Web-based Graphical Interface Research Articles

A web-based design support system for fashion technical sketches

Purpose – To better respond to today’s volatile and changing fashion market, the purpose of this paper is to develop a web-based design support system that enables users to design realistic and interesting skirts in the form of technical sketches over the internet. Design/methodology/approach – The proposed system mainly consists of a sketch representation and composing method (SRCM), a graphic user interface (GUI) and a controller. The SRCM is implemented at the server end that generates technical sketches according to user defined parameters and features via the web-based GUI at the client side. The controller manages the workflows between the server and the clients. Findings – To evaluate the effectiveness of the proposed system, a survey was conducted by inviting 30 subjects (professional designers or undergraduate students studying fashion design) to have trial run of the system in Hong Kong and in the USA. Positive comments and feedbacks were received, and valuable suggestions were also obtained in regard to the prototype system. Originality/value – Compared with traditional computer-aided design (CAD) systems, the proposed system is more effective and easier to operate as users can create technical sketches in accurate proportions with simple computer operations in a few mouse clicks. Besides, the output sketches are fully compatible with most commercial CAD software. The system is developed based on web technologies, thus fashion sketches can be easily designed using any computer connected to the internet; it can be implemented on Android or iOS platform in the future.

AEGIS: a wildfire prevention and management information system

Abstract. We describe a Web-GIS wildfire prevention and management platform (AEGIS) developed as an integrated and easy-to-use decision support tool to manage wildland fire hazards in Greece (http://aegis.aegean.gr). The AEGIS platform assists with early fire warning, fire planning, fire control and coordination of firefighting forces by providing online access to information that is essential for wildfire management. The system uses a number of spatial and non-spatial data sources to support key system functionalities. Land use/land cover maps were produced by combining field inventory data with high-resolution multispectral satellite images (RapidEye). These data support wildfire simulation tools that allow the users to examine potential fire behavior and hazard with the Minimum Travel Time fire spread algorithm. End-users provide a minimum number of inputs such as fire duration, ignition point and weather information to conduct a fire simulation. AEGIS offers three types of simulations, i.e., single-fire propagation, point-scale calculation of potential fire behavior, and burn probability analysis, similar to the FlamMap fire behavior modeling software. Artificial neural networks (ANNs) were utilized for wildfire ignition risk assessment based on various parameters, training methods, activation functions, pre-processing methods and network structures. The combination of ANNs and expected burned area maps are used to generate integrated output map of fire hazard prediction. The system also incorporates weather information obtained from remote automatic weather stations and weather forecast maps. The system and associated computation algorithms leverage parallel processing techniques (i.e., High Performance Computing and Cloud Computing) that ensure computational power required for real-time application. All AEGIS functionalities are accessible to authorized end-users through a web-based graphical user interface. An innovative smartphone application, AEGIS App, also provides mobile access to the web-based version of the system.

CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare complex molecular simulation systems and input files (CHARMM, NAMD, GROMACS, AMBER, OpenMM, CHARMM/OpenMM) to facilitate the usage of common and advanced simulation techniques. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations: PDB Reader & Manipulator for reading PDB structure files and modifying side chains (e.g., mutation, phosphorylation, protonation, lipid-tail linkers, spin labels, fluorophores, and unnatural amino acids), Glycan Reader for preparation of simulation systems containing carbohydrates or glycoproteins, Quick MD Simulator for solution simulation system generation, Membrane Builder for bilayer simulation system generation, HMMM Builder for HMMM-based bilayer system generation, Monolayer Builder for monolayer simulation system generation, Micelle Builder for micelle simulation system generation, PACE CG Builder for coarse-grained simulation system preparation using the PACE force field. Martini Maker for coarse-grained simulation system preparation using the Martini force field, PBEQ-Solver for electrostatic potential visualization, Ligand Binder for free energy perturbation molecular dynamics simulations for protein-ligand binding affinity calculations, Drude Prepper for conversion of CHARMM additive FF-based systems to Drude polarizable FF-based systems, and GCMC/BD ion simulator for Brownian dynamics of ions across ion channels. Recently, new modules have been integrated into CHARMM-GUI, such as Ligand Reader & Modeler for generation of the CHARMM-compatible topology and parameter files of ligands, Glycolipid Modeler for generation of various glycolipid structures, LPS Modeler for generation of various lipopolysaccharide structures. These new features together with existing modules are expected to be useful in advanced biomolecular modeling and simulation.

Subsea Condition Monitoring: Does Effective Diagnosis Increase Availability?

