BioDat is a software tool that simplifies routine recording, storing and analyzing technical and biological 1D signals. The basic features of the BioDat software are: database format based on PhysioNet, a shared database of signals running in network environment accessible for users with permissions, importing and/or exporting data from and/or to different formats (d-file, EDF, ASCII, Matlab), accessing the database through HTTP(S) and ordinary web browsers. The application is written in Java and runs both standalone and as installation-free Java applet.
Enzymes are in high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field.
- MeSH
- Biotechnology * MeSH
- Internet * MeSH
- Solubility MeSH
- Computational Biology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
V rámci konference seznamujeme s e-learningovým kurzem “Management kvality ve zdravotnických organizacích”, který prošel akreditací příslušných ministerstev v několika státech EU. Současně předvedeme software “Simulační hra manažerských rolí – QM-RPS”. V současnosti jsou dostupné čtyři základní a deset volitelných modulů (různé kurzy/předměty v závislosti na individuálních požadavcích zákazníků). Kurz naplňje požadavky harmonizovaného schématu Evropské organizace pro kvalitu (EOQ) pro manažéry kvality. Ozřejmíme požadavek na potřebné zapojení laické komunity (občanů) do oblasti managementu kvality ve zdravotnickém prostředí. Kurz lze provozovat v rámci různých prostředí Webu. Předkládáme průběžné poznatky získané v rámci empirického výzkumu projektů Leonardo da Vinci SK 03/B/F/PP – 177014 “IMPROHEALTH", SK/06/3/F/PP – 177443 "IMPROHEALTH _COLLABORATIVE" and KEGA 3-4121-06 “Webové portály nástrojů, metod a případových studií managementu kvality, (“Web portal of tools, methods and case studies of the quality management".)
The aim of this paper is to present courseware "Quality Management in Healthcare Organization" supported by international projects and accredited by the respective ministries in some EU countries, and software "Quality Management Role-Play Simulation QM-RPS”. Four basic and ten optional modules (courses/subjects according to special custom requirements) have been developed. The course is in concert with the requirements of the harmonized scheme of the European Organization for Quality (EOQ) as related to quality nanagers. A claim for involvement of laypeople (citizens) in healthcare quality management will be discussed. Examples of "Quality Management in Healthcare" and application of Role-Play Simulation will be shown. The courseware and simulation can be embedded into different Web learning environments. We present ongoing and continuous knowledge acquired from theoretical and empirical research in projects Leonardo da Vinci SK 03/B/F/PP – 177014 “IMPROHEALTH", SK/06/3/F/PP – 177443 "IMPROHEALTH _COLLABORATIVE" and KEGA 3-4121-06 “Web portal of tools, methods and case studies of quality management".
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.
- MeSH
- Alleles * MeSH
- Arabidopsis * genetics MeSH
- Data Mining * methods MeSH
- Datasets as Topic * MeSH
- Gene Frequency MeSH
- Genotype MeSH
- Glycine max * genetics MeSH
- Internet * MeSH
- Zea mays * genetics MeSH
- Metadata MeSH
- Mutation MeSH
- Pigmentation genetics MeSH
- Genes, Plant genetics MeSH
- Software * MeSH
- Amino Acid Substitution MeSH
- Plant Dormancy genetics MeSH
- Data Visualization MeSH
- Publication type
- Journal Article MeSH
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.
Background: The aim of this review was to summarise the experience on implementation of information technology to support the teaching and learning process in medicine. Particular attention was paid to web-based tutorials, their impact on increasing the effectiveness of medical instruction and motivation of students towards self-directed learning. Most of the studies selected for the purpose of the review comprised evaluation of the web-tutorials in view of practical implementation, strengths, weaknesses, and main preferences in comparison with traditional lecture-based education. METHOD AND RESULTS: We searched MEDLINE via PubMed using MeSH term "computer-assisted learning" between 1996 and 2005 and selected for inclusion in this review were studies on the implementation and evaluation of web based tutorials in medical education. Additional related papers were obtained through cross-referencing. We found that overall, students prefer Web tutorials to traditional lecture-based classes for accessibility, ease of use, freedom of navigation, high medical image quality and advantage of repeated practice, that web-based learning has been continually developing and that it is a very important tool in Evidence Based Medicine. CONCLUSIONS: Web based education is an important tool in medical training. It will require transformation in the way medicine is taught from instructor based to self directed learning. It is above all seen as a device for information retrieval and storage.
