psb.ugent.be/webtools/tapir. Supplementary data are available at Bioinformatics online.

PREFMD: a web server for protein structure refinement via molecular dynamics simulations.

PubMed

Heo, Lim; Feig, Michael

2018-03-15

Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. PREFMD is freely available as a web server at http://feiglab.org/prefmd. Scripts for running PREFMD as a stand-alone package are available at https://github.com/feiglab/prefmd.git. feig@msu.edu. Supplementary data are available at Bioinformatics online.

Using NetCloak to develop server-side Web-based experiments without writing CGI programs.

PubMed

Wolfe, Christopher R; Reyna, Valerie F

2002-05-01

Server-side experiments use the Web server, rather than the participant's browser, to handle tasks such as random assignment, eliminating inconsistencies with JAVA and other client-side applications. Heretofore, experimenters wishing to create server-side experiments have had to write programs to create common gateway interface (CGI) scripts in programming languages such as Perl and C++. NetCloak uses simple, HTML-like commands to create CGIs. We used NetCloak to implement an experiment on probability estimation. Measurements of time on task and participants' IP addresses assisted quality control. Without prior training, in less than 1 month, we were able to use NetCloak to design and create a Web-based experiment and to help graduate students create three Web-based experiments of their own.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

PubMed Central

Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

2011-01-01

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

Installation of the National Transport Code Collaboration Data Server at the ITPA International Multi-tokamak Confinement Profile Database

NASA Astrophysics Data System (ADS)

Roach, Colin; Carlsson, Johan; Cary, John R.; Alexander, David A.

2002-11-01

The National Transport Code Collaboration (NTCC) has developed an array of software, including a data client/server. The data server, which is written in C++, serves local data (in the ITER Profile Database format) as well as remote data (by accessing one or several MDS+ servers). The client, a web-invocable Java applet, provides a uniform, intuitive, user-friendly, graphical interface to the data server. The uniformity of the interface relieves the user from the trouble of mastering the differences between different data formats and lets him/her focus on the essentials: plotting and viewing the data. The user runs the client by visiting a web page using any Java capable Web browser. The client is automatically downloaded and run by the browser. A reference to the data server is then retrieved via the standard Web protocol (HTTP). The communication between the client and the server is then handled by the mature, industry-standard CORBA middleware. CORBA has bindings for all common languages and many high-quality implementations are available (both Open Source and commercial). The NTCC data server has been installed at the ITPA International Multi-tokamak Confinement Profile Database, which is hosted by the UKAEA at Culham Science Centre. The installation of the data server is protected by an Internet firewall. To make it accessible to clients outside the firewall some modifications of the server were required. The working version of the ITPA confinement profile database is not open to the public. Authentification of legitimate users is done utilizing built-in Java security features to demand a password to download the client. We present an overview of the NTCC data client/server and some details of how the CORBA firewall-traversal issues were resolved and how the user authentification is implemented.

Experimental Internet Environment Software Development

NASA Technical Reports Server (NTRS)

Maddux, Gary A.

1998-01-01

Geographically distributed project teams need an Internet based collaborative work environment or "Intranet." The Virtual Research Center (VRC) is an experimental Intranet server that combines several services such as desktop conferencing, file archives, on-line publishing, and security. Using the World Wide Web (WWW) as a shared space paradigm, the Graphical User Interface (GUI) presents users with images of a lunar colony. Each project has a wing of the colony and each wing has a conference room, library, laboratory, and mail station. In FY95, the VRC development team proved the feasibility of this shared space concept by building a prototype using a Netscape commerce server and several public domain programs. Successful demonstrations of the prototype resulted in approval for a second phase. Phase 2, documented by this report, will produce a seamlessly integrated environment by introducing new technologies such as Java and Adobe Web Links to replace less efficient interface software.

Computational resources for ribosome profiling: from database to Web server and software.

PubMed

Wang, Hongwei; Wang, Yan; Xie, Zhi

2017-08-14

Ribosome profiling is emerging as a powerful technique that enables genome-wide investigation of in vivo translation at sub-codon resolution. The increasing application of ribosome profiling in recent years has achieved remarkable progress toward understanding the composition, regulation and mechanism of translation. This benefits from not only the awesome power of ribosome profiling but also an extensive range of computational resources available for ribosome profiling. At present, however, a comprehensive review on these resources is still lacking. Here, we survey the recent computational advances guided by ribosome profiling, with a focus on databases, Web servers and software tools for storing, visualizing and analyzing ribosome profiling data. This review is intended to provide experimental and computational biologists with a reference to make appropriate choices among existing resources for the question at hand. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A web-based approach for electrocardiogram monitoring in the home.

PubMed

Magrabi, F; Lovell, N H; Celler, B G

1999-05-01

A Web-based electrocardiogram (ECG) monitoring service in which a longitudinal clinical record is used for management of patients, is described. The Web application is used to collect clinical data from the patient's home. A database on the server acts as a central repository where this clinical information is stored. A Web browser provides access to the patient's records and ECG data. We discuss the technologies used to automate the retrieval and storage of clinical data from a patient database, and the recording and reviewing of clinical measurement data. On the client's Web browser, ActiveX controls embedded in the Web pages provide a link between the various components including the Web server, Web page, the specialised client side ECG review and acquisition software, and the local file system. The ActiveX controls also implement FTP functions to retrieve and submit clinical data to and from the server. An intelligent software agent on the server is activated whenever new ECG data is sent from the home. The agent compares historical data with newly acquired data. Using this method, an optimum patient care strategy can be evaluated, a summarised report along with reminders and suggestions for action is sent to the doctor and patient by email.

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes.

PubMed

Olechnovič, Kliment; Venclovas, Ceslovas

2014-07-01

The Contact Area Difference score (CAD-score) web server provides a universal framework to compute and analyze discrepancies between different 3D structures of the same biological macromolecule or complex. The server accepts both single-subunit and multi-subunit structures and can handle all the major types of macromolecules (proteins, RNA, DNA and their complexes). It can perform numerical comparison of both structures and interfaces. In addition to entire structures and interfaces, the server can assess user-defined subsets. The CAD-score server performs both global and local numerical evaluations of structural differences between structures or interfaces. The results can be explored interactively using sortable tables of global scores, profiles of local errors, superimposed contact maps and 3D structure visualization. The web server could be used for tasks such as comparison of models with the native (reference) structure, comparison of X-ray structures of the same macromolecule obtained in different states (e.g. with and without a bound ligand), analysis of nuclear magnetic resonance (NMR) structural ensemble or structures obtained in the course of molecular dynamics simulation. The web server is freely accessible at: http://www.ibt.lt/bioinformatics/cad-score. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web-Beagle: a web server for the alignment of RNA secondary structures.

PubMed

Mattei, Eugenio; Pietrosanto, Marco; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2015-07-01

Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

PubMed

Miao, Zhichao; Westhof, Eric

2016-07-08

RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Blackboard Technologies: A Vehicle to Promote Student Motivation and Learning in Physics

ERIC Educational Resources Information Center

Larkin, Teresa L.; Belson, Sarah Irvine

2005-01-01

The Blackboard Learning System™, a Web-based server software system, is widely used on many college and university campuses today. This paper explores the use of the Blackboard system as a teaching and learning tool. Particular emphasis is placed on the online chat feature available through the Blackboard interface. During the fall 2002 pilot…

Casting the Net: The Development of a Resource Collection for an Internet Database.

ERIC Educational Resources Information Center

McKiernan, Gerry

CyberStacks(sm), a demonstration prototype World Wide Web information service, was established on the home page server at Iowa State University with the intent of facilitating identification and use of significant Internet resources in science and technology. CyberStacks(sm) was created in response to perceived deficiencies in early efforts to…

Online Survey, Enrollment, and Examination: Special Internet Applications in Teacher Education.

ERIC Educational Resources Information Center

Tu, Jho-Ju; Babione, Carolyn; Chen, Hsin-Chu

The Teachers College at Emporia State University in Kansas is now utilizing World Wide Web technology for automating the application procedure for student teaching. The general concepts and some of the key terms that are important for understanding the process involved in this project include: a client-server model, HyperText Markup Language,…

Network oriented radiological and medical archive

NASA Astrophysics Data System (ADS)

Ferraris, M.; Frixione, P.; Squarcia, S.

2001-10-01

In this paper the basic ideas of NORMA (Network Oriented Radiological and Medical Archive) are discussed. NORMA is an original project built by a team of physicists in collaboration with radiologists in order to select the best Treatment Planning in radiotherapy. It allows physicians and health physicists, working in different places, to discuss on interesting clinical cases visualizing the same diagnostic images, at the same time, and highlighting zones of interest (tumors and organs at risk). NORMA has a client/server architecture in order to be platform independent. Applying World Wide Web technologies, it can be easily used by people with no specific computer knowledge providing a verbose help to guide the user through the right steps of execution. The client side is an applet while the server side is a Java application. In order to optimize execution the project also includes a proprietary protocol, lying over TCP/IP suite, that organizes data exchanges and control messages. Diagnostic images are retrieved from a relational database or from a standard DICOM (Digital Images and COmmunications in Medicine) PACS through the DICOM-WWW gateway allowing connection of the usual Web browsers, used by the NORMA system, to DICOM applications via the HTTP protocol. Browser requests are sent to the gateway from the Web server through CGI (Common Gateway Interface). DICOM software translates the requests in DICOM messages and organizes the communication with the remote DICOM Application.

OPeNDAP servers like Hyrax and TDS can easily support common single-sign-on authentication protocols using the Apache httpd and related software; adding support for these protocols to clients can be more challenging

NASA Astrophysics Data System (ADS)

Gallagher, J. H. R.; Potter, N.; Evans, B. J. K.

2016-12-01

OPeNDAP, in conjunction with the Australian National University, documented the installation process needed to add authentication to OPeNDAP-enabled data servers (Hyrax, TDS, etc.) and examined 13 OPeNDAP clients to determine how best to add authentication using LDAP, Shibboleth and OAuth2 (we used NASA's URS). We settled on a server configuration (architecture) that uses the Apache web server and a collection of open-source modules to perform the authentication and authorization actions. This is not the only way to accomplish those goals, but using Apache represents a good balance between functionality, leveraging existing work that has been well vetted and includes support for a wide variety of web services, include those that depend on a servlet engine such as tomcat (which both Hyrax and TDS do). Or work shows how LDAP, OAuth2 and Shibboleth can all be accommodated using this readily available software stack. Also important is that the Apache software is very widely used and is fairly robust - extremely important for security software components. In order to make use of a server requiring authentication, clients must support the authentication process. Because HTTP has included authentication for well over a decade, and because HTTP/HTTPS can be used by simply linking programs with a library, both the LDAP and OAuth2/URS authentication schemes have almost universal support within the OPeNDAP client base. The clients, i.e. the HTTP client libraries they employ, understand how to submit the credentials to the correct server when confronted by an HTTP/S Unauthorized (401) response. Interestingly OAuth2 can achieve it's SSO objectives while relying entirely on normative HTTP transport. All 13 of the clients examined worked.The situation with Shibboleth is different. While Shibboleth does use HTTP, it also requires the client to either scrape a web page or support the SAML2.0 ECP profile, which, for programmatic clients, means using SOAP messages. Since working with SOAP is outside the scope of HTTP, support for Shibboleth must be added explicitly into the client software. Some of the potential burden of enabling OPeNDAP clients to work with Shibboleth may be mitigated by getting both NetCDF-C and NetCDF-Java libraries to use the Shibboleth ECP profile. If done, this would get 9 of the 13 clients we examined working.

Molray--a web interface between O and the POV-Ray ray tracer.

PubMed

Harris, M; Jones, T A

2001-08-01

A publicly available web-based interface is presented for producing high-quality ray-traced images and movies from the molecular-modelling program O [Jones et al. (1991), Acta Cryst. A47, 110-119]. The interface allows the user to select O-plot files and set parameters to create standard input files for the popular ray-tracing renderer POV-Ray, which can then produce publication-quality still images or simple movies. To ensure ease of use, we have made this service available to the O user community via the World Wide Web. The public Molray server is available at http://xray.bmc.uu.se/molray.

Integrated web-based viewing and secure remote access to a clinical data repository and diverse clinical systems.

PubMed

Duncan, R G; Saperia, D; Dulbandzhyan, R; Shabot, M M; Polaschek, J X; Jones, D T

2001-01-01

The advent of the World-Wide-Web protocols and client-server technology has made it easy to build low-cost, user-friendly, platform-independent graphical user interfaces to health information systems and to integrate the presentation of data from multiple systems. The authors describe a Web interface for a clinical data repository (CDR) that was moved from concept to production status in less than six months using a rapid prototyping approach, multi-disciplinary development team, and off-the-shelf hardware and software. The system has since been expanded to provide an integrated display of clinical data from nearly 20 disparate information systems.

SMPBS: Web server for computing biomolecular electrostatics using finite element solvers of size modified Poisson-Boltzmann equation.

PubMed

Xie, Yang; Ying, Jinyong; Xie, Dexuan

2017-03-30

SMPBS (Size Modified Poisson-Boltzmann Solvers) is a web server for computing biomolecular electrostatics using finite element solvers of the size modified Poisson-Boltzmann equation (SMPBE). SMPBE not only reflects ionic size effects but also includes the classic Poisson-Boltzmann equation (PBE) as a special case. Thus, its web server is expected to have a broader range of applications than a PBE web server. SMPBS is designed with a dynamic, mobile-friendly user interface, and features easily accessible help text, asynchronous data submission, and an interactive, hardware-accelerated molecular visualization viewer based on the 3Dmol.js library. In particular, the viewer allows computed electrostatics to be directly mapped onto an irregular triangular mesh of a molecular surface. Due to this functionality and the fast SMPBE finite element solvers, the web server is very efficient in the calculation and visualization of electrostatics. In addition, SMPBE is reconstructed using a new objective electrostatic free energy, clearly showing that the electrostatics and ionic concentrations predicted by SMPBE are optimal in the sense of minimizing the objective electrostatic free energy. SMPBS is available at the URL: smpbs.math.uwm.edu © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database.

PubMed

Wang, Xia; Shen, Yihang; Wang, Shiwei; Li, Shiliang; Zhang, Weilin; Liu, Xiaofeng; Lai, Luhua; Pei, Jianfeng; Li, Honglin

2017-07-03

The PharmMapper online tool is a web server for potential drug target identification by reversed pharmacophore matching the query compound against an in-house pharmacophore model database. The original version of PharmMapper includes more than 7000 target pharmacophores derived from complex crystal structures with corresponding protein target annotations. In this article, we present a new version of the PharmMapper web server, of which the backend pharmacophore database is six times larger than the earlier one, with a total of 23 236 proteins covering 16 159 druggable pharmacophore models and 51 431 ligandable pharmacophore models. The expanded target data cover 450 indications and 4800 molecular functions compared to 110 indications and 349 molecular functions in our last update. In addition, the new web server is united with the statistically meaningful ranking of the identified drug targets, which is achieved through the use of standard scores. It also features an improved user interface. The proposed web server is freely available at http://lilab.ecust.edu.cn/pharmmapper/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

PubMed

Jiménez-García, Brian; Pons, Carles; Fernández-Recio, Juan

2013-07-01

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy. The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock. Supplementary data are available at Bioinformatics online.

KAGLVis - On-line 3D Visualisation of Earth-observing-satellite Data

NASA Astrophysics Data System (ADS)

Szuba, Marek; Ameri, Parinaz; Grabowski, Udo; Maatouki, Ahmad; Meyer, Jörg

2015-04-01

One of the goals of the Large-Scale Data Management and Analysis project is to provide a high-performance framework facilitating management of data acquired by Earth-observing satellites such as Envisat. On the client-facing facet of this framework, we strive to provide visualisation and basic analysis tool which could be used by scientists with minimal to no knowledge of the underlying infrastructure. Our tool, KAGLVis, is a JavaScript client-server Web application which leverages modern Web technologies to provide three-dimensional visualisation of satellite observables on a wide range of client systems. It takes advantage of the WebGL API to employ locally available GPU power for 3D rendering; this approach has been demonstrated to perform well even on relatively weak hardware such as integrated graphics chipsets found in modern laptop computers and with some user-interface tuning could even be usable on embedded devices such as smartphones or tablets. Data is fetched from the database back-end using a ReST API and cached locally, both in memory and using HTML5 Web Storage, to minimise network use. Computations, calculation of cloud altitude from cloud-index measurements for instance, can depending on configuration be performed on either the client or the server side. Keywords: satellite data, Envisat, visualisation, 3D graphics, Web application, WebGL, MEAN stack.

Implementing a Dynamic Database-Driven Course Using LAMP

ERIC Educational Resources Information Center

Laverty, Joseph Packy; Wood, David; Turchek, John

2011-01-01

This paper documents the formulation of a database driven open source architecture web development course. The design of a web-based curriculum faces many challenges: a) relative emphasis of client and server-side technologies, b) choice of a server-side language, and c) the cost and efficient delivery of a dynamic web development, database-driven…

PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

PubMed

Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

2016-07-08

The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Risk Assessment of the Naval Postgraduate School Gigabit Network

DTIC Science & Technology

2004-09-01

Management Server (1) • Ras Server (1) • Remedy Server (1) • Samba Server(2) • SQL Servers (3) • Web Servers (3) • WINS Server (1) • Library...Server Bob Sharp INCA Windows 2000 Advanced Server NPGS Landesk SQL 2000 Alan Pires eagle Microsoft Windows 2000 Advanced Server EWS NPGS Landesk...Advanced Server Special Projects NPGS SQL Alan Pires MC01BDB Microsoft Windows 2000 Advanced Server Special Projects NPGS SQL 2000 Alan Pires

Embedded PLC Webserver and Possibilities of its Utilization

NASA Astrophysics Data System (ADS)

Kopček, Michal

2016-12-01

The concept Industry 4.0 is a top theme of recent times. Even if it represents the so-called 4th industrial revolution its main ideas could be used also to support the education of subjects from IT and automation. Furthermore, the basic IT and web technologies inherited by this concept are very well known to students. This paper introduces the embedded webserver of PLC and the options for its optimal utilization. The web server is essentially a simple and widely well-known technology, therefore it was chosen as an example.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks.

PubMed

Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar; Ruan, Yijun; Menghi, Francesca; Shin, Dong-Guk; Stitzel, Michael L; Vera-Licona, Paola; Ucar, Duygu

2016-06-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. QuIN's web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/.

WMT: The CSDMS Web Modeling Tool

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E. W. H.; Overeem, I.; Syvitski, J. P.

2015-12-01

The Community Surface Dynamics Modeling System (CSDMS) has a mission to enable model use and development for research in earth surface processes. CSDMS strives to expand the use of quantitative modeling techniques, promotes best practices in coding, and advocates for the use of open-source software. To streamline and standardize access to models, CSDMS has developed the Web Modeling Tool (WMT), a RESTful web application with a client-side graphical interface and a server-side database and API that allows users to build coupled surface dynamics models in a web browser on a personal computer or a mobile device, and run them in a high-performance computing (HPC) environment. With WMT, users can: Design a model from a set of components Edit component parameters Save models to a web-accessible server Share saved models with the community Submit runs to an HPC system Download simulation results The WMT client is an Ajax application written in Java with GWT, which allows developers to employ object-oriented design principles and development tools such as Ant, Eclipse and JUnit. For deployment on the web, the GWT compiler translates Java code to optimized and obfuscated JavaScript. The WMT client is supported on Firefox, Chrome, Safari, and Internet Explorer. The WMT server, written in Python and SQLite, is a layered system, with each layer exposing a web service API: wmt-db: database of component, model, and simulation metadata and output wmt-api: configure and connect components wmt-exe: launch simulations on remote execution servers The database server provides, as JSON-encoded messages, the metadata for users to couple model components, including descriptions of component exchange items, uses and provides ports, and input parameters. Execution servers are network-accessible computational resources, ranging from HPC systems to desktop computers, containing the CSDMS software stack for running a simulation. Once a simulation completes, its output, in NetCDF, is packaged and uploaded to a data server where it is stored and from which a user can download it as a single compressed archive file.

The DICOM-based radiation therapy information system

NASA Astrophysics Data System (ADS)

Law, Maria Y. Y.; Chan, Lawrence W. C.; Zhang, Xiaoyan; Zhang, Jianguo

2004-04-01

Similar to DICOM for PACS (Picture Archiving and Communication System), standards for radiotherapy (RT) information have been ratified with seven DICOM-RT objects and their IODs (Information Object Definitions), which are more than just images. This presentation describes how a DICOM-based RT Information System Server can be built based on the PACS technology and its data model for a web-based distribution. Methods: The RT information System consists of a Modality Simulator, a data format translator, a RT Gateway, the DICOM RT Server, and the Web-based Application Server. The DICOM RT Server was designed based on a PACS data model and was connected to a Web application Server for distribution of the RT information including therapeutic plans, structures, dose distribution, images and records. Various DICOM RT objects of the patient transmitted to the RT Server were routed to the Web Application Server where the contents of the DICOM RT objects were decoded and mapped to the corresponding location of the RT data model for display in the specially-designed Graphic User Interface. The non-DICOM objects were first rendered to DICOM RT Objects in the translator before they were sent to the RT Server. Results: Ten clinical cases have been collected from different hopsitals for evaluation of the DICOM-based RT Information System. They were successfully routed through the data flow and displayed in the client workstation of the RT information System. Conclusion: Using the DICOM-RT standards, integration of RT data from different vendors is possible.

A Digital Library for the National Advisory Committee for Aeronautics

NASA Technical Reports Server (NTRS)

Nelson, Michael L.

1999-01-01

We describe the digital library (DL) for the National Advisory Committee for Aeronautics (NACA), the NACA Technical Report Server (NACATRS). The predecessor organization for the National Aeronautics and Space Administration (NASA), NACA existed from 1915 until 1958. The primary manifestation of NACA's research was the NACA report series. We describe the process of converting this collection of reports to digital format and making it available on the World Wide Web (WWW) and is a node in the NASA Technical Report Server (NTRS). We describe the current state of the project, the resulting DL technology developed from the project, and the future plans for NACATRS.

MovieMaker: a web server for rapid rendering of protein motions and interactions.

PubMed

Maiti, Rajarshi; Van Domselaar, Gary H; Wishart, David S

2005-07-01

MovieMaker is a web server that allows short ( approximately 10 s), downloadable movies of protein motions to be generated. It accepts PDB files or PDB accession numbers as input and automatically calculates, renders and merges the necessary image files to create colourful animations covering a wide range of protein motions and other dynamic processes. Users have the option of animating (i) simple rotation, (ii) morphing between two end-state conformers, (iii) short-scale, picosecond vibrations, (iv) ligand docking, (v) protein oligomerization, (vi) mid-scale nanosecond (ensemble) motions and (vii) protein folding/unfolding. MovieMaker does not perform molecular dynamics calculations. Instead it is an animation tool that uses a sophisticated superpositioning algorithm in conjunction with Cartesian coordinate interpolation to rapidly and automatically calculate the intermediate structures needed for many of its animations. Users have extensive control over the rendering style, structure colour, animation quality, background and other image features. MovieMaker is intended to be a general-purpose server that allows both experts and non-experts to easily generate useful, informative protein animations for educational and illustrative purposes. MovieMaker is accessible at http://wishart.biology.ualberta.ca/moviemaker.

REMORA: a pilot in the ocean of BioMoby web-services.

PubMed

Carrere, Sébastien; Gouzy, Jérôme

2006-04-01

Emerging web-services technology allows interoperability between multiple distributed architectures. Here, we present REMORA, a web server implemented according to the BioMoby web-service specifications, providing life science researchers with an easy-to-use workflow generator and launcher, a repository of predefined workflows and a survey system. Jerome.Gouzy@toulouse.inra.fr The REMORA web server is freely available at http://bioinfo.genopole-toulouse.prd.fr/remora, sources are available upon request from the authors.

Building a Library Web Server on a Budget.

ERIC Educational Resources Information Center

Orr, Giles

1998-01-01

Presents a method for libraries with limited budgets to create reliable Web servers with existing hardware and free software available via the Internet. Discusses staff, hardware and software requirements, and security; outlines the assembly process. (PEN)

A Design of a Network Model to the Electric Power Trading System Using Web Services

NASA Astrophysics Data System (ADS)

Maruo, Tomoaki; Matsumoto, Keinosuke; Mori, Naoki; Kitayama, Masashi; Izumi, Yoshio

Web services are regarded as a new application paradigm in the world of the Internet. On the other hand, many business models of a power trading system has been proposed to aim at load reduction by consumers cooperating with electric power suppliers in an electric power market. Then, we propose a network model of power trading system using Web service in this paper. The adaptability of Web services to power trading system was checked in the prototype of our network model and we got good results for it. Each server provides functions as a SOAP server, and it is coupled loosely with each other through SOAP. Storing SOAP message in HTTP packet can establish the penetration communication way that is not conscious of a firewall. Switching of a dynamic server is possible by means of rewriting the server point information on WSDL at the time of obstacle generating.

FRASS: the web-server for RNA structural comparison

PubMed Central

2010-01-01

Background The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA, SARSA, and LaJolla) are available for the structural comparison of large and intact RNA molecules. Results The FRASS web-server represents a RNA chain with its Gauss integrals and allows one to compare structures of RNA chains and to find similar entries in a database derived from the Protein Data Bank. We observed that FRASS scores correlate well with the ARTS and LaJolla similarity scores. Moreover, the-web server can also reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR functions that was obtained by the SARA method. Conclusions The FRASS web-server can be easily used to detect relationships among RNA molecules and to scan efficiently the rapidly enlarging structural databases. PMID:20553602

miRNAFold: a web server for fast miRNA precursor prediction in genomes.

PubMed

Tav, Christophe; Tempel, Sébastien; Poligny, Laurent; Tahi, Fariza

2016-07-08

Computational methods are required for prediction of non-coding RNAs (ncRNAs), which are involved in many biological processes, especially at post-transcriptional level. Among these ncRNAs, miRNAs have been largely studied and biologists need efficient and fast tools for their identification. In particular, ab initio methods are usually required when predicting novel miRNAs. Here we present a web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high sensitivity. miRNAFold is implemented as a web server with an intuitive and user-friendly interface, as well as a standalone version. The web server is freely available at: http://EvryRNA.ibisc.univ-evry.fr/miRNAFold. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Radiology information system using HTML, JavaScript, and Web server].

PubMed

Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

1997-12-01

We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

NASA Technical Reports Server (NTRS)

Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

2000-01-01

This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

CABS-fold: Server for the de novo and consensus-based prediction of protein structure.

PubMed

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-07-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold.

CABS-fold: server for the de novo and consensus-based prediction of protein structure

PubMed Central

Blaszczyk, Maciej; Jamroz, Michal; Kmiecik, Sebastian; Kolinski, Andrzej

2013-01-01

The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competitions as one of the leading approaches for de novo and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold. PMID:23748950

Improving the quality of e-commerce web service: what is important for the request scheduling algorithm?

NASA Astrophysics Data System (ADS)

Suchacka, Grazyna

2005-02-01

The paper concerns a new research area that is Quality of Web Service (QoWS). The need for QoWS is motivated by a still growing number of Internet users, by a steady development and diversification of Web services, and especially by popularization of e-commerce applications. The goal of the paper is a critical analysis of the literature concerning scheduling algorithms for e-commerce Web servers. The paper characterizes factors affecting the load of the Web servers and discusses ways of improving their efficiency. Crucial QoWS requirements of the business Web server are identified: serving requests before their individual deadlines, supporting user session integrity, supporting different classes of users and minimizing a number of rejected requests. It is justified that meeting these requirements and implementing them in an admission control (AC) and scheduling algorithm for the business Web server is crucial to the functioning of e-commerce Web sites and revenue generated by them. The paper presents results of the literature analysis and discusses algorithms that implement these important QoWS requirements. The analysis showed that very few algorithms take into consideration the above mentioned factors and that there is a need for designing an algorithm implementing them.