Management The challenges encountered in deepwater development have led to the use of increasingly complex subsea systems. Consequently, operators have become more reliant on subsea monitoring equipment and instrumentation to provide field information for understanding production and equipment conditions. Production monitoring is typically the field operator’s main priority, and equipment condition and performance are sometimes overlooked, resulting in equipment failures and long production downtimes because of unplanned maintenance. Equipment failures often occur without warning and may sometimes, when caused by environmental factors, become inevitable. To determine the cause, field operators sift through vast amounts of distributed data from the subsea control system. The system downtime can be reduced and system availability can be increased by performing effective equipment diagnosis. With the current low-oil-price environment, subsea operators are looking to maximize returns on investment, and condition-based monitoring offers the possibility of lowering operational expenses while increasing field production. Condition Monitoring Condition monitoring is a proactive maintenance strategy combining software and people. Data are used to diagnose changes in the integrity of a system such that corrective action may be planned in a cost-effective manner to increase system availability. Condition monitoring is not a novel technology and is currently used in the aeronautical and automobile industries. The condition monitoring system takes integrity monitoring beyond traditional key performance indicators by utilizing all available data and information from the system and looking for trends of equipment degradation prior to equipment failure. A condition monitoring system is typically based on the following three-step monitoring process: Data Collection: Read-only software to acquire real-time and historical knowledge from the subsea control system. Storing historical data and supporting analysis based on historical trends. Analysis: Onshore analysis server applies statistical analysis, signal processing, mathematical modeling, and simulations to ascertain system conditions. Requires experience-based product knowledge and reliability analysis to target known failure modes and performance issues. System may be tuned and updated in order to continuously improve its online diagnostic performance. Collaboration and Discussion: Estimation of potential impact on production (availability) is built into the system based on operational and maintenance philosophy. With remote surveillance, multiple onshore and offshore users are able to operate the system on a web-based graphical user interface for monitoring and troubleshooting of the subsea field. To simplify monitoring, each component and associated potential failure mode is designed with its individual user interface.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients

PurposeMRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients’ progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. MethodAn imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists’ contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. SummaryThe MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record.

MT-ComparEval: Graphical evaluation interface for Machine Translation development

Abstract The tool described in this article has been designed to help MT developers by implementing a web-based graphical user interface that allows to systematically compare and evaluate various MT engines/experiments using comparative analysis via automatic measures and statistics. The evaluation panel provides graphs, tests for statistical significance and n-gram statistics. We also present a demo server http://wmt.ufal.cz with WMT14 and WMT15 translations.

DNA microarray integromics analysis platform

BackgroundThe study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray Integromics Analysis Platform, a unique web application that focuses on computational integration and analysis of “multi-omics” data. Our tool supports a range of complex analyses, including – among others – low- and high-level analyses of DNA microarray data, integrated analysis of transcriptomics and lipidomics data and the ability to infer miRNA-mRNA interactions.ResultsWe demonstrate the characteristics and benefits of the DNA Microarray Integromics Analysis Platform using two different test cases. The first test case involves the analysis of the nutrimouse dataset, which contains measurements of the expression of genes involved in nutritional problems and the concentrations of hepatic fatty acids. The second test case involves the analysis of miRNA-mRNA interactions in polysaccharide-stimulated human dermal fibroblasts infected with porcine endogenous retroviruses.ConclusionsThe DNA Microarray Integromics Analysis Platform is a web-based graphical user interface for “multi-omics” data management and analysis. Its intuitive nature and wide range of available workflows make it an effective tool for molecular biology research. The platform is hosted at https://lifescience.plgrid.pl/.

Data mining in newt-omics, the repository for omics data from the newt.

Salamanders are an excellent model organism to study regenerative processes due to their unique ability to regenerate lost appendages or organs. Straightforward bioinformatics tools to analyze and take advantage of the growing number of "omics" studies performed in salamanders were lacking so far. To overcome this limitation, we have generated a comprehensive data repository for the red-spotted newt Notophthalmus viridescens, named newt-omics, merging omics style datasets on the transcriptome and proteome level including expression values and annotations. The resource is freely available via a user-friendly Web-based graphical user interface ( http://newt-omics.mpi-bn.mpg.de) that allows access and queries to the database without prior bioinformatical expertise. The repository is updated regularly, incorporating new published datasets from omics technologies.

SEMERGY.net: automatically identifying and optimizing energy-efficient building designs

A central goal of European and national climate and energy programs is to reduce the greenhouse gas emission of buildings. SEMERGY is a web-based optimization environment, which supports users in decision-making regarding energy-efficient building designs. Taking the user-specified criteria investment costs, final energy demand of the building, and environmental impact of used building products into account, the system identifies efficient building designs and retrofit options. The following steps were taken: (i) development of a comprehensive building data model, (ii) creation of an ontology of linked building product data, (iii) development of a rule-based system to automatically identify valid construction alternatives for building components, (iv) development of a multi-objective optimization procedure, and (v) creation of a web-based Graphical User Interface to enable data entry and user interaction. The present contribution provides an overview of the progress made in the above mentioned domains.

Monitoring activities of daily living based on wearable wireless body sensor network.

