Biomolecular structural knowledge is important to understand the biological processes and the mechanisms underlying human diseases. In silico modeling plays a vital role in de novo design and docking ...of biomacromolecules as well as in exploring their conformational dynamics. Additionally, it has a major role in acquiring the structural insights using the parameters derived from experimental techniques such as cryo-electron microscopy. Steric hindrance is one of the important measures to validate the accuracy of the modeled biomolecular structures. A web user interface (WUI), namely, STRIDER (steric hindrance and metal coordination identifier) (www.iith.ac.in/strider/) estimates and reports pairwise inter- and intra- molecular steric hindrances using the van der Waals radius of 117 elements. STRIDER identifies and reports the coordination pattern of 64 metals in an interactive mode. It can provide conformer wise interaction pattern(s) of an ensemble of conformers which is needed in circumventing sampling issue in flexible docking, protein folding and structure based virtual screening. Further, it generates a pymol session file which highlights the aforementioned interaction for an offline analysis. Since STRIDER simply requires the Cartesian coordinates of a molecule in PDB format, any chemical structure can be given as an input. Functionality of STRIDER is illustrated here by considering several examples.
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•STRIDER estimates pairwise inter- and intra- molecular short-contacts using the van der Waals radius of 117 elements.•STRIDER provides an interactive view of all the short-contact regions for a single conformer or an ensemble of conformers.•STRIDER identifies and reports the coordination pattern of 64 metals in an interactive mode.•STRIDER can act as an essential tool in modeling the three-dimensional structure of any biomolecules.
As digital systems continue to grow in popularity, they also become more vulnerable to various forms of attacks with various motives, including financial gain and political influence. In response, ...engineers must consider system security from the design phase. However, defining security requirements at this stage can be challenging. To address this challenge, we propose E-SCORE, a web-based tool that streamlines the security requirements engineering process. E-SCORE implements the SCORE (Security Criteria Ontology for security Requirements Engineering) (i) to suggest security mechanisms and additional criteria to enhance security coverage and (ii) to facilitate security analysis of the system. An example of banking system usage is provided. Through our approach, we could define ten additional security requirements for a single requirement. Therefore, E-SCORE offers a valuable resource for engineers to ensure the security of digital systems across various domains.
Web2.0 has led to the common age of the Internet. Users not only passively read information online, but also actively become information producers. Therefore, humanization has become an increasingly ...important topic in network interface design. Whether the design of the web interfaces is consistent with the cognitive characteristics of the user, and whether it is conducive to the organization and processing of the consciousness, will affect the effectiveness, efficiency and satisfaction of the user interface. This article explores the relationship between designers and users through literature and case analysis, starting from cognitive psychology. Through analysis of a series of psychological activities such as perception, the goal of humanizing the web interface is finally achieved. Cognitive psychology is an effective means to improve the level of web interface design in the Web2.0 era. Learning and research on it can promote the construction of user-friendly web sites that are easy to use and loved by users.
An automated fruit identification system may be used in the supermarket to help consumers determine the type and standard of fruits. Automatic fruit categorization and recognition is becoming ...increasingly popular, but it is also becoming more difficult due to low contrast and ambiguous characteristics. Proposed research used deep learning algorithms to classify fruit images and developed a web-based system for autonomous fruit identification. However, autonomous fruit categorization is not a relatively easy process that is dependent on the locations, shapes, colors, and sizes of the objects. Proposed study collected samples from different local places, then removed images backdrops and improved them for a more accurate result. ResNet-50, VGG-19, Inception-V3, and MobileNet were utilized to achieve more precise feature extraction. Among these, MobileNet achieved 99.21% accuracy in feature extraction, outperforming previously proposed machine learning techniques. 3240 samples of eight different fruits are collected from the Bangladeshi countryside, including Carambola, Bilimbi, Elephant Apple, Emblica, Burmese Grape, Sapodilla, Tamarind, and Wood Apple. As a consequence of this research, the proposed approach will aid individuals and industry in recognizing local fruits due to its high accuracy rate and web-based system.
We present PALEO-SEAL, a simple web interface that allows visualizing, querying and downloading Holocene sea-level datapoints formatted following the HOLSEA data template. The data is hosted on a ...mySQL database, and the interface uses AngularJS. PALEO-SEAL is scalable to large datasets and can be deployed in few easy steps, that require only basic knowledge of SQL and HTML. The tool is released in the open domain.