The ClusPro web server for protein-protein docking

PubMed Central

Kozakov, Dima; Hall, David R.; Xia, Bing; Porter, Kathryn A.; Padhorny, Dzmitry; Yueh, Christine; Beglov, Dmitri; Vajda, Sandor

2017-01-01

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank format. However, ClusPro also offers a number of advanced options to modify the search that include the removal of unstructured protein regions, applying attraction or repulsion, accounting for pairwise distance restraints, constructing homo-multimers, considering small angle X-ray scattering (SAXS) data, and finding heparin binding sites. Six different energy functions can be used depending on the type of proteins. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in < 4 hours. PMID:28079879

RaptorX server: a resource for template-based protein structure modeling.

PubMed

Källberg, Morten; Margaryan, Gohar; Wang, Sheng; Ma, Jianzhu; Xu, Jinbo

2014-01-01

Assigning functional properties to a newly discovered protein is a key challenge in modern biology. To this end, computational modeling of the three-dimensional atomic arrangement of the amino acid chain is often crucial in determining the role of the protein in biological processes. We present a community-wide web-based protocol, RaptorX server ( http://raptorx.uchicago.edu ), for automated protein secondary structure prediction, template-based tertiary structure modeling, and probabilistic alignment sampling.Given a target sequence, RaptorX server is able to detect even remotely related template sequences by means of a novel nonlinear context-specific alignment potential and probabilistic consistency algorithm. Using the protocol presented here it is thus possible to obtain high-quality structural models for many target protein sequences when only distantly related protein domains have experimentally solved structures. At present, RaptorX server can perform secondary and tertiary structure prediction of a 200 amino acid target sequence in approximately 30 min.

DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008

PlanetServer: Innovative approaches for the online analysis of hyperspectral satellite data from Mars

NASA Astrophysics Data System (ADS)

Oosthoek, J. H. P.; Flahaut, J.; Rossi, A. P.; Baumann, P.; Misev, D.; Campalani, P.; Unnithan, V.

2014-06-01

PlanetServer is a WebGIS system, currently under development, enabling the online analysis of Compact Reconnaissance Imaging Spectrometer (CRISM) hyperspectral data from Mars. It is part of the EarthServer project which builds infrastructure for online access and analysis of huge Earth Science datasets. Core functionality consists of the rasdaman Array Database Management System (DBMS) for storage, and the Open Geospatial Consortium (OGC) Web Coverage Processing Service (WCPS) for data querying. Various WCPS queries have been designed to access spatial and spectral subsets of the CRISM data. The client WebGIS, consisting mainly of the OpenLayers javascript library, uses these queries to enable online spatial and spectral analysis. Currently the PlanetServer demonstration consists of two CRISM Full Resolution Target (FRT) observations, surrounding the NASA Curiosity rover landing site. A detailed analysis of one of these observations is performed in the Case Study section. The current PlanetServer functionality is described step by step, and is tested by focusing on detecting mineralogical evidence described in earlier Gale crater studies. Both the PlanetServer methodology and its possible use for mineralogical studies will be further discussed. Future work includes batch ingestion of CRISM data and further development of the WebGIS and analysis tools.

Hardware Assisted Stealthy Diversity (CHECKMATE)

DTIC Science & Technology

2013-09-01

applicable across multiple architectures. Figure 29 shows an example an attack against an interpreted environment with a Java executable. CHECKMATE can...Architectures ARM PPCx86 Java VM Java VMJava VM Java Executable Attack APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED 33 a user executes “/usr/bin/wget...Server 1 - Administration Server 2 – Database ( mySQL ) Server 3 – Web server (Mongoose) Server 4 – File server (SSH) Server 5 – Email server

Development and process evaluation of a Web-based responsible beverage service training program.

PubMed

Danaher, Brian G; Dresser, Jack; Shaw, Tracy; Severson, Herbert H; Tyler, Milagra S; Maxwell, Elisabeth D; Christiansen, Steve M

2012-09-22

Responsible beverage service (RBS) training designed to improve the appropriate service of alcohol in commercial establishments is typically delivered in workshops. Recently, Web-based RBS training programs have emerged. This report describes the formative development and subsequent design of an innovative Web-delivered RBS program, and evaluation of the impact of the program on servers' knowledge, attitudes, and self-efficacy. Formative procedures using focus groups and usability testing were used to develop a Web-based RBS training program. Professional alcohol servers (N = 112) who worked as servers and/or mangers in alcohol service settings were recruited to participate. A pre-post assessment design was used to assess changes associated with using the program. Participants who used the program showed significant improvements in their RBS knowledge, attitudes, and self-efficacy. Although the current study did not directly observe and determine impact of the intervention on server behaviors, it demonstrated that the development process incorporating input from a multidisciplinary team in conjunction with feedback from end-users resulted in creation of a Web-based RBS program that was well-received by servers and that changed relevant knowledge, attitudes, and self-efficacy. The results also help to establish a needed evidence base in support of the use of online RBS training, which has been afforded little research attention.

The Most Popular Astronomical Web Server in China

NASA Astrophysics Data System (ADS)

Cui, Chenzhou; Zhao, Yongheng

Affected by the consistent depressibility of IT economy free homepage space is becoming less and less. It is more and more difficult to construct websites for amateur astronomers who do not have ability to pay for commercial space. In last May with the support of Chinese National Astronomical Observatory and Large Sky Area Multi-Object Fiber Spectroscopic Telescope project we setup a special web server (amateur.lamost.org) to provide free huge stable and no-advertisement homepage space to Chinese amateur astronomers and non-professional organizations. After only one year there has been more than 80 websites hosted on the server. More than 10000 visitors from nearly 40 countries visit the server and the amount of data downloaded by them exceeds 4 Giga-Bytes per day. The server has become the most popular amateur astronomical web server in China. It stores the most abundant Chinese amateur astronomical resources. Because of the extremely success our service has been drawing tremendous attentions from related institutions. Recently Chinese National Natural Science Foundation shows great interest to support the service. In the paper the emergence of the thought construction of the server and its present utilization and our future plan are introduced

HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry.

PubMed

Yan, Yumeng; Tao, Huanyu; Huang, Sheng-You

2018-05-26

A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling of the symmetric protein complexes is important for understanding the molecular mechanism of related biological processes. Although several symmetric docking algorithms have been developed for Cn symmetry, few docking servers have been proposed for Dn symmetry. Here, we present HSYMDOCK, a web server of our hierarchical symmetric docking algorithm that supports both Cn and Dn symmetry. The HSYMDOCK server was extensively evaluated on three benchmarks of symmetric protein complexes, including the 20 CASP11-CAPRI30 homo-oligomer targets, the symmetric docking benchmark of 213 Cn targets and 35 Dn targets, and a nonredundant test set of 55 transmembrane proteins. It was shown that HSYMDOCK obtained a significantly better performance than other similar docking algorithms. The server supports both sequence and structure inputs for the monomer/subunit. Users have an option to provide the symmetry type of the complex, or the server can predict the symmetry type automatically. The docking process is fast and on average consumes 10∼20 min for a docking job. The HSYMDOCK web server is available at http://huanglab.phys.hust.edu.cn/hsymdock/.

Integration of multiple DICOM Web servers into an enterprise-wide Web-based electronic medical record

NASA Astrophysics Data System (ADS)

Stewart, Brent K.; Langer, Steven G.; Martin, Kelly P.

1999-07-01

The purpose of this paper is to integrate multiple DICOM image webservers into the currently existing enterprises- wide web-browsable electronic medical record. Over the last six years the University of Washington has created a clinical data repository combining in a distributed relational database information from multiple departmental databases (MIND). A character cell-based view of this data called the Mini Medical Record (MMR) has been available for four years, MINDscape, unlike the text-based MMR. provides a platform independent, dynamic, web browser view of the MIND database that can be easily linked with medical knowledge resources on the network, like PubMed and the Federated Drug Reference. There are over 10,000 MINDscape user accounts at the University of Washington Academic Medical Centers. The weekday average number of hits to MINDscape is 35,302 and weekday average number of individual users is 1252. DICOM images from multiple webservers are now being viewed through the MINDscape electronic medical record.

Dynamic online surveys and experiments with the free open-source software dynQuest.

PubMed

Rademacher, Jens D M; Lippke, Sonia

2007-08-01

With computers and the World Wide Web widely available, collecting data through Web browsers is an attractive method utilized by the social sciences. In this article, conducting PC- and Web-based trials with the software package dynQuest is described. The software manages dynamic questionnaire-based trials over the Internet or on single computers, possibly as randomized control trials (RCT), if two or more groups are involved. The choice of follow-up questions can depend on previous responses, as needed for matched interventions. Data are collected in a simple text-based database that can be imported easily into other programs for postprocessing and statistical analysis. The software consists of platform-independent scripts written in the programming language PERL that use the common gateway interface between Web browser and server for submission of data through HTML forms. Advantages of dynQuest are parsimony, simplicity in use and installation, transparency, and reliability. The program is available as open-source freeware from the authors.

The World Wide Web: a review of an emerging internet-based technology for the distribution of biomedical information.

PubMed Central

Lowe, H J; Lomax, E C; Polonkey, S E

1996-01-01

The Internet is rapidly evolving from a resource used primarily by the research community to a true global information network offering a wide range of databases and services. This evolution presents many opportunities for improved access to biomedical information, but Internet-based resources have often been difficult for the non-expert to develop and use. The World Wide Web (WWW) supports an inexpensive, easy-to-use, cross-platform, graphic interface to the Internet that may radically alter the way we retrieve and disseminate medical data. This paper summarizes the Internet and hypertext origins of the WWW, reviews WWW-specific technologies, and describes current and future applications of this technology in medicine and medical informatics. The paper also includes an appendix of useful biomedical WWW servers. PMID:8750386

INFO-RNA--a server for fast inverse RNA folding satisfying sequence constraints.

PubMed

Busch, Anke; Backofen, Rolf

2007-07-01

INFO-RNA is a new web server for designing RNA sequences that fold into a user given secondary structure. Furthermore, constraints on the sequence can be specified, e.g. one can restrict sequence positions to a fixed nucleotide or to a set of nucleotides. Moreover, the user can allow violations of the constraints at some positions, which can be advantageous in complicated cases. The INFO-RNA web server allows biologists to design RNA sequences in an automatic manner. It is clearly and intuitively arranged and easy to use. The procedure is fast, as most applications are completed within seconds and it proceeds better and faster than other existing tools. The INFO-RNA web server is freely available at http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/

INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints

PubMed Central

Busch, Anke; Backofen, Rolf

2007-01-01

INFO-RNA is a new web server for designing RNA sequences that fold into a user given secondary structure. Furthermore, constraints on the sequence can be specified, e.g. one can restrict sequence positions to a fixed nucleotide or to a set of nucleotides. Moreover, the user can allow violations of the constraints at some positions, which can be advantageous in complicated cases. The INFO-RNA web server allows biologists to design RNA sequences in an automatic manner. It is clearly and intuitively arranged and easy to use. The procedure is fast, as most applications are completed within seconds and it proceeds better and faster than other existing tools. The INFO-RNA web server is freely available at http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/ PMID:17452349

The World Wide Web: A Web Even a Fly Would Love

NASA Astrophysics Data System (ADS)

Bryson, E.

Ever since my introduction to the World Wide Web (WWW), it's been love at first byte. Searching on the WWW is similar to being able to go to a public library and allow yourself to be transported to any other book or library around the world by looking at a reference or index and clicking your heels together like Dorothy did in "The Wizard of Oz", only the clicking is done with a computer mouse. During this presentation, we will explore the WWW protocols which allow clients and servers to communicate on the Internet. We will demonstrate the ease with which users can navigate the virtual tidal wave of information available with a mere click of a button. In addition, the workshop will discuss the revolutionary aspects of this network information system and how it's impacting our libraries as a primary mechanism for rapid dissemination of knowledge.

PINTA: a web server for network-based gene prioritization from expression data

PubMed Central

Nitsch, Daniela; Tranchevent, Léon-Charles; Gonçalves, Joana P.; Vogt, Josef Korbinian; Madeira, Sara C.; Moreau, Yves

2011-01-01

PINTA (available at http://www.esat.kuleuven.be/pinta/; this web site is free and open to all users and there is no login requirement) is a web resource for the prioritization of candidate genes based on the differential expression of their neighborhood in a genome-wide protein–protein interaction network. Our strategy is meant for biological and medical researchers aiming at identifying novel disease genes using disease specific expression data. PINTA supports both candidate gene prioritization (starting from a user defined set of candidate genes) as well as genome-wide gene prioritization and is available for five species (human, mouse, rat, worm and yeast). As input data, PINTA only requires disease specific expression data, whereas various platforms (e.g. Affymetrix) are supported. As a result, PINTA computes a gene ranking and presents the results as a table that can easily be browsed and downloaded by the user. PMID:21602267

Web data mining

NASA Astrophysics Data System (ADS)

Wibonele, Kasanda J.; Zhang, Yanqing

2002-03-01

A web data mining system using granular computing and ASP programming is proposed. This is a web based application, which allows web users to submit survey data for many different companies. This survey is a collection of questions that will help these companies develop and improve their business and customer service with their clients by analyzing survey data. This web application allows users to submit data anywhere. All the survey data is collected into a database for further analysis. An administrator of this web application can login to the system and view all the data submitted. This web application resides on a web server, and the database resides on the MS SQL server.

A Services-Oriented Architecture for Water Observations Data

NASA Astrophysics Data System (ADS)

Maidment, D. R.; Zaslavsky, I.; Valentine, D.; Tarboton, D. G.; Whitenack, T.; Whiteaker, T.; Hooper, R.; Kirschtel, D.

2009-04-01

Water observations data are time series of measurements made at point locations of water level, flow, and quality and corresponding data for climatic observations at point locations such as gaged precipitation and weather variables. A services-oriented architecture has been built for such information for the United States that has three components: hydrologic information servers, hydrologic information clients, and a centralized metadata cataloging system. These are connected using web services for observations data and metadata defined by an XML-based language called WaterML. A Hydrologic Information Server can be built by storing observations data in a relational database schema in the CUAHSI Observations Data Model, in which case, web services access to the data and metadata is automatically provided by query functions for WaterML that are wrapped around the relational database within a web server. A Hydrologic Information Server can also be constructed by custom-programming an interface to an existing water agency web site so that responds to the same queries by producing data in WaterML as do the CUAHSI Observations Data Model based servers. A Hydrologic Information Client is one which can interpret and ingest WaterML metadata and data. We have two client applications for Excel and ArcGIS and have shown how WaterML web services can be ingested into programming environments such as Matlab and Visual Basic. HIS Central, maintained at the San Diego Supercomputer Center is a repository of observational metadata for WaterML web services which presently indexes 342 million data measured at 1.75 million locations. This is the largest catalog water observational data for the United States presently in existence. As more observation networks join what we term "CUAHSI Water Data Federation", and the system accommodates a growing number of sites, measured parameters, applications, and users, rapid and reliable access to large heterogeneous hydrologic data repositories becomes critical. The CUAHSI HIS solution to the scalability and heterogeneity challenges has several components. Structural differences across the data repositories are addressed by building a standard services foundation for the exchange of hydrologic data, as derived from a common information model for observational data measured at stationary points and its implementation as a relational schema (ODM) and an XML schema (WaterML). Semantic heterogeneity is managed by mapping water quantity, water quality, and other parameters collected by government agencies and academic projects to a common ontology. The WaterML-compliant web services are indexed in a community services registry called HIS Central (hiscentral.cuahsi.org). Once a web service is registered in HIS Central, its metadata (site and variable characteristics, period of record for each variable at each site, etc.) is harvested and appended to the central catalog. The catalog is further updated as the service publisher associates the variables in the published service with ontology concepts. After this, the newly published service becomes available for spatial and semantics-based queries from online and desktop client applications developed by the project. Hydrologic system server software is now deployed at more than a dozen locations in the United States and Australia. To provide rapid access to data summaries, in particular for several nation-wide data repositories including EPA STORET, USGS NWIS, and USDA SNOTEL, we convert the observation data catalogs and databases with harvested data values into special representations that support high-performance analysis and visualization. The construction of OLAP (Online Analytical Processing) cubes, often called data cubes, is an approach to organizing and querying large multi-dimensional data collections. We have applied the OLAP techniques, as implemented in Microsoft SQL Server 2005/2008, to the analysis of the catalogs from several agencies. OLAP analysis results reflect geography and history of observation data availability from USGS NWIS, EPA STORET, and USDA SNOTEL repositories, and spatial and temporal dynamics of the available measurements for several key nutrient-related parameters. Our experience developing the CUAHSI HIS cyberinfrastructure demonstrated that efficient integration of hydrologic observations from multiple government and academic sources requires a range of technical approaches focused on managing different components of data heterogeneity and system scalability. While this submission addresses technical aspects of developing a national-scale information system for hydrologic observations, the challenges of explicating shared semantics of hydrologic observations and building a community of HIS users and developers remain critical in constructing a nation-wide federation of water data services.

Contingency Contractor Optimization Phase 3 Sustainment Third-Party Software List - Contingency Contractor Optimization Tool - Prototype

DOE Office of Scientific and Technical Information (OSTI.GOV)

Durfee, Justin David; Frazier, Christopher Rawls; Bandlow, Alisa

2016-05-01

The Contingency Contractor Optimization Tool - Prototype (CCOT-P) requires several third-party software packages. These are documented below for each of the CCOT-P elements: client, web server, database server, solver, web application and polling application.

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

Escape Excel: A tool for preventing gene symbol and accession conversion errors.

PubMed

Welsh, Eric A; Stewart, Paul A; Kuenzi, Brent M; Eschrich, James A

2017-01-01

Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications.

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leung, Elo; Huang, Amy; Cadag, Eithon

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

DOE PAGES

Leung, Elo; Huang, Amy; Cadag, Eithon; ...

2016-01-20

In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online

PubMed Central

Posada, David

2006-01-01

ModelTest server is a web-based application for the selection of models of nucleotide substitution using the program ModelTest. The server takes as input a text file with likelihood scores for the set of candidate models. Models can be selected with hierarchical likelihood ratio tests, or with the Akaike or Bayesian information criteria. The output includes several statistics for the assessment of model selection uncertainty, for model averaging or to estimate the relative importance of model parameters. The server can be accessed at . PMID:16845102

The widest practicable dissemination: The NASA technical report server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Binkley, Robert L.; Kellogg, Yvonne D.; Paulson, Sharon S.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael; Accomazzi, Alberto

1995-01-01

The search for innovative methods to distribute NASA's information lead a gross-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the services over the initial 6-month period. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained will allow NASA to ensure that its institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

PANNZER2: a rapid functional annotation web server.

PubMed

Törönen, Petri; Medlar, Alan; Holm, Liisa

2018-05-08

The unprecedented growth of high-throughput sequencing has led to an ever-widening annotation gap in protein databases. While computational prediction methods are available to make up the shortfall, a majority of public web servers are hindered by practical limitations and poor performance. Here, we introduce PANNZER2 (Protein ANNotation with Z-scoRE), a fast functional annotation web server that provides both Gene Ontology (GO) annotations and free text description predictions. PANNZER2 uses SANSparallel to perform high-performance homology searches, making bulk annotation based on sequence similarity practical. PANNZER2 can output GO annotations from multiple scoring functions, enabling users to see which predictions are robust across predictors. Finally, PANNZER2 predictions scored within the top 10 methods for molecular function and biological process in the CAFA2 NK-full benchmark. The PANNZER2 web server is updated on a monthly schedule and is accessible at http://ekhidna2.biocenter.helsinki.fi/sanspanz/. The source code is available under the GNU Public Licence v3.

Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity.

PubMed

Marini, Simone; Nazzicari, Nelson; Biscarini, Filippo; Wang, Guang-Zhong

2017-06-15

Formation of homodimers by identical Dscam1 protein isomers on cell surface is the key factor for the self-avoidance of growing neurites. Dscam1 immense diversity has a critical role in the formation of arthropod neuronal circuit, showing unique evolutionary properties when compared to other cell surface proteins. Experimental measures are available for 89 self-binding and 1722 hetero-binding protein samples, out of more than 19 thousands (self-binding) and 350 millions (hetero-binding) possible isomer combinations. We developed Dscam1 Web Server to quickly predict Dscam1 self- and hetero- binding affinity for batches of Dscam1 isomers. The server can help the study of Dscam1 affinity and help researchers navigate through the tens of millions of possible isomer combinations to isolate the strong-binding ones. Dscam1 Web Server is freely available at: http://bioinformatics.tecnoparco.org/Dscam1-webserver . Web server code is available at https://gitlab.com/ne1s0n/Dscam1-binding . simone.marini@unipv.it or guangzhong.wang@picb.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

PubMed Central

Thibodeau, Asa; Márquez, Eladio J.; Luo, Oscar; Ruan, Yijun; Shin, Dong-Guk; Stitzel, Michael L.; Ucar, Duygu

2016-01-01

Recent studies of the human genome have indicated that regulatory elements (e.g. promoters and enhancers) at distal genomic locations can interact with each other via chromatin folding and affect gene expression levels. Genomic technologies for mapping interactions between DNA regions, e.g., ChIA-PET and HiC, can generate genome-wide maps of interactions between regulatory elements. These interaction datasets are important resources to infer distal gene targets of non-coding regulatory elements and to facilitate prioritization of critical loci for important cellular functions. With the increasing diversity and complexity of genomic information and public ontologies, making sense of these datasets demands integrative and easy-to-use software tools. Moreover, network representation of chromatin interaction maps enables effective data visualization, integration, and mining. Currently, there is no software that can take full advantage of network theory approaches for the analysis of chromatin interaction datasets. To fill this gap, we developed a web-based application, QuIN, which enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions. AVAILABILITY: QuIN’s web server is available at http://quin.jax.org QuIN is developed in Java and JavaScript, utilizing an Apache Tomcat web server and MySQL database and the source code is available under the GPLV3 license available on GitHub: https://github.com/UcarLab/QuIN/. PMID:27336171

A Web Terminology Server Using UMLS for the Description of Medical Procedures

PubMed Central

Burgun, Anita; Denier, Patrick; Bodenreider, Olivier; Botti, Geneviève; Delamarre, Denis; Pouliquen, Bruno; Oberlin, Philippe; Lévéque, Jean M.; Lukacs, Bertrand; Kohler, François; Fieschi, Marius; Le Beux, Pierre

1997-01-01

Abstract The Model for Assistance in the Orientation of a User within Coding Systems (MAOUSSC) project has been designed to provide a representation for medical and surgical procedures that allows several applications to be developed from several viewpoints. It is based on a conceptual model, a controlled set of terms, and Web server development. The design includes the UMLS knowledge sources associated with additional knowledge about medico-surgical procedures. The model was implemented using a relational database. The authors developed a complete interface for the Web presentation, with the intermediary layer being written in PERL. The server has been used for the representation of medico-surgical procedures that occur in the discharge summaries of the national survey of hospital activities that is performed by the French Health Statistics Agency in order to produce inpatient profiles. The authors describe the current status of the MAOUSSC server and discuss their interest in using such a server to assist in the coordination of terminology tasks and in the sharing of controlled terminologies. PMID:9292841

Template-based protein structure modeling using the RaptorX web server.

PubMed

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2012-07-19

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.

Template-based protein structure modeling using the RaptorX web server

PubMed Central

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2016-01-01

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world. PMID:22814390

Secure remote access to a clinical data repository using a wireless personal digital assistant (PDA).

PubMed

Duncan, R G; Shabot, M M

2000-01-01

TCP/IP and World-Wide-Web (WWW) technology have become the universal standards for networking and delivery of information. Personal digital assistants (PDAs), cellular telephones, and alphanumeric pagers are rapidly converging on a single pocket device that will leverage wireless TCP/IP networks and WWW protocols and can be used to deliver clinical information and alerts anytime, anywhere. We describe a wireless interface to clinical information for physicians based on Palm Corp.'s Palm VII pocket computer, a wireless digital network, encrypted data transmission, secure web servers, and a clinical data repository (CDR).

Secure remote access to a clinical data repository using a wireless personal digital assistant (PDA).

PubMed Central

Duncan, R. G.; Shabot, M. M.

2000-01-01

TCP/IP and World-Wide-Web (WWW) technology have become the universal standards for networking and delivery of information. Personal digital assistants (PDAs), cellular telephones, and alphanumeric pagers are rapidly converging on a single pocket device that will leverage wireless TCP/IP networks and WWW protocols and can be used to deliver clinical information and alerts anytime, anywhere. We describe a wireless interface to clinical information for physicians based on Palm Corp.'s Palm VII pocket computer, a wireless digital network, encrypted data transmission, secure web servers, and a clinical data repository (CDR). PMID:11079875

LigSearch: a knowledge-based web server to identify likely ligands for a protein target

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beer, Tjaart A. P. de; Laskowski, Roman A.; Duban, Mark-Eugene

LigSearch is a web server for identifying ligands likely to bind to a given protein. Identifying which ligands might bind to a protein before crystallization trials could provide a significant saving in time and resources. LigSearch, a web server aimed at predicting ligands that might bind to and stabilize a given protein, has been developed. Using a protein sequence and/or structure, the system searches against a variety of databases, combining available knowledge, and provides a clustered and ranked output of possible ligands. LigSearch can be accessed at http://www.ebi.ac.uk/thornton-srv/databases/LigSearch.

MultiSETTER: web server for multiple RNA structure comparison.

PubMed

Čech, Petr; Hoksza, David; Svozil, Daniel

2015-08-12

Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in a reasonable time, large structures represent much bigger challenge. Therefore, we have developed a fast and accurate algorithm for RNA pairwise structure superposition called SETTER and implemented it in the SETTER web server. However, though biological relationships can be inferred by a pairwise structure alignment, key features preserved by evolution can be identified only from a multiple structure alignment. Thus, we extended the SETTER algorithm to the alignment of multiple RNA structures and developed the MultiSETTER algorithm. In this paper, we present the updated version of the SETTER web server that implements a user friendly interface to the MultiSETTER algorithm. The server accepts RNA structures either as the list of PDB IDs or as user-defined PDB files. After the superposition is computed, structures are visualized in 3D and several reports and statistics are generated. To the best of our knowledge, the MultiSETTER web server is the first publicly available tool for a multiple RNA structure alignment. The MultiSETTER server offers the visual inspection of an alignment in 3D space which may reveal structural and functional relationships not captured by other multiple alignment methods based either on a sequence or on secondary structure motifs.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Database Organisation in a Web-Enabled Free and Open-Source Software (foss) Environment for Spatio-Temporal Landslide Modelling

NASA Astrophysics Data System (ADS)

Das, I.; Oberai, K.; Sarathi Roy, P.

