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Ústav zdravotnických informