BACKGROUND: Hierarchical clustering is an exploratory data analysis method that reveals the groups (clusters) of similar objects. The result of the hierarchical clustering is a tree structure called dendrogram that shows the arrangement of individual clusters. To investigate the row/column hierarchical cluster structure of a data matrix, a visualization tool called 'cluster heatmap' is commonly employed. In the cluster heatmap, the data matrix is displayed as a heatmap, a 2-dimensional array in which the colour of each element corresponds to its value. The rows/columns of the matrix are ordered such that similar rows/columns are near each other. The ordering is given by the dendrogram which is displayed on the side of the heatmap. RESULTS: We developed InCHlib (Interactive Cluster Heatmap Library), a highly interactive and lightweight JavaScript library for cluster heatmap visualization and exploration. InCHlib enables the user to select individual or clustered heatmap rows, to zoom in and out of clusters or to flexibly modify heatmap appearance. The cluster heatmap can be augmented with additional metadata displayed in a different colour scale. In addition, to further enhance the visualization, the cluster heatmap can be interconnected with external data sources or analysis tools. Data clustering and the preparation of the input file for InCHlib is facilitated by the Python utility script inchlib_clust. CONCLUSIONS: The cluster heatmap is one of the most popular visualizations of large chemical and biomedical data sets originating, e.g., in high-throughput screening, genomics or transcriptomics experiments. The presented JavaScript library InCHlib is a client-side solution for cluster heatmap exploration. InCHlib can be easily deployed into any modern web application and configured to cooperate with external tools and data sources. Though InCHlib is primarily intended for the analysis of chemical or biological data, it is a versatile tool which application domain is not limited to the life sciences only.

• Klíčová slova
• Big data, Client-side scripting, Cluster heatmap, Data clustering, Exploration, JavaScript library, Scientific visualization, Web integration,
• Publikační typ
• časopisecké články MeSH

Large-scale biodiversity data, for example, on species distribution and richness information, are being mobilized and becoming available at an increasing rate. Interactive web applications like atlases have been developed to visualize available datasets and make them accessible to a wider audience. Web mapping tools are changing rapidly, and different underlying concepts have been developed to visualize datasets at a high cartographic standard.Here, we introduce the Combined Atlas Framework for the development of interactive web atlases for ecological data visualization. We combine two existing approaches: the five stages of the user-centred design approach for web mapping applications and the three U approach for interface success.Subsequently, we illustrate the use of this framework by developing the Atlas of Plant Invasions based on the Global Naturalized Alien Flora (GloNAF) database. This case study illustrates how the newly developed Combined Atlas Framework with a user-centred design philosophy can generate measurable success through communication with the target user group, iterative prototyping and competitive analysis of other existing web mapping approaches.The framework is useful in creating an atlas that employs user feedback to determine usability and utility features within an interactive atlas system. Finally, this framework will enable a better-informed development process of future visualization and dissemination of biodiversity data through web mapping applications and interactive atlases.

• Klíčová slova
• D3, GloNAF, JavaScript, atlas, cartography, framework development, invasive alien species, web mapping, workflow,
• Publikační typ
• časopisecké články MeSH

PDBsum is a web server providing structural information on the entries in the Protein Data Bank (PDB). The analyses are primarily image-based and include protein secondary structure, protein-ligand and protein-DNA interactions, PROCHECK analyses of structural quality, and many others. The 3D structures can be viewed interactively in RasMol, PyMOL, and a JavaScript viewer called 3Dmol.js. Users can upload their own PDB files and obtain a set of password-protected PDBsum analyses for each. The server is freely accessible to all at: http://www.ebi.ac.uk/pdbsum.

• Klíčová slova
• 3D protein structure, PDB, PDBsum, enzymes, molecular interactions, protein database, protein structure analysis, schematic diagrams,
• MeSH
• databáze proteinů * MeSH
• internet * MeSH
• molekulární modely * MeSH
• sekundární struktura proteinů * MeSH
• software * MeSH
• zobrazování trojrozměrné * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The Hypertext Atlas of Dermatopathology, the Atlas of Fetal and Neonatal Pathology and Hypertext Atlas of Pathology (this one in Czech only) are available at http://www.muni.cz/atlases. These atlases offer many clinical, macroscopic and microscopic images, together with short introductory texts. Most of the images are annotated and arrows pointing to the important parts of the image can be activated.The Virtual Microscope interface is used for the access to the histological images obtained in high resolution using automated microscope and image stitching, possibly in more focusing planes. Parts of the image prepared in advance are downloaded on demand to save the memory of the user's computer. The virtual microscope is programmed in JavaScript only, works in Firefox/Mozilla and MSIE browsers without need to install any additional software.

• Publikační typ
• časopisecké články MeSH

SUMMARY: Amino acid residues showing above background levels of conservation are often indicative of functionally significant regions within a protein. Understanding how the sequence conservation profile relates in space requires projection onto a protein structure, a potentially time-consuming process. 3DPatch is a web application that streamlines this task by automatically generating multiple sequence alignments (where appropriate) and finding structural homologs, presenting the user with a choice of structures matching their query, annotated with residue conservation scores in a matter of seconds. AVAILABILITY AND IMPLEMENTATION: 3DPatch is written in JavaScript and is freely available at http://www.skylign.org/3DPatch/. Mozilla Firefox, Google Chrome, and Safari web browsers are supported. Source code is available under MIT license at https://github.com/davidjakubec/3DPatch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• databáze proteinů MeSH
• internetový prohlížeč MeSH
• konformace proteinů * MeSH
• lidé MeSH
• sekvenční seřazení * MeSH
• software * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The "quick mode" allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The "normal mode" integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.

• Klíčová slova
• 2D structure, SNFG notation, carbohydrate, software,
• MeSH
• internetový prohlížeč * MeSH
• polysacharidy chemie   MeSH
• software * MeSH
• výpočetní biologie metody   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• polysacharidy MeSH

Data visualization is a pivotal component of a structural biologist's arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While Mol* provides a wide range of functionality, it has a steep learning curve and is only available via a JavaScript interface. To enhance the accessibility and usability of web-based molecular visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), a standardized approach for defining molecular visualizations that decouples the definition of complex molecular scenes from their rendering. Scene definition can include references to commonly used structural, volumetric, and annotation data formats together with a description of how the data should be visualized and paired with optional annotations specifying colors, labels, measurements, and custom 3D geometries. Developed as an open standard, this solution paves the way for broader interoperability and support across different programming languages and molecular viewers, enabling more streamlined, standardized, and reproducible visual molecular analyses. MolViewSpec is freely available as a Mol* extension and a standalone Python package.

• MeSH
• internet MeSH
• počítačová grafika * MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: Simulators used in teaching are interactive applications comprising a mathematical model of the system under study and a graphical user interface (GUI) that allows the user to control the model inputs and visualize the model results in an intuitive and educational way. Well-designed simulators promote active learning, enhance problem-solving skills, and encourage collaboration and small group discussion. However, creating simulators for teaching purposes is a challenging process that requires many contributors including educators, modelers, graphic designers, and programmers. The availability of a toolchain of user-friendly software tools for building simulators can facilitate this complex task. OBJECTIVE: This paper aimed to describe an open-source software toolchain termed Bodylight.js that facilitates the creation of browser-based client-side simulators for teaching purposes, which are platform independent, do not require any installation, and can work offline. The toolchain interconnects state-of-the-art modeling tools with current Web technologies and is designed to be resilient to future changes in the software ecosystem. METHODS: We used several open-source Web technologies, namely, WebAssembly and JavaScript, combined with the power of the Modelica modeling language and deployed them on the internet with interactive animations built using Adobe Animate. RESULTS: Models are implemented in the Modelica language using either OpenModelica or Dassault Systèmes Dymola and exported to a standardized Functional Mock-up Unit (FMU) to ensure future compatibility. The C code from the FMU is further compiled to WebAssembly using Emscripten. Industry-standard Adobe Animate is used to create interactive animations. A new tool called Bodylight.js Composer was developed for the toolchain that enables one to create the final simulator by composing the GUI using animations, plots, and control elements in a drag-and-drop style and binding them to the model variables. The resulting simulators are stand-alone HyperText Markup Language files including JavaScript and WebAssembly. Several simulators for physiology education were created using the Bodylight.js toolchain and have been received with general acclaim by teachers and students alike, thus validating our approach. The Nephron, Circulation, and Pressure-Volume Loop simulators are presented in this paper. Bodylight.js is licensed under General Public License 3.0 and is free for anyone to use. CONCLUSIONS: Bodylight.js enables us to effectively develop teaching simulators. Armed with this technology, we intend to focus on the development of new simulators and interactive textbooks for medical education. Bodylight.js usage is not limited to developing simulators for medical education and can facilitate the development of simulators for teaching complex topics in a variety of different fields.

