Biological interpretation of gene/protein lists resulting from -omics experiments can be a complex task. A common approach consists of reviewing Gene Ontology (GO) annotations for entries in such ...lists and searching for enrichment patterns. Unfortunately, there is a gap between machine-readable output of GO software and its human-interpretable form. This gap can be bridged by allowing users to simultaneously visualize and interact with term-term and gene-term relationships.
We created the open-source GOnet web-application (available at http://tools.dice-database.org/GOnet/ ), which takes a list of gene or protein entries from human or mouse data and performs GO term annotation analysis (mapping of provided entries to GO subsets) or GO term enrichment analysis (scanning for GO categories overrepresented in the input list). The application is capable of producing parsable data formats and importantly, interactive visualizations of the GO analysis results. The interactive results allow exploration of genes and GO terms as a graph that depicts the natural hierarchy of the terms and retains relationships between terms and genes/proteins. As a result, GOnet provides insight into the functional interconnection of the submitted entries.
The application can be used for GO analysis of any biological data sources resulting in gene/protein lists. It can be helpful for experimentalists as well as computational biologists working on biological interpretation of -omics data resulting in such lists.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Membaca merupakan proses memahami, menafsirkan, dan mengekstraksi informasi dari serangkaian kata yang memerlukan waktu. Melalui internet, akses membaca semakin luas dengan adanya konten seperti ...artikel, e-book, jurnal, dan lainnya yang mayoritas disajikan dalam bahasa Inggris. Melalui survei terhadap 30 mahasiswa mengenai kegiatan membaca cepat dan relevansinya terhadap bahasa Inggris, sebanyak 76.7% darinya tidak mengetahui kecepatan membaca mereka dan 56.7% mengaku sering membaca teks berbahasa Inggris. Ada baiknya jika kemampuan membaca cepat dilatih dengan penggunaan bahasa Inggris untuk membangun motivasi terhadap literasi digital yang luas. Melalui pengamatan tersebut, dikembangkan aplikasi berbasis progressive web app (PWA) menggunakan metode SDLC prototyping. Melalui proses prototyping sebanyak 2 kali iterasi, dihasilkan aplikasi PWA ‘Speed Reader’ yang bertujuan untuk membantu berlatih membaca cepat secara senyap dengan materi bacaan berbahasa Inggris. Hasil evaluasi pengujian menunjukkan bahwa aplikasi ini kompatibel pada perangkat mobile dan dapat berjalan secara cross-browser. Setiap fitur berhasil dijalankan dengan tingkat validitas 100% pada pengujian efektivitas. Melalui pengujian efisiensi, didapatkan waktu penyelesaian tugas sebesar 0,156 tugas per detik. Hasil pengujian kepuasan pengguna melalui pengukuran System Usability Scale (SUS) mencapai nilai 84 dengan kategori grade B dan tergolong acceptable. Dengan demikian, dapat disimpulkan bahwa pengguna berhasil mencapai tujuan mereka dan aplikasi ini layak untuk digunakan.
Abstract
Reading is a process of understanding, interpreting, and extracting information from a series of words that takes time. The internet has significantly broadened reading access, providing abundant content like articles, e-books, journals, predominantly in English. A survey conducted among 30 students explored their engagement in speed reading and its relevance to English. Surprisingly, 76.7% of participants were unaware of their reading speed, while 56.7% acknowledged frequent reading of English texts. To foster extensive digital literacy, it is advisable to train speed reading skills specifically using the English language. Based on this observation, a Progressive Web App (PWA) was developed utilizing the SDLC prototyping method. The development of an app called 'Speed Reader' was aimed to facilitate the practice of silent speed reading with English materials. Evaluation tests demonstrated the application's compatibility with mobile devices and its cross-browser functionality. Each feature achieved a 100% validity rate in effectiveness testing. Moreover, efficiency testing revealed a task completion time of 0.156 tasks per second. User satisfaction assessments, conducted using the SUS method, yielded a score of 84, categorizing it as grade B and considered acceptable. It can be concluded that the users have successfully achieved their goals, and this application is deemed suitable.