- MeSH
- Internet MeSH
- Computer-Assisted Instruction MeSH
- Education, Medical, Undergraduate MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
- Geographicals
- Czech Republic MeSH
MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introduce microRNA sponge generator and tester (miRNAsong), a freely available web-based tool for generation and in silico testing of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation. URL: http://www.med.muni.cz/histology/miRNAsong/.
- MeSH
- HEK293 Cells MeSH
- Internet * MeSH
- Humans MeSH
- RNA, Messenger metabolism MeSH
- MicroRNAs genetics metabolism MeSH
- Computer Simulation MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The change in pedagogy relates partly to the development of electronic media and communication possibilities that are available in networked environments. This new technology dominates and supports the international educational content and learning. The aim of our study was to evaluate this progress in dental edu cation. The education was compared parallel in two groups of Czech and international students. Groups and teaching hours were in the fourth year of the MD curriculum. Stomatology course materials were prepared and published on the portals of the individual dental study programs 1 . The lectures had different access levels, ranging from materials that were freely available to all International WEB dental faculties’ sources to materials that were accessible only after receiving permission from the authors. A number of software tools were used for the creation of e-learning courses, such as, e.g., WebCT, Blackboard, Adobe Connect or Microsoft Class Server. The 291 stu - dents who were included in our study were divided into two groups according to the e-learning program. The goal of our study was to check student activities during the educational process, namely online work – lessons, articles, videos, lite rature, quiz - zes and direct Internet access. The statisticaly significant differences were found in the results of the questionnaire based on five-point Likert scale. The Mann Whitney non- parametric test was used to evaluate students’ activities during the edu cation process. The e-learning course had a direct influence on learning experiences, dental informa - tion, opinions and comments. Our results verified that satisfaction is an important and influential factor in determining whether a student decides to choose a dentistry and maxillofacial surgery course. Students prefer to have more time for practical therapy in the clinic. It was demonstrated that examination results did not correspond to the type of education but it was confirmed that e-learning helped to prepare students for practical training.
- MeSH
- Internet MeSH
- Humans MeSH
- Computer-Assisted Instruction * classification statistics & numerical data trends MeSH
- Surveys and Questionnaires MeSH
- Oral Medicine education MeSH
- Students, Dental MeSH
- Education, Dental methods MeSH
- Dentistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
The paper is a presentation of the current state of development for the Atlas of Physiology and Pathophysiology (Atlas). Our main aim is to provide a novel interactive multimedia application that can be used for biomedical education where (a) simulations are combined with tutorials and (b) the presentation layer is simplified while the underlying complexity of the model is retained. The development of the Atlas required the cooperation of many professionals including teachers, system analysts, artists, and programmers. During the design of the Atlas, tools were developed that allow for component-based creation of simulation models, creation of interactive multimedia and their final coordination into a compact unit based on the given design. The Atlas is a freely available online application, which can help to explain the function of individual physiological systems and the causes and symptoms of their disorders.
- MeSH
- Atlases as Topic MeSH
- Physiology MeSH
- Internet MeSH
- Computer Simulation MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Partial atomic charges serve as a simple model for the electrostatic distribution of a molecule that drives its interactions with its surroundings. Since partial atomic charges are frequently used in computational chemistry, chemoinformatics and bioinformatics, many computational approaches for calculating them have been introduced. The most applicable are fast and reasonably accurate empirical charge calculation approaches. Here, we introduce Atomic Charge Calculator II (ACC II), a web application that enables the calculation of partial atomic charges via all the main empirical approaches and for all types of molecules. ACC II implements 17 empirical charge calculation methods, including the highly cited (QEq, EEM), the recently published (EQeq, EQeq+C), and the old but still often used (PEOE). ACC II enables the fast calculation of charges even for large macromolecular structures. The web server also offers charge visualization, courtesy of the powerful LiteMol viewer. The calculation setup of ACC II is very straightforward and enables the quick calculation of high-quality partial charges. The application is available at https://acc2.ncbr.muni.cz.
- MeSH
- Phenols chemistry MeSH
- Internet MeSH
- Models, Molecular * MeSH
- Molecular Structure MeSH
- Receptors, Nicotinic chemistry MeSH
- bcl-2-Associated X Protein chemistry MeSH
- Software * MeSH
- Static Electricity MeSH
- Hydrogen chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
