Access To Web Services Research Articles

Fixing Accessibility Issues in Open-Source Teaching Repositories

In the LINTI, New Information Technologies Research Laboratory at the Computer Science School, in the National University of La Plata, it is being developed a project that involves the integration of the repository, implemented using DSpace, with different tools and platforms used in academic tasks. Accessibility is a process that cuts across all software development stages, so when using a free software product it is important to evaluate it in order to correct faults if it´s necessary. This article describes a DSpace repository accessibility validation, using screen readers for manual test, automatic validation with software tools and experimental test with users with and without disabilities. The evaluation involves the proper basic functions and the implemented extensions. The original DSpace software was extended through the integration with different tools and platforms, such as Moodle LMS, the library management system called Meran, file management services like DropBox and GoogleDrive and the social network Facebook. The tools used during accessibility evaluation were Examinator, Google ChromeVox and one entirely implemented in the LINTI, called SiMor. The experimental tests were made with blind and deaf persons, most of them college students. All the validation results are detailed using tables and graphs, where it can observe the measured values. It is also described the changes that was necessary to carry out in the repository to improve the user experience and ensure Web service accessibility.

Validation of Structures in the Protein Data Bank

SummaryThe Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for three-dimensional structures of biological macromolecules are produced. These reports are based on recommendations of expert task forces representing crystallography, nuclear magnetic resonance, and cryoelectron microscopy communities. The reports provide useful metrics with which depositors can evaluate the quality of the experimental data, the structural model, and the fit between them. The validation module is also available as a stand-alone web server and as a programmatically accessible web service. A growing number of journals require the official wwPDB validation reports (produced at biocuration) to accompany manuscripts describing macromolecular structures. Upon public release of the structure, the validation report becomes part of the public PDB archive. Geometric quality scores for proteins in the PDB archive have improved over the past decade.

UFace: Your universal password that no one can see

Due to the ease of use, face authentication could be a promising way to replace hard-to-remember passwords to access web services. However, to make face authentication suitable for web services, there are still several critical security and privacy challenges unaddressed. First, the existing authentication servers typically collect the plaintext of users' facial images in order to conduct authentication. If the servers are compromised, the attackers would obtain the users' facial images and can easily impersonate the users in any other applications that use face authentication. Second, it is also hard to prevent attackers from using facial images published in social network sites to impersonate the true user. In this paper, we conquered these two issues by proposing a novel secure face authentication system, called UFace. UFace uses special close-up facial images (which cannot be found online) for authentication. To further ensure the confidentiality of these close-up images, UFace guarantees that these images are only stored at user side and the servers have not any plaintext of these images. The face authentication is conducted securely with two collaborative authentication servers. UFace was implemented through both an Android application and multiple server side programs which were then evaluated in a real setting. The experimental results demonstrate that the UFace system can accurately authenticate users within a few seconds.

Proteome-wide prediction and annotation of mitochondrial and sub-mitochondrial proteins by incorporating domain information

Mitochondrion is one of the most important subcellular organelle of eukaryotic cells. It carries out several biochemical functions that are extremely vital for cells. Defects in mitochondria also play an important role in the development and progression of different types of cancer. Therefore knowledge of complete mitochondrial protein repertoire is essential to understand overall mitochondrial functionality, maintenance, dynamics and metabolism. It would be of a great practical significance to develop an automated and reliable approach that can identify the mitochondrial proteins and their sub-mitochondrial location. In the present study, we report a two level prediction method, named as SubMitoPred, which predicts mitochondrial proteins (at first level) and their sub-mitochondrial localization (at second level). Our approach is based on combined usage of Pfam domain information and support vector machine model. During training we achieved an overall prediction accuracy of 94.37% at first level while at the second level a prediction accuracy of 74.91% for inner membrane, 82.98% for outer membrane, 71.23% for inter-membrane space and 81.58% accuracy was achieved for matrix. Evaluation on independent data shows better performance of SubMitoPred. Benchmarking showed that SubMitoPred performed better than other existing methods. We also annotated human proteome using SubMitoPred. We also developed a freely accessible web-server as well as standalone software for the use of scientific community, which is available at http://proteininformatics.org/mkumar/submitopred/.