With recent advances in microprocessor chip technology, wireless communication, and biomedical engineering it is possible to develop miniaturized ubiquitous health monitoring devices that are capable of recording physiological and movement signals during daily life activities. The aim of the research is to implement and test the prototype of health monitoring system. The system consists of the body central unit with Bluetooth module and wearable sensors: the custom-designed ECG sensor, the temperature sensor, the skin humidity sensor and accelerometers placed on the human body or integrated with clothes and a network gateway to forward data to a remote medical server. The system includes custom-designed transmission protocol and remote web-based graphical user interface for remote real time data analysis. Experimental results for a group of humans who performed various activities (eg. working, running, etc.) showed maximum 5% absolute error compared to certified medical devices. The results are promising and indicate that developed wireless wearable monitoring system faces challenges of multi-sensor human health monitoring during performing daily activities and opens new opportunities in developing novel healthcare services.

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present a novel model-based approach (MiClip) to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments. The MiClip algorithm has been tested in both HITS-CLIP and PAR-CLIP datasets. In the HITS-CLIP dataset, the signal/noise ratios of miRNA seed motif enrichment produced by the MiClip approach are between 17% and 301% higher than those by the ad hoc method for the top 10 most enriched miRNAs. In the PAR-CLIP dataset, the MiClip approach can identify ∼50% more validated binding targets than the original ad hoc method and two recently published methods. To facilitate the application of the algorithm, we have released an R package, MiClip ( http://cran.r-project.org/web/packages/MiClip/index.html ), and a public web-based graphical user interface software (http://galaxy.qbrc.org/tool_runner?tool_id=mi_clip) for customized analysis.

RTANDEM, an R/Bioconductor package for MS/MS protein identification

rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca Supplementary data are available at Bioinformatics online.

ST‐analyzer: A web‐based user interface for simulation trajectory analysis

Molecular dynamics (MD) simulation has become one of the key tools to obtain deeper insights into biological systems using various levels of descriptions such as all-atom, united-atom, and coarse-grained models. Recent advances in computing resources and MD programs have significantly accelerated the simulation time and thus increased the amount of trajectory data. Although many laboratories routinely perform MD simulations, analyzing MD trajectories is still time consuming and often a difficult task. ST-analyzer, http://im.bioinformatics.ku.edu/st-analyzer, is a standalone graphical user interface (GUI) toolset to perform various trajectory analyses. ST-analyzer has several outstanding features compared to other existing analysis tools: (i) handling various formats of trajectory files from MD programs, such as CHARMM, NAMD, GROMACS, and Amber, (ii) intuitive web-based GUI environment--minimizing administrative load and reducing burdens on the user from adapting new software environments, (iii) platform independent design--working with any existing operating system, (iv) easy integration into job queuing systems--providing options of batch processing either on the cluster or in an interactive mode, and (v) providing independence between foreground GUI and background modules--making it easier to add personal modules or to recycle/integrate pre-existing scripts utilizing other analysis tools. The current ST-analyzer contains nine main analysis modules that together contain 18 options, including density profile, lipid deuterium order parameters, surface area per lipid, and membrane hydrophobic thickness. This article introduces ST-analyzer with its design, implementation, and features, and also illustrates practical analysis of lipid bilayer simulations.

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

High-throughput RNA sequencing (RNA-seq) has become an instrumental assay for the analysis of multiple aspects of an organism's transcriptome. Further, the analysis of a biological specimen's associated microbiome can also be performed using RNA-seq data and this application is gaining interest in the scientific community. There are many existing bioinformatics tools designed for analysis and visualization of transcriptome data. Despite the availability of an array of next generation sequencing (NGS) analysis tools, the analysis of RNA-seq data sets poses a challenge for many biomedical researchers who are not familiar with command-line tools. Here we present RNA CoMPASS, a comprehensive RNA-seq analysis pipeline for the simultaneous analysis of transcriptomes and metatranscriptomes from diverse biological specimens. RNA CoMPASS leverages existing tools and parallel computing technology to facilitate the analysis of even very large datasets. RNA CoMPASS has a web-based graphical user interface with intrinsic queuing to control a distributed computational pipeline. RNA CoMPASS was evaluated by analyzing RNA-seq data sets from 45 B-cell samples. Twenty-two of these samples were derived from lymphoblastoid cell lines (LCLs) generated by the infection of naïve B-cells with the Epstein Barr virus (EBV), while another 23 samples were derived from Burkitt's lymphomas (BL), some of which arose in part through infection with EBV. Appropriately, RNA CoMPASS identified EBV in all LCLs and in a fraction of the BLs. Cluster analysis of the human transcriptome component of the RNA CoMPASS output clearly separated the BLs (which have a germinal center-like phenotype) from the LCLs (which have a blast-like phenotype) with evidence of activated MYC signaling and lower interferon and NF-kB signaling in the BLs. Together, this analysis illustrates the utility of RNA CoMPASS in the simultaneous analysis of transcriptome and metatranscriptome data. RNA CoMPASS is freely available at http://rnacompass.sourceforge.net/.