Sample automation and management is increasingly important as the number and size of population-scale and high-throughput projects grow. This is particularly the case in large-scale population ...studies where sample size is far outpacing the commonly used 96-well plate format. To facilitate management and transfer of samples in this format, we present Samasy, a web-based application for the construction of a sample database, intuitive display of sample and batch information, and facilitation of automated sample transfer or subset. Samasy is designed with ease-of-use in mind, can be quickly set up, and runs in any web browser.
A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is ...however still challenging, as it requires sufficient computer programing and command-line knowledge. Furthermore, researchers often need to evaluate and visualize interactively the effect of using differential statistical and error models, assess the impact of selecting different parameters and cutoffs, and finally explore the overlapping consensus of cross-validated results obtained with different methods. This represents a bottleneck that slows down or impedes the adoption of NGS technologies in many labs.
We developed DEApp, an interactive and dynamic web application for differential expression analysis of count based NGS data. This application enables models selection, parameter tuning, cross validation and visualization of results in a user-friendly interface.
DEApp enables labs with no access to full time bioinformaticians to exploit the advantages of NGS applications in biomedical research. This application is freely available at https://yanli.shinyapps.io/DEAppand https://gallery.shinyapps.io/DEApp.
The rapid identification of pathogen clones is pivotal for effective epidemiological control strategies in hospital settings. High Resolution Melting (HRM) is a molecular biology technique suitable ...for fast and inexpensive pathogen typing protocols. Unfortunately, the mathematical/informatics skills required to analyse HRM data for pathogen typing likely limit the application of this promising technique in hospital settings.
MeltingPlot is the first tool specifically designed for epidemiological investigations using HRM data, easing the application of HRM typing to large real-time surveillance and rapid outbreak reconstructions. MeltingPlot implements a graph-based algorithm designed to discriminate pathogen clones on the basis of HRM data, producing portable typing results. The tool also merges typing information with isolates and patients metadata to create graphical and tabular outputs useful in epidemiological investigations and it runs in a few seconds even with hundreds of isolates.
https://skynet.unimi.it/index.php/tools/meltingplot/ .
The analysis and result interpretation of HRM typing protocols can be not trivial and this likely limited its application in hospital settings. MeltingPlot is a web tool designed to help the user to reconstruct epidemiological events by combining HRM-based clustering methods and the isolate/patient metadata. The tool can be used for the implementation of HRM based real time large scale surveillance programs in hospital settings.
An efficient implementation of the generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J Phys. Chem. A 2007, 111, 2193) for treating a wide range of large molecules is ...presented. In this implementation, the fragmentation process can be automatically done for a general molecule, with only some functional groups defined by users. A new and fast scheme is designed for the generation of various subsystems and the derivation of their coefficients. The newly implemented GEBF approach has been applied to several large molecules including proteins, nucleic acids, and supermolecules with fused aromatic rings. Test calculations within the Hartree−Fock (HF) and density functional theory (DFT) framework demonstrate that the GEBF approach can provide reasonably accurate ground-state energies and optimized structures, which are in good agreement with those from conventional HF or DFT calculations. The GEBF approach implemented in this work can now be employed by nonexpert users to compute energies, optimized structures, and some molecular properties at various ab initio levels for a broad range of large molecules on ordinary PC workstations.
Open Data is considered a key to scientific innovations. These freely available datasets can also be used as a foundation to enhance the digital and data literacies among the younger generation of ...school pupils. This article presents the design and prototype of an Open Data web interface based on the Enterprise Architecture Oriented Requirements Engineering (EAORE) approach for Open Data usage as an educational resource in Danish public schools. We first systematically review the literature on Open Data use in educational fields and selected 14 research articles with a particular focus on the use of Open Data in the educational domain after prescribing an inclusion/exclusion criteria on 101 research articles identified initially. The review indicates that there is a gap between Open Data opportunities within the educational domain and in exploring the use of Open Data as a source to develop twenty-first-century skills, specifically digital and data literacies among younger school pupils. To fill this gap, we propose an EAORE approach that represents how Enterprise Architecture (EA) models can guide the overall Requirements Engineering (RE) process for the use of Open Data in Danish public schools. Based on these EA models, we designed the prototype of an Open Data web interface for schools.
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