The increased availability of user‐friendly and accessible computational tools for biomolecular modeling would expand the reach and application of biomolecular engineering and design. For protein ...modeling, one key challenge is to reduce the complexities of 3D protein folds to sets of parametric equations that nonetheless capture the salient features of these structures accurately. At present, this is possible for a subset of proteins, namely, repeat proteins. The α‐helical coiled coil provides one such example, which represents ≈ 3–5% of all known protein‐encoding regions of DNA. Coiled coils are bundles of α helices that can be described by a small set of structural parameters. Here we describe how this parametric description can be implemented in an easy‐to‐use web application, called CCBuilder 2.0, for modeling and optimizing both α‐helical coiled coils and polyproline‐based collagen triple helices. This has many applications from providing models to aid molecular replacement for X‐ray crystallography, in silico model building and engineering of natural and designed protein assemblies, and through to the creation of completely de novo “dark matter” protein structures. CCBuilder 2.0 is available as a web‐based application, the code for which is open‐source and can be downloaded freely. http://coiledcoils.chm.bris.ac.uk/ccbuilder2.
Lay Summary
We have created CCBuilder 2.0, an easy to use web‐based application that can model structures for a whole class of proteins, the α‐helical coiled coil, which is estimated to account for 3–5% of all proteins in nature. CCBuilder 2.0 will be of use to a large number of protein scientists engaged in fundamental studies, such as protein structure determination, through to more‐applied research including designing and engineering novel proteins that have potential applications in biotechnology.
The beginning of the coronavirus disease (COVID-19) epidemic dates back to December 31, 2019, when the first cases were reported in the People's Republic of China. In the Czech Republic, the first ...three cases of infection with the novel coronavirus were confirmed on March 1, 2020. The joint effort of state authorities and researchers gave rise to a unique team, which combines methodical knowledge of real-world processes with the know-how needed for effective processing, analysis, and online visualization of data.
Due to an urgent need for a tool that presents important reports based on valid data sources, a team of government experts and researchers focused on the design and development of a web app intended to provide a regularly updated overview of COVID-19 epidemiology in the Czech Republic to the general population.
The cross-industry standard process for data mining model was chosen for the complex solution of analytical processing and visualization of data that provides validated information on the COVID-19 epidemic across the Czech Republic. Great emphasis was put on the understanding and a correct implementation of all six steps (business understanding, data understanding, data preparation, modelling, evaluation, and deployment) needed in the process, including the infrastructure of a nationwide information system; the methodological setting of communication channels between all involved stakeholders; and data collection, processing, analysis, validation, and visualization.
The web-based overview of the current spread of COVID-19 in the Czech Republic has been developed as an online platform providing a set of outputs in the form of tables, graphs, and maps intended for the general public. On March 12, 2020, the first version of the web portal, containing fourteen overviews divided into five topical sections, was released. The web portal's primary objective is to publish a well-arranged visualization and clear explanation of basic information consisting of the overall numbers of performed tests, confirmed cases of COVID-19, COVID-19-related deaths, the daily and cumulative overviews of people with a positive COVID-19 case, performed tests, location and country of infection of people with a positive COVID-19 case, hospitalizations of patients with COVID-19, and distribution of personal protective equipment.
The online interactive overview of the current spread of COVID-19 in the Czech Republic was launched on March 11, 2020, and has immediately become the primary communication channel employed by the health care sector to present the current situation regarding the COVID-19 epidemic. This complex reporting of the COVID-19 epidemic in the Czech Republic also shows an effective way to interconnect knowledge held by various specialists, such as regional and national methodology experts (who report positive cases of the disease on a daily basis), with knowledge held by developers of central registries, analysts, developers of web apps, and leaders in the health care sector.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Odour nuisance has a not negligible impact on the quality of life of the population affected by it, yet tracing the source of malodorous releases is challenging. Numerical models may be profitably ...used, to support both the identification of the potential source areas and the execution of timely field measurements. In this frame, a new methodology has been developed with the aim of tracing backward the origin of odour nuisance, starting from citizens’ notifications. A numerical procedure processing the alerts received through the Web-App NOSE, has been developed to produce the proper input to the dispersion module of the SMART meteo-dispersive modelling system. Then, a post-processing numerical code elaborates the simulation output based on a combination of puffs of Lagrangian stochastic particles, released backward in time from the locations and at the time of the citizens’ notifications. This novel approach is presented, it is applied to three real case studies occurred in the area of Siracusa province (Sicily, Italy), then related results are discussed. The new methodology proved to be reliable and effective in identifying the most probable zones that can originate the nuisance.
Display omitted
•Citizen cooperation in support to odour nuisance tracing.•Lagrangian backward numerical modelling to identify source areas.•A new approach to use citizens’ notifications as input to numerical model simulations.•A new methodology to elaborate probability distribution maps of source locations.
•Diatoms are widely used to detect changes in water quality.•Biotic indices, ecological and morphological traits are the most commonly used tools.•DiaThor is a free and open source R package for ...calculating diatoms metrics and indices.•It contains 24 functions that provide ecological and morphological metrics and indices.•DiaThor package aims to contribute to the water quality assessment based on diatom.
Diatom-based tools like biotic indices, ecological and morphological traits, are widely used to detect changes in water quality. Here we present DiaThor, a free and open source R package for calculating biotic and ecological indices and metrics for diatom samples. A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment.
Website ”XYZ” merupakan aplikasi yang mempunyai fungsi dalam layanan pembuatan dokumen kependudukan, layanan pendaftaran akses masuk, dan fitur login. Penilaian kerawanan secara berkala diperlukan ...untuk menjamin kehandalan dari aplikasi. Penilaian kerawanan dengan menggunakan tool uji saja sekarang tidak dirasa cukup sehingga memerlukan validasi. Salah satu validasi tersebut adalah menggunakan penetration testing. Uji penetrasi pada Website XYZ Kabupaten XYZ dilaksanakan dengan mengacu kepada Open Web Application Security Project (OWASP) Top 10-2021. Penetration testing dilaksanakan dengan metode black box untuk mendapatkan hasil pengukuran tingkat kerentanan pada aplikasi. Keseluruhan penilaian kerentanan dilakukan dalam empat tahap yaitu planning, information gathering, vulnerability scanning menggunakan 2 tools otomatis yaitu Vega dan OWASP ZAP sebagai upaya untuk mendapatkan cakupan yang lebih luas terkait kerentanan yang ditemukan dikuti dengan validasi dilanjutkan tahap analysis and reporting. Hasil tahap vulnerability scanning menghasilkan 9 jenis kerentanan dengan sebaran 2 high, 1 medium, dan 6 low. Pengujian penetrasi untuk validasi mengacu pada dokumen panduan Web Security Testing Guide (WSTG) versi 4.2. Hasil proses akhir berupa rekomendasi dapat digunakan sebagai referensi pengembang aplikasi web untuk menangani kerentanan khususnya hilangnya ketersediaan layanan dan kebocoran data.
A thesis is a scientific work completed by students with the aim of developing the knowledge gained during the lecture period. Students at Universitas Trunojoyo Madura (UTM), Faculty of Engineering, ...particularly Informatics Engineering, carry out their theses manually and on paper. Thesis Management System (TMS) is software designed to help with the thesis execution process by reducing paper usage and increasing time efficiency. Monolithic system development can disrupt the service process if improvements are being made to the system. Therefore, in this research, a Thesis Management System (TMS) will be built using a microservice approach to make it easier to maintain and develop the system, for example, system scalability. As a means of communication between services, TMS is designed and developed using the REST API. TMS has undergone system performance testing to verify that it performs well under certain conditions. The results show that the number of requests increases the performance response time, CPU usage, and memory consumption, with an average resource usage of each service based on a response time of 61.64 ms, CPU usage of 8.64%, and memory usage of 89.47 Mb. As the number of requests on the service increases, so does resource usage in each service, but this has no effect on device performance because the increase is so low.
In recent years, social media disinformation had a significant impact on real-world events. Consequently, to fight disinformation, a large number of fake news detection models have been proposed. ...However, the theory behind these models has become increasingly sophisticated and complex. Thus, despite the high precision, most of these systems classify text without explaining why since they inherently use advanced and complex technology that is not understandable to humans. In the particular case of disinformation, users are already susceptible to their prior beliefs (i.e., preconceived bias). Consequently, without a proper aid to understand the classification of a certain text, users' trust in these models is likely to be small. Therefore, we propose a reliability detection application for Twitter messages that not only produces a classification but also attempts to explain it by providing a set of graphical cues commonly used to differentiate between reliable and unreliable content.
The sensing behavior of a MoS2-functionalized paper sensor towards dopamine was explored through a combinatorial approach of theoretical analysis, subsequent experimental validation, and ...machine-learning-driven predictive modeling of the measured electrochemical outputs. The suitability of the chosen 2D material for efficient detection of dopamine was confirmed using density functional theory. The physisorption behavior along with electrostatic interaction due to the incorporation of dopamine on MoS2 was unraveled under the purview of theoretically estimated noncovalent interaction and charge density difference plot. The theoretical Löwdin population analysis elucidates the alteration in oxidation potential of dopamine, as observed in electrochemical experiments. The electrochemical responses of the developed sensor with the spiked serum samples showed an average accuracy of more than 96% with a limit of detection of 10 nM. Furthermore, implementation of a machine-intelligent interactive web app interface improved the resolution of the sensing platform significantly with an enhanced accuracy of nearly 99%.
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