DEVELOPING A SPATIAL PROCESSING SERVICE FOR AUTOMATIC CALCULATION OF STORM INUNDATION

Abstract. With the increase in urbanization, the surface of earth and its climate are changing. These changes resulted in more frequent floodingand storm inundation in urban areas. The challenges of flooding can be addressed through several computational procedures. Due to its numerous advantages, accessible web services can be chosen as a proper format for determining the storm inundation. Web services have facilitated the integration and interactivity of the web applications. Such services made the interaction between machines more feasible. Web services enable the heterogeneous software systems to communicate with each other. A Web Processing Service (WPS) makes it possible to process spatial data with different formats. In this study, we developed a WPS to automatically calculate the amount of storm inundation caused by rainfall in urban areas. The method we used for calculating the storm inundation is based on a simplified hydrologic model which estimates the final status of inundation. The simulation process and water transfer between subcatchments are carried out respectively, without user’s interference. The implementation of processing functions in a form of processing web services gives the capability to reuse the services and apply them in other services. As a result, it would avoid creating the duplicate resources.

IPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.

Being responsible for initiating transaction of a particular gene in genome, promoter is a short region of DNA. Promoters have various types with different functions. Owing to their importance in biological process, it is highly desired to develop computational tools for timely identifying promoters and their types. Such a challenge has become particularly critical and urgent in facing the avalanche of DNA sequences discovered in the postgenomic age. Although some prediction methods were developed, they can only be used to discriminate a specific type of promoters from non-promoters. None of them has the ability to identify the types of promoters. This is due to the facts that different types of promoters may share quite similar consensus sequence pattern, and that the promoters of same type may have considerably different consensus sequences. To overcome such difficulty, using the multi-window-based PseKNC (pseudo K-tuple nucleotide composition) approach to incorporate the short-, middle-, and long-range sequence information, we have developed a two-layer seamless predictor named as 'iPromoter-2 L'. The first layer serves to identify a query DNA sequence as a promoter or non-promoter, and the second layer to predict which of the following six types the identified promoter belongs to: σ24, σ28, σ32, σ38, σ54 and σ70. For the convenience of most experimental scientists, a user-friendly and publicly accessible web-server for the powerful new predictor has been established at http://bioinformatics.hitsz.edu.cn/iPromoter-2L/. It is anticipated that iPromoter-2 L will become a very useful high throughput tool for genome analysis. bliu@hit.edu.cn or dshuang@tongji.edu.cn or kcchou@gordonlifescience.org. Supplementary data are available at Bioinformatics online.

MLACP: machine-learning-based prediction of anticancer peptides.

Cancer is the second leading cause of death globally, and use of therapeutic peptides to target and kill cancer cells has received considerable attention in recent years. Identification of anticancer peptides (ACPs) through wet-lab experimentation is expensive and often time consuming; therefore, development of an efficient computational method is essential to identify potential ACP candidates prior to in vitro experimentation. In this study, we developed support vector machine- and random forest-based machine-learning methods for the prediction of ACPs using the features calculated from the amino acid sequence, including amino acid composition, dipeptide composition, atomic composition, and physicochemical properties. We trained our methods using the Tyagi-B dataset and determined the machine parameters by 10-fold cross-validation. Furthermore, we evaluated the performance of our methods on two benchmarking datasets, with our results showing that the random forest-based method outperformed the existing methods with an average accuracy and Matthews correlation coefficient value of 88.7% and 0.78, respectively. To assist the scientific community, we also developed a publicly accessible web server at www.thegleelab.org/MLACP.html.

Interactive, Web-Based Calculator of Neutron and X-ray Reflectivity.

For many users of the neutron and X-ray reflectometry instruments at NIST, these measurements represent a relatively small and specialized part of their research portfolio. As such, providing calculation and modeling tools that are as accessible and easy-to-use as possible is a high priority of the facility. In order to meet this need, a purely web-browser-based calculator for reflectivity modeling and rudimentary fitting has been developed and provided on a publicly accessible web server. Going to https://www.ncnr.nist.gov/instruments/magik/calculators/reflectivity-calculator.html, will load a one-page web application into the browser. Any relatively modern browser with support for ECMAScript 5 will be able to load and run the application. A calculator for magnetic samples can be found at https://www.ncnr.nist.gov/instruments/magik/calculators/magnetic-reflectivity-calculator.html.

Reducing Parental Uncertainty Around Childhood Cancer: Implementation Decisions and Design Trade-Offs in Developing an Electronic Health Record-Linked Mobile App.