• Klíčová slova
• Web browser, Web technologies, computer simulation, education, modeling, physiology,
• MeSH
• internet MeSH
• lidé MeSH
• software normy   MeSH
• studium lékařství metody   MeSH
• uživatelské rozhraní počítače * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Rhinosinusitis is an inflammation of the sinonasal cavity which affects roughly one in seven people per year. Acute rhinosinusitis (ARS) is mostly, apart from allergic etiology, caused by a viral infection and, in some cases (30-50%), by a bacterial superinfection. Antibiotics, indicated only in rare cases according to EPOS guidelines, are nevertheless prescribed in more than 80% of ARS cases, which increases the resistant bacterial strains in the population. METHODS: We have designed a clinical decision support system (CDSS), RHINA, based on a web application created in HTML 5, using JavaScript, jQuery, CCS3 and PHP scripting language. The presented CDSS RHINA helps general physicians to decide whether or not to prescribe antibiotics in patients with rhinosinusitis. RESULTS: In a retrospective study of a total of 1465 patients with rhinosinusitis, the CDSS RHINA presented a 90.2% consistency with the diagnosis and treatment made by the ENT specialist. CONCLUSION: Patients assessed with the assistance of our CDSS RHINA would decrease the over-prescription of antibiotics, which in turn would help to reduce the bacterial resistance to the most commonly prescribed antibiotics.

• Klíčová slova
• Antibiotic resistance, Clinical decision support system, EPOS, Rhinosinusitis,
• MeSH
• chronická nemoc MeSH
• lidé MeSH
• retrospektivní studie MeSH
• rýma * diagnóza   farmakoterapie   MeSH
• sinusitida * diagnóza   farmakoterapie   MeSH
• systémy pro podporu klinického rozhodování * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

SUMMARY: Structures in PDB tend to contain errors. This is a very serious issue for authors that rely on such potentially problematic data. The community of structural biologists develops validation methods as countermeasures, which are also included in the PDB deposition system. But how are these validation efforts influencing the structure quality of subsequently published data? Which quality aspects are improving, and which remain problematic? We developed ValTrendsDB, a database that provides the results of an extensive exploratory analysis of relationships between quality criteria, size and metadata of biomacromolecules. Key input data are sourced from PDB. The discovered trends are presented via precomputed information-rich plots. ValTrendsDB also supports the visualization of a set of user-defined structures on top of general quality trends. Therefore, ValTrendsDB enables users to see the quality of structures published by selected author, laboratory or journal, discover quality outliers, etc. ValTrendsDB is updated weekly. AVAILABILITY AND IMPLEMENTATION: Freely accessible at http://ncbr.muni.cz/ValTrendsDB. The web interface was implemented in JavaScript. The database was implemented in C++. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• databáze proteinů MeSH
• internet MeSH
• proteiny MeSH
• software * MeSH
• uživatelské rozhraní počítače MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• proteiny MeSH