Graphical user interface
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BACKGROUND: Microarray technologies now belong to the standard functional genomics toolbox and have undergone massive development leading to increased genome coverage, accuracy and reliability. The number of experiments exploiting microarray technology has markedly increased in recent years. In parallel with the rapid accumulation of transcriptomic data, on-line analysis tools are being introduced to simplify their use. Global statistical data analysis methods contribute to the development of overall concepts about gene expression patterns and to query and compose working hypotheses. More recently, these applications are being supplemented with more specialized products offering visualization and specific data mining tools. We present a curated gene family-oriented gene expression database, Arabidopsis Gene Family Profiler (aGFP; http://agfp.ueb.cas.cz), which gives the user access to a large collection of normalised Affymetrix ATH1 microarray datasets. The database currently contains NASC Array and AtGenExpress transcriptomic datasets for various tissues at different developmental stages of wild type plants gathered from nearly 350 gene chips. RESULTS: The Arabidopsis GFP database has been designed as an easy-to-use tool for users needing an easily accessible resource for expression data of single genes, pre-defined gene families or custom gene sets, with the further possibility of keyword search. Arabidopsis Gene Family Profiler presents a user-friendly web interface using both graphic and text output. Data are stored at the MySQL server and individual queries are created in PHP script. The most distinguishable features of Arabidopsis Gene Family Profiler database are: 1) the presentation of normalized datasets (Affymetrix MAS algorithm and calculation of model-based gene-expression values based on the Perfect Match-only model); 2) the choice between two different normalization algorithms (Affymetrix MAS4 or MAS5 algorithms); 3) an intuitive interface; 4) an interactive "virtual plant" visualizing the spatial and developmental expression profiles of both gene families and individual genes. CONCLUSION: Arabidopsis GFP gives users the possibility to analyze current Arabidopsis developmental transcriptomic data starting with simple global queries that can be expanded and further refined to visualize comparative and highly selective gene expression profiles.
A tangible user interface or TUI connects physical objects and digital interfaces. It is more interactive and interesting for users than a classic graphic user interface. This article presents a descriptive overview of TUI's real-world applications sorted into ten main application areas-teaching of traditional subjects, medicine and psychology, programming, database development, music and arts, modeling of 3D objects, modeling in architecture, literature and storytelling, adjustable TUI solutions, and commercial TUI smart toys. The paper focuses on TUI's technical solutions and a description of technical constructions that influences the applicability of TUIs in the real world. Based on the review, the technical concept was divided into two main approaches: the sensory technical concept and technology based on a computer vision algorithm. The sensory technical concept is processed to use wireless technology, sensors, and feedback possibilities in TUI applications. The image processing approach is processed to a marker and markerless approach for object recognition, the use of cameras, and the use of computer vision platforms for TUI applications.
- Klíčová slova
- augmented reality, education, sensors, smart object, tangible, tangible user interface,
- MeSH
- hra a hračky * MeSH
- lidé MeSH
- uživatelské rozhraní počítače * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
UNLABELLED: The new version of the TRITON program provides user-friendly graphical tools for modeling protein mutants using the external program MODELLER and for docking ligands into the mutants using the external program AutoDock. TRITON can now be used to design ligand-binding proteins, to study protein-ligand binding mechanisms or simply to dock any ligand to a protein. AVAILABILITY: Executable files of TRITON are available free of charge for academic users at http://ncbr.chemi.muni.cz/triton/
- MeSH
- algoritmy MeSH
- chemické modely * MeSH
- ligandy MeSH
- molekulární modely * MeSH
- počítačová grafika * MeSH
- počítačová simulace MeSH
- proteinové inženýrství metody MeSH
- proteiny chemie ultrastruktura MeSH
- racionální návrh léčiv MeSH
- software * MeSH
- uživatelské rozhraní počítače MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- ligandy MeSH
- proteiny MeSH
With the advent of OMICs technologies, both individual research groups and consortia have spear-headed the characterization of human samples of multiple pathophysiologic origins, resulting in thousands of archived genomes and transcriptomes. Although a variety of web tools are now available to extract information from OMICs data, their utility has been limited by the capacity of nonbioinformatician researchers to exploit the information. To address this problem, we have developed CANCERTOOL, a web-based interface that aims to overcome the major limitations of public transcriptomics dataset analysis for highly prevalent types of cancer (breast, prostate, lung, and colorectal). CANCERTOOL provides rapid and comprehensive visualization of gene expression data for the gene(s) of interest in well-annotated cancer datasets. This visualization is accompanied by generation of reports customized to the interest of the researcher (e.g., editable figures, detailed statistical analyses, and access to raw data for reanalysis). It also carries out gene-to-gene correlations in multiple datasets at the same time or using preset patient groups. Finally, this new tool solves the time-consuming task of performing functional enrichment analysis with gene sets of interest using up to 11 different databases at the same time. Collectively, CANCERTOOL represents a simple and freely accessible interface to interrogate well-annotated datasets and obtain publishable representations that can contribute to refinement and guidance of cancer-related investigations at all levels of hypotheses and design.Significance: In order to facilitate access of research groups without bioinformatics support to public transcriptomics data, we have developed a free online tool with an easy-to-use interface that allows researchers to obtain quality information in a readily publishable format. Cancer Res; 78(21); 6320-8. ©2018 AACR.
- MeSH
- algoritmy MeSH
- databáze faktografické MeSH
- databáze genetické MeSH
- genomika MeSH
- internet MeSH
- lékařská onkologie MeSH
- lidé MeSH
- nádory genetika MeSH
- počítačová grafika MeSH
- proteomika MeSH
- průběh práce MeSH
- software MeSH
- transkriptom MeSH
- uživatelské rozhraní počítače MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
UNLABELLED: The transport of ligands, ions or solvent molecules into proteins with buried binding sites or through the membrane is enabled by protein tunnels and channels. CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures. It provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. AVAILABILITY AND IMPLEMENTATION: CAVER Analyst is a multi-platform software written in JAVA. Binaries and documentation are freely available for non-commercial use at http://www.caver.cz.
Ever-increasing availability of experimental volumetric data (e.g., in .ccp4, .mrc, .map, .rec, .zarr, .ome.tif formats) and advances in segmentation software (e.g., Amira, Segger, IMOD) and formats (e.g., .am, .seg, .mod, etc.) have led to a demand for efficient web-based visualization tools. Despite this, current solutions remain scarce, hindering data interpretation and dissemination. Previously, we introduced Mol* Volumes & Segmentations (Mol* VS), a web application for the visualization of volumetric, segmentation, and annotation data (e.g., semantically relevant information on biological entities corresponding to individual segmentations such as Gene Ontology terms or PDB IDs). However, this lacked important features such as the ability to edit annotations (e.g., assigning user-defined descriptions of a segment) and seamlessly share visualizations. Additionally, setting up Mol* VS required a substantial programming background. This article presents an updated version, Mol* VS 2.0, that addresses these limitations. As part of Mol* VS 2.0, we introduce the Annotation Editor, a user-friendly graphical interface for editing annotations, and the Volumes & Segmentations Toolkit (VSToolkit) for generating shareable files with visualization data. The outlined protocols illustrate the utilization of Mol* VS 2.0 for visualization of volumetric and segmentation data across various scales, showcasing the progress in the field of molecular complex visualization. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: VSToolkit-setting up and visualizing a user-constructed Mol* VS 2.0 database entry Basic Protocol 2: VSToolkit-visualizing multiple time frames and volume channels Support Protocol 1: Example: Adding database entry idr-13457537 Alternate Protocol 1: Local-server-and-viewer-visualizing multiple time frames and volume channels Support Protocol 2: Addition of database entry custom-tubhiswt Basic Protocol 3: VSToolkit-visualizing a specific channel and time frame Basic Protocol 4: VSToolkit-visualizing geometric segmentation Basic Protocol 5: VSToolkit-visualizing lattice segmentations Alternate Protocol 2: "Local-server-and-viewer"-visualizing lattice segmentations Basic Protocol 6: "Local-server-and-viewer"-visualizing multiple volume channels Support Protocol 3: Deploying a server API Support Protocol 4: Hosting Mol* viewer with VS extension 2.0 Support Protocol 5: Example: Addition of database entry empiar-11756 Support Protocol 6: Example: Addition of database entry emd-1273 Support Protocol 7: Editing annotations Support Protocol 8: Addition of database entry idr-5025553.
- Klíčová slova
- 3D visualization tools, annotation data, large‐scale datasets, segmentation data, volumetric data,
- MeSH
- internet MeSH
- počítačová grafika MeSH
- software * MeSH
- uživatelské rozhraní počítače MeSH
- vizualizace dat MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND AND OBJECTIVE: Functional magnetic resonance imaging (fMRI) studies of the human brain are appearing in increasing numbers, providing interesting information about this complex system. Unique information about healthy and diseased brains is inferred using many types of experiments and analyses. In order to obtain reliable information, it is necessary to conduct consistent experiments with large samples of subjects and to involve statistical methods to confirm or reject any tested hypotheses. Group analysis is performed for all voxels within a group mask, i.e. a common space where all of the involved subjects contribute information. To our knowledge, a user-friendly interface with the ability to visualize subject-specific details in a common analysis space did not yet exist. The purpose of our work is to develop and present such interface. METHODS: Several pitfalls have to be avoided while preparing fMRI data for group analysis. One such pitfall is spurious non-detection, caused by inferring conclusions in the volume of a group mask that has been corrupted due to a preprocessing failure. We describe a MATLAB toolbox, called the mask_explorer, designed for prevention of this pitfall. RESULTS: The mask_explorer uses a graphical user interface, enables a user-friendly exploration of subject masks and is freely available. It is able to compute subject masks from raw data and create lists of subjects with potentially problematic data. It runs under MATLAB with the widely used SPM toolbox. Moreover, we present several practical examples where the mask_explorer is usefully applied. CONCLUSIONS: The mask_explorer is designed to quickly control the quality of the group fMRI analysis volume and to identify specific failures related to preprocessing steps and acquisition. It helps researchers detect subjects with potentially problematic data and consequently enables inspection of the data.
- Klíčová slova
- Dataset explorer, Group analysis, Preprocessing, Statistical parametric mapping, Tool, fMRI,
- MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody MeSH
- mozek fyziologie MeSH
- počítačová grafika MeSH
- uživatelské rozhraní počítače MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
UNLABELLED: Expertomica Cells is a program for the creation and analysis of pedigree plots from time-lapse micrographs of cell monolayers. It enables recording the basic events in a cell cycle, cell neighbourhoods and spatial migration. The output is both numeric and graphical. The software helps to lower main hurdles in the manual analysis of cell monolayer development to practical limits; it reduces the operator processing time of typical experiment containing 5000 consecutive images from the usual 3 months to 3-10 h. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at http://www.expertomicacells.tk or http://www.expertomicacells.wu.cz. The source code is implemented in JAVA 6 and supported by Linux, Mac and MS Windows. SUPPLEMENTARY INFORMATION: Supplementary data available at Bioinformatics online.
The design of new materials for technological applications is increasingly being assisted by online computational tools that facilitate the study of their properties. In this work, based on modern web application frameworks, the online app MAELASviewer has been developed to visualize and analyze magnetostriction via a user-friendly interactive graphical interface. The features and technical details of this new tool are described in detail. Among other applications, it could potentially be used for the design of magnetostrictive materials for sensors and actuators.
- Klíčová slova
- graphical user interface, magnetoelastic effects, magnetostriction, visualization, web application,
- Publikační typ
- dopisy 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