BackgroundParents of children newly diagnosed with cancer are confronted with multiple stressors that place them at risk for significant psychological distress. One strategy that has been shown to help reduce uncertainty is the provision of basic information; however, families of newly diagnosed cancer patients are often bombarded with educational material. Technology has the potential to help families manage their informational needs and move towards normalization.ObjectiveThe aim of this study was to create a mobile app that pulls together data from both the electronic health record (EHR) and vetted external information resources to provide tailored information to parents of newly diagnosed children as one method to reduce the uncertainty around their child’s illness. This app was developed to be used by families in a National Institutes of Health (NIH)-funded randomized controlled trial (RCT) aimed at decreasing uncertainty and the subsequent psychological distress.MethodsA 2-phase qualitative study was conducted to elicit the features and content of the mobile app based on the needs and experience of parents of children newly diagnosed with cancer and their providers. Example functions include the ability to view laboratory results, look up appointments, and to access educational material. Educational material was obtained from databases maintained by the National Cancer Institute (NCI) as well as from groups like the Children’s Oncology Group (COG) and care teams within Cincinnati Children’s Hospital Medical Center (CCHMC). The use of EHR-based Web services was explored to allow data like laboratory results to be retrieved in real-time.ResultsThe ethnographic design process resulted in a framework that divided the content of the mobile app into the following 4 sections: (1) information about the patient’s current treatment and other data from the EHR; (2) educational background material; (3) a calendar to view upcoming appointments at their medical center; and (4) a section where participants in the RCT document the study data. Integration with the NCI databases was straightforward; however, accessing the EHR Web services posed a challenge, though the roadblocks were not technical in nature. The lack of a formal, end-to-end institutional process for requesting Web service access and a mechanism to shepherd the request through all stages of implementation proved to be the biggest barrier.ConclusionsWe successfully deployed a mobile app with a custom user interface that can integrate with the EHR to retrieve laboratory results and appointment information using vendor-provided Web services. Developers should expect to face hurdles when integrating with the EHR, but many of them can be addressed with frequent communication and thorough documentation. Executive sponsorship is also a key factor for success.Trial RegistrationClinicalTrials.gov NCT02505165; https://clinicaltrials.gov/ct2/show/NCT02505165 (Archived by WebCite at http://www.Webcitation.org/6r9ZSUgoT)

An Approach To Webpage Prediction Method Using Variable Order Markov Model In Recommendation Systems

With the continuous increase of web applications and services, web usage data have been overloaded and handling that dynamic web information is very challenging task. Personalized web recommender systems are evolving to provide better and tailored experiences for online users than ever before. The personalization technique is carried out for the each individual user by considering their interests and search behavior stored in the web server access logs. Recently a variety of recommendation systems to predict user future request has been proposed, but the quality of these system results only low prediction accuracy. Hence this paper presents a new framework for effective recommendation system to reduce the searching time of the user and to reach the user’s future intention (request) webpage with the improved prediction accuracy by integrating fuzzy cmeans clustering and variable order markov model recommendation system. Experimental setups are carried out initially by applying preprocessing technique on the web log followed by fuzzy c-means clustering process to identify the similarity patterns. Finally web page recommendation is performed using variable order markov model to predict the user’s next web page access by reducing the search time and better prediction accuracy.

Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield

Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for Function) to query protein function from ≥1 µs long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions.

Accessibility analysis of web browsers

Web portals have become widely accepted and convenient means of electronic presence for organisations, businesses, and governments. As a result, a plethora of information services are now being delivered by organisations be it government, business firms, or academic institutions across the world. This has raised concern for accessibility of such web services by users belonging to different age groups, physical challenges, ethnicity, and levels of literacy. In order to enhance web accessibility, one must consider the accessibility of both web portals and web browsers. Towards this end, in this paper, we have studied the accessibility compliance of some popular web browsers with respect to User Agent Accessibility Guideline (UAAG 2.0). We have provided a quantitative evaluation of different aspects of accessibility of web browsers which we believe can help in the better designing of web browsers by taking care of the deficiencies inherent to them.

Data Analysis Protocol for the Development and Evaluation of Population Pharmacokinetic Models for Incorporation Into the Web-Accessible Population Pharmacokinetic Service - Hemophilia (WAPPS-Hemo).

