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: Remote measurement technology (RMT) involves the use of wearable devices and smartphone apps to measure health outcomes in everyday life. RMT with feedback in the form of data visual representations can facilitate self-management of chronic health conditions, promote health care engagement, and present opportunities for intervention. Studies to date focus broadly on multiple dimensions of service users' design preferences and RMT user experiences (eg, health variables of perceived importance and perceived quality of medical advice provided) as opposed to data visualization preferences. OBJECTIVE: This study aims to explore data visualization preferences and priorities in RMT, with individuals living with depression, those with epilepsy, and those with multiple sclerosis (MS). METHODS: A triangulated qualitative study comparing and thematically synthesizing focus group discussions with user reviews of existing self-management apps and a systematic review of RMT data visualization preferences. A total of 45 people participated in 6 focus groups across the 3 health conditions (depression, n=17; epilepsy, n=11; and MS, n=17). RESULTS: Thematic analysis validated a major theme around design preferences and recommendations and identified a further four minor themes: (1) data reporting, (2) impact of visualization, (3) moderators of visualization preferences, and (4) system-related factors and features. CONCLUSIONS: When used effectively, data visualizations are valuable, engaging components of RMT. Easy to use and intuitive data visualization design was lauded by individuals with neurological and psychiatric conditions. Apps design needs to consider the unique requirements of service users. Overall, this study offers RMT developers a comprehensive outline of the data visualization preferences of individuals living with depression, epilepsy, and MS.
- Klíčová slova
- application, data, data visualization, depression, devices, epilepsy, feedback, mHealth, mobile phone, multiple sclerosis, qualitative, smartphone apps, technology, users, wearables,
- MeSH
- deprese * psychologie MeSH
- dospělí MeSH
- epilepsie * psychologie MeSH
- kvalitativní výzkum * MeSH
- lidé středního věku MeSH
- lidé MeSH
- mobilní aplikace MeSH
- nositelná elektronika MeSH
- pacientova volba psychologie statistika a číselné údaje MeSH
- roztroušená skleróza * psychologie MeSH
- senioři MeSH
- telemedicína MeSH
- vizualizace dat MeSH
- zjišťování skupinových postojů * MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
OBJECTIVE: Dynamic systems theory and complexity theory (DST/CT) is a framework explaining how complex systems change and adapt over time. In psychotherapy, DST/CT can be used to understand how a person's mental and emotional state changes during therapy incorporating higher levels of complexity. This study aimed to systematically review the variability of DST/CT methods applied in psychotherapy research. METHODS: A primary studies search was conducted in the EBSCO and Web of Knowledge databases, extracting information about the analyzed DST/CT phenomena, employed mathematical methods to investigate these phenomena, descriptions of specified dynamic models, psychotherapy phenomena, and other information regarding studies with empirical data (e.g., measurement granularity). RESULTS: After screening 38,216 abstracts and 4,194 full texts, N = 41 studies published from 1990 to 2021 were identified. The employed methods typically included measures of dynamic complexity or chaoticity. Computational and simulation studies most often employed first-order ordinary differential equations and typically focused on describing the time evolution of client-therapist dyadic influences. Eligible studies with empirical data were usually based on case studies and focused on data with high time intensity of within-session dynamics. CONCLUSION: This review provides a descriptive synthesis of the current state of the proliferation of DST/CT methods in the psychotherapy research field.
- Klíčová slova
- chaos theory, complex systems, differential equations, nonlinearity, psychotherapy, systematic review,
- MeSH
- adaptace psychologická MeSH
- lidé MeSH
- nelineární dynamika * MeSH
- psychologie * metody MeSH
- psychoterapie * MeSH
- systémová teorie * MeSH
- teoretické modely MeSH
- vizualizace dat MeSH
- výzkumný projekt * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- systematický přehled MeSH
BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
- Klíčová slova
- Allele Catalog Pipeline, Allele Catalog Tool, Alleles in Gene, Data Visualization, Variant Calling Pipeline,
- MeSH
- alely * MeSH
- Arabidopsis * genetika MeSH
- data mining * metody MeSH
- datové soubory jako téma * MeSH
- frekvence genu MeSH
- genotyp MeSH
- Glycine max * genetika MeSH
- internet * MeSH
- kukuřice setá * genetika MeSH
- metadata MeSH
- mutace MeSH
- pigmentace genetika MeSH
- rostlinné geny genetika MeSH
- software * MeSH
- substituce aminokyselin MeSH
- vegetační klid genetika MeSH
- vizualizace dat MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- DOG1 protein, Arabidopsis MeSH Prohlížeč
During the time of the novel coronavirus disease 2019 (COVID-19) pandemic, it has been crucial to search for novel antiviral drugs from plants and well as other natural sources as alternatives for prophylaxis. This work reviews the antiviral potential of plant extracts, and the results of previous research for the treatment and prophylaxis of coronavirus disease and previous kinds of representative coronaviruses group. Detailed descriptions of medicinal herbs and crops based on their origin native area, plant parts used, and their antiviral potentials have been conducted. The possible role of plant-derived natural antiviral compounds for the development of plant-based drugs against coronavirus has been described. To identify useful scientific trends, VOSviewer visualization of presented scientific data analysis was used.
- Klíčová slova
- COVID-19, biological active compounds, coronaviruses group, plant chemo-diversity,
- MeSH
- alkaloidy chemie farmakologie MeSH
- antivirové látky chemie terapeutické užití MeSH
- COVID-19 prevence a kontrola MeSH
- farmakoterapie COVID-19 MeSH
- flavonoidy chemie farmakologie MeSH
- léčivé rostliny chemie MeSH
- lidé MeSH
- rostlinné extrakty chemie farmakologie terapeutické užití MeSH
- terpeny chemie farmakologie MeSH
- vizualizace dat MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- alkaloidy MeSH
- antivirové látky MeSH
- flavonoidy MeSH
- rostlinné extrakty MeSH
- terpeny MeSH