2012-07-01

Landslides exhibit themselves in different mass movement processes and are considered among the most complex natural hazards occurring on the earth surface. Making landslide database available online via WWW (World Wide Web) promotes the spreading and reaching out of the landslide information to all the stakeholders. The aim of this research is to present a comprehensive database for generating landslide hazard scenario with the help of available historic records of landslides and geo-environmental factors and make them available over the Web using geospatial Free & Open Source Software (FOSS). FOSS reduces the cost of the project drastically as proprietary software's are very costly. Landslide data generated for the period 1982 to 2009 were compiled along the national highway road corridor in Indian Himalayas. All the geo-environmental datasets along with the landslide susceptibility map were served through WEBGIS client interface. Open source University of Minnesota (UMN) mapserver was used as GIS server software for developing web enabled landslide geospatial database. PHP/Mapscript server-side application serve as a front-end application and PostgreSQL with PostGIS extension serve as a backend application for the web enabled landslide spatio-temporal databases. This dynamic virtual visualization process through a web platform brings an insight into the understanding of the landslides and the resulting damage closer to the affected people and user community. The landslide susceptibility dataset is also made available as an Open Geospatial Consortium (OGC) Web Feature Service (WFS) which can be accessed through any OGC compliant open source or proprietary GIS Software.

Sirepo for Synchrotron Radiation Workshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

Web Monitoring of EOS Front-End Ground Operations, Science Downlinks and Level 0 Processing

NASA Technical Reports Server (NTRS)

Cordier, Guy R.; Wilkinson, Chris; McLemore, Bruce

2008-01-01

This paper addresses the efforts undertaken and the technology deployed to aggregate and distribute the metadata characterizing the real-time operations associated with NASA Earth Observing Systems (EOS) high-rate front-end systems and the science data collected at multiple ground stations and forwarded to the Goddard Space Flight Center for level 0 processing. Station operators, mission project management personnel, spacecraft flight operations personnel and data end-users for various EOS missions can retrieve the information at any time from any location having access to the internet. The users are distributed and the EOS systems are distributed but the centralized metadata accessed via an external web server provide an effective global and detailed view of the enterprise-wide events as they are happening. The data-driven architecture and the implementation of applied middleware technology, open source database, open source monitoring tools, and external web server converge nicely to fulfill the various needs of the enterprise. The timeliness and content of the information provided are key to making timely and correct decisions which reduce project risk and enhance overall customer satisfaction. The authors discuss security measures employed to limit access of data to authorized users only.

TRFolder-W: a web server for telomerase RNA structure prediction in yeast genomes.

PubMed

Zhang, Dong; Xue, Xingran; Malmberg, Russell L; Cai, Liming

2012-10-15

TRFolder-W is a web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. TRFolder is a command-line Python toolkit for TR-specific structure prediction. We developed a web-version built on the django web framework, leveraging the work done previously, to include enhancements to increase flexibility of usage. To date, there are five core sub-structures commonly found in TR of fungal species, which are the template region, downstream pseudoknot, boundary element, core-closing stem and triple helix. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species. The web server TRFolder-W is available at http://rna-informatics.uga.edu/?f=software&p=TRFolder-w.

New web technologies for astronomy

NASA Astrophysics Data System (ADS)

Sprimont, P.-G.; Ricci, D.; Nicastro, L.

2014-12-01

Thanks to the new HTML5 capabilities and the huge improvements of the JavaScript language, it is now possible to design very complex and interactive web user interfaces. On top of that, the once monolithic and file-server oriented web servers are evolving into easily programmable server applications capable to cope with the complex interactions made possible by the new generation of browsers. We believe that the whole community of amateur and professionals astronomers can benefit from the potential of these new technologies. New web interfaces can be designed to provide the user with a large deal of much more intuitive and interactive tools. Accessing astronomical data archives, schedule, control and monitor observatories, and in particular robotic telescopes, supervising data reduction pipelines, all are capabilities that can now be implemented in a JavaScript web application. In this paper we describe the Sadira package we are implementing exactly to this aim.

EnviroAtlas - Metrics for Austin, TX

EPA Pesticide Factsheets

This EnviroAtlas web service supports research and online mapping activities related to EnviroAtlas (https://enviroatlas.epa.gov/EnviroAtlas). The layers in this web service depict ecosystem services at the census block group level for the community of Austin, Texas. These layers illustrate the ecosystems and natural resources that are associated with clean air (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_CleanAir/MapServer); clean and plentiful water (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_CleanPlentifulWater/MapServer); natural hazard mitigation (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_NaturalHazardMitigation/MapServer); climate stabilization (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_ClimateStabilization/MapServer); food, fuel, and materials (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_FoodFuelMaterials/MapServer); recreation, culture, and aesthetics (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_RecreationCultureAesthetics/MapServer); and biodiversity conservation (https://enviroatlas.epa.gov/arcgis/rest/services/Communities/ESC_ATX_BiodiversityConservation/MapServer), and factors that place stress on those resources. EnviroAtlas allows the user to interact with a web-based, easy-to-use, mapping application to view and analyze multiple ecosystem services for the conterminous United States as well as de

SCENERY: a web application for (causal) network reconstruction from cytometry data

PubMed Central

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper

2017-01-01

Abstract Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. PMID:28525568

Development of a 3D WebGIS System for Retrieving and Visualizing CityGML Data Based on their Geometric and Semantic Characteristics by Using Free and Open Source Technology

NASA Astrophysics Data System (ADS)

Pispidikis, I.; Dimopoulou, E.

2016-10-01

CityGML is considered as an optimal standard for representing 3D city models. However, international experience has shown that visualization of the latter is quite difficult to be implemented on the web, due to the large size of data and the complexity of CityGML. As a result, in the context of this paper, a 3D WebGIS application is developed in order to successfully retrieve and visualize CityGML data in accordance with their respective geometric and semantic characteristics. Furthermore, the available web technologies and the architecture of WebGIS systems are investigated, as provided by international experience, in order to be utilized in the most appropriate way for the purposes of this paper. Specifically, a PostgreSQL/ PostGIS Database is used, in compliance with the 3DCityDB schema. At Server tier, Apache HTTP Server and GeoServer are utilized, while a Server Side programming language PHP is used. At Client tier, which implemented the interface of the application, the following technologies were used: JQuery, AJAX, JavaScript, HTML5, WebGL and Ol3-Cesium. Finally, it is worth mentioning that the application's primary objectives are a user-friendly interface and a fully open source development.

Library Web Proxy Use Survey Results.

ERIC Educational Resources Information Center

Murray, Peter E.

2001-01-01

Outlines the use of proxy Web servers by libraries and reports on a survey on their use in libraries. Highlights include proxy use for remote resource access, for filtering, for bandwidth conservation, and for gathering statistics; privacy policies regarding the use of proxy server log files; and a copy of the survey. (LRW)

Adding tools to the open source toolbox: The Internet

NASA Technical Reports Server (NTRS)

Porth, Tricia

1994-01-01

The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

A web service framework for astronomical remote observation in Antarctica by using satellite link

NASA Astrophysics Data System (ADS)

Jia, M.-h.; Chen, Y.-q.; Zhang, G.-y.; Jiang, P.; Zhang, H.; Wang, J.

2018-07-01

Many telescopes are deployed in Antarctica as it offers excellent astronomical observation conditions. However, because Antarctica's environment is harsh to humans, remote operation of telescope is necessary for observation. Furthermore, communication to devices in Antarctica through satellite link with low bandwidth and high latency limits the effectiveness of remote observation. This paper introduces a web service framework for remote astronomical observation in Antarctica. The framework is based on Python Tornado. RTS2-HTTPD and REDIS are used as the access interface to the telescope control system in Antarctica. The web service provides real-time updates through WebSocket. To improve user experience and control effectiveness under the poor satellite link condition, an agent server is deployed in the mainland to synchronize the Antarctic server's data and send it to domestic users in China. The agent server will forward the request of domestic users to the Antarctic master server. The web service was deployed and tested on Bright Star Survey Telescope (BSST) in Antarctica. Results show that the service meets the demands of real-time, multiuser remote observation and domestic users have a better experience of remote operation.

Development of a web geoservices platform for School of Environmental Sciences, Mahatma Gandhi University, Kerala, India

NASA Astrophysics Data System (ADS)

Satheendran, S.; John, C. M.; Fasalul, F. K.; Aanisa, K. M.

2014-11-01

Web geoservices is the obvious graduation of Geographic Information System in a distributed environment through a simple browser. It enables organizations to share domain-specific rich and dynamic spatial information over the web. The present study attempted to design and develop a web enabled GIS application for the School of Environmental Sciences, Mahatma Gandhi University, Kottayam, Kerala, India to publish various geographical databases to the public through its website. The development of this project is based upon the open source tools and techniques. The output portal site is platform independent. The premier webgis frame work `Geomoose' is utilized. Apache server is used as the Web Server and the UMN Map Server is used as the map server for this project. It provides various customised tools to query the geographical database in different ways and search for various facilities in the geographical area like banks, attractive places, hospitals, hotels etc. The portal site was tested with the output geographical database of 2 projects of the School such as 1) the Tourism Information System for the Malabar region of Kerala State consisting of 5 northern districts 2) the geoenvironmental appraisal of the Athirappilly Hydroelectric Project covering the entire Chalakkudy river basin.

Providing Web Interfaces to the NSF EarthScope USArray Transportable Array

NASA Astrophysics Data System (ADS)

Vernon, Frank; Newman, Robert; Lindquist, Kent

2010-05-01

Since April 2004 the EarthScope USArray seismic network has grown to over 850 broadband stations that stream multi-channel data in near real-time to the Array Network Facility in San Diego. Providing secure, yet open, access to real-time and archived data for a broad range of audiences is best served by a series of platform agnostic low-latency web-based applications. We present a framework of tools that mediate between the world wide web and Boulder Real Time Technologies Antelope Environmental Monitoring System data acquisition and archival software. These tools provide comprehensive information to audiences ranging from network operators and geoscience researchers, to funding agencies and the general public. This ranges from network-wide to station-specific metadata, state-of-health metrics, event detection rates, archival data and dynamic report generation over a station's two year life span. Leveraging open source web-site development frameworks for both the server side (Perl, Python and PHP) and client-side (Flickr, Google Maps/Earth and jQuery) facilitates the development of a robust extensible architecture that can be tailored on a per-user basis, with rapid prototyping and development that adheres to web-standards. Typical seismic data warehouses allow online users to query and download data collected from regional networks, without the scientist directly visually assessing data coverage and/or quality. Using a suite of web-based protocols, we have recently developed an online seismic waveform interface that directly queries and displays data from a relational database through a web-browser. Using the Python interface to Datascope and the Python-based Twisted network package on the server side, and the jQuery Javascript framework on the client side to send and receive asynchronous waveform queries, we display broadband seismic data using the HTML Canvas element that is globally accessible by anyone using a modern web-browser. We are currently creating additional interface tools to create a rich-client interface for accessing and displaying seismic data that can be deployed to any system running the Antelope Real Time System. The software is freely available from the Antelope contributed code Git repository (http://www.antelopeusersgroup.org).

Visualization and interaction tools for aerial photograph mosaics

NASA Astrophysics Data System (ADS)

Fernandes, João Pedro; Fonseca, Alexandra; Pereira, Luís; Faria, Adriano; Figueira, Helder; Henriques, Inês; Garção, Rita; Câmara, António

1997-05-01

This paper describes the development of a digital spatial library based on mosaics of digital orthophotos, called Interactive Portugal, that will enable users both to retrieve geospatial information existing in the Portuguese National System for Geographic Information World Wide Web server, and to develop local databases connected to the main system. A set of navigation, interaction, and visualization tools are proposed and discussed. They include sketching, dynamic sketching, and navigation capabilities over the digital orthophotos mosaics. Main applications of this digital spatial library are pointed out and discussed, namely for education, professional, and tourism markets. Future developments are considered. These developments are related to user reactions, technological advancements, and projects that also aim at delivering and exploring digital imagery on the World Wide Web. Future capabilities for site selection and change detection are also considered.

'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.

PubMed

Baksi, Krishanu D; Kuntal, Bhusan K; Mande, Sharmila S

2018-01-01

Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data. The TIME web-server is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples, defined by a series of longitudinal time points along with their metadata information, can be compared in order to interactively visualize the temporal variations. In addition to standard microbiome data analytics, the web server implements popular time series analysis methods like Dynamic time warping, Granger causality and Dickey Fuller test to generate interactive layouts for facilitating easy biological inferences. Apart from this, a new metric for comparing metagenomic time series data has been introduced to effectively visualize the similarities/differences in the trends of the resident microbial groups. Augmenting the visualizations with the stationarity information pertaining to the microbial groups is utilized to predict the microbial competition as well as community structure. Additionally, the 'causality graph analysis' module incorporated in TIME allows predicting taxa that might have a higher influence on community structure in different conditions. TIME also allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis. We illustrate the utility of the web-server features on a few published time series microbiome data and demonstrate the ease with which it can be used to perform complex analysis.

The Live Access Server - A Web-Services Framework for Earth Science Data

NASA Astrophysics Data System (ADS)

Schweitzer, R.; Hankin, S. C.; Callahan, J. S.; O'Brien, K.; Manke, A.; Wang, X. Y.

2005-12-01

The Live Access Server (LAS) is a general purpose Web-server for delivering services related to geo-science data sets. Data providers can use the LAS architecture to build custom Web interfaces to their scientific data. Users and client programs can then access the LAS site to search the provider's on-line data holdings, make plots of data, create sub-sets in a variety of formats, compare data sets and perform analysis on the data. The Live Access server software has continued to evolve by expanding the types of data (in-situ observations and curvilinear grids) it can serve and by taking advantages of advances in software infrastructure both in the earth sciences community (THREDDS, the GrADS Data Server, the Anagram framework and Java netCDF 2.2) and in the Web community (Java Servlet and the Apache Jakarta frameworks). This presentation will explore the continued evolution of the LAS architecture towards a complete Web-services-based framework. Additionally, we will discuss the redesign and modernization of some of the support tools available to LAS installers. Soon after the initial implementation, the LAS architecture was redesigned to separate the components that are responsible for the user interaction (the User Interface Server) from the components that are responsible for interacting with the data and producing the output requested by the user (the Product Server). During this redesign, we changed the implementation of the User Interface Server from CGI and JavaScript to the Java Servlet specification using Apache Jakarta Velocity backed by a database store for holding the user interface widget components. The User Interface server is now quite flexible and highly configurable because we modernized the components used for the implementation. Meanwhile, the implementation of the Product Server has remained a Perl CGI-based system. Clearly, the time has come to modernize this part of the LAS architecture. Before undertaking such a modernization it is important to understand what we hope to gain. Specifically we would like to make it even easier to add new output products into our core system based on the Ferret analysis and visualization package. By carefully factoring the tasks needed to create a product we will be able to create new products simply by adding a description of the product into the configuration and by writing the Ferret script needed to create the product. No code will need to be added to the Product Server to bring the new product on-line. The new architecture should be faster at extracting and processing configuration information needed to address each request. Finally, the new Product Server architecture should make it even easier to pass specialized configuration information to the Product Server to deal with unanticipated special data structures or processing requirements.

Sequence harmony: detecting functional specificity from alignments

PubMed Central

Feenstra, K. Anton; Pirovano, Walter; Krab, Klaas; Heringa, Jaap

2007-01-01

Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww. PMID:17584793

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis.

PubMed

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/.

Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank.

PubMed

Collier, James H; Lesk, Arthur M; Garcia de la Banda, Maria; Konagurthu, Arun S

2012-07-01

Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80,500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from: http://lcb.infotech.monash.edu.au/super.

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis

PubMed Central

Jalili, Mahdi; Salehzadeh-Yazdi, Ali; Asgari, Yazdan; Arab, Seyed Shahriar; Yaghmaie, Marjan; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran

2015-01-01

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/ PMID:26571275

LDAP: a web server for lncRNA-disease association prediction.

PubMed

Lan, Wei; Li, Min; Zhao, Kaijie; Liu, Jin; Wu, Fang-Xiang; Pan, Yi; Wang, Jianxin

2017-02-01

Increasing evidences have demonstrated that long noncoding RNAs (lncRNAs) play important roles in many human diseases. Therefore, predicting novel lncRNA-disease associations would contribute to dissect the complex mechanisms of disease pathogenesis. Some computational methods have been developed to infer lncRNA-disease associations. However, most of these methods infer lncRNA-disease associations only based on single data resource. In this paper, we propose a new computational method to predict lncRNA-disease associations by integrating multiple biological data resources. Then, we implement this method as a web server for lncRNA-disease association prediction (LDAP). The input of the LDAP server is the lncRNA sequence. The LDAP predicts potential lncRNA-disease associations by using a bagging SVM classifier based on lncRNA similarity and disease similarity. The web server is available at http://bioinformatics.csu.edu.cn/ldap jxwang@mail.csu.edu.cn. Supplementary data are available at Bioinformatics online.

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services

PubMed Central

Gessler, Damian DG; Schiltz, Gary S; May, Greg D; Avraham, Shulamit; Town, Christopher D; Grant, David; Nelson, Rex T

2009-01-01

Background SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. Results There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at , developer tools at , and a portal to third-party ontologies at (a "swap meet"). Conclusion SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs. PMID:19775460

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan

NASA Astrophysics Data System (ADS)

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

iScreen: world's first cloud-computing web server for virtual screening and de novo drug design based on TCM database@Taiwan.

PubMed

Tsai, Tsung-Ying; Chang, Kai-Wei; Chen, Calvin Yu-Chian

2011-06-01

The rapidly advancing researches on traditional Chinese medicine (TCM) have greatly intrigued pharmaceutical industries worldwide. To take initiative in the next generation of drug development, we constructed a cloud-computing system for TCM intelligent screening system (iScreen) based on TCM Database@Taiwan. iScreen is compacted web server for TCM docking and followed by customized de novo drug design. We further implemented a protein preparation tool that both extract protein of interest from a raw input file and estimate the size of ligand bind site. In addition, iScreen is designed in user-friendly graphic interface for users who have less experience with the command line systems. For customized docking, multiple docking services, including standard, in-water, pH environment, and flexible docking modes are implemented. Users can download first 200 TCM compounds of best docking results. For TCM de novo drug design, iScreen provides multiple molecular descriptors for a user's interest. iScreen is the world's first web server that employs world's largest TCM database for virtual screening and de novo drug design. We believe our web server can lead TCM research to a new era of drug development. The TCM docking and screening server is available at http://iScreen.cmu.edu.tw/.

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

LocExpress: a web server for efficiently estimating expression of novel transcripts.

PubMed

Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

2016-12-22

The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

That's My Bailiwick: A Library-Sponsored Faculty Research Web Server.

ERIC Educational Resources Information Center

Soderdahl, Paul A.; Hughes, Carol Ann

2000-01-01

Describes Bailiwick, a project at the University of Iowa library that provides Web space for faculty, staff, and graduate students to focus on particular areas of scholarly interest such as Internet bibliographies, multimedia essays, scholarly research, and collaborative research. Also explains a MOO project and a streaming video server. (LRW)

Development of a web database portfolio system with PACS connectivity for undergraduate health education and continuing professional development.

PubMed

Ng, Curtise K C; White, Peter; McKay, Janice C

2009-04-01

Increasingly, the use of web database portfolio systems is noted in medical and health education, and for continuing professional development (CPD). However, the functions of existing systems are not always aligned with the corresponding pedagogy and hence reflection is often lost. This paper presents the development of a tailored web database portfolio system with Picture Archiving and Communication System (PACS) connectivity, which is based on the portfolio pedagogy. Following a pre-determined portfolio framework, a system model with the components of web, database and mail servers, server side scripts, and a Query/Retrieve (Q/R) broker for conversion between Hypertext Transfer Protocol (HTTP) requests and Q/R service class of Digital Imaging and Communication in Medicine (DICOM) standard, is proposed. The system was piloted with seventy-seven volunteers. A tailored web database portfolio system (http://radep.hti.polyu.edu.hk) was developed. Technological arrangements for reinforcing portfolio pedagogy include popup windows (reminders) with guidelines and probing questions of 'collect', 'select' and 'reflect' on evidence of development/experience, limitation in the number of files (evidence) to be uploaded, the 'Evidence Insertion' functionality to link the individual uploaded artifacts with reflective writing, capability to accommodate diversity of contents and convenient interfaces for reviewing portfolios and communication. Evidence to date suggests the system supports users to build their portfolios with sound hypertext reflection under a facilitator's guidance, and with reviewers to monitor students' progress providing feedback and comments online in a programme-wide situation.

"Just Another Tool for Online Studies” (JATOS): An Easy Solution for Setup and Management of Web Servers Supporting Online Studies

PubMed Central

Lange, Kristian; Kühn, Simone; Filevich, Elisa

2015-01-01

We present here “Just Another Tool for Online Studies” (JATOS): an open source, cross-platform web application with a graphical user interface (GUI) that greatly simplifies setting up and communicating with a web server to host online studies that are written in JavaScript. JATOS is easy to install in all three major platforms (Microsoft Windows, Mac OS X, and Linux), and seamlessly pairs with a database for secure data storage. It can be installed on a server or locally, allowing researchers to try the application and feasibility of their studies within a browser environment, before engaging in setting up a server. All communication with the JATOS server takes place via a GUI (with no need to use a command line interface), making JATOS an especially accessible tool for researchers without a strong IT background. We describe JATOS’ main features and implementation and provide a detailed tutorial along with example studies to help interested researchers to set up their online studies. JATOS can be found under the Internet address: www.jatos.org. PMID:26114751

ASPEN--A Web-Based Application for Managing Student Server Accounts

ERIC Educational Resources Information Center

Sandvig, J. Christopher

2004-01-01

The growth of the Internet has greatly increased the demand for server-side programming courses at colleges and universities. Students enrolled in such courses must be provided with server-based accounts that support the technologies that they are learning. The process of creating, managing and removing large numbers of student server accounts is…

iSeq: Web-Based RNA-seq Data Analysis and Visualization.

PubMed

Zhang, Chao; Fan, Caoqi; Gan, Jingbo; Zhu, Ping; Kong, Lei; Li, Cheng

2018-01-01

Transcriptome sequencing (RNA-seq) is becoming a standard experimental methodology for genome-wide characterization and quantification of transcripts at single base-pair resolution. However, downstream analysis of massive amount of sequencing data can be prohibitively technical for wet-lab researchers. A functionally integrated and user-friendly platform is required to meet this demand. Here, we present iSeq, an R-based Web server, for RNA-seq data analysis and visualization. iSeq is a streamlined Web-based R application under the Shiny framework, featuring a simple user interface and multiple data analysis modules. Users without programming and statistical skills can analyze their RNA-seq data and construct publication-level graphs through a standardized yet customizable analytical pipeline. iSeq is accessible via Web browsers on any operating system at http://iseq.cbi.pku.edu.cn .

Escape Excel: A tool for preventing gene symbol and accession conversion errors

PubMed Central

Stewart, Paul A.; Kuenzi, Brent M.; Eschrich, James A.

2017-01-01

Background Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text into dates, scientific notation, and other numerical representations. These conversions lead to subsequent, irreversible, corruption of the imported text. A recent survey of popular genomic literature estimates that one-fifth of all papers with supplementary gene lists suffer from this issue. Results Here, we present an open-source tool, Escape Excel, which prevents these erroneous conversions by generating an escaped text file that can be safely imported into Excel. Escape Excel is implemented in a variety of formats (http://www.github.com/pstew/escape_excel), including a command line based Perl script, a Windows-only Excel Add-In, an OS X drag-and-drop application, a simple web-server, and as a Galaxy web environment interface. Test server implementations are accessible as a Galaxy interface (http://apostl.moffitt.org) and simple non-Galaxy web server (http://apostl.moffitt.org:8000/). Conclusions Escape Excel detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Examples of problematic strings include date-like strings, time-like strings, leading zeroes in front of numbers, and long numeric and alphanumeric identifiers that should not be automatically converted into scientific notation. It is hoped that greater awareness of these potential data corruption issues, together with diligent escaping of text files prior to importation into Excel, will help to reduce the amount of Excel-corrupted data in scientific analyses and publications. PMID:28953918

DIANA-microT web server: elucidating microRNA functions through target prediction.

PubMed

Maragkakis, M; Reczko, M; Simossis, V A; Alexiou, P; Papadopoulos, G L; Dalamagas, T; Giannopoulos, G; Goumas, G; Koukis, E; Kourtis, K; Vergoulis, T; Koziris, N; Sellis, T; Tsanakas, P; Hatzigeorgiou, A G

2009-07-01

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

PubMed

Tong, Jing; Pei, Jimin; Grishin, Nick V

2015-09-03

Protein sequence alignment is essential for a variety of tasks such as homology modeling and active site prediction. Alignment errors remain the main cause of low-quality structure models. A bioinformatics tool to refine alignments is needed to make protein alignments more accurate. We developed the SFESA web server to refine pairwise protein sequence alignments. Compared to the previous version of SFESA, which required a set of 3D coordinates for a protein, the new server will search a sequence database for the closest homolog with an available 3D structure to be used as a template. For each alignment block defined by secondary structure elements in the template, SFESA evaluates alignment variants generated by local shifts and selects the best-scoring alignment variant. A scoring function that combines the sequence score of profile-profile comparison and the structure score of template-derived contact energy is used for evaluation of alignments. PROMALS pairwise alignments refined by SFESA are more accurate than those produced by current advanced alignment methods such as HHpred and CNFpred. In addition, SFESA also improves alignments generated by other software. SFESA is a web-based tool for alignment refinement, designed for researchers to compute, refine, and evaluate pairwise alignments with a combined sequence and structure scoring of alignment blocks. To our knowledge, the SFESA web server is the only tool that refines alignments by evaluating local shifts of secondary structure elements. The SFESA web server is available at http://prodata.swmed.edu/sfesa.

Development of a mobile emergency patient information and imaging communication system based on CDMA-1X EVDO

NASA Astrophysics Data System (ADS)

Yang, Keon Ho; Jung, Haijo; Kang, Won-Suk; Jang, Bong Mun; Kim, Joong Il; Han, Dong Hoon; Yoo, Sun-Kook; Yoo, Hyung-Sik; Kim, Hee-Joung

2006-03-01

The wireless mobile service with a high bit rate using CDMA-1X EVDO is now widely used in Korea. Mobile devices are also increasingly being used as the conventional communication mechanism. We have developed a web-based mobile system that communicates patient information and images, using CDMA-1X EVDO for emergency diagnosis. It is composed of a Mobile web application system using the Microsoft Windows 2003 server and an internet information service. Also, a mobile web PACS used for a database managing patient information and images was developed by using Microsoft access 2003. A wireless mobile emergency patient information and imaging communication system is developed by using Microsoft Visual Studio.NET, and JPEG 2000 ActiveX control for PDA phone was developed by using the Microsoft Embedded Visual C++. Also, the CDMA-1X EVDO is used for connections between mobile web servers and the PDA phone. This system allows fast access to the patient information database, storing both medical images and patient information anytime and anywhere. Especially, images were compressed into a JPEG2000 format and transmitted from a mobile web PACS inside the hospital to the radiologist using a PDA phone located outside the hospital. Also, this system shows radiological images as well as physiological signal data, including blood pressure, vital signs and so on, in the web browser of the PDA phone so radiologists can diagnose more effectively. Also, we acquired good results using an RW-6100 PDA phone used in the university hospital system of the Sinchon Severance Hospital in Korea.

Some Programs Should Not Run on Laptops - Providing Programmatic Access to Applications Via Web Services

NASA Astrophysics Data System (ADS)

Gupta, V.; Gupta, N.; Gupta, S.; Field, E.; Maechling, P.

2003-12-01

Modern laptop computers, and personal computers, can provide capabilities that are, in many ways, comparable to workstations or departmental servers. However, this doesn't mean we should run all computations on our local computers. We have identified several situations in which it preferable to implement our seismological application programs in a distributed, server-based, computing model. In this model, application programs on the user's laptop, or local computer, invoke programs that run on an organizational server, and the results are returned to the invoking system. Situations in which a server-based architecture may be preferred include: (a) a program is written in a language, or written for an operating environment, that is unsupported on the local computer, (b) software libraries or utilities required to execute a program are not available on the users computer, (c) a computational program is physically too large, or computationally too expensive, to run on a users computer, (d) a user community wants to enforce a consistent method of performing a computation by standardizing on a single implementation of a program, and (e) the computational program may require current information, that is not available to all client computers. Until recently, distributed, server-based, computational capabilities were implemented using client/server architectures. In these architectures, client programs were often written in the same language, and they executed in the same computing environment, as the servers. Recently, a new distributed computational model, called Web Services, has been developed. Web Services are based on Internet standards such as XML, SOAP, WDSL, and UDDI. Web Services offer the promise of platform, and language, independent distributed computing. To investigate this new computational model, and to provide useful services to the SCEC Community, we have implemented several computational and utility programs using a Web Service architecture. We have hosted these Web Services as a part of the SCEC Community Modeling Environment (SCEC/CME) ITR Project (http://www.scec.org/cme). We have implemented Web Services for several of the reasons sited previously. For example, we implemented a FORTRAN-based Earthquake Rupture Forecast (ERF) as a Web Service for use by client computers that don't support a FORTRAN runtime environment. We implemented a Generic Mapping Tool (GMT) Web Service for use by systems that don't have local access to GMT. We implemented a Hazard Map Calculator Web Service to execute Hazard calculations that are too computationally intensive to run on a local system. We implemented a Coordinate Conversion Web Service to enforce a standard and consistent method for converting between UTM and Lat/Lon. Our experience developing these services indicates both strengths and weakness in current Web Service technology. Client programs that utilize Web Services typically need network access, a significant disadvantage at times. Programs with simple input and output parameters were the easiest to implement as Web Services, while programs with complex parameter-types required a significant amount of additional development. We also noted that Web services are very data-oriented, and adapting object-oriented software into the Web Service model proved problematic. Also, the Web Service approach of converting data types into XML format for network transmission has significant inefficiencies for some data sets.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families.

PubMed

Suplatov, Dmitry; Sharapova, Yana; Timonina, Daria; Kopylov, Kirill; Švedas, Vytas

2018-04-01

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand's binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design

PubMed Central

2015-01-01

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser.1 One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing’s capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of “re-dockings” with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing’s docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening. PMID:25151852

Fragment-based docking: development of the CHARMMing Web user interface as a platform for computer-aided drug design.

PubMed

Pevzner, Yuri; Frugier, Emilie; Schalk, Vinushka; Caflisch, Amedeo; Woodcock, H Lee

2014-09-22

Web-based user interfaces to scientific applications are important tools that allow researchers to utilize a broad range of software packages with just an Internet connection and a browser. One such interface, CHARMMing (CHARMM interface and graphics), facilitates access to the powerful and widely used molecular software package CHARMM. CHARMMing incorporates tasks such as molecular structure analysis, dynamics, multiscale modeling, and other techniques commonly used by computational life scientists. We have extended CHARMMing's capabilities to include a fragment-based docking protocol that allows users to perform molecular docking and virtual screening calculations either directly via the CHARMMing Web server or on computing resources using the self-contained job scripts generated via the Web interface. The docking protocol was evaluated by performing a series of "re-dockings" with direct comparison to top commercial docking software. Results of this evaluation showed that CHARMMing's docking implementation is comparable to many widely used software packages and validates the use of the new CHARMM generalized force field for docking and virtual screening.

Web-based health services and clinical decision support.

PubMed

Jegelevicius, Darius; Marozas, Vaidotas; Lukosevicius, Arunas; Patasius, Martynas

2004-01-01

The purpose of this study was the development of a Web-based e-health service for comprehensive assistance and clinical decision support. The service structure consists of a Web server, a PHP-based Web interface linked to a clinical SQL database, Java applets for interactive manipulation and visualization of signals and a Matlab server linked with signal and data processing algorithms implemented by Matlab programs. The service ensures diagnostic signal- and image analysis-sbased clinical decision support. By using the discussed methodology, a pilot service for pathology specialists for automatic calculation of the proliferation index has been developed. Physicians use a simple Web interface for uploading the pictures under investigation to the server; subsequently a Java applet interface is used for outlining the region of interest and, after processing on the server, the requested proliferation index value is calculated. There is also an "expert corner", where experts can submit their index estimates and comments on particular images, which is especially important for system developers. These expert evaluations are used for optimization and verification of automatic analysis algorithms. Decision support trials have been conducted for ECG and ophthalmology ultrasonic investigations of intraocular tumor differentiation. Data mining algorithms have been applied and decision support trees constructed. These services are under implementation by a Web-based system too. The study has shown that the Web-based structure ensures more effective, flexible and accessible services compared with standalone programs and is very convenient for biomedical engineers and physicians, especially in the development phase.

Web server for priority ordered multimedia services

NASA Astrophysics Data System (ADS)

Celenk, Mehmet; Godavari, Rakesh K.; Vetnes, Vermund

2001-10-01

In this work, our aim is to provide finer priority levels in the design of a general-purpose Web multimedia server with provisions of the CM services. The type of services provided include reading/writing a web page, downloading/uploading an audio/video stream, navigating the Web through browsing, and interactive video teleconferencing. The selected priority encoding levels for such operations follow the order of admin read/write, hot page CM and Web multicasting, CM read, Web read, CM write and Web write. Hot pages are the most requested CM streams (e.g., the newest movies, video clips, and HDTV channels) and Web pages (e.g., portal pages of the commercial Internet search engines). Maintaining a list of these hot Web pages and CM streams in a content addressable buffer enables a server to multicast hot streams with lower latency and higher system throughput. Cold Web pages and CM streams are treated as regular Web and CM requests. Interactive CM operations such as pause (P), resume (R), fast-forward (FF), and rewind (RW) have to be executed without allocation of extra resources. The proposed multimedia server model is a part of the distributed network with load balancing schedulers. The SM is connected to an integrated disk scheduler (IDS), which supervises an allocated disk manager. The IDS follows the same priority handling as the SM, and implements a SCAN disk-scheduling method for an improved disk access and a higher throughput. Different disks are used for the Web and CM services in order to meet the QoS requirements of CM services. The IDS ouput is forwarded to an Integrated Transmission Scheduler (ITS). The ITS creates a priority ordered buffering of the retrieved Web pages and CM data streams that are fed into an auto regressive moving average (ARMA) based traffic shaping circuitry before being transmitted through the network.

WebEAV

PubMed Central

Nadkarni, Prakash M.; Brandt, Cynthia M.; Marenco, Luis

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples. PMID:10887163

A Semantics-Based Information Distribution Framework for Large Web-Based Course Forum System

ERIC Educational Resources Information Center

Chim, Hung; Deng, Xiaotie

2008-01-01

We propose a novel data distribution framework for developing a large Web-based course forum system. In the distributed architectural design, each forum server is fully equipped with the ability to support some course forums independently. The forum servers collaborating with each other constitute the whole forum system. Therefore, the workload of…

Development of a Web-Enabled Learning Platform for Geospatial Laboratories: Improving the Undergraduate Learning Experience

ERIC Educational Resources Information Center

Mui, Amy B.; Nelson, Sarah; Huang, Bruce; He, Yuhong; Wilson, Kathi

2015-01-01

This paper describes a web-enabled learning platform providing remote access to geospatial software that extends the learning experience outside of the laboratory setting. The platform was piloted in two undergraduate courses, and includes a software server, a data server, and remote student users. The platform was designed to improve the quality…

Parmodel: a web server for automated comparative modeling of proteins.

PubMed

Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

2004-12-24

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

WebEAV: automatic metadata-driven generation of web interfaces to entity-attribute-value databases.

PubMed

Nadkarni, P M; Brandt, C M; Marenco, L

2000-01-01

The task of creating and maintaining a front end to a large institutional entity-attribute-value (EAV) database can be cumbersome when using traditional client-server technology. Switching to Web technology as a delivery vehicle solves some of these problems but introduces others. In particular, Web development environments tend to be primitive, and many features that client-server developers take for granted are missing. WebEAV is a generic framework for Web development that is intended to streamline the process of Web application development for databases having a significant EAV component. It also addresses some challenging user interface issues that arise when any complex system is created. The authors describe the architecture of WebEAV and provide an overview of its features with suitable examples.

Space Physics Data Facility Web Services

NASA Technical Reports Server (NTRS)

Candey, Robert M.; Harris, Bernard T.; Chimiak, Reine A.

2005-01-01

The Space Physics Data Facility (SPDF) Web services provides a distributed programming interface to a portion of the SPDF software. (A general description of Web services is available at http://www.w3.org/ and in many current software-engineering texts and articles focused on distributed programming.) The SPDF Web services distributed programming interface enables additional collaboration and integration of the SPDF software system with other software systems, in furtherance of the SPDF mission to lead collaborative efforts in the collection and utilization of space physics data and mathematical models. This programming interface conforms to all applicable Web services specifications of the World Wide Web Consortium. The interface is specified by a Web Services Description Language (WSDL) file. The SPDF Web services software consists of the following components: 1) A server program for implementation of the Web services; and 2) A software developer s kit that consists of a WSDL file, a less formal description of the interface, a Java class library (which further eases development of Java-based client software), and Java source code for an example client program that illustrates the use of the interface.

SCOPE: a web server for practical de novo motif discovery.

PubMed

Carlson, Jonathan M; Chakravarty, Arijit; DeZiel, Charles E; Gross, Robert H

2007-07-01

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at .

Implementation of an Embedded Web Server Application for Wireless Control of Brain Computer Interface Based Home Environments.

PubMed

Aydın, Eda Akman; Bay, Ömer Faruk; Güler, İnan

2016-01-01

Brain Computer Interface (BCI) based environment control systems could facilitate life of people with neuromuscular diseases, reduces dependence on their caregivers, and improves their quality of life. As well as easy usage, low-cost, and robust system performance, mobility is an important functionality expected from a practical BCI system in real life. In this study, in order to enhance users' mobility, we propose internet based wireless communication between BCI system and home environment. We designed and implemented a prototype of an embedded low-cost, low power, easy to use web server which is employed in internet based wireless control of a BCI based home environment. The embedded web server provides remote access to the environmental control module through BCI and web interfaces. While the proposed system offers to BCI users enhanced mobility, it also provides remote control of the home environment by caregivers as well as the individuals in initial stages of neuromuscular disease. The input of BCI system is P300 potentials. We used Region Based Paradigm (RBP) as stimulus interface. Performance of the BCI system is evaluated on data recorded from 8 non-disabled subjects. The experimental results indicate that the proposed web server enables internet based wireless control of electrical home appliances successfully through BCIs.

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

PubMed Central

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Švedas, Vytas

2014-01-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure–function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. PMID:24852248

NMRPro: an integrated web component for interactive processing and visualization of NMR spectra.

PubMed

Mohamed, Ahmed; Nguyen, Canh Hao; Mamitsuka, Hiroshi

2016-07-01

The popularity of using NMR spectroscopy in metabolomics and natural products has driven the development of an array of NMR spectral analysis tools and databases. Particularly, web applications are well used recently because they are platform-independent and easy to extend through reusable web components. Currently available web applications provide the analysis of NMR spectra. However, they still lack the necessary processing and interactive visualization functionalities. To overcome these limitations, we present NMRPro, a web component that can be easily incorporated into current web applications, enabling easy-to-use online interactive processing and visualization. NMRPro integrates server-side processing with client-side interactive visualization through three parts: a python package to efficiently process large NMR datasets on the server-side, a Django App managing server-client interaction, and SpecdrawJS for client-side interactive visualization. Demo and installation instructions are available at http://mamitsukalab.org/tools/nmrpro/ mohamed@kuicr.kyoto-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

Joint Force Quarterly. Number 31, Summer 2002

DTIC Science & Technology

2002-09-01

College of the Armed Forces COL Timothy S. Heinemann, USA ■ U.S. Army Command and General Staff College CAPT Chester E. Helms, USN ■ Naval War College...Announcing the next event in the 2002– 2003 symposia program Pacific Symposium Towards a Durable Security Strategy (Co-sponsored with U.S. Pacific...Command) March 25–27, 2003 Information on symposia is available via the National Defense University World Wide Web server. Access by addressing

Implementation of a World Wide Web server for the oil and gas industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blaylock, R.E.; Martin, F.D.; Emery, R.

1995-12-31

The Gas and Oil Technology Exchange and Communication Highway, (GO-TECH), provides an electronic information system for the petroleum community for the purpose of exchanging ideas, data, and technology. The personal computer-based system fosters communication and discussion by linking oil and gas producers with resource centers, government agencies, consulting firms, service companies, national laboratories, academic research groups, and universities throughout the world. The oil and gas producers are provided access to the GO-TECH World Wide Web home page via modem links, as well as Internet. The future GO-TECH applications will include the establishment of{open_quote}Virtual corporations {close_quotes} consisting of consortiums of smallmore » companies, consultants, and service companies linked by electronic information systems. These virtual corporations will have the resources and expertise previously found only in major corporations.« less

Implementation of a World Wide Web server for the oil and gas industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Blaylock, R.E.; Martin, F.D.; Emery, R.

1996-10-01

The Gas and Oil Technology Exchange and Communication Highway (GO-TECH) provides an electronic information system for the petroleum community for exchanging ideas, data, and technology. The PC-based system fosters communication and discussion by linking the oil and gas producers with resource centers, government agencies, consulting firms, service companies, national laboratories, academic research groups, and universities throughout the world. The oil and gas producers can access the GO-TECH World Wide Web (WWW) home page through modem links, as well as through the Internet. Future GO-TECH applications will include the establishment of virtual corporations consisting of consortia of small companies, consultants, andmore » service companies linked by electronic information systems. These virtual corporations will have the resources and expertise previously found only in major corporations.« less

Develop, Build, and Test a Virtual Lab to Support a Vulnerability Training System

DTIC Science & Technology

2004-09-01

docs.us.dell.com/support/edocs/systems/pe1650/ en /it/index.htm> (20 August 2004) “HOWTO: Installing Web Services with Linux /Tomcat/Apache/Struts...configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web server was configured as the external interface to...1650, dual processor, blade servers were configured as host machines with VMware and VNC running on a Linux RedHat 9 Kernel. An Apache-Tomcat web

Web-Based Distributed Simulation of Aeronautical Propulsion System

NASA Technical Reports Server (NTRS)

Zheng, Desheng; Follen, Gregory J.; Pavlik, William R.; Kim, Chan M.; Liu, Xianyou; Blaser, Tammy M.; Lopez, Isaac

2001-01-01

An application was developed to allow users to run and view the Numerical Propulsion System Simulation (NPSS) engine simulations from web browsers. Simulations were performed on multiple INFORMATION POWER GRID (IPG) test beds. The Common Object Request Broker Architecture (CORBA) was used for brokering data exchange among machines and IPG/Globus for job scheduling and remote process invocation. Web server scripting was performed by JavaServer Pages (JSP). This application has proven to be an effective and efficient way to couple heterogeneous distributed components.

Creating Web-Based Scientific Applications Using Java Servlets

NASA Technical Reports Server (NTRS)

Palmer, Grant; Arnold, James O. (Technical Monitor)

2001-01-01

There are many advantages to developing web-based scientific applications. Any number of people can access the application concurrently. The application can be accessed from a remote location. The application becomes essentially platform-independent because it can be run from any machine that has internet access and can run a web browser. Maintenance and upgrades to the application are simplified since only one copy of the application exists in a centralized location. This paper details the creation of web-based applications using Java servlets. Java is a powerful, versatile programming language that is well suited to developing web-based programs. A Java servlet provides the interface between the central server and the remote client machines. The servlet accepts input data from the client, runs the application on the server, and sends the output back to the client machine. The type of servlet that supports the HTTP protocol will be discussed in depth. Among the topics the paper will discuss are how to write an http servlet, how the servlet can run applications written in Java and other languages, and how to set up a Java web server. The entire process will be demonstrated by building a web-based application to compute stagnation point heat transfer.

The pepATTRACT web server for blind, large-scale peptide-protein docking.

PubMed

de Vries, Sjoerd J; Rey, Julien; Schindler, Christina E M; Zacharias, Martin; Tuffery, Pierre

2017-07-03

Peptide-protein interactions are ubiquitous in the cell and form an important part of the interactome. Computational docking methods can complement experimental characterization of these complexes, but current protocols are not applicable on the proteome scale. pepATTRACT is a novel docking protocol that is fully blind, i.e. it does not require any information about the binding site. In various stages of its development, pepATTRACT has participated in CAPRI, making successful predictions for five out of seven protein-peptide targets. Its performance is similar or better than state-of-the-art local docking protocols that do require binding site information. Here we present a novel web server that carries out the rigid-body stage of pepATTRACT. On the peptiDB benchmark, the web server generates a correct model in the top 50 in 34% of the cases. Compared to the full pepATTRACT protocol, this leads to some loss of performance, but the computation time is reduced from ∼18 h to ∼10 min. Combined with the fact that it is fully blind, this makes the web server well-suited for large-scale in silico protein-peptide docking experiments. The rigid-body pepATTRACT server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Flexible software architecture for user-interface and machine control in laboratory automation.

PubMed

Arutunian, E B; Meldrum, D R; Friedman, N A; Moody, S E

1998-10-01

We describe a modular, layered software architecture for automated laboratory instruments. The design consists of a sophisticated user interface, a machine controller and multiple individual hardware subsystems, each interacting through a client-server architecture built entirely on top of open Internet standards. In our implementation, the user-interface components are built as Java applets that are downloaded from a server integrated into the machine controller. The user-interface client can thereby provide laboratory personnel with a familiar environment for experiment design through a standard World Wide Web browser. Data management and security are seamlessly integrated at the machine-controller layer using QNX, a real-time operating system. This layer also controls hardware subsystems through a second client-server interface. This architecture has proven flexible and relatively easy to implement and allows users to operate laboratory automation instruments remotely through an Internet connection. The software architecture was implemented and demonstrated on the Acapella, an automated fluid-sample-processing system that is under development at the University of Washington.

THttpServer class in ROOT

NASA Astrophysics Data System (ADS)

Adamczewski-Musch, Joern; Linev, Sergey

2015-12-01

The new THttpServer class in ROOT implements HTTP server for arbitrary ROOT applications. It is based on Civetweb embeddable HTTP server and provides direct access to all objects registered for the server. Objects data could be provided in different formats: binary, XML, GIF/PNG, and JSON. A generic user interface for THttpServer has been implemented with HTML/JavaScript based on JavaScript ROOT development. With any modern web browser one could list, display, and monitor objects available on the server. THttpServer is used in Go4 framework to provide HTTP interface to the online analysis.

CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments.

PubMed

Cao, Qingyi; Ma, Jian; Chen, Chen-Hao; Xu, Han; Chen, Zhi; Li, Wei; Liu, X Shirley

2017-01-01

The recently developed CRISPR screen technology, based on the CRISPR/Cas9 genome editing system, enables genome-wide interrogation of gene functions in an efficient and cost-effective manner. Although many computational algorithms and web servers have been developed to design single-guide RNAs (sgRNAs) with high specificity and efficiency, algorithms specifically designed for conducting CRISPR screens are still lacking. Here we present CRISPR-FOCUS, a web-based platform to search and prioritize sgRNAs for CRISPR screen experiments. With official gene symbols or RefSeq IDs as the only mandatory input, CRISPR-FOCUS filters and prioritizes sgRNAs based on multiple criteria, including efficiency, specificity, sequence conservation, isoform structure, as well as genomic variations including Single Nucleotide Polymorphisms and cancer somatic mutations. CRISPR-FOCUS also provides pre-defined positive and negative control sgRNAs, as well as other necessary sequences in the construct (e.g., U6 promoters to drive sgRNA transcription and RNA scaffolds of the CRISPR/Cas9). These features allow users to synthesize oligonucleotides directly based on the output of CRISPR-FOCUS. Overall, CRISPR-FOCUS provides a rational and high-throughput approach for sgRNA library design that enables users to efficiently conduct a focused screen experiment targeting up to thousands of genes. (CRISPR-FOCUS is freely available at http://cistrome.org/crispr-focus/).

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

Web Proxy Auto Discovery for the WLCG

NASA Astrophysics Data System (ADS)

Dykstra, D.; Blomer, J.; Blumenfeld, B.; De Salvo, A.; Dewhurst, A.; Verguilov, V.

2017-10-01

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily support that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which they direct to the nearest publicly accessible web proxy servers. The responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.

Web Proxy Auto Discovery for the WLCG

DOE PAGES

Dykstra, D.; Blomer, J.; Blumenfeld, B.; ...

2017-11-23

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

Web Proxy Auto Discovery for the WLCG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dykstra, D.; Blomer, J.; Blumenfeld, B.

All four of the LHC experiments depend on web proxies (that is, squids) at each grid site to support software distribution by the CernVM FileSystem (CVMFS). CMS and ATLAS also use web proxies for conditions data distributed through the Frontier Distributed Database caching system. ATLAS & CMS each have their own methods for their grid jobs to find out which web proxies to use for Frontier at each site, and CVMFS has a third method. Those diverse methods limit usability and flexibility, particularly for opportunistic use cases, where an experiment’s jobs are run at sites that do not primarily supportmore » that experiment. This paper describes a new Worldwide LHC Computing Grid (WLCG) system for discovering the addresses of web proxies. The system is based on an internet standard called Web Proxy Auto Discovery (WPAD). WPAD is in turn based on another standard called Proxy Auto Configuration (PAC). Both the Frontier and CVMFS clients support this standard. The input into the WLCG system comes from squids registered in the ATLAS Grid Information System (AGIS) and CMS SITECONF files, cross-checked with squids registered by sites in the Grid Configuration Database (GOCDB) and the OSG Information Management (OIM) system, and combined with some exceptions manually configured by people from ATLAS and CMS who operate WLCG Squid monitoring. WPAD servers at CERN respond to http requests from grid nodes all over the world with a PAC file that lists available web proxies, based on IP addresses matched from a database that contains the IP address ranges registered to organizations. Large grid sites are encouraged to supply their own WPAD web servers for more flexibility, to avoid being affected by short term long distance network outages, and to offload the WLCG WPAD servers at CERN. The CERN WPAD servers additionally support requests from jobs running at non-grid sites (particularly for LHC@Home) which it directs to the nearest publicly accessible web proxy servers. Furthermore, the responses to those requests are geographically ordered based on a separate database that maps IP addresses to longitude and latitude.« less

The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data

PubMed Central

Ramos, H.; Shannon, P.; Aebersold, R.

2008-01-01

Motivation: Mass spectrometry experiments in the field of proteomics produce lists containing tens to thousands of identified proteins. With the protein information and property explorer (PIPE), the biologist can acquire functional annotations for these proteins and explore the enrichment of the list, or fraction thereof, with respect to functional classes. These protein lists may be saved for access at a later time or different location. The PIPE is interoperable with the Firegoose and the Gaggle, permitting wide-ranging data exploration and analysis. The PIPE is a rich-client web application which uses AJAX capabilities provided by the Google Web Toolkit, and server-side data storage using Hibernate. Availability: http://pipe.systemsbiology.net Contact: pshannon@systemsbiology.org PMID:18635572

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

SCENERY: a web application for (causal) network reconstruction from cytometry data.

PubMed

Papoutsoglou, Georgios; Athineou, Giorgos; Lagani, Vincenzo; Xanthopoulos, Iordanis; Schmidt, Angelika; Éliás, Szabolcs; Tegnér, Jesper; Tsamardinos, Ioannis

2017-07-03

Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data. To bridge this gap, we present Single CEll NEtwork Reconstruction sYstem (SCENERY), a web server featuring several standard and advanced cytometry data analysis methods coupled with NR algorithms in a user-friendly, on-line environment. In SCENERY, users may upload their data and set their own study design. The server offers several data analysis options categorized into three classes of methods: data (pre)processing, statistical analysis and NR. The server also provides interactive visualization and download of results as ready-to-publish images or multimedia reports. Its core is modular and based on the widely-used and robust R platform allowing power users to extend its functionalities by submitting their own NR methods. SCENERY is available at scenery.csd.uoc.gr or http://mensxmachina.org/en/software/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web Service Distributed Management Framework for Autonomic Server Virtualization

NASA Astrophysics Data System (ADS)

Solomon, Bogdan; Ionescu, Dan; Litoiu, Marin; Mihaescu, Mircea

Virtualization for the x86 platform has imposed itself recently as a new technology that can improve the usage of machines in data centers and decrease the cost and energy of running a high number of servers. Similar to virtualization, autonomic computing and more specifically self-optimization, aims to improve server farm usage through provisioning and deprovisioning of instances as needed by the system. Autonomic systems are able to determine the optimal number of server machines - real or virtual - to use at a given time, and add or remove servers from a cluster in order to achieve optimal usage. While provisioning and deprovisioning of servers is very important, the way the autonomic system is built is also very important, as a robust and open framework is needed. One such management framework is the Web Service Distributed Management (WSDM) system, which is an open standard of the Organization for the Advancement of Structured Information Standards (OASIS). This paper presents an open framework built on top of the WSDM specification, which aims to provide self-optimization for applications servers residing on virtual machines.

Super: a web server to rapidly screen superposable oligopeptide fragments from the protein data bank

PubMed Central

Collier, James H.; Lesk, Arthur M.; Garcia de la Banda, Maria; Konagurthu, Arun S.

2012-01-01

Searching for well-fitting 3D oligopeptide fragments within a large collection of protein structures is an important task central to many analyses involving protein structures. This article reports a new web server, Super, dedicated to the task of rapidly screening the protein data bank (PDB) to identify all fragments that superpose with a query under a prespecified threshold of root-mean-square deviation (RMSD). Super relies on efficiently computing a mathematical bound on the commonly used structural similarity measure, RMSD of superposition. This allows the server to filter out a large proportion of fragments that are unrelated to the query; >99% of the total number of fragments in some cases. For a typical query, Super scans the current PDB containing over 80 500 structures (with ∼40 million potential oligopeptide fragments to match) in under a minute. Super web server is freely accessible from: http://lcb.infotech.monash.edu.au/super. PMID:22638586

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts

PubMed Central

Naito, Yuki; Bono, Hidemasa

2012-01-01

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users. PMID:22641850

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

PubMed

Naito, Yuki; Bono, Hidemasa

2012-07-01

GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant RefSeq transcripts. A typical search takes just a few seconds, which dramatically enhances the usability of routine searching. In particular, GGRNA can search sequences as short as 10 nt or 4 amino acids, which cannot be handled easily by popular sequence analysis tools. Nucleotide sequences can be searched allowing up to three mismatches, or the query sequences may contain degenerate nucleotide codes (e.g. N, R, Y, S). Furthermore, Gene Ontology annotations, Enzyme Commission numbers and probe sequences of catalog microarrays are also incorporated into GGRNA, which may help users to conduct searches by various types of keywords. GGRNA web server will provide a simple and powerful interface for finding genes and transcripts for a wide range of users. All services at GGRNA are provided free of charge to all users.

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences.

PubMed

Chen, Zhen; Zhao, Pei; Li, Fuyi; Leier, André; Marquez-Lago, Tatiana T; Wang, Yanan; Webb, Geoffrey I; Smith, A Ian; Daly, Roger J; Chou, Kuo-Chen; Song, Jiangning

2018-03-08

Structural and physiochemical descriptors extracted from sequence data have been widely used to represent sequences and predict structural, functional, expression and interaction profiles of proteins and peptides as well as DNAs/RNAs. Here, we present iFeature, a versatile Python-based toolkit for generating various numerical feature representation schemes for both protein and peptide sequences. iFeature is capable of calculating and extracting a comprehensive spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. It also allows users to extract specific amino acid properties from the AAindex database. Furthermore, iFeature integrates 12 different types of commonly used feature clustering, selection, and dimensionality reduction algorithms, greatly facilitating training, analysis, and benchmarking of machine-learning models. The functionality of iFeature is made freely available via an online web server and a stand-alone toolkit. http://iFeature.erc.monash.edu/; https://github.com/Superzchen/iFeature/. jiangning.song@monash.edu; kcchou@gordonlifescience.org; roger.daly@monash.edu. Supplementary data are available at Bioinformatics online.

In-house access to PACS images and related data through World Wide Web

NASA Astrophysics Data System (ADS)

Mascarini, Christian; Ratib, Osman M.; Trayser, Gerhard; Ligier, Yves; Appel, R. D.

1996-05-01

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing an user interface which is the same independently of the platform being used (Mac, Windows, UNIX, ...), and an easy integration of different types of documents (text, images, ...). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

PubMed Central

Di Tommaso, Paolo; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

2014-01-01

This article introduces the SARA-Coffee web server; a service allowing the online computation of 3D structure based multiple RNA sequence alignments. The server makes it possible to combine sequences with and without known 3D structures. Given a set of sequences SARA-Coffee outputs a multiple sequence alignment along with a reliability index for every sequence, column and aligned residue. SARA-Coffee combines SARA, a pairwise structural RNA aligner with the R-Coffee multiple RNA aligner in a way that has been shown to improve alignment accuracy over most sequence aligners when enough structural data is available. The server can be accessed from http://tcoffee.crg.cat/apps/tcoffee/do:saracoffee. PMID:24972831

Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

PubMed Central

Kirshner, Daniel A.; Nilmeier, Jerome P.; Lightstone, Felice C.

2013-01-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov. PMID:23680785

Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

PubMed

Kirshner, Daniel A; Nilmeier, Jerome P; Lightstone, Felice C

2013-07-01

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl.gov.

EarthServer - an FP7 project to enable the web delivery and analysis of 3D/4D models

NASA Astrophysics Data System (ADS)

Laxton, John; Sen, Marcus; Passmore, James

2013-04-01

EarthServer aims at open access and ad-hoc analytics on big Earth Science data, based on the OGC geoservice standards Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS). The WCS model defines "coverages" as a unifying paradigm for multi-dimensional raster data, point clouds, meshes, etc., thereby addressing a wide range of Earth Science data including 3D/4D models. WCPS allows declarative SQL-style queries on coverages. The project is developing a pilot implementing these standards, and will also investigate the use of GeoSciML to describe coverages. Integration of WCPS with XQuery will in turn allow coverages to be queried in combination with their metadata and GeoSciML description. The unified service will support navigation, extraction, aggregation, and ad-hoc analysis on coverage data from SQL. Clients will range from mobile devices to high-end immersive virtual reality, and will enable 3D model visualisation using web browser technology coupled with developing web standards. EarthServer is establishing open-source client and server technology intended to be scalable to Petabyte/Exabyte volumes, based on distributed processing, supercomputing, and cloud virtualization. Implementation will be based on the existing rasdaman server technology developed. Services using rasdaman technology are being installed serving the atmospheric, oceanographic, geological, cryospheric, planetary and general earth observation communities. The geology service (http://earthserver.bgs.ac.uk/) is being provided by BGS and at present includes satellite imagery, superficial thickness data, onshore DTMs and 3D models for the Glasgow area. It is intended to extend the data sets available to include 3D voxel models. Use of the WCPS standard allows queries to be constructed against single or multiple coverages. For example on a single coverage data for a particular area can be selected or data with a particular range of pixel values. Queries on multiple surfaces can be constructed to calculate, for example, the thickness between two surfaces in a 3D model or the depth from ground surface to the top of a particular geologic unit. In the first version of the service a simple interface showing some example queries has been implemented in order to show the potential of the technologies. The project aims to develop the services available in light of user feedback, both in terms of the data available, the functionality and the interface. User feedback on the services guides the software and standards development aspects of the project, leading to enhanced versions of the software which will be implemented in upgraded versions of the services during the lifetime of the project.

A geospatial search engine for discovering multi-format geospatial data across the web

Treesearch

Christopher Bone; Alan Ager; Ken Bunzel; Lauren Tierney

2014-01-01

The volume of publically available geospatial data on the web is rapidly increasing due to advances in server-based technologies and the ease at which data can now be created. However, challenges remain with connecting individuals searching for geospatial data with servers and websites where such data exist. The objective of this paper is to present a publically...

Using a Java Web-based Graphical User Interface to access the SOHO Data Arch ive

NASA Astrophysics Data System (ADS)

Scholl, I.; Girard, Y.; Bykowski, A.

This paper presents the architecture of a Java web-based graphical interface dedicated to the access of the SOHO Data archive. This application allows local and remote users to search in the SOHO data catalog and retrieve the SOHO data files from the archive. It has been developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France), which is one of the European Archives for the SOHO data. This development is part of a joint effort between ESA, NASA and IAS in order to implement long term archive systems for the SOHO data. The software architecture is built as a client-server application using Java language and SQL above a set of components such as an HTTP server, a JDBC gateway, a RDBMS server, a data server and a Web browser. Since HTML pages and CGI scripts are not powerful enough to allow user interaction during a multi-instrument catalog search, this type of requirement enforces the choice of Java as the main language. We also discuss performance issues, security problems and portability on different Web browsers and operating syste ms.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services.

PubMed

Gessler, Damian D G; Schiltz, Gary S; May, Greg D; Avraham, Shulamit; Town, Christopher D; Grant, David; Nelson, Rex T

2009-09-23

SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at http://sswap.info (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at http://sswap.info/protocol.jsp, developer tools at http://sswap.info/developer.jsp, and a portal to third-party ontologies at http://sswapmeet.sswap.info (a "swap meet"). SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.

Webmail: an Automated Web Publishing System

NASA Astrophysics Data System (ADS)

Bell, David

A system for publishing frequently updated information to the World Wide Web will be described. Many documents now hosted by the NOAO Web server require timely posting and frequent updates, but need only minor changes in markup or are in a standard format requiring only conversion to HTML. These include information from outside the organization, such as electronic bulletins, and a number of internal reports, both human and machine generated. Webmail uses procmail and Perl scripts to process incoming email messages in a variety of ways. This processing may include wrapping or conversion to HTML, posting to the Web or internal newsgroups, updating search indices or links on related pages, and sending email notification of the new pages to interested parties. The Webmail system has been in use at NOAO since early 1997 and has steadily grown to include fourteen recipes that together handle about fifty messages per week.

On-demand server-side image processing for web-based DICOM image display

NASA Astrophysics Data System (ADS)

Sakusabe, Takaya; Kimura, Michio; Onogi, Yuzo

2000-04-01

Low cost image delivery is needed in modern networked hospitals. If a hospital has hundreds of clients, cost of client systems is a big problem. Naturally, a Web-based system is the most effective solution. But a Web browser could not display medical images with certain image processing such as a lookup table transformation. We developed a Web-based medical image display system using Web browser and on-demand server-side image processing. All images displayed on a Web page are generated from DICOM files on a server, delivered on-demand. User interaction on the Web page is handled by a client-side scripting technology such as JavaScript. This combination makes a look-and-feel of an imaging workstation not only for its functionality but also for its speed. Real time update of images with tracing mouse motion is achieved on Web browser without any client-side image processing which may be done by client-side plug-in technology such as Java Applets or ActiveX. We tested performance of the system in three cases. Single client, small number of clients in a fast speed network, and large number of clients in a normal speed network. The result shows that there are very slight overhead for communication and very scalable in number of clients.

T-Epitope Designer: A HLA-peptide binding prediction server.

PubMed

Kangueane, Pandjassarame; Sakharkar, Meena Kishore

2005-05-15

The current challenge in synthetic vaccine design is the development of a methodology to identify and test short antigen peptides as potential T-cell epitopes. Recently, we described a HLA-peptide binding model (using structural properties) capable of predicting peptides binding to any HLA allele. Consequently, we have developed a web server named T-EPITOPE DESIGNER to facilitate HLA-peptide binding prediction. The prediction server is based on a model that defines peptide binding pockets using information gleaned from X-ray crystal structures of HLA-peptide complexes, followed by the estimation of peptide binding to binding pockets. Thus, the prediction server enables the calculation of peptide binding to HLA alleles. This model is superior to many existing methods because of its potential application to any given HLA allele whose sequence is clearly defined. The web server finds potential application in T cell epitope vaccine design. http://www.bioinformation.net/ted/

A web-based solution for 3D medical image visualization

NASA Astrophysics Data System (ADS)

Hou, Xiaoshuai; Sun, Jianyong; Zhang, Jianguo

2015-03-01

In this presentation, we present a web-based 3D medical image visualization solution which enables interactive large medical image data processing and visualization over the web platform. To improve the efficiency of our solution, we adopt GPU accelerated techniques to process images on the server side while rapidly transferring images to the HTML5 supported web browser on the client side. Compared to traditional local visualization solution, our solution doesn't require the users to install extra software or download the whole volume dataset from PACS server. By designing this web-based solution, it is feasible for users to access the 3D medical image visualization service wherever the internet is available.

Virtual reality for spherical images

NASA Astrophysics Data System (ADS)

Pilarczyk, Rafal; Skarbek, Władysław

2017-08-01

Paper presents virtual reality application framework and application concept for mobile devices. Framework uses Google Cardboard library for Android operating system. Framework allows to create virtual reality 360 video player using standard OpenGL ES rendering methods. Framework provides network methods in order to connect to web server as application resource provider. Resources are delivered using JSON response as result of HTTP requests. Web server also uses Socket.IO library for synchronous communication between application and server. Framework implements methods to create event driven process of rendering additional content based on video timestamp and virtual reality head point of view.

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2012-01-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

A genetic algorithm for replica server placement

NASA Astrophysics Data System (ADS)

Eslami, Ghazaleh; Toroghi Haghighat, Abolfazl

2011-12-01

Modern distribution systems use replication to improve communication delay experienced by their clients. Some techniques have been developed for web server replica placement. One of the previous studies was Greedy algorithm proposed by Qiu et al, that needs knowledge about network topology. In This paper, first we introduce a genetic algorithm for web server replica placement. Second, we compare our algorithm with Greedy algorithm proposed by Qiu et al, and Optimum algorithm. We found that our approach can achieve better results than Greedy algorithm proposed by Qiu et al but it's computational time is more than Greedy algorithm.

Hypertext-based computer vision teaching packages

NASA Astrophysics Data System (ADS)

Marshall, A. David

1994-10-01

The World Wide Web Initiative has provided a means for providing hypertext and multimedia based information across the whole INTERNET. Many applications have been developed on such http servers. At Cardiff we have developed a http hypertext based multimedia server, the Cardiff Information Server, using the widely available Mosaic system. The server provides a variety of information ranging from the provision of teaching modules, on- line documentation, timetables for departmental activities to more light hearted hobby interests. One important and novel development to the server has been the development of courseware facilities. This ranges from the provision of on-line lecture notes, exercises and their solutions to more interactive teaching packages. A variety of disciplines have benefitted notably Computer Vision, and Image Processing but also C programming, X Windows, Computer Graphics and Parallel Computing. This paper will address the issues of the implementation of the Computer Vision and Image Processing packages, the advantages gained from using a hypertext based system and also will relate practical experiences of using the packages in a class environment. The paper addresses issues of how best to provide information in such a hypertext based system and how interactive image processing packages can be developed and integrated into courseware. The suite of tools developed facilitates a flexible and powerful courseware package that has proved popular in the classroom and over the Internet. The paper will also detail many future developments we see possible. One of the key points raised in the paper is that Mosaic's hypertext language (html) is extremely powerful and yet relatively straightforward to use. It is also possible to link in Unix calls so that programs and shells can be executed. This provides a powerful suite of utilities that can be exploited to develop many packages.

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families.

PubMed

Suplatov, Dmitry; Kirilin, Eugeny; Arbatsky, Mikhail; Takhaveev, Vakil; Svedas, Vytas

2014-07-01

The new web-server pocketZebra implements the power of bioinformatics and geometry-based structural approaches to identify and rank subfamily-specific binding sites in proteins by functional significance, and select particular positions in the structure that determine selective accommodation of ligands. A new scoring function has been developed to annotate binding sites by the presence of the subfamily-specific positions in diverse protein families. pocketZebra web-server has multiple input modes to meet the needs of users with different experience in bioinformatics. The server provides on-site visualization of the results as well as off-line version of the output in annotated text format and as PyMol sessions ready for structural analysis. pocketZebra can be used to study structure-function relationship and regulation in large protein superfamilies, classify functionally important binding sites and annotate proteins with unknown function. The server can be used to engineer ligand-binding sites and allosteric regulation of enzymes, or implemented in a drug discovery process to search for potential molecular targets and novel selective inhibitors/effectors. The server, documentation and examples are freely available at http://biokinet.belozersky.msu.ru/pocketzebra and there are no login requirements. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.

PubMed

Krystkowiak, Izabella; Manguy, Jean; Davey, Norman E

2018-06-05

There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.

QuadBase2: web server for multiplexed guanine quadruplex mining and visualization

PubMed Central

Dhapola, Parashar; Chowdhury, Shantanu

2016-01-01

DNA guanine quadruplexes or G4s are non-canonical DNA secondary structures which affect genomic processes like replication, transcription and recombination. G4s are computationally identified by specific nucleotide motifs which are also called putative G4 (PG4) motifs. Despite the general relevance of these structures, there is currently no tool available that can allow batch queries and genome-wide analysis of these motifs in a user-friendly interface. QuadBase2 (quadbase.igib.res.in) presents a completely reinvented web server version of previously published QuadBase database. QuadBase2 enables users to mine PG4 motifs in up to 178 eukaryotes through the EuQuad module. This module interfaces with Ensembl Compara database, to allow users mine PG4 motifs in the orthologues of genes of interest across eukaryotes. PG4 motifs can be mined across genes and their promoter sequences in 1719 prokaryotes through ProQuad module. This module includes a feature that allows genome-wide mining of PG4 motifs and their visualization as circular histograms. TetraplexFinder, the module for mining PG4 motifs in user-provided sequences is now capable of handling up to 20 MB of data. QuadBase2 is a comprehensive PG4 motif mining tool that further expands the configurations and algorithms for mining PG4 motifs in a user-friendly way. PMID:27185890

Providing the Persistent Data Storage in a Software Engineering Environment Using Java/COBRA and a DBMS

NASA Technical Reports Server (NTRS)

Dhaliwal, Swarn S.

1997-01-01

An investigation was undertaken to build the software foundation for the WHERE (Web-based Hyper-text Environment for Requirements Engineering) project. The TCM (Toolkit for Conceptual Modeling) was chosen as the foundation software for the WHERE project which aims to provide an environment for facilitating collaboration among geographically distributed people involved in the Requirements Engineering process. The TCM is a collection of diagram and table editors and has been implemented in the C++ programming language. The C++ implementation of the TCM was translated into Java in order to allow the editors to be used for building various functionality of the WHERE project; the WHERE project intends to use the Web as its communication back- bone. One of the limitations of the translated software (TcmJava), which militated against its use in the WHERE project, was persistent data management mechanisms which it inherited from the original TCM; it was designed to be used in standalone applications. Before TcmJava editors could be used as a part of the multi-user, geographically distributed applications of the WHERE project, a persistent storage mechanism must be built which would allow data communication over the Internet, using the capabilities of the Web. An approach involving features of Java, CORBA (Common Object Request Broker), the Web, a middle-ware (Java Relational Binding (JRB)), and a database server was used to build the persistent data management infrastructure for the WHERE project. The developed infrastructure allows a TcmJava editor to be downloaded and run from a network host by using a JDK 1.1 (Java Developer's Kit) compatible Web-browser. The aforementioned editor establishes connection with a server by using the ORB (Object Request Broker) software and stores/retrieves data in/from the server. The server consists of a CORBA object or objects depending upon whether the data is to be made persistent on a single server or multiple servers. The CORBA object providing the persistent data server is implemented using the Java progranu-ning language. It uses the JRB to store/retrieve data in/from a relational database server. The persistent data management system provides transaction and user management facilities which allow multi-user, distributed access to the stored data in a secure manner.

UAV field demonstration of social media enabled tactical data link

NASA Astrophysics Data System (ADS)

Olson, Christopher C.; Xu, Da; Martin, Sean R.; Castelli, Jonathan C.; Newman, Andrew J.

2015-05-01

This paper addresses the problem of enabling Command and Control (C2) and data exfiltration functions for missions using small, unmanned, airborne surveillance and reconnaissance platforms. The authors demonstrated the feasibility of using existing commercial wireless networks as the data transmission infrastructure to support Unmanned Aerial Vehicle (UAV) autonomy functions such as transmission of commands, imagery, metadata, and multi-vehicle coordination messages. The authors developed and integrated a C2 Android application for ground users with a common smart phone, a C2 and data exfiltration Android application deployed on-board the UAVs, and a web server with database to disseminate the collected data to distributed users using standard web browsers. The authors performed a mission-relevant field test and demonstration in which operators commanded a UAV from an Android device to search and loiter; and remote users viewed imagery, video, and metadata via web server to identify and track a vehicle on the ground. Social media served as the tactical data link for all command messages, images, videos, and metadata during the field demonstration. Imagery, video, and metadata were transmitted from the UAV to the web server via multiple Twitter, Flickr, Facebook, YouTube, and similar media accounts. The web server reassembled images and video with corresponding metadata for distributed users. The UAV autopilot communicated with the on-board Android device via on-board Bluetooth network.

Development and process evaluation of a web-based responsible beverage service training program

PubMed Central

2012-01-01

Background Responsible beverage service (RBS) training designed to improve the appropriate service of alcohol in commercial establishments is typically delivered in workshops. Recently, Web-based RBS training programs have emerged. This report describes the formative development and subsequent design of an innovative Web-delivered RBS program, and evaluation of the impact of the program on servers’ knowledge, attitudes, and self-efficacy. Methods Formative procedures using focus groups and usability testing were used to develop a Web-based RBS training program. Professional alcohol servers (N = 112) who worked as servers and/or mangers in alcohol service settings were recruited to participate. A pre-post assessment design was used to assess changes associated with using the program. Results Participants who used the program showed significant improvements in their RBS knowledge, attitudes, and self-efficacy. Conclusions Although the current study did not directly observe and determine impact of the intervention on server behaviors, it demonstrated that the development process incorporating input from a multidisciplinary team in conjunction with feedback from end-users resulted in creation of a Web-based RBS program that was well-received by servers and that changed relevant knowledge, attitudes, and self-efficacy. The results also help to establish a needed evidence base in support of the use of online RBS training, which has been afforded little research attention. PMID:22999419

StarScan: a web server for scanning small RNA targets from degradome sequencing data.

PubMed

Liu, Shun; Li, Jun-Hao; Wu, Jie; Zhou, Ke-Ren; Zhou, Hui; Yang, Jian-Hua; Qu, Liang-Hu

2015-07-01

Endogenous small non-coding RNAs (sRNAs), including microRNAs, PIWI-interacting RNAs and small interfering RNAs, play important gene regulatory roles in animals and plants by pairing to the protein-coding and non-coding transcripts. However, computationally assigning these various sRNAs to their regulatory target genes remains technically challenging. Recently, a high-throughput degradome sequencing method was applied to identify biologically relevant sRNA cleavage sites. In this study, an integrated web-based tool, StarScan (sRNA target Scan), was developed for scanning sRNA targets using degradome sequencing data from 20 species. Given a sRNA sequence from plants or animals, our web server performs an ultrafast and exhaustive search for potential sRNA-target interactions in annotated and unannotated genomic regions. The interactions between small RNAs and target transcripts were further evaluated using a novel tool, alignScore. A novel tool, degradomeBinomTest, was developed to quantify the abundance of degradome fragments located at the 9-11th nucleotide from the sRNA 5' end. This is the first web server for discovering potential sRNA-mediated RNA cleavage events in plants and animals, which affords mechanistic insights into the regulatory roles of sRNAs. The StarScan web server is available at http://mirlab.sysu.edu.cn/starscan/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Leveraging the Cloud for Integrated Network Experimentation

DTIC Science & Technology

2014-03-01

kernel settings, or any of the low-level subcomponents. 3. Scalable Solutions: Businesses can build scalable solutions for their clients , ranging from...values. These values 13 can assume several distributions that include normal, Pareto , uniform, exponential and Poisson, among others [21]. Additionally, D...communication, the web client establishes a connection to the server before traffic begins to flow. Web servers do not initiate connections to clients in

Supply Chain Collaboration: Information Sharing in a Tactical Operating Environment

DTIC Science & Technology

2013-06-01

architecture, there are four tiers: Client (Web Application Clients ), Presentation (Web-Server), Processing (Application-Server), Data (Database...organization in each period. This data will be collected to analyze. i) Analyses and Validation: We will do a statistics test in this data, Pareto ...notes, outstanding deliveries, and inventory. i) Analyses and Validation: We will do a statistics test in this data, Pareto analyses and confirmation

A WebGIS-based system for analyzing and visualizing air quality data for Shanghai Municipality

NASA Astrophysics Data System (ADS)

Wang, Manyi; Liu, Chaoshun; Gao, Wei

2014-10-01

An online visual analytical system based on Java Web and WebGIS for air quality data for Shanghai Municipality was designed and implemented to quantitatively analyze and qualitatively visualize air quality data. By analyzing the architecture of WebGIS and Java Web, we firstly designed the overall scheme for system architecture, then put forward the software and hardware environment and also determined the main function modules for the system. The visual system was ultimately established with the DIV + CSS layout method combined with JSP, JavaScript, and some other computer programming languages based on the Java programming environment. Moreover, Struts, Spring, and Hibernate frameworks (SSH) were integrated in the system for the purpose of easy maintenance and expansion. To provide mapping service and spatial analysis functions, we selected ArcGIS for Server as the GIS server. We also used Oracle database and ESRI file geodatabase to store spatial data and non-spatial data in order to ensure the data security. In addition, the response data from the Web server are resampled to implement rapid visualization through the browser. The experimental successes indicate that this system can quickly respond to user's requests, and efficiently return the accurate processing results.

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

MEGANTE: A Web-Based System for Integrated Plant Genome Annotation

PubMed Central

Numa, Hisataka; Itoh, Takeshi

2014-01-01

The recent advancement of high-throughput genome sequencing technologies has resulted in a considerable increase in demands for large-scale genome annotation. While annotation is a crucial step for downstream data analyses and experimental studies, this process requires substantial expertise and knowledge of bioinformatics. Here we present MEGANTE, a web-based annotation system that makes plant genome annotation easy for researchers unfamiliar with bioinformatics. Without any complicated configuration, users can perform genomic sequence annotations simply by uploading a sequence and selecting the species to query. MEGANTE automatically runs several analysis programs and integrates the results to select the appropriate consensus exon–intron structures and to predict open reading frames (ORFs) at each locus. Functional annotation, including a similarity search against known proteins and a functional domain search, are also performed for the predicted ORFs. The resultant annotation information is visualized with a widely used genome browser, GBrowse. For ease of analysis, the results can be downloaded in Microsoft Excel format. All of the query sequences and annotation results are stored on the server side so that users can access their own data from virtually anywhere on the web. The current release of MEGANTE targets 24 plant species from the Brassicaceae, Fabaceae, Musaceae, Poaceae, Salicaceae, Solanaceae, Rosaceae and Vitaceae families, and it allows users to submit a sequence up to 10 Mb in length and to save up to 100 sequences with the annotation information on the server. The MEGANTE web service is available at https://megante.dna.affrc.go.jp/. PMID:24253915

Optimizing real-time Web-based user interfaces for observatories

NASA Astrophysics Data System (ADS)

Gibson, J. Duane; Pickering, Timothy E.; Porter, Dallan; Schaller, Skip

2008-08-01

In using common HTML/Ajax approaches for web-based data presentation and telescope control user interfaces at the MMT Observatory (MMTO), we rapidly were confronted with web browser performance issues. Much of the operational data at the MMTO is highly dynamic and is constantly changing during normal operations. Status of telescope subsystems must be displayed with minimal latency to telescope operators and other users. A major motivation of migrating toward web-based applications at the MMTO is to provide easy access to current and past observatory subsystem data for a wide variety of users on their favorite operating system through a familiar interface, their web browser. Performance issues, especially for user interfaces that control telescope subsystems, led to investigations of more efficient use of HTML/Ajax and web server technologies as well as other web-based technologies, such as Java and Flash/Flex. The results presented here focus on techniques for optimizing HTML/Ajax web applications with near real-time data display. This study indicates that direct modification of the contents or "nodeValue" attribute of text nodes is the most efficient method of updating data values displayed on a web page. Other optimization techniques are discussed for web-based applications that display highly dynamic data.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Mathew; Bowen, Brian; Coles, Dwight

The Middleware Automated Deployment Utilities consists the these three components: MAD: Utility designed to automate the deployment of java applications to multiple java application servers. The product contains a front end web utility and backend deployment scripts. MAR: Web front end to maintain and update the components inside database. MWR-Encrypt: Web utility to convert a text string to an encrypted string that is used by the Oracle Weblogic application server. The encryption is done using the built in functions if the Oracle Weblogic product and is mainly used to create an encrypted version of a database password.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

BEAM web server: a tool for structural RNA motif discovery.

PubMed

Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

2018-03-15

RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks.

PubMed

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-06-01

The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-independent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL

GSCALite: A Web Server for Gene Set Cancer Analysis.

PubMed

Liu, Chun-Jie; Hu, Fei-Fei; Xia, Mengxuan; Han, Leng; Zhang, Qiong; Guo, An-Yuan

2018-05-22

The availability of cancer genomic data makes it possible to analyze genes related to cancer. Cancer is usually the result of a set of genes and the signal of a single gene could be covered by background noise. Here, we present a web server named Gene Set Cancer Analysis (GSCALite) to analyze a set of genes in cancers with the following functional modules. (i) Differential expression in tumor vs normal, and the survival analysis; (ii) Genomic variations and their survival analysis; (iii) Gene expression associated cancer pathway activity; (iv) miRNA regulatory network for genes; (v) Drug sensitivity for genes; (vi) Normal tissue expression and eQTL for genes. GSCALite is a user-friendly web server for dynamic analysis and visualization of gene set in cancer and drug sensitivity correlation, which will be of broad utilities to cancer researchers. GSCALite is available on http://bioinfo.life.hust.edu.cn/web/GSCALite/. guoay@hust.edu.cn or zhangqiong@hust.edu.cn. Supplementary data are available at Bioinformatics online.

Reliability Information Analysis Center 1st Quarter 2007, Technical Area Task (TAT) Report

DTIC Science & Technology

2007-02-05

34* Created new SQL server database for "PC Configuration" web application. Added roles for security closed 4235 and posted application to production. "e Wrote...and ran SQL Server scripts to migrate production databases to new server . "e Created backup jobs for new SQL Server databases. "* Continued...second phase of the TENA demo. Extensive tasking was established and assigned. A TENA interface to EW Server was reaffirmed after some uncertainty about

Effect of Temporal Relationships in Associative Rule Mining for Web Log Data

PubMed Central

Mohd Khairudin, Nazli; Mustapha, Aida

2014-01-01

The advent of web-based applications and services has created such diverse and voluminous web log data stored in web servers, proxy servers, client machines, or organizational databases. This paper attempts to investigate the effect of temporal attribute in relational rule mining for web log data. We incorporated the characteristics of time in the rule mining process and analysed the effect of various temporal parameters. The rules generated from temporal relational rule mining are then compared against the rules generated from the classical rule mining approach such as the Apriori and FP-Growth algorithms. The results showed that by incorporating the temporal attribute via time, the number of rules generated is subsequently smaller but is comparable in terms of quality. PMID:24587757

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks.

PubMed

Hamed, Mohamed; Spaniol, Christian; Nazarieh, Maryam; Helms, Volkhard

2015-07-01

TFmiR is a freely available web server for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. Since the inner workings of cells rely on the correct functioning of an enormously complex system of activating and repressing interactions that can be perturbed in many ways, TFmiR helps to better elucidate cellular mechanisms at the molecular level from a network perspective. The provided topological and functional analyses promote TFmiR as a reliable systems biology tool for researchers across the life science communities. TFmiR web server is accessible through the following URL: http://service.bioinformatik.uni-saarland.de/tfmir. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization.

PubMed

Wolff, Joachim; Bhardwaj, Vivek; Nothjunge, Stephan; Richard, Gautier; Renschler, Gina; Gilsbach, Ralf; Manke, Thomas; Backofen, Rolf; Ramírez, Fidel; Grüning, Björn A

2018-06-13

Galaxy HiCExplorer is a web server that facilitates the study of the 3D conformation of chromatin by allowing Hi-C data processing, analysis and visualization. With the Galaxy HiCExplorer web server, users with little bioinformatic background can perform every step of the analysis in one workflow: mapping of the raw sequence data, creation of Hi-C contact matrices, quality assessment, correction of contact matrices and identification of topological associated domains (TADs) and A/B compartments. Users can create publication ready plots of the contact matrix, A/B compartments, and TADs on a selected genomic locus, along with additional information like gene tracks or ChIP-seq signals. Galaxy HiCExplorer is freely usable at: https://hicexplorer.usegalaxy.eu and is available as a Docker container: https://github.com/deeptools/docker-galaxy-hicexplorer.

Image-based electronic patient records for secured collaborative medical applications.

PubMed

Zhang, Jianguo; Sun, Jianyong; Yang, Yuanyuan; Liang, Chenwen; Yao, Yihong; Cai, Weihua; Jin, Jin; Zhang, Guozhen; Sun, Kun

2005-01-01

We developed a Web-based system to interactively display image-based electronic patient records (EPR) for secured intranet and Internet collaborative medical applications. The system consists of four major components: EPR DICOM gateway (EPR-GW), Image-based EPR repository server (EPR-Server), Web Server and EPR DICOM viewer (EPR-Viewer). In the EPR-GW and EPR-Viewer, the security modules of Digital Signature and Authentication are integrated to perform the security processing on the EPR data with integrity and authenticity. The privacy of EPR in data communication and exchanging is provided by SSL/TLS-based secure communication. This presentation gave a new approach to create and manage image-based EPR from actual patient records, and also presented a way to use Web technology and DICOM standard to build an open architecture for collaborative medical applications.

Improving Internet Archive Service through Proxy Cache.

ERIC Educational Resources Information Center

Yu, Hsiang-Fu; Chen, Yi-Ming; Wang, Shih-Yong; Tseng, Li-Ming

2003-01-01

Discusses file transfer protocol (FTP) servers for downloading archives (files with particular file extensions), and the change to HTTP (Hypertext transfer protocol) with increased Web use. Topics include the Archie server; proxy cache servers; and how to improve the hit rate of archives by a combination of caching and better searching mechanisms.…

Web-based access to near real-time and archived high-density time-series data: cyber infrastructure challenges & developments in the open-source Waveform Server

NASA Astrophysics Data System (ADS)

Reyes, J. C.; Vernon, F. L.; Newman, R. L.; Steidl, J. H.

2010-12-01

The Waveform Server is an interactive web-based interface to multi-station, multi-sensor and multi-channel high-density time-series data stored in Center for Seismic Studies (CSS) 3.0 schema relational databases (Newman et al., 2009). In the last twelve months, based on expanded specifications and current user feedback, both the server-side infrastructure and client-side interface have been extensively rewritten. The Python Twisted server-side code-base has been fundamentally modified to now present waveform data stored in cluster-based databases using a multi-threaded architecture, in addition to supporting the pre-existing single database model. This allows interactive web-based access to high-density (broadband @ 40Hz to strong motion @ 200Hz) waveform data that can span multiple years; the common lifetime of broadband seismic networks. The client-side interface expands on it's use of simple JSON-based AJAX queries to now incorporate a variety of User Interface (UI) improvements including standardized calendars for defining time ranges, applying on-the-fly data calibration to display SI-unit data, and increased rendering speed. This presentation will outline the various cyber infrastructure challenges we have faced while developing this application, the use-cases currently in existence, and the limitations of web-based application development.

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

ProTox: a web server for the in silico prediction of rodent oral toxicity

PubMed Central

Drwal, Malgorzata N.; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R.; Preissner, Robert

2014-01-01

Animal trials are currently the major method for determining the possible toxic effects of drug candidates and cosmetics. In silico prediction methods represent an alternative approach and aim to rationalize the preclinical drug development, thus enabling the reduction of the associated time, costs and animal experiments. Here, we present ProTox, a web server for the prediction of rodent oral toxicity. The prediction method is based on the analysis of the similarity of compounds with known median lethal doses (LD50) and incorporates the identification of toxic fragments, therefore representing a novel approach in toxicity prediction. In addition, the web server includes an indication of possible toxicity targets which is based on an in-house collection of protein–ligand-based pharmacophore models (‘toxicophores’) for targets associated with adverse drug reactions. The ProTox web server is open to all users and can be accessed without registration at: http://tox.charite.de/tox. The only requirement for the prediction is the two-dimensional structure of the input compounds. All ProTox methods have been evaluated based on a diverse external validation set and displayed strong performance (sensitivity, specificity and precision of 76, 95 and 75%, respectively) and superiority over other toxicity prediction tools, indicating their possible applicability for other compound classes. PMID:24838562

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

LocalMove: computing on-lattice fits for biopolymers

PubMed Central

Ponty, Y.; Istrate, R.; Porcelli, E.; Clote, P.

2008-01-01

Given an input Protein Data Bank file (PDB) for a protein or RNA molecule, LocalMove is a web server that determines an on-lattice representation for the input biomolecule. The web server implements a Markov Chain Monte-Carlo algorithm with simulated annealing to compute an approximate fit for either the coarse-grain model or backbone model on either the cubic or face-centered cubic lattice. LocalMove returns a PDB file as output, as well as dynamic movie of 3D images of intermediate conformations during the computation. The LocalMove server is publicly available at http://bioinformatics.bc.edu/clotelab/localmove/. PMID:18556754

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.

PubMed

Tubiana, Luca; Polles, Guido; Orlandini, Enzo; Micheletti, Cristian

2018-06-07

The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .

The new protein topology graph library web server.

PubMed

Schäfer, Tim; Scheck, Andreas; Bruneß, Daniel; May, Patrick; Koch, Ina

2016-02-01

We present a new, extended version of the Protein Topology Graph Library web server. The Protein Topology Graph Library describes the protein topology on the super-secondary structure level. It allows to compute and visualize protein ligand graphs and search for protein structural motifs. The new server features additional information on ligand binding to secondary structure elements, increased usability and an application programming interface (API) to retrieve data, allowing for an automated analysis of protein topology. The Protein Topology Graph Library server is freely available on the web at http://ptgl.uni-frankfurt.de. The website is implemented in PHP, JavaScript, PostgreSQL and Apache. It is supported by all major browsers. The VPLG software that was used to compute the protein ligand graphs and all other data in the database is available under the GNU public license 2.0 from http://vplg.sourceforge.net. tim.schaefer@bioinformatik.uni-frankfurt.de; ina.koch@bioinformatik.uni-frankfurt.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm.

PubMed

Zhou, Pei; Jin, Bowen; Li, Hao; Huang, Sheng-You

2018-05-09

Protein-peptide interactions are crucial in many cellular functions. Therefore, determining the structure of protein-peptide complexes is important for understanding the molecular mechanism of related biological processes and developing peptide drugs. HPEPDOCK is a novel web server for blind protein-peptide docking through a hierarchical algorithm. Instead of running lengthy simulations to refine peptide conformations, HPEPDOCK considers the peptide flexibility through an ensemble of peptide conformations generated by our MODPEP program. For blind global peptide docking, HPEPDOCK obtained a success rate of 33.3% in binding mode prediction on a benchmark of 57 unbound cases when the top 10 models were considered, compared to 21.1% for pepATTRACT server. HPEPDOCK also performed well in docking against homology models and obtained a success rate of 29.8% within top 10 predictions. For local peptide docking, HPEPDOCK achieved a high success rate of 72.6% on a benchmark of 62 unbound cases within top 10 predictions, compared to 45.2% for HADDOCK peptide protocol. Our HPEPDOCK server is computationally efficient and consumed an average of 29.8 mins for a global peptide docking job and 14.2 mins for a local peptide docking job. The HPEPDOCK web server is available at http://huanglab.phys.hust.edu.cn/hpepdock/.

DOE Office of Scientific and Technical Information (OSTI.GOV)

The system is developed to collect, process, store and present the information provided by the radio frequency identification (RFID) devices. The system contains three parts, the application software, the database and the web page. The application software manages multiple RFID devices, such as readers and portals, simultaneously. It communicates with the devices through application programming interface (API) provided by the device vendor. The application software converts data collected by the RFID readers and portals to readable information. It is capable of encrypting data using 256 bits advanced encryption standard (AES). The application software has a graphical user interface (GUI). Themore » GUI mimics the configurations of the nucler material storage sites or transport vehicles. The GUI gives the user and system administrator an intuitive way to read the information and/or configure the devices. The application software is capable of sending the information to a remote, dedicated and secured web and database server. Two captured screen samples, one for storage and transport, are attached. The database is constructed to handle a large number of RFID tag readers and portals. A SQL server is employed for this purpose. An XML script is used to update the database once the information is sent from the application software. The design of the web page imitates the design of the application software. The web page retrieves data from the database and presents it in different panels. The user needs a user name combined with a password to access the web page. The web page is capable of sending e-mail and text messages based on preset criteria, such as when alarm thresholds are excceeded. A captured screen sample is attached. The application software is designed to be installed on a local computer. The local computer is directly connected to the RFID devices and can be controlled locally or remotely. There are multiple local computers managing different sites or transport vehicles. The control from remote sites and information transmitted to a central database server is through secured internet. The information stored in the central databaser server is shown on the web page. The users can view the web page on the internet. A dedicated and secured web and database server (https) is used to provide information security.« less

JADDS - towards a tailored global atmospheric composition data service for CAMS forecasts and reanalysis

NASA Astrophysics Data System (ADS)

Stein, Olaf; Schultz, Martin G.; Rambadt, Michael; Saini, Rajveer; Hoffmann, Lars; Mallmann, Daniel

2017-04-01

Global model data of atmospheric composition produced by the Copernicus Atmospheric Monitoring Service (CAMS) is collected since 2010 at FZ Jülich and serves as boundary condition for use by Regional Air Quality (RAQ) modellers world-wide. RAQ models need time-resolved meteorological as well as chemical lateral boundary conditions for their individual model domains. While the meteorological data usually come from well-established global forecast systems, the chemical boundary conditions are not always well defined. In the past, many models used 'climatic' boundary conditions for the tracer concentrations, which can lead to significant concentration biases, particularly for tracers with longer lifetimes which can be transported over long distances (e.g. over the whole northern hemisphere) with the mean wind. The Copernicus approach utilizes extensive near-realtime data assimilation of atmospheric composition data observed from space which gives additional reliability to the global modelling data and is well received by the RAQ communities. An existing Web Coverage Service (WCS) for sharing these individually tailored model results is currently being re-engineered to make use of a modern, scalable database technology in order to improve performance, enhance flexibility, and allow the operation of catalogue services. The new Jülich Atmospheric Data Distributions Server (JADDS) adheres to the Web Coverage Service WCS2.0 standard as defined by the Open Geospatial Consortium OGC. This enables the user groups to flexibly define datasets they need by selecting a subset of chemical species or restricting geographical boundaries or the length of the time series. The data is made available in the form of different catalogues stored locally on our server. In addition, the Jülich OWS Interface (JOIN) provides interoperable web services allowing for easy download and visualization of datasets delivered from WCS servers via the internet. We will present the prototype JADDS server and address the major issues identified when relocating large four-dimensional datasets into a RASDAMAN raster array database. So far the RASDAMAN support for data available in netCDF format is limited with respect to metadata related to variables and axes. For community-wide accepted solutions, selected data coverages shall result in downloadable netCDF files including metadata complying with the netCDF CF Metadata Conventions standard (http://cfconventions.org/). This can be achieved by adding custom metadata elements for RASDAMAN bands (model levels) on data ingestion. Furthermore, an optimization strategy for ingestion of several TB of 4D model output data will be outlined.

Web-based network analysis and visualization using CellMaps

PubMed Central

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-01-01

Summary: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. Availability and Implementation: The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps. The client is implemented in JavaScript and the server in C and Java. Contact: jdopazo@cipf.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27296979

Web-based network analysis and visualization using CellMaps.

PubMed

Salavert, Francisco; García-Alonso, Luz; Sánchez, Rubén; Alonso, Roberto; Bleda, Marta; Medina, Ignacio; Dopazo, Joaquín

2016-10-01

: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API. The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java. jdopazo@cipf.es Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Applying World Wide Web technology to the study of patients with rare diseases.

PubMed

de Groen, P C; Barry, J A; Schaller, W J

1998-07-15

Randomized, controlled trials of sporadic diseases are rarely conducted. Recent developments in communication technology, particularly the World Wide Web, allow efficient dissemination and exchange of information. However, software for the identification of patients with a rare disease and subsequent data entry and analysis in a secure Web database are currently not available. To study cholangiocarcinoma, a rare cancer of the bile ducts, we developed a computerized disease tracing system coupled with a database accessible on the Web. The tracing system scans computerized information systems on a daily basis and forwards demographic information on patients with bile duct abnormalities to an electronic mailbox. If informed consent is given, the patient's demographic and preexisting medical information available in medical database servers are electronically forwarded to a UNIX research database. Information from further patient-physician interactions and procedures is also entered into this database. The database is equipped with a Web user interface that allows data entry from various platforms (PC-compatible, Macintosh, and UNIX workstations) anywhere inside or outside our institution. To ensure patient confidentiality and data security, the database includes all security measures required for electronic medical records. The combination of a Web-based disease tracing system and a database has broad applications, particularly for the integration of clinical research within clinical practice and for the coordination of multicenter trials.

ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.

PubMed

Zhang, Kunlin; Chang, Suhua; Cui, Sijia; Guo, Liyuan; Zhang, Liuyan; Wang, Jing

2011-07-01

Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation is to identify causal SNPs and provide profound evidence on how they affect the trait. Currently, researches are focusing on identification of candidate causal variants from the most significant SNPs of GWAS, while there is lack of support on biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed to identify disease-related pathways by analyzing the full list of SNPs from GWAS, it does not emphasize on interpreting causal SNPs. To our knowledge, so far there is no web server available to solve the challenge for GWAS data interpretation within one analytical framework. ICSNPathway is developed to identify candidate causal SNPs and their corresponding candidate causal pathways from GWAS by integrating linkage disequilibrium (LD) analysis, functional SNP annotation and PBA. ICSNPathway provides a feasible solution to bridge the gap between GWAS and disease mechanism study by generating hypothesis of SNP → gene → pathway(s). The ICSNPathway server is freely available at http://icsnpathway.psych.ac.cn/.

TBI server: a web server for predicting ion effects in RNA folding.

PubMed

Zhu, Yuhong; He, Zhaojian; Chen, Shi-Jie

2015-01-01

Metal ions play a critical role in the stabilization of RNA structures. Therefore, accurate prediction of the ion effects in RNA folding can have a far-reaching impact on our understanding of RNA structure and function. Multivalent ions, especially Mg²⁺, are essential for RNA tertiary structure formation. These ions can possibly become strongly correlated in the close vicinity of RNA surface. Most of the currently available software packages, which have widespread success in predicting ion effects in biomolecular systems, however, do not explicitly account for the ion correlation effect. Therefore, it is important to develop a software package/web server for the prediction of ion electrostatics in RNA folding by including ion correlation effects. The TBI web server http://rna.physics.missouri.edu/tbi_index.html provides predictions for the total electrostatic free energy, the different free energy components, and the mean number and the most probable distributions of the bound ions. A novel feature of the TBI server is its ability to account for ion correlation and ion distribution fluctuation effects. By accounting for the ion correlation and fluctuation effects, the TBI server is a unique online tool for computing ion-mediated electrostatic properties for given RNA structures. The results can provide important data for in-depth analysis for ion effects in RNA folding including the ion-dependence of folding stability, ion uptake in the folding process, and the interplay between the different energetic components.

Connection Map for Compounds (CMC): A Server for Combinatorial Drug Toxicity and Efficacy Analysis.

PubMed

Liu, Lei; Tsompana, Maria; Wang, Yong; Wu, Dingfeng; Zhu, Lixin; Zhu, Ruixin

2016-09-26

Drug discovery and development is a costly and time-consuming process with a high risk for failure resulting primarily from a drug's associated clinical safety and efficacy potential. Identifying and eliminating inapt candidate drugs as early as possible is an effective way for reducing unnecessary costs, but limited analytical tools are currently available for this purpose. Recent growth in the area of toxicogenomics and pharmacogenomics has provided with a vast amount of drug expression microarray data. Web servers such as CMap and LTMap have used this information to evaluate drug toxicity and mechanisms of action independently; however, their wider applicability has been limited by the lack of a combinatorial drug-safety type of analysis. Using available genome-wide drug transcriptional expression profiles, we developed the first web server for combinatorial evaluation of toxicity and efficacy of candidate drugs named "Connection Map for Compounds" (CMC). Using CMC, researchers can initially compare their query drug gene signatures with prebuilt gene profiles generated from two large-scale toxicogenomics databases, and subsequently perform a drug efficacy analysis for identification of known mechanisms of drug action or generation of new predictions. CMC provides a novel approach for drug repositioning and early evaluation in drug discovery with its unique combination of toxicity and efficacy analyses, expansibility of data and algorithms, and customization of reference gene profiles. CMC can be freely accessed at http://cadd.tongji.edu.cn/webserver/CMCbp.jsp .

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

DXplain on the Internet.

PubMed

Barnett, G O; Famiglietti, K T; Kim, R J; Hoffer, E P; Feldman, M J

1998-01-01

DXplain, a computer-based medical education, reference and decision support system has been used by thousands of physicians and medical students on stand-alone systems and over communications networks. For the past two years, we have made DXplain available over the Internet in order to provide DXplain's knowledge and analytical capabilities as a resource to other applications within Massachusetts General Hospital (MGH) and at outside institutions. We describe and provide the user experience with two different protocols through which users can access DXplain through the World Wide Web (WWW). The first allows the user to have direct interaction with all the functionality of DXplain where the MGH server controls the interaction and the mode of presentation. In the second mode, the MGH server provides the DXplain functionality as a series of services, which can be called independently by the user application program.

NUREBASE: database of nuclear hormone receptors.

PubMed

Duarte, Jorge; Perrière, Guy; Laudet, Vincent; Robinson-Rechavi, Marc

2002-01-01

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.

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

SCit: web tools for protein side chain conformation analysis.

PubMed

Gautier, R; Camproux, A-C; Tufféry, P

2004-07-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank.

PubMed

Chen, Junjie; Guo, Mingyue; Li, Shumin; Liu, Bin

2017-11-01

As one of the most important tasks in protein sequence analysis, protein remote homology detection is critical for both basic research and practical applications. Here, we present an effective web server for protein remote homology detection called ProtDec-LTR2.0 by combining ProtDec-Learning to Rank (LTR) and pseudo protein representation. Experimental results showed that the detection performance is obviously improved. The web server provides a user-friendly interface to explore the sequence and structure information of candidate proteins and find their conserved domains by launching a multiple sequence alignment tool. The web server is free and open to all users with no login requirement at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR2.0/. bliu@hit.edu.cn. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Developing Server-Side Infrastructure for Large-Scale E-Learning of Web Technology

ERIC Educational Resources Information Center

Simpkins, Neil

2010-01-01

The growth of E-business has made experience in server-side technology an increasingly important area for educators. Server-side skills are in increasing demand and recognised to be of relatively greater value than comparable client-side aspects (Ehie, 2002). In response to this, many educational organisations have developed E-business courses,…

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data.

PubMed

Ambrosini, Giovanna; Dreos, René; Kumar, Sunil; Bucher, Philipp

2016-11-18

ChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data. Here we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade. The various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/ .

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Dcs Data Viewer, an Application that Accesses ATLAS DCS Historical Data

NASA Astrophysics Data System (ADS)

Tsarouchas, C.; Schlenker, S.; Dimitrov, G.; Jahn, G.

2014-06-01

The ATLAS experiment at CERN is one of the four Large Hadron Collider experiments. The Detector Control System (DCS) of ATLAS is responsible for the supervision of the detector equipment, the reading of operational parameters, the propagation of the alarms and the archiving of important operational data in a relational database (DB). DCS Data Viewer (DDV) is an application that provides access to the ATLAS DCS historical data through a web interface. Its design is structured using a client-server architecture. The pythonic server connects to the DB and fetches the data by using optimized SQL requests. It communicates with the outside world, by accepting HTTP requests and it can be used stand alone. The client is an AJAX (Asynchronous JavaScript and XML) interactive web application developed under the Google Web Toolkit (GWT) framework. Its web interface is user friendly, platform and browser independent. The selection of metadata is done via a column-tree view or with a powerful search engine. The final visualization of the data is done using java applets or java script applications as plugins. The default output is a value-over-time chart, but other types of outputs like tables, ascii or ROOT files are supported too. Excessive access or malicious use of the database is prevented by a dedicated protection mechanism, allowing the exposure of the tool to hundreds of inexperienced users. The current configuration of the client and of the outputs can be saved in an XML file. Protection against web security attacks is foreseen and authentication constrains have been taken into account, allowing the exposure of the tool to hundreds of users world wide. Due to its flexible interface and its generic and modular approach, DDV could be easily used for other experiment control systems.

The NASA Technical Report Server

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Gottlich, Gretchen L.; Bianco, David J.; Paulson, Sharon S.; Binkley, Robert L.; Kellogg, Yvonne D.; Beaumont, Chris J.; Schmunk, Robert B.; Kurtz, Michael J.; Accomazzi, Alberto

1995-01-01

The National Aeronautics and Space Act of 1958 established NASA and charged it to "provide for the widest practicable and appropriate dissemination of information concerning its activities and the results thereof." The search for innovative methods to distribute NASA's information lead a grass-roots team to create the NASA Technical Report Server (NTRS), which uses the World Wide Web and other popular Internet-based information systems as search engines. The NTRS is an inter-center effort which provides uniform access to various distributed publication servers residing on the Internet. Users have immediate desktop access to technical publications from NASA centers and institutes. The NTRS is comprised of several units, some constructed especially for inclusion in NTRS, and others that are existing NASA publication services that NTRS reuses. This paper presents the NTRS architecture, usage metrics, and the lessons learned while implementing and maintaining the service. The NTRS is largely constructed with freely available software running on existing hardware. NTRS builds upon existing hardware and software, and the resulting additional exposure for the body of literature contained ensures that NASA's institutional knowledge base will continue to receive the widest practicable and appropriate dissemination.

Biographer: web-based editing and rendering of SBGN compliant biochemical networks

PubMed Central

Krause, Falko; Schulz, Marvin; Ripkens, Ben; Flöttmann, Max; Krantz, Marcus; Klipp, Edda; Handorf, Thomas

2013-01-01

Motivation: The rapid accumulation of knowledge in the field of Systems Biology during the past years requires advanced, but simple-to-use, methods for the visualization of information in a structured and easily comprehensible manner. Results: We have developed biographer, a web-based renderer and editor for reaction networks, which can be integrated as a library into tools dealing with network-related information. Our software enables visualizations based on the emerging standard Systems Biology Graphical Notation. It is able to import networks encoded in various formats such as SBML, SBGN-ML and jSBGN, a custom lightweight exchange format. The core package is implemented in HTML5, CSS and JavaScript and can be used within any kind of web-based project. It features interactive graph-editing tools and automatic graph layout algorithms. In addition, we provide a standalone graph editor and a web server, which contains enhanced features like web services for the import and export of models and visualizations in different formats. Availability: The biographer tool can be used at and downloaded from the web page http://biographer.biologie.hu-berlin.de/. The different software packages, including a server-indepenent version as well as a web server for Windows and Linux based systems, are available at http://code.google.com/p/biographer/ under the open-source license LGPL. Contact: edda.klipp@biologie.hu-berlin.de or handorf@physik.hu-berlin.de PMID:23574737

Comprehensive Metabolite Identification Strategy Using Multiple Two-Dimensional NMR Spectra of a Complex Mixture Implemented in the COLMARm Web Server

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bingol, Kerem; Li, Da-Wei; Zhang, Bo

Identification of metabolites in complex mixtures represents a key step in metabolomics. A new strategy is introduced, which is implemented in a new public web server, COLMARm, that permits the co-analysis of up to three 2D NMR spectra, namely 13C-1H HSQC, 1H-1H TOCSY, and 13C-1H HSQC-TOCSY for the comprehensive, accurate, and efficient performance of this task. The highly versatile and interactive nature of COLMARm permits its application to a wide range of metabolomics samples independent of the magnetic field. Database query is performed using the HSQC spectrum and the top metabolite hits are then validated against the TOCSY-type experiment(s) bymore » superimposing the expected cross-peaks on the mixture spectrum. In this way the user can directly accept or reject candidate metabolites by taking advantage of the complementary spectral information offered by these experiments and their different sensitivities. The power of COLMARm is demonstrated for a human serum sample uncovering the existence of 14 metabolites that hitherto were not identified by NMR.« less

Digging into the low molecular weight peptidome with the OligoNet web server.

PubMed

Liu, Youzhong; Forcisi, Sara; Lucio, Marianna; Harir, Mourad; Bahut, Florian; Deleris-Bou, Magali; Krieger-Weber, Sibylle; Gougeon, Régis D; Alexandre, Hervé; Schmitt-Kopplin, Philippe

2017-09-15

Bioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as "hidden treasure" of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases. The web server OligoNet responds to this challenge by attempting to decompose each individual mass into a combination of amino acids out of metabolomics datasets. It provides an additional network-based data interpretation named "Peptide degradation network" (PDN), which unravels interesting relations between annotated peptides and generates potential functional patterns. The ab initio PDN built from yeast metabolic profiling data shows a great similarity with well-known metabolic networks, and could aid biological interpretation. OligoNet allows also an easy evaluation and interpretation of annotated peptides in systems biology, and is freely accessible at https://daniellyz200608105.shinyapps.io/OligoNet/ .

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

PubMed

Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

2011-07-01

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation.

PubMed

Li, Ying; Shi, Xiaohu; Liang, Yanchun; Xie, Juan; Zhang, Yu; Ma, Qin

2017-01-21

RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms. An alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package. RNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/ .

ORBIT: an integrated environment for user-customized bioinformatics tools.

PubMed

Bellgard, M I; Hiew, H L; Hunter, A; Wiebrands, M

1999-10-01

There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as 'default' advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet. We have implemented a client/server system called ORBIT (Online Researcher's Bioinformatics Interface Tools) where individual clients can have interfaces created and customized to command-line-driven, server-side programs. Thus, Internet-based interfaces can be tailored to a user's specific bioinformatic needs. As interfaces are created on the client machine independent of the server, there can be different interfaces to the same server-side program to cater for different parameter settings. The interface customization is relatively quick (between 10 and 60 min) and all client interfaces are integrated into a single modular environment which will run on any computer platform supporting Java. The system has been developed to allow for a number of future enhancements and features. ORBIT represents an important advance in the way researchers gain access to bioinformatics tools on the Internet.

Adaptive proxy map server for efficient vector spatial data rendering

NASA Astrophysics Data System (ADS)

Sayar, Ahmet

2013-01-01

The rapid transmission of vector map data over the Internet is becoming a bottleneck of spatial data delivery and visualization in web-based environment because of increasing data amount and limited network bandwidth. In order to improve both the transmission and rendering performances of vector spatial data over the Internet, we propose a proxy map server enabling parallel vector data fetching as well as caching to improve the performance of web-based map servers in a dynamic environment. Proxy map server is placed seamlessly anywhere between the client and the final services, intercepting users' requests. It employs an efficient parallelization technique based on spatial proximity and data density in case distributed replica exists for the same spatial data. The effectiveness of the proposed technique is proved at the end of the article by the application of creating map images enriched with earthquake seismic data records.

Introduction to the Space Weather Monitoring System at KASI

NASA Astrophysics Data System (ADS)

Baek, J.; Choi, S.; Kim, Y.; Cho, K.; Bong, S.; Lee, J.; Kwak, Y.; Hwang, J.; Park, Y.; Hwang, E.

2014-05-01

We have developed the Space Weather Monitoring System (SWMS) at the Korea Astronomy and Space Science Institute (KASI). Since 2007, the system has continuously evolved into a better system. The SWMS consists of several subsystems: applications which acquire and process observational data, servers which run the applications, data storage, and display facilities which show the space weather information. The applications collect solar and space weather data from domestic and oversea sites. The collected data are converted to other format and/or visualized in real time as graphs and illustrations. We manage 3 data acquisition and processing servers, a file service server, a web server, and 3 sets of storage systems. We have developed 30 applications for a variety of data, and the volume of data is about 5.5 GB per day. We provide our customers with space weather contents displayed at the Space Weather Monitoring Lab (SWML) using web services.

DNA barcode goes two-dimensions: DNA QR code web server.

PubMed

Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition.

PubMed

Chen, Wei; Lei, Tian-Yu; Jin, Dian-Chuan; Lin, Hao; Chou, Kuo-Chen

2014-07-01

The pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition (PseKNC), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides. Therefore, the PseKNC approach may hold very high potential for enhancing the power in dealing with many problems in computational genomics and genome sequence analysis. However, dealing with different DNA or RNA problems may need different kinds of PseKNC. Here, we present a flexible and user-friendly web server for PseKNC (at http://lin.uestc.edu.cn/pseknc/default.aspx) by which users can easily generate many different modes of PseKNC according to their need by selecting various parameters and physicochemical properties. Furthermore, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the current web server to generate their desired PseKNC without the need to follow the complicated mathematical equations, which are presented in this article just for the integrity of PseKNC formulation and its development. It is anticipated that the PseKNC web server will become a very useful tool in computational genomics and genome sequence analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

ProTox: a web server for the in silico prediction of rodent oral toxicity.

PubMed

Drwal, Malgorzata N; Banerjee, Priyanka; Dunkel, Mathias; Wettig, Martin R; Preissner, Robert

2014-07-01

Animal trials are currently the major method for determining the possible toxic effects of drug candidates and cosmetics. In silico prediction methods represent an alternative approach and aim to rationalize the preclinical drug development, thus enabling the reduction of the associated time, costs and animal experiments. Here, we present ProTox, a web server for the prediction of rodent oral toxicity. The prediction method is based on the analysis of the similarity of compounds with known median lethal doses (LD50) and incorporates the identification of toxic fragments, therefore representing a novel approach in toxicity prediction. In addition, the web server includes an indication of possible toxicity targets which is based on an in-house collection of protein-ligand-based pharmacophore models ('toxicophores') for targets associated with adverse drug reactions. The ProTox web server is open to all users and can be accessed without registration at: http://tox.charite.de/tox. The only requirement for the prediction is the two-dimensional structure of the input compounds. All ProTox methods have been evaluated based on a diverse external validation set and displayed strong performance (sensitivity, specificity and precision of 76, 95 and 75%, respectively) and superiority over other toxicity prediction tools, indicating their possible applicability for other compound classes. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Web-based Electronic Sharing and RE-allocation of Assets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leverett, Dave; Miller, Robert A.; Berlin, Gary J.

2002-09-09

The Electronic Asses Sharing Program is a web-based application that provides the capability for complex-wide sharing and reallocation of assets that are excess, under utilized, or un-utilized. through a web-based fron-end and supporting has database with a search engine, users can search for assets that they need, search for assets needed by others, enter assets they need, and enter assets they have available for reallocation. In addition, entire listings of available assets and needed assets can be viewed. The application is written in Java, the hash database and search engine are in Object-oriented Java Database Management (OJDBM). The application willmore » be hosted on an SRS-managed server outside the Firewall and access will be controlled via a protected realm. An example of the application can be viewed at the followinig (temporary) URL: http://idgdev.srs.gov/servlet/srs.weshare.WeShare« less

Web-based training: a new paradigm in computer-assisted instruction in medicine.

PubMed

Haag, M; Maylein, L; Leven, F J; Tönshoff, B; Haux, R

1999-01-01

Computer-assisted instruction (CAI) programs based on internet technologies, especially on the world wide web (WWW), provide new opportunities in medical education. The aim of this paper is to examine different aspects of such programs, which we call 'web-based training (WBT) programs', and to differentiate them from conventional CAI programs. First, we will distinguish five different interaction types: presentation; browsing; tutorial dialogue; drill and practice; and simulation. In contrast to conventional CAI, there are four architectural types of WBT programs: client-based; remote data and knowledge; distributed teaching; and server-based. We will discuss the implications of the different architectures for developing WBT software. WBT programs have to meet other requirements than conventional CAI programs. The most important tools and programming languages for developing WBT programs will be listed and assigned to the architecture types. For the future, we expect a trend from conventional CAI towards WBT programs.

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

PubMed Central

2014-01-01

Background The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. Results Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. Conclusion Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment. PMID:25521245

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

PubMed Central

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

2017-01-01

Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein–protein and protein–DNA benchmarks and performed better than template-based modeling on the three protein–RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

A Web Server for MACCS Magnetometer Data

NASA Technical Reports Server (NTRS)

Engebretson, Mark J.

1998-01-01

NASA Grant NAG5-3719 was provided to Augsburg College to support the development of a web server for the Magnetometer Array for Cusp and Cleft Studies (MACCS), a two-dimensional array of fluxgate magnetometers located at cusp latitudes in Arctic Canada. MACCS was developed as part of the National Science Foundation's GEM (Geospace Environment Modeling) Program, which was designed in part to complement NASA's Global Geospace Science programs during the decade of the 1990s. This report describes the successful use of these grant funds to support a working web page that provides both daily plots and file access to any user accessing the worldwide web. The MACCS home page can be accessed at http://space.augsburg.edu/space/MaccsHome.html.

The Next Linear Collider Program

Science.gov Websites

Navbar Other Address Books: Laboratory Phone/Email Web Directory SLAC SLAC Phonebook Entire SLAC Web FNAL Telephone Directory Fermilab Search LLNL Phone Book LLNL Web Servers LBNL Directory Services Web Search: A-Z Index KEK E-mail Database Research Projects NLC Website Search: Entire SLAC Web | Help

Design and Implementation of an Architectural Framework for Web Portals in a Ubiquitous Pervasive Environment

PubMed Central

Raza, Muhammad Taqi; Yoo, Seung-Wha; Kim, Ki-Hyung; Joo, Seong-Soon; Jeong, Wun-Cheol

2009-01-01

Web Portals function as a single point of access to information on the World Wide Web (WWW). The web portal always contacts the portal’s gateway for the information flow that causes network traffic over the Internet. Moreover, it provides real time/dynamic access to the stored information, but not access to the real time information. This inherent functionality of web portals limits their role for resource constrained digital devices in the Ubiquitous era (U-era). This paper presents a framework for the web portal in the U-era. We have introduced the concept of Local Regions in the proposed framework, so that the local queries could be solved locally rather than having to route them over the Internet. Moreover, our framework enables one-to-one device communication for real time information flow. To provide an in-depth analysis, firstly, we provide an analytical model for query processing at the servers for our framework-oriented web portal. At the end, we have deployed a testbed, as one of the world’s largest IP based wireless sensor networks testbed, and real time measurements are observed that prove the efficacy and workability of the proposed framework. PMID:22346693

Design and implementation of an architectural framework for web portals in a ubiquitous pervasive environment.

PubMed

Raza, Muhammad Taqi; Yoo, Seung-Wha; Kim, Ki-Hyung; Joo, Seong-Soon; Jeong, Wun-Cheol

2009-01-01

Web Portals function as a single point of access to information on the World Wide Web (WWW). The web portal always contacts the portal's gateway for the information flow that causes network traffic over the Internet. Moreover, it provides real time/dynamic access to the stored information, but not access to the real time information. This inherent functionality of web portals limits their role for resource constrained digital devices in the Ubiquitous era (U-era). This paper presents a framework for the web portal in the U-era. We have introduced the concept of Local Regions in the proposed framework, so that the local queries could be solved locally rather than having to route them over the Internet. Moreover, our framework enables one-to-one device communication for real time information flow. To provide an in-depth analysis, firstly, we provide an analytical model for query processing at the servers for our framework-oriented web portal. At the end, we have deployed a testbed, as one of the world's largest IP based wireless sensor networks testbed, and real time measurements are observed that prove the efficacy and workability of the proposed framework.

The ABCs of PDFs.

ERIC Educational Resources Information Center

Adler, Steve

2000-01-01

Explains the use of Adobe Acrobat's Portable Document Format (PDF) for school Web sites and Intranets. Explains the PDF workflow; components for Web-based PDF delivery, including the Web server, preparing content of the PDF files, and the browser; incorporating PDFs into the Web site; incorporating multimedia; and software. (LRW)

Wide Area Information Servers: An Executive Information System for Unstructured Files.

ERIC Educational Resources Information Center

Kahle, Brewster; And Others

1992-01-01

Describes the Wide Area Information Servers (WAIS) system, an integrated information retrieval system for corporate end users. Discussion covers general characteristics of the system, search techniques, protocol development, user interfaces, servers, selective dissemination of information, nontextual data, access to other servers, and description…

Global ISR: Toward a Comprehensive Defense Against Unauthorized Code Execution

DTIC Science & Technology

2010-10-01

implementation using two of the most popular open- source servers: the Apache web server, and the MySQL database server. For Apache, we measure the effect that...utility ab. T o ta l T im e ( s e c ) 0 500 1000 1500 2000 2500 3000 Native Null ISR ISR−MP Fig. 3. The MySQL test-insert bench- mark measures...various SQL operations. The figure draws total execution time as reported by the benchmark utility. Finally, we benchmarked a MySQL database server using

1995 Joseph E. Whitley, MD, Award. A World Wide Web gateway to the radiologic learning file.

PubMed

Channin, D S

1995-12-01

Computer networks in general, and the Internet specifically, are changing the way information is manipulated in the world at large and in radiology. The goal of this project was to develop a computer system in which images from the Radiologic Learning File, available previously only via a single-user laser disc, are made available over a generic, high-availability computer network to many potential users simultaneously. Using a networked workstation in our laboratory and freely available distributed hypertext software, we established a World Wide Web (WWW) information server for radiology. Images from the Radiologic Learning File are requested through the WWW client software, digitized from a single laser disc containing the entire teaching file and then transmitted over the network to the client. The text accompanying each image is incorporated into the transmitted document. The Radiologic Learning File is now on-line, and requests to view the cases result in the delivery of the text and images. Image digitization via a frame grabber takes 1/30th of a second. Conversion of the image to a standard computer graphic format takes 45-60 sec. Text and image transmission speed on a local area network varies between 200 and 400 kilobytes (KB) per second depending on the network load. We have made images from a laser disc of the Radiologic Learning File available through an Internet-based hypertext server. The images previously available through a single-user system located in a remote section of our department are now ubiquitously available throughout our department via the department's computer network. We have thus converted a single-user, limited functionality system into a multiuser, widely available resource.

ClusterControl: a web interface for distributing and monitoring bioinformatics applications on a Linux cluster.

PubMed

Stocker, Gernot; Rieder, Dietmar; Trajanoski, Zlatko

2004-03-22

ClusterControl is a web interface to simplify distributing and monitoring bioinformatics applications on Linux cluster systems. We have developed a modular concept that enables integration of command line oriented program into the application framework of ClusterControl. The systems facilitate integration of different applications accessed through one interface and executed on a distributed cluster system. The package is based on freely available technologies like Apache as web server, PHP as server-side scripting language and OpenPBS as queuing system and is available free of charge for academic and non-profit institutions. http://genome.tugraz.at/Software/ClusterControl

SCit: web tools for protein side chain conformation analysis

PubMed Central

Gautier, R.; Camproux, A.-C.; Tufféry, P.

2004-01-01

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

CircularLogo: A lightweight web application to visualize intra-motif dependencies.

PubMed

Ye, Zhenqing; Ma, Tao; Kalmbach, Michael T; Dasari, Surendra; Kocher, Jean-Pierre A; Wang, Liguo

2017-05-22

The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies. Applying CircularLogo to HNF6 binding sites and tRNA sequences demonstrated its ability to show intra-motif dependencies and intuitively reveal biomolecular structure. CircularLogo is implemented in JavaScript and Python based on the Django web framework. The program's source code and user's manual are freely available at http://circularlogo.sourceforge.net . CircularLogo web server can be accessed from http://bioinformaticstools.mayo.edu/circularlogo/index.html . CircularLogo is an innovative web application that is specifically designed to visualize and interactively explore intra-motif dependencies.

Web-Based Course Management and Web Services

ERIC Educational Resources Information Center

Mandal, Chittaranjan; Sinha, Vijay Luxmi; Reade, Christopher M. P.

2004-01-01

The architecture of a web-based course management tool that has been developed at IIT [Indian Institute of Technology], Kharagpur and which manages the submission of assignments is discussed. Both the distributed architecture used for data storage and the client-server architecture supporting the web interface are described. Further developments…

WEB-BASED MODELING OF A FERTILIZER SOLUTION SPILL IN THE OHIO RIVER

EPA Science Inventory

Environmental computer models are usually desktop models. Some web-enabled models are beginning to appear where the user can use a browser to run the models on a central web server. Several issues arise when a desktop model is transferred to a web architecture. This paper discuss...

Development of wide area environment accelerator operation and diagnostics method

NASA Astrophysics Data System (ADS)

Uchiyama, Akito; Furukawa, Kazuro

2015-08-01

Remote operation and diagnostic systems for particle accelerators have been developed for beam operation and maintenance in various situations. Even though fully remote experiments are not necessary, the remote diagnosis and maintenance of the accelerator is required. Considering remote-operation operator interfaces (OPIs), the use of standard protocols such as the hypertext transfer protocol (HTTP) is advantageous, because system-dependent protocols are unnecessary between the remote client and the on-site server. Here, we have developed a client system based on WebSocket, which is a new protocol provided by the Internet Engineering Task Force for Web-based systems, as a next-generation Web-based OPI using the Experimental Physics and Industrial Control System Channel Access protocol. As a result of this implementation, WebSocket-based client systems have become available for remote operation. Also, as regards practical application, the remote operation of an accelerator via a wide area network (WAN) faces a number of challenges, e.g., the accelerator has both experimental device and radiation generator characteristics. Any error in remote control system operation could result in an immediate breakdown. Therefore, we propose the implementation of an operator intervention system for remote accelerator diagnostics and support that can obviate any differences between the local control room and remote locations. Here, remote-operation Web-based OPIs, which resolve security issues, are developed.

RaptorX-Property: a web server for protein structure property prediction.

PubMed

Wang, Sheng; Li, Wei; Liu, Shiwang; Xu, Jinbo

2016-07-08

RaptorX Property (http://raptorx2.uchicago.edu/StructurePropertyPred/predict/) is a web server predicting structure property of a protein sequence without using any templates. It outperforms other servers, especially for proteins without close homologs in PDB or with very sparse sequence profile (i.e. carries little evolutionary information). This server employs a powerful in-house deep learning model DeepCNF (Deep Convolutional Neural Fields) to predict secondary structure (SS), solvent accessibility (ACC) and disorder regions (DISO). DeepCNF not only models complex sequence-structure relationship by a deep hierarchical architecture, but also interdependency between adjacent property labels. Our experimental results show that, tested on CASP10, CASP11 and the other benchmarks, this server can obtain ∼84% Q3 accuracy for 3-state SS, ∼72% Q8 accuracy for 8-state SS, ∼66% Q3 accuracy for 3-state solvent accessibility, and ∼0.89 area under the ROC curve (AUC) for disorder prediction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrated technologies for solid waste bin monitoring system.

PubMed

Arebey, Maher; Hannan, M A; Basri, Hassan; Begum, R A; Abdullah, Huda

2011-06-01

The integration of communication technologies such as radio frequency identification (RFID), global positioning system (GPS), general packet radio system (GPRS), and geographic information system (GIS) with a camera are constructed for solid waste monitoring system. The aim is to improve the way of responding to customer's inquiry and emergency cases and estimate the solid waste amount without any involvement of the truck driver. The proposed system consists of RFID tag mounted on the bin, RFID reader as in truck, GPRS/GSM as web server, and GIS as map server, database server, and control server. The tracking devices mounted in the trucks collect location information in real time via the GPS. This information is transferred continuously through GPRS to a central database. The users are able to view the current location of each truck in the collection stage via a web-based application and thereby manage the fleet. The trucks positions and trash bin information are displayed on a digital map, which is made available by a map server. Thus, the solid waste of the bin and the truck are being monitored using the developed system.

CCTOP: a Consensus Constrained TOPology prediction web server.

PubMed

Dobson, László; Reményi, István; Tusnády, Gábor E

2015-07-01

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Molecular structure input on the web.

PubMed

Ertl, Peter

2010-02-02

A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

High-Performance Tiled WMS and KML Web Server

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2007-01-01

This software is an Apache 2.0 module implementing a high-performance map server to support interactive map viewers and virtual planet client software. It can be used in applications that require access to very-high-resolution geolocated images, such as GIS, virtual planet applications, and flight simulators. It serves Web Map Service (WMS) requests that comply with a given request grid from an existing tile dataset. It also generates the KML super-overlay configuration files required to access the WMS image tiles.

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

PubMed Central

Metsalu, Tauno; Vilo, Jaak

2015-01-01

The Principal Component Analysis (PCA) is a widely used method of reducing the dimensionality of high-dimensional data, often followed by visualizing two of the components on the scatterplot. Although widely used, the method is lacking an easy-to-use web interface that scientists with little programming skills could use to make plots of their own data. The same applies to creating heatmaps: it is possible to add conditional formatting for Excel cells to show colored heatmaps, but for more advanced features such as clustering and experimental annotations, more sophisticated analysis tools have to be used. We present a web tool called ClustVis that aims to have an intuitive user interface. Users can upload data from a simple delimited text file that can be created in a spreadsheet program. It is possible to modify data processing methods and the final appearance of the PCA and heatmap plots by using drop-down menus, text boxes, sliders etc. Appropriate defaults are given to reduce the time needed by the user to specify input parameters. As an output, users can download PCA plot and heatmap in one of the preferred file formats. This web server is freely available at http://biit.cs.ut.ee/clustvis/. PMID:25969447

GLobal Integrated Design Environment (GLIDE): A Concurrent Engineering Application

NASA Technical Reports Server (NTRS)

McGuire, Melissa L.; Kunkel, Matthew R.; Smith, David A.

2010-01-01

The GLobal Integrated Design Environment (GLIDE) is a client-server software application purpose-built to mitigate issues associated with real time data sharing in concurrent engineering environments and to facilitate discipline-to-discipline interaction between multiple engineers and researchers. GLIDE is implemented in multiple programming languages utilizing standardized web protocols to enable secure parameter data sharing between engineers and researchers across the Internet in closed and/or widely distributed working environments. A well defined, HyperText Transfer Protocol (HTTP) based Application Programming Interface (API) to the GLIDE client/server environment enables users to interact with GLIDE, and each other, within common and familiar tools. One such common tool, Microsoft Excel (Microsoft Corporation), paired with its add-in API for GLIDE, is discussed in this paper. The top-level examples given demonstrate how this interface improves the efficiency of the design process of a concurrent engineering study while reducing potential errors associated with manually sharing information between study participants.

Image Reference Database in Teleradiology: Migrating to WWW

NASA Astrophysics Data System (ADS)

Pasqui, Valdo

The paper presents a multimedia Image Reference Data Base (IRDB) used in Teleradiology. The application was developed at the University of Florence in the framework of the European Community TELEMED Project. TELEMED overall goals and IRDB requirements are outlined and the resulting architecture is described. IRDB is a multisite database containing radiological images, selected because their scientific interest, and their related information. The architecture consists of a set of IRDB Installations which are accessed from Viewing Stations (VS) located at different medical sites. The interaction between VS and IRDB Installations follows the client-server paradigm and uses an OSI level-7 protocol, named Telemed Communication Language. After reviewing Florence prototype implementation and experimentation, IRDB migration to World Wide Web (WWW) is discussed. A possible scenery to implement IRDB on the basis of WWW model is depicted in order to exploit WWW servers and browsers capabilities. Finally, the advantages of this conversion are outlined.

The Internet for Librarians

NASA Astrophysics Data System (ADS)

Grothkopf, U.

Librarianship is currently undergoing major changes. New information sources, accessible via the "network of networks", the Internet, offer opportunities which were previously unknown, but which require continuous ongoing learning. The Internet seems to be organized badly or not at all. The poor appearance might lead to an underestimation of its value. In the following, an introduction to the main functions will be given in order to facilitate understanding and use of the Internet. E-Mail, FTP (File Transfer Protocol) and Telnet will be covered, as well as Mailing lists, Newsgroups and the tools Archie, Gopher, Veronica, WAIS (Wide Area Information Server) and the World Wide Web (WWW). Examples will be given to show possible applications for library services.

Security Proof for Password Authentication in TLS-Verifier-based Three-Party Group Diffie-Hellman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chevassut, Olivier; Milner, Joseph; Pointcheval, David

2008-04-21

The internet has grown greatly in the past decade, by some numbers exceeding 47 million active web sites and a total aggregate exceeding100 million web sites. What is common practice today on the Internet is that servers have public keys, but clients are largely authenticated via short passwords. Protecting these passwords by not storing them in the clear on institutions's servers has become a priority. This paper develops password-based ciphersuites for the Transport Layer Security (TLS) protocol that are: (1) resistant to server compromise; (2) provably secure; (3) believed to be free from patent and licensing restrictions based on anmore » analysis of relevant patents in the area.« less

Analysis of web-related threats in ten years of logs from a scientific portal

NASA Astrophysics Data System (ADS)

Santos, Rafael D. C.; Grégio, André R. A.; Raddick, Jordan; Vattki, Vamsi; Szalay, Alex

2012-06-01

SkyServer is an Internet portal to data from the Sloan Digital Sky Survey, the largest online archive of astronomy data in the world. provides free access to hundreds of millions of celestial objects for science, education and outreach purposes. Logs of accesses to SkyServer comprise around 930 million hits, 140 million web services accesses and 170 million SQL submitted queries, collected over the past 10 years. These logs also contain indications of compromise attempts on the servers. In this paper, we show some threats that were detected in ten years of stored logs, and compare them with known threats in those years. Also, we present an analysis of the evolution of those threats over these years.

WebGeocalc and Cosmographia: Modern Tools to Access SPICE Archives

NASA Astrophysics Data System (ADS)

Semenov, B. V.; Acton, C. H.; Bachman, N. J.; Ferguson, E. W.; Rose, M. E.; Wright, E. D.

2017-06-01

The WebGeocalc (WGC) web client-server tool and the SPICE-enhanced Cosmographia visualization program are two new ways for accessing space mission geometry data provided in the PDS SPICE kernel archives and by mission operational SPICE kernel sets.

[A web-based biomedical image mosaicing system].

PubMed

Zhang, Meng; Yan, Zhuang-zhi; Pan, Zhi-jun; Shao, Shi-jie

2006-11-01

This paper describes a web service for biomedical image mosaicing. A web site based on CGI (Common Gateway Interface) is implemented. The system is based on Browser/Server model and is tested in www. Finally implementation examples and experiment results are provided.

Healthcare

MedlinePlus

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Delivering Electronic Resources with Web OPACs and Other Web-based Tools: Needs of Reference Librarians.

ERIC Educational Resources Information Center

Bordeianu, Sever; Carter, Christina E.; Dennis, Nancy K.

2000-01-01

Describes Web-based online public access catalogs (Web OPACs) and other Web-based tools as gateway methods for providing access to library collections. Addresses solutions for overcoming barriers to information, such as through the implementation of proxy servers and other authentication tools for remote users. (Contains 18 references.)…

Remote vibration monitoring system using wireless internet data transfer

NASA Astrophysics Data System (ADS)

Lemke, John

2000-06-01

Vibrations from construction activities can affect infrastructure projects in several ways. Within the general vicinity of a construction site, vibrations can result in damage to existing structures, disturbance to people, damage to sensitive machinery, and degraded performance of precision instrumentation or motion sensitive equipment. Current practice for monitoring vibrations in the vicinity of construction sites commonly consists of measuring free field or structural motions using velocity transducers connected to a portable data acquisition unit via cables. This paper describes an innovative way to collect, process, transmit, and analyze vibration measurements obtained at construction sites. The system described measures vibration at the sensor location, performs necessary signal conditioning and digitization, and sends data to a Web server using wireless data transmission and Internet protocols. A Servlet program running on the Web server accepts the transmitted data and incorporates it into a project database. Two-way interaction between the Web-client and the Web server is accomplished through the use of a Servlet program and a Java Applet running inside a browser located on the Web client's computer. Advantages of this system over conventional vibration data logging systems include continuous unattended monitoring, reduced costs associated with field data collection, instant access to data files and graphs by project team members, and the ability to remotely modify data sampling schemes.

Mobile cloud-computing-based healthcare service by noncontact ECG monitoring.

PubMed

Fong, Ee-May; Chung, Wan-Young

2013-12-02

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service.

A new reference implementation of the PSICQUIC web service.

PubMed

del-Toro, Noemi; Dumousseau, Marine; Orchard, Sandra; Jimenez, Rafael C; Galeota, Eugenia; Launay, Guillaume; Goll, Johannes; Breuer, Karin; Ono, Keiichiro; Salwinski, Lukasz; Hermjakob, Henning

2013-07-01

The Proteomics Standard Initiative Common QUery InterfaCe (PSICQUIC) specification was created by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI) to enable computational access to molecular-interaction data resources by means of a standard Web Service and query language. Currently providing >150 million binary interaction evidences from 28 servers globally, the PSICQUIC interface allows the concurrent search of multiple molecular-interaction information resources using a single query. Here, we present an extension of the PSICQUIC specification (version 1.3), which has been released to be compliant with the enhanced standards in molecular interactions. The new release also includes a new reference implementation of the PSICQUIC server available to the data providers. It offers augmented web service capabilities and improves the user experience. PSICQUIC has been running for almost 5 years, with a user base growing from only 4 data providers to 28 (April 2013) allowing access to 151 310 109 binary interactions. The power of this web service is shown in PSICQUIC View web application, an example of how to simultaneously query, browse and download results from the different PSICQUIC servers. This application is free and open to all users with no login requirement (http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml).

Systematic plan of building Web geographic information system based on ActiveX control

NASA Astrophysics Data System (ADS)

Zhang, Xia; Li, Deren; Zhu, Xinyan; Chen, Nengcheng

2003-03-01

A systematic plan of building Web Geographic Information System (WebGIS) using ActiveX technology is proposed in this paper. In the proposed plan, ActiveX control technology is adopted in building client-side application, and two different schemas are introduced to implement communication between controls in users¡ browser and middle application server. One is based on Distribute Component Object Model (DCOM), the other is based on socket. In the former schema, middle service application is developed as a DCOM object that communicates with ActiveX control through Object Remote Procedure Call (ORPC) and accesses data in GIS Data Server through Open Database Connectivity (ODBC). In the latter, middle service application is developed using Java language. It communicates with ActiveX control through socket based on TCP/IP and accesses data in GIS Data Server through Java Database Connectivity (JDBC). The first one is usually developed using C/C++, and it is difficult to develop and deploy. The second one is relatively easy to develop, but its performance of data transfer relies on Web bandwidth. A sample application is developed using the latter schema. It is proved that the performance of the sample application is better than that of some other WebGIS applications in some degree.

Mobile Cloud-Computing-Based Healthcare Service by Noncontact ECG Monitoring

PubMed Central

Fong, Ee-May; Chung, Wan-Young

2013-01-01

Noncontact electrocardiogram (ECG) measurement technique has gained popularity these days owing to its noninvasive features and convenience in daily life use. This paper presents mobile cloud computing for a healthcare system where a noncontact ECG measurement method is employed to capture biomedical signals from users. Healthcare service is provided to continuously collect biomedical signals from multiple locations. To observe and analyze the ECG signals in real time, a mobile device is used as a mobile monitoring terminal. In addition, a personalized healthcare assistant is installed on the mobile device; several healthcare features such as health status summaries, medication QR code scanning, and reminders are integrated into the mobile application. Health data are being synchronized into the healthcare cloud computing service (Web server system and Web server dataset) to ensure a seamless healthcare monitoring system and anytime and anywhere coverage of network connection is available. Together with a Web page application, medical data are easily accessed by medical professionals or family members. Web page performance evaluation was conducted to ensure minimal Web server latency. The system demonstrates better availability of off-site and up-to-the-minute patient data, which can help detect health problems early and keep elderly patients out of the emergency room, thus providing a better and more comprehensive healthcare cloud computing service. PMID:24316562

minepath.org: a free interactive pathway analysis web server.

PubMed

Koumakis, Lefteris; Roussos, Panos; Potamias, George

2017-07-03

( www.minepath.org ) is a web-based platform that elaborates on, and radically extends the identification of differentially expressed sub-paths in molecular pathways. Besides the network topology, the underlying MinePath algorithmic processes exploit exact gene-gene molecular relationships (e.g. activation, inhibition) and are able to identify differentially expressed pathway parts. Each pathway is decomposed into all its constituent sub-paths, which in turn are matched with corresponding gene expression profiles. The highly ranked, and phenotype inclined sub-paths are kept. Apart from the pathway analysis algorithm, the fundamental innovation of the MinePath web-server concerns its advanced visualization and interactive capabilities. To our knowledge, this is the first pathway analysis server that introduces and offers visualization of the underlying and active pathway regulatory mechanisms instead of genes. Other features include live interaction, immediate visualization of functional sub-paths per phenotype and dynamic linked annotations for the engaged genes and molecular relations. The user can download not only the results but also the corresponding web viewer framework of the performed analysis. This feature provides the flexibility to immediately publish results without publishing source/expression data, and get all the functionality of a web based pathway analysis viewer. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemozart: a web-based 3D molecular structure editor and visualizer platform.

PubMed

Mohebifar, Mohamad; Sajadi, Fatemehsadat

2015-01-01

Chemozart is a 3D Molecule editor and visualizer built on top of native web components. It offers an easy to access service, user-friendly graphical interface and modular design. It is a client centric web application which communicates with the server via a representational state transfer style web service. Both client-side and server-side application are written in JavaScript. A combination of JavaScript and HTML is used to draw three-dimensional structures of molecules. With the help of WebGL, three-dimensional visualization tool is provided. Using CSS3 and HTML5, a user-friendly interface is composed. More than 30 packages are used to compose this application which adds enough flexibility to it to be extended. Molecule structures can be drawn on all types of platforms and is compatible with mobile devices. No installation is required in order to use this application and it can be accessed through the internet. This application can be extended on both server-side and client-side by implementing modules in JavaScript. Molecular compounds are drawn on the HTML5 Canvas element using WebGL context. Chemozart is a chemical platform which is powerful, flexible, and easy to access. It provides an online web-based tool used for chemical visualization along with result oriented optimization for cloud based API (application programming interface). JavaScript libraries which allow creation of web pages containing interactive three-dimensional molecular structures has also been made available. The application has been released under Apache 2 License and is available from the project website https://chemozart.com.

Hazardous Drugs

MedlinePlus

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Winter Weather

MedlinePlus

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SITEHOUND-web: a server for ligand binding site identification in protein structures.

PubMed

Hernandez, Marylens; Ghersi, Dario; Sanchez, Roberto

2009-07-01

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.

A Powerful, Cost Effective, Web Based Engineering Solution Supporting Conjunction Detection and Visual Analysis

NASA Astrophysics Data System (ADS)

Novak, Daniel M.; Biamonti, Davide; Gross, Jeremy; Milnes, Martin

2013-08-01

An innovative and visually appealing tool is presented for efficient all-vs-all conjunction analysis on a large catalogue of objects. The conjunction detection uses a nearest neighbour search algorithm, based on spatial binning and identification of pairs of objects in adjacent bins. This results in the fastest all vs all filtering the authors are aware of. The tool is constructed on a server-client architecture, where the server broadcasts to the client the conjunction data and ephemerides, while the client supports the user interface through a modern browser, without plug-in. In order to make the tool flexible and maintainable, Java software technologies were used on the server side, including Spring, Camel, ActiveMQ and CometD. The user interface and visualisation are based on the latest web technologies: HTML5, WebGL, THREE.js. Importance has been given on the ergonomics and visual appeal of the software. In fact certain design concepts have been borrowed from the gaming industry.

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

PubMed

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Web-based system for surgical planning and simulation

NASA Astrophysics Data System (ADS)

Eldeib, Ayman M.; Ahmed, Mohamed N.; Farag, Aly A.; Sites, C. B.

1998-10-01

The growing scientific knowledge and rapid progress in medical imaging techniques has led to an increasing demand for better and more efficient methods of remote access to high-performance computer facilities. This paper introduces a web-based telemedicine project that provides interactive tools for surgical simulation and planning. The presented approach makes use of client-server architecture based on new internet technology where clients use an ordinary web browser to view, send, receive and manipulate patients' medical records while the server uses the supercomputer facility to generate online semi-automatic segmentation, 3D visualization, surgical simulation/planning and neuroendoscopic procedures navigation. The supercomputer (SGI ONYX 1000) is located at the Computer Vision and Image Processing Lab, University of Louisville, Kentucky. This system is under development in cooperation with the Department of Neurological Surgery, Alliant Health Systems, Louisville, Kentucky. The server is connected via a network to the Picture Archiving and Communication System at Alliant Health Systems through a DICOM standard interface that enables authorized clients to access patients' images from different medical modalities.

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.

PubMed

Lowe, Todd M; Chan, Patricia P

2016-07-08

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Connection Admission Control Method for Web Server Systems

NASA Astrophysics Data System (ADS)

Satake, Shinsuke; Inai, Hiroshi; Saito, Tomoya; Arai, Tsuyoshi

Most browsers establish multiple connections and download files in parallel to reduce the response time. On the other hand, a web server limits the total number of connections to prevent from being overloaded. That could decrease the response time, but would increase the loss probability, the probability of which a newly arriving client is rejected. This paper proposes a connection admission control method which accepts only one connection from a newly arriving client when the number of connections exceeds a threshold, but accepts new multiple connections when the number of connections is less than the threshold. Our method is aimed at reducing the response time by allowing as many clients as possible to establish multiple connections, and also reducing the loss probability. In order to reduce spending time to examine an adequate threshold for web server administrators, we introduce a procedure which approximately calculates the loss probability under a condition that the threshold is given. Via simulation, we validate the approximation and show effectiveness of the admission control.

MetCCS predictor: a web server for predicting collision cross-section values of metabolites in ion mobility-mass spectrometry based metabolomics.

PubMed

Zhou, Zhiwei; Xiong, Xin; Zhu, Zheng-Jiang

2017-07-15

In metabolomics, rigorous structural identification of metabolites presents a challenge for bioinformatics. The use of collision cross-section (CCS) values of metabolites derived from ion mobility-mass spectrometry effectively increases the confidence of metabolite identification, but this technique suffers from the limit number of available CCS values. Currently, there is no software available for rapidly generating the metabolites' CCS values. Here, we developed the first web server, namely, MetCCS Predictor, for predicting CCS values. It can predict the CCS values of metabolites using molecular descriptors within a few seconds. Common users with limited background on bioinformatics can benefit from this software and effectively improve the metabolite identification in metabolomics. The web server is freely available at: http://www.metabolomics-shanghai.org/MetCCS/ . jiangzhu@sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Chemotext: A Publicly Available Web Server for Mining Drug-Target-Disease Relationships in PubMed.

PubMed

Capuzzi, Stephen J; Thornton, Thomas E; Liu, Kammy; Baker, Nancy; Lam, Wai In; O'Banion, Colin P; Muratov, Eugene N; Pozefsky, Diane; Tropsha, Alexander

2018-02-26

Elucidation of the mechanistic relationships between drugs, their targets, and diseases is at the core of modern drug discovery research. Thousands of studies relevant to the drug-target-disease (DTD) triangle have been published and annotated in the Medline/PubMed database. Mining this database affords rapid identification of all published studies that confirm connections between vertices of this triangle or enable new inferences of such connections. To this end, we describe the development of Chemotext, a publicly available Web server that mines the entire compendium of published literature in PubMed annotated by Medline Subject Heading (MeSH) terms. The goal of Chemotext is to identify all known DTD relationships and infer missing links between vertices of the DTD triangle. As a proof-of-concept, we show that Chemotext could be instrumental in generating new drug repurposing hypotheses or annotating clinical outcomes pathways for known drugs. The Chemotext Web server is freely available at http://chemotext.mml.unc.edu .

The HMMER Web Server for Protein Sequence Similarity Search.

PubMed

Prakash, Ananth; Jeffryes, Matt; Bateman, Alex; Finn, Robert D

2017-12-08

Protein sequence similarity search is one of the most commonly used bioinformatics methods for identifying evolutionarily related proteins. In general, sequences that are evolutionarily related share some degree of similarity, and sequence-search algorithms use this principle to identify homologs. The requirement for a fast and sensitive sequence search method led to the development of the HMMER software, which in the latest version (v3.1) uses a combination of sophisticated acceleration heuristics and mathematical and computational optimizations to enable the use of profile hidden Markov models (HMMs) for sequence analysis. The HMMER Web server provides a common platform by linking the HMMER algorithms to databases, thereby enabling the search for homologs, as well as providing sequence and functional annotation by linking external databases. This unit describes three basic protocols and two alternate protocols that explain how to use the HMMER Web server using various input formats and user defined parameters. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

PubMed

van der Schot, Gijs; Bonvin, Alexandre M J J

2015-08-01

We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

Patient-Centered Access to Secure Systems Online (PCASSO): a secure approach to clinical data access via the World Wide Web.

PubMed Central

Masys, D. R.; Baker, D. B.

1997-01-01

The Internet's World-Wide Web (WWW) provides an appealing medium for the communication of health related information due to its ease of use and growing popularity. But current technologies for communicating data between WWW clients and servers are systematically vulnerable to certain types of security threats. Prominent among these threats are "Trojan horse" programs running on client workstations, which perform some useful and known function for a user, while breaching security via background functions that are not apparent to the user. The Patient-Centered Access to Secure Systems Online (PCASSO) project of SAIC and UCSD is a research, development and evaluation project to exploit state-of-the-art security and WWW technology for health care. PCASSO is designed to provide secure access to clinical data for healthcare providers and their patients using the Internet. PCASSO will be evaluated for both safety and effectiveness, and may provide a model for secure communications via public data networks. PMID:9357644

NOAA Operational Model Archive Distribution System (NOMADS): High Availability Applications for Reliable Real Time Access to Operational Model Data

NASA Astrophysics Data System (ADS)

Alpert, J. C.; Wang, J.

2009-12-01

To reduce the impact of natural hazards and environmental changes, the National Centers for Environmental Prediction (NCEP) provide first alert and a preferred partner for environmental prediction services, and represents a critical national resource to operational and research communities affected by climate, weather and water. NOMADS is now delivering high availability services as part of NOAA’s official real time data dissemination at its Web Operations Center (WOC) server. The WOC is a web service used by organizational units in and outside NOAA, and acts as a data repository where public information can be posted to a secure and scalable content server. A goal is to foster collaborations among the research and education communities, value added retailers, and public access for science and development efforts aimed at advancing modeling and GEO-related tasks. The user (client) executes what is efficient to execute on the client and the server efficiently provides format independent access services. Client applications can execute on the server, if it is desired, but the same program can be executed on the client side with no loss of efficiency. In this way this paradigm lends itself to aggregation servers that act as servers of servers listing, searching catalogs of holdings, data mining, and updating information from the metadata descriptions that enable collections of data in disparate places to be simultaneously accessed, with results processed on servers and clients to produce a needed answer. The services used to access the operational model data output are the Open-source Project for a Network Data Access Protocol (OPeNDAP), implemented with the Grid Analysis and Display System (GrADS) Data Server (GDS), and applications for slicing, dicing and area sub-setting the large matrix of real time model data holdings. This approach insures an efficient use of computer resources because users transmit/receive only the data necessary for their tasks including metadata. Data sets served in this way with a high availability server offer vast possibilities for the creation of new products for value added retailers and the scientific community. We demonstrate how users can use NOMADS services to select the values of Ensemble model runs over the ith Ensemble component, (forecast) time, vertical levels, global horizontal location, and by variable, virtually a 6-Dimensional data cube of access across the internet. The example application called the “Ensemble Probability Tool” make probability predictions of user defined weather events that can be used in remote areas for weather vulnerable circumstances. An application to access data for a verification pilot study is shown in detail in a companion paper (U06) collaboration with the World Bank and is an example of high value, usability and relevance of NCEP products and service capability over a wide spectrum of user and partner needs.

Cybersecurity, massive data processing, community interaction, and other developments at WWW-based computational X-ray Server

NASA Astrophysics Data System (ADS)

Stepanov, Sergey

2013-03-01

X-Ray Server (x-server.gmca.aps.anl.gov) is a WWW-based computational server for modeling of X-ray diffraction, reflection and scattering data. The modeling software operates directly on the server and can be accessed remotely either from web browsers or from user software. In the later case the server can be deployed as a software library or a data fitting engine. As the server recently surpassed the milestones of 15 years online and 1.5 million calculations, it accumulated a number of technical solutions that are discussed in this paper. The developed approaches to detecting physical model limits and user calculations failures, solutions to spam and firewall problems, ways to involve the community in replenishing databases and methods to teach users automated access to the server programs may be helpful for X-ray researchers interested in using the server or sharing their own software online.

Computers in Small Libraries: Learning Server-Side Scripting

ERIC Educational Resources Information Center

Roberts, Gary

2005-01-01

In this column, the author compares and contrasts the most popular scripting languages that are used to create truly dynamic service-oriented Web sites, building a conceptual framework that be can used as a starting point for specific server-side library projects.

Computer Workstations: Desks

MedlinePlus

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Access Control of Web- and Java-Based Applications

NASA Technical Reports Server (NTRS)

Tso, Kam S.; Pajevski, Michael J.

2013-01-01

Cybersecurity has become a great concern as threats of service interruption, unauthorized access, stealing and altering of information, and spreading of viruses have become more prevalent and serious. Application layer access control of applications is a critical component in the overall security solution that also includes encryption, firewalls, virtual private networks, antivirus, and intrusion detection. An access control solution, based on an open-source access manager augmented with custom software components, was developed to provide protection to both Web-based and Javabased client and server applications. The DISA Security Service (DISA-SS) provides common access control capabilities for AMMOS software applications through a set of application programming interfaces (APIs) and network- accessible security services for authentication, single sign-on, authorization checking, and authorization policy management. The OpenAM access management technology designed for Web applications can be extended to meet the needs of Java thick clients and stand alone servers that are commonly used in the JPL AMMOS environment. The DISA-SS reusable components have greatly reduced the effort for each AMMOS subsystem to develop its own access control strategy. The novelty of this work is that it leverages an open-source access management product that was designed for Webbased applications to provide access control for Java thick clients and Java standalone servers. Thick clients and standalone servers are still commonly used in businesses and government, especially for applications that require rich graphical user interfaces and high-performance visualization that cannot be met by thin clients running on Web browsers

DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

PubMed Central

Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, “DNA barcode” actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

NASA Astrophysics Data System (ADS)

Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

2014-05-01

The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web application enables an intuitive navigation through all available information and allows the visualization of geological maps (2D), seismic transects (2D/3D), wells (2D/3D), and the 3D-model. These achievements will alleviate spatial and geological data management within the German State Geological Offices and foster the interoperability of heterogeneous systems. It will provide guidance to a systematic subsurface management across system, domain and administrative boundaries on the basis of a federated spatial data infrastructure, and include the public in the decision processes (e-Governance). Yet, the interoperability of the systems has to be strongly propelled forward through agreements on standards that need to be decided upon in responsible committees. The project B3D is funded with resources from the European Fund for Regional Development (EFRE).

Broadband network on-line data acquisition system with web based interface for control and basic analysis

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Grad, Marek

2016-04-01

Passive seismic experiment "13BB Star" is operated since mid 2013 in northern Poland and consists of 13 broadband seismic stations. One of the elements of this experiment is dedicated on-line data acquisition system comprised of both client (station) side and server side modules with web based interface that allows monitoring of network status and provides tools for preliminary data analysis. Station side is controlled by ARM Linux board that is programmed to maintain 3G/EDGE internet connection, receive data from digitizer, send data do central server among with additional auxiliary parameters like temperatures, voltages and electric current measurements. Station side is controlled by set of easy to install PHP scripts. Data is transmitted securely over SSH protocol to central server. Central server is a dedicated Linux based machine. Its duty is receiving and processing all data from all stations including auxiliary parameters. Server side software is written in PHP and Python. Additionally, it allows remote station configuration and provides web based interface for user friendly interaction. All collected data can be displayed for each day and station. It also allows manual creation of event oriented plots with different filtering abilities and provides numerous status and statistic information. Our solution is very flexible and easy to modify. In this presentation we would like to share our solution and experience. National Science Centre Poland provided financial support for this work via NCN grant DEC-2011/02/A/ST10/00284.

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

PubMed

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

2017-07-03

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Recommendations for Benchmarking Web Site Usage among Academic Libraries.

ERIC Educational Resources Information Center

Hightower, Christy; Sih, Julie; Tilghman, Adam

1998-01-01

To help library directors and Web developers create a benchmarking program to compare statistics of academic Web sites, the authors analyzed the Web server log files of 14 university science and engineering libraries. Recommends a centralized voluntary reporting structure coordinated by the Association of Research Libraries (ARL) and a method for…

ITMS: Individualized Teaching Material System: Adaptive Integration of Web Pages Distributed in Some Servers.

ERIC Educational Resources Information Center

Mitsuhara, Hiroyuki; Kurose, Yoshinobu; Ochi, Youji; Yano, Yoneo

The authors developed a Web-based Adaptive Educational System (Web-based AES) named ITMS (Individualized Teaching Material System). ITMS adaptively integrates knowledge on the distributed Web pages and generates individualized teaching material that has various contents. ITMS also presumes the learners' knowledge levels from the states of their…

Availability of the OGC geoprocessing standard: March 2011 reality check

NASA Astrophysics Data System (ADS)

Lopez-Pellicer, Francisco J.; Rentería-Agualimpia, Walter; Béjar, Rubén; Muro-Medrano, Pedro R.; Zarazaga-Soria, F. Javier

2012-10-01

This paper presents an investigation about the servers available in March 2011 conforming to the Web Processing Service interface specification published by the geospatial standards organization Open Geospatial Consortium (OGC) in 2007. This interface specification gives support to standard Web-based geoprocessing. The data used in this research were collected using a focused crawler configured for finding OGC Web services. The research goals are (i) to provide a reality check of the availability of Web Processing Service servers, (ii) to provide quantitative data about the use of different features defined in the standard that are relevant for a scalable Geoprocessing Web (e.g. long-running processes, Web-accessible data outputs), and (iii) to test if the advances in the use of search engines and focused crawlers for finding Web services can be applied for finding geoscience processing systems. Research results show the feasibility of the discovery approach and provide data about the implementation of the Web Processing Service specification. These results also show extensive use of features related to scalability, except for those related to technical and semantic interoperability.

CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyagi, Sonika; Vaz, Candida; Gupta, Vipin

2008-08-08

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filteringmore » systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)« less

A Web-Based Information System for Field Data Management

NASA Astrophysics Data System (ADS)

Weng, Y. H.; Sun, F. S.

2014-12-01

A web-based field data management system has been designed and developed to allow field geologists to store, organize, manage, and share field data online. System requirements were analyzed and clearly defined first regarding what data are to be stored, who the potential users are, and what system functions are needed in order to deliver the right data in the right way to the right user. A 3-tiered architecture was adopted to create this secure, scalable system that consists of a web browser at the front end while a database at the back end and a functional logic server in the middle. Specifically, HTML, CSS, and JavaScript were used to implement the user interface in the front-end tier, the Apache web server runs PHP scripts, and MySQL to server is used for the back-end database. The system accepts various types of field information, including image, audio, video, numeric, and text. It allows users to select data and populate them on either Google Earth or Google Maps for the examination of the spatial relations. It also makes the sharing of field data easy by converting them into XML format that is both human-readable and machine-readable, and thus ready for reuse.

COMAN: a web server for comprehensive metatranscriptomics analysis.

PubMed

Ni, Yueqiong; Li, Jun; Panagiotou, Gianni

2016-08-11

Microbiota-oriented studies based on metagenomic or metatranscriptomic sequencing have revolutionised our understanding on microbial ecology and the roles of both clinical and environmental microbes. The analysis of massive metatranscriptomic data requires extensive computational resources, a collection of bioinformatics tools and expertise in programming. We developed COMAN (Comprehensive Metatranscriptomics Analysis), a web-based tool dedicated to automatically and comprehensively analysing metatranscriptomic data. COMAN pipeline includes quality control of raw reads, removal of reads derived from non-coding RNA, followed by functional annotation, comparative statistical analysis, pathway enrichment analysis, co-expression network analysis and high-quality visualisation. The essential data generated by COMAN are also provided in tabular format for additional analysis and integration with other software. The web server has an easy-to-use interface and detailed instructions, and is freely available at http://sbb.hku.hk/COMAN/ CONCLUSIONS: COMAN is an integrated web server dedicated to comprehensive functional analysis of metatranscriptomic data, translating massive amount of reads to data tables and high-standard figures. It is expected to facilitate the researchers with less expertise in bioinformatics in answering microbiota-related biological questions and to increase the accessibility and interpretation of microbiota RNA-Seq data.

Suspension Trauma / Orthostatic Intolerance

MedlinePlus

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Computer Workstation: Pointer/Mouse

MedlinePlus

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ACFIS: a web server for fragment-based drug discovery

PubMed Central

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-01-01

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown ‘chemical space’ to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for ‘chemical space’, which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. PMID:27150808

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles

PubMed Central

Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G.; Gelly, Jean-Christophe

2016-01-01

Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation —with Protein Blocks—, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the ‘Hard’ category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/. PMID:27319297

AlignMe—a membrane protein sequence alignment web server

PubMed Central

Stamm, Marcus; Staritzbichler, René; Khafizov, Kamil; Forrest, Lucy R.

2014-01-01

We present a web server for pair-wise alignment of membrane protein sequences, using the program AlignMe. The server makes available two operational modes of AlignMe: (i) sequence to sequence alignment, taking two sequences in fasta format as input, combining information about each sequence from multiple sources and producing a pair-wise alignment (PW mode); and (ii) alignment of two multiple sequence alignments to create family-averaged hydropathy profile alignments (HP mode). For the PW sequence alignment mode, four different optimized parameter sets are provided, each suited to pairs of sequences with a specific similarity level. These settings utilize different types of inputs: (position-specific) substitution matrices, secondary structure predictions and transmembrane propensities from transmembrane predictions or hydrophobicity scales. In the second (HP) mode, each input multiple sequence alignment is converted into a hydrophobicity profile averaged over the provided set of sequence homologs; the two profiles are then aligned. The HP mode enables qualitative comparison of transmembrane topologies (and therefore potentially of 3D folds) of two membrane proteins, which can be useful if the proteins have low sequence similarity. In summary, the AlignMe web server provides user-friendly access to a set of tools for analysis and comparison of membrane protein sequences. Access is available at http://www.bioinfo.mpg.de/AlignMe PMID:24753425

ACFIS: a web server for fragment-based drug discovery.

PubMed

Hao, Ge-Fei; Jiang, Wen; Ye, Yuan-Nong; Wu, Feng-Xu; Zhu, Xiao-Lei; Guo, Feng-Biao; Yang, Guang-Fu

2016-07-08

In order to foster innovation and improve the effectiveness of drug discovery, there is a considerable interest in exploring unknown 'chemical space' to identify new bioactive compounds with novel and diverse scaffolds. Hence, fragment-based drug discovery (FBDD) was developed rapidly due to its advanced expansive search for 'chemical space', which can lead to a higher hit rate and ligand efficiency (LE). However, computational screening of fragments is always hampered by the promiscuous binding model. In this study, we developed a new web server Auto Core Fragment in silico Screening (ACFIS). It includes three computational modules, PARA_GEN, CORE_GEN and CAND_GEN. ACFIS can generate core fragment structure from the active molecule using fragment deconstruction analysis and perform in silico screening by growing fragments to the junction of core fragment structure. An integrated energy calculation rapidly identifies which fragments fit the binding site of a protein. We constructed a simple interface to enable users to view top-ranking molecules in 2D and the binding mode in 3D for further experimental exploration. This makes the ACFIS a highly valuable tool for drug discovery. The ACFIS web server is free and open to all users at http://chemyang.ccnu.edu.cn/ccb/server/ACFIS/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles.

PubMed

Ghouzam, Yassine; Postic, Guillaume; Guerin, Pierre-Edouard; de Brevern, Alexandre G; Gelly, Jean-Christophe

2016-06-20

Protein structure prediction based on comparative modeling is the most efficient way to produce structural models when it can be performed. ORION is a dedicated webserver based on a new strategy that performs this task. The identification by ORION of suitable templates is performed using an original profile-profile approach that combines sequence and structure evolution information. Structure evolution information is encoded into profiles using structural features, such as solvent accessibility and local conformation -with Protein Blocks-, which give an accurate description of the local protein structure. ORION has recently been improved, increasing by 5% the quality of its results. The ORION web server accepts a single protein sequence as input and searches homologous protein structures within minutes. Various databases such as PDB, SCOP and HOMSTRAD can be mined to find an appropriate structural template. For the modeling step, a protein 3D structure can be directly obtained from the selected template by MODELLER and displayed with global and local quality model estimation measures. The sequence and the predicted structure of 4 examples from the CAMEO server and a recent CASP11 target from the 'Hard' category (T0818-D1) are shown as pertinent examples. Our web server is accessible at http://www.dsimb.inserm.fr/ORION/.