BackgroundHemophilia is an inherited bleeding disorder caused by a deficiency in a specific clotting factor. This results in spontaneous bleeding episodes and eventual arthropathy. The mainstay of hemophilia treatment is prophylactic replacement of the missing factor, but an optimal regimen remains to be determined. Rather, individualized prophylaxis has been suggested to improve both patient safety and resource utilization. However, uptake of this approach has been hampered by the demanding sampling schedules and complex calculations required to obtain individual estimates of pharmacokinetic (PK) parameters. The use of population pharmacokinetics (PopPK) can alleviate this burden by reducing the number of plasma samples required for accurate estimation, but few tools incorporating this approach are readily available to clinicians.ObjectiveThe Web-accessible Population Pharmacokinetic Service - Hemophilia (WAPPS-Hemo) project aims to bridge this gap by providing a Web-accessible service for the reliable estimation of individual PK parameters from only a few patient samples. This service is predicated on the development of validated brand-specific PopPK models.MethodsWe describe the data analysis plan for the development and evaluation of each PopPK model to be incorporated into the WAPPS-Hemo platform. The data sources and structure of the dataset are discussed first, followed by the procedures for handling both data below limit of quantification (BLQ) and absence of such BLQ data. Next, we outline the strategies for building the appropriate structural and covariate models, including the possible need for a process algorithm when PK behavior varies between subjects or significant covariates are not provided. Prior to use in a prospective manner, the models will undergo extensive evaluation using a variety of techniques such as diagnostic plots, bootstrap analysis and cross-validation. Finally, we describe the incorporation of a validated PopPK model into the Bayesian post hoc model to produce individualized estimates of PK parameters.ResultsDense PK data has been collected for more than 20 brands of factor concentrate from both industry-sponsored and investigator-driven studies. The model development process is underway for the majority of molecules, with refinement and validation to be completed in 2017. Further, the WAPPS-Hemo co-investigator network has contributed more than 300 PK assessments for use in model development and evaluation. This constitutes the largest repository of this type of PK data globally.ConclusionsThe WAPPS-Hemo service aims to eliminate barriers to the uptake of individualized PK-tailored hemophilia treatment. By incorporating this tool into routine practice, clinicians can implement a personalized dosing strategy without performing rigorous sampling or complex calculations. This service is centred on validated models developed according to the robust approach to PopPK modeling described herein.ClinicalTrialClinicalTrials.gov NCT02061072; https://clinicaltrials.gov/ct2/show/NCT02061072 (Archived by WebCite at http://www.webcitation.org/6mRIXJh55)

A novel method to authenticate in website using CAPTCHA‐based validation

AbstractWeb security has become vital, as the practice of internet is embryonic nowadays. To protect network from adversaries and to improve web security, researches has been done for a long time. The most solemn issue is phishing attack as well as access of web services by illicit users. Many users are not even sentient about phishing websites. Phishing is a kind of falsified approach employed by an attacker to get sensitive information from the users who are unaware of phishing attacks. User authorization is a noteworthy security measure that confirms the integrity of the user and ensures the confidentiality associated user data. The significant work done here is to prevent web users from entering into phishing websites and to provide web access only to authorized users via web server. Applications based on CAPTCHA provides more security against attacks. The proposed novel technique identifies phishing websites and authorized web access using Cropped Image CAPTCHA algorithm. The image CAPTCHA technique is not easily prone to web attacks moreover. Threshold values and conditions are defined. Based on this, Cropping‐Based Image CAPTCHA System appraises if the website is phishing website or legitimate website furthermore denies acquiescence to web admittance for unconstitutional users. Copyright © 2017 John Wiley & Sons, Ltd.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts.

SummaryThe lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting.Availability and implementationThe source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com. This software is designed to run on a Java EE application server and store data in a relational database.

Featured Collection Introduction: Open Water Data Initiative

Featured Collection Introduction: Open Water Data Initiative

AN ONLINE EXPERT SYSTEM FOR CONSULTATION SERVICES USING A MOBILE APPLICATION INTERFACE

An expert system service that deals with public problems or wide ranges of users basically requires an alternative medium, which is accessible. This paper proposes interface expansion for Web and WAP based expert system consulting application using an Android application interface. An open and accessible web service is developed to provide an access to the Android application to reach the knowledge base in the form of a decision tree stored in a particular database. The Android application employs HTTP for accessing data in a JSON format through web service. Then, the consultation mechanism would run interactively following an available path in the decision tree model from initial symptom identification to reach a conclusion.

Technical note: Harmonising metocean model data via standard web services within small research groups

Abstract. Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Development of two novel face-recognition CAPTCHAs: A security and usability study

CAPTCHAs are challenge-response tests that aim at preventing unwanted machines, including bots, from accessing web services while providing easy access for humans. Recent advances in artificial-intelligence based attacks show that the level of security provided by many state-of-the-art text-based CAPTCHAs is declining. At the same time, techniques for distorting and obscuring the text, which are used to maintain the level of security, make text-based CAPTCHAs difficult to solve for humans, and thereby further degrade usability. The need for developing alternative types of CAPTCHAs that improve both the current security and the usability levels has been emphasized widely.With this study, we contribute to research through (1) the development of two new face recognition CAPTCHAs (Farett-Gender and Farett-Gender&Age), (2) the security analysis of both procedures, and (3) the provision of empirical evidence that one of the suggested CAPTCHAs (Farett-Gender) is similar to Google's reCAPTCHA and better than KCAPTCHA concerning effectiveness (error rates), superior to both regarding learnability and satisfaction but not efficiency.