Extracting structured data from publications in the Art Conservation Domain

The most common method of publishing new discoveries about art conservation techniques and research has been through traditional full-text publications. Such corpora typically only support searching via metadata (e.g. title, authors, or keywords) and full-text. In particular, it is difficult to discover valuable information about the chemical processes, experimental results, or preservation treatments associated with the conservation of paintings from a specific genre. This article addresses this problem by focusing on the extraction of structured data (that complies with a pre-defined ontology) from a distributed corpus of publications about painting conservation. Our specific extraction method involves a unique combination of named entity recognition (using gazetteer-based and machine learning-based methods) followed by relationship extraction (using rule-based and machine learning-based methods). The resulting structured data are stored in a resource description framework triple store, and a Web-based graphical user interface enables the SPARQL querying, retrieval, and display of the search results. The results from applying our techniques to a corpus of publications on art conservation indicate that our approach achieves higher quality precision and recall in extracting named entities and relations from publications, relative to alternative existing approaches.

R2oDNA designer: computational design of biologically neutral synthetic DNA sequences.

R2oDNA Designer is a web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.

SEMERGY: Performance-Guided Building Design and Refurbishment within a Semantically Augmented Optimization Environment

This contribution illustrates recent efforts in the research project SEMERGY, a computational environment, which incorporates semantic web technologies to support building design and refurbishment optimization. A major part of the necessary information for energy efficient building planning is implicitly available in the World Wide Web. However, this theoretically valuable repository of information cannot be practically used, given its ill-structured nature. SEMERGY addresses this very problem through a number of developments. Specifically, SEMERGY: 1) embeds a comprehensive building data model, 2) incorporates an Ontology for building product data, 3) deploys a rule-based logic for identification of valid building construction alternatives, 4) provides an easy-to-use optimization procedure evaluating energy demand, environmental impact, and investment costs of alternatives, and 5) offers a web-based Graphical User Interface. The present contribution provides a general overview of the whole project and documents the state of its development.

ISTSOS, SENSOR OBSERVATION MANAGEMENT SYSTEM: A REAL CASE APPLICATION OF HYDRO-METEOROLOGICAL DATA FOR FLOOD PROTECTION

Abstract. istSOS (Istituto scienze della Terra Sensor Observation Service) is an implementation of the Sensor Observation Service standard from Open Geospatial Consortium (OGC). The development of istSOS started in 2009 in order to provide a simple implementation of the Sensor Observation Service (SOS) standard for the management, provision and integration of hydro-meteorological data collected in Canton Ticino (Southern Switzerland). istSOS is entirely written in Python and is based on reliable open source software like PostgreSQL/PostGIS and Apache/mod_wsgi. The authors during this presentation want to illustrate the latest software enhancements together with a real case in a production environment. Latest software enhancement includes the development of a RESTful service and of a Web-based graphical user interface that allows hydrologists a better interaction with measurements. This includes the ability of new services creation, addition of new sensors and relative metadata, visualization and manipulation of stored observations, registration of new measures and setting of system properties like observable properties and data quality codes. The study will show a real case application of the system for the provision of data to interregional partners and to a hydrological model for lake level forecasting and flooding hazard assessment. The hydrological model uses a combination of WPS (Web Processing Service) and SOS for the generation of model input data. This system is linked with a dedicated geo-portal used by the civil protection for the management, alert and protection of population and assets of the Locarno area (Verbano Lake flooding). Practical considerations and technical issues will be presented and discussed.

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.

IstSOS, a new sensor observation management system: software architecture and a real-case application for flood protection

istSOS (Istituto scienze della Terra Sensor Observation Service) is an implementation of the Sensor Observation Service (SOS) standard from the Open Geospatial Consortium. The development of istSOS started in 2009 in order to provide a simple implementation of the SOS for the management, provision and integration of hydro-meteorological data collected in Canton Ticino (Southern Switzerland). istSOS is an Open Source, entirely written in Python and based on reliable software like PostgreSQL/PostGIS and Apache/mod_wsgi. This paper illustrates the latest software enhancements, including a RESTful Web service and a Web-based graphical user interface, which enable a better and simplified interaction with measurements and SOS service settings. The robustness of the implemented solution has been validated in a real-case application: the Verbano Lake Early Warning System. In this application, near real-time data have to be exchanged by inter-regional partners and used in a hydrological model for lake level forecasting and flooding hazard assessment. This system is linked with a dedicated geoportal used by the civil protection for the management, alert and protection of the population and the assets of the Locarno area. Practical considerations, technical issues and foreseen improvements are presented and discussed.