Graphical user interface
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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
- financování organizované 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
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.
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
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.
- 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
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.
Přehledový článek seznámí v přiměřeném detailu s řízenou klinickou terminologií SNOMED CT, se souvisejícími přístupy, postupy, principy a technologiemi. Hlavními tématy jsou terminologický obsah, logický model, principy a možnosti pre- a post-koordinace a využití SNOMED CT v grafickém uživatelském rozhraní klinického informačního systému. Článek odkazuje na klíčové zdroje o SNOMED CT a tak může posloužit jako výchozí studijní materiál pro hlubší seznámení se a detailní studium SNOMED CT.
This overview article introduces controlled clinical terminology SNOMED CT in a reasonable detail suitable for the Czech national environment. Not only the content of the terminology is described but it also deals with related approaches, methods, principles and technologies. The main topics are terminological content, logical model, principles and possibilities of pre- and post-coordination and use of SNOMED CT in the graphical user interface of clinical information systems. The article refers to key resources of SNOMED CT and thus may serve as a starting point for a deeper study of SNOMED CT.
- MeSH
- databáze jako téma MeSH
- SNOMED * MeSH
- terminologie jako téma MeSH
- uživatelské rozhraní počítače MeSH
- Publikační typ
- přehledy 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.
- 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
A new portable CE instrument is presented. The instrument features the concurrent separation of anions and cations in parallel channels. Each channel has a separate buffer container to allow independent optimization of separation conditions. The microfluidics circuit is based on off-the-shelf parts, and can be easily replicated; only four valves are present in the design. The system employs a miniature automated syringe pump, which can apply both positive and negative pressures (-100 to 800 kPa). The application of negative pressure allows a semi-automatic mode of operation for introducing volume-limited samples. The separations are performed in a thermostatted compartment for improved reproducibility in field conditions. The instrument has a compact design, with all components, save for batteries and power supplies, arranged in a briefcase with dimensions of 52 × 34 × 18 cm and a weight of less than 15 kg. The system runs automatically and is controlled by a purpose-made graphical user interface on a connected computer. For demonstration, the system was successfully employed for the concurrent separation and analysis of inorganic cations and anions in sediment porewater samples from Lake Baldegg in Switzerland and of metal ions in a sample from the tailing pond of an abandoned mine in Argentina.
In this work, a MATLAB-based graphical user interface is proposed for the visual examination of several eye movements. The proposed solution is algorithm-based, which localizes the area of the eye movement, removes artifacts, and calculates the view trajectory in terms of direction and orb deviation. To compute the algorithm, a five-electrode configuration is needed. The goodness of the proposed MATLAB-based graphical user interface has been validated, at the Clinic of Child Neurology of University Hospital of Ostrava, through the EEG Wave Program, which was considered as "gold standard" test. The proposed solution can help physicians on studying cerebral diseases, or to be used for the development of human-machine interfaces useful for the improvement of the digital era that surrounds us today.
- Klíčová slova
- Matlab,
- MeSH
- dospělí MeSH
- elektrookulografie * metody MeSH
- lidé MeSH
- měření pohybů očí MeSH
- mrkání MeSH
- pohyby očí MeSH
- software MeSH
- technologie sledování pohybu očí MeSH
- uživatelské rozhraní počítače MeSH
- výzkum MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
- práce podpořená grantem MeSH
S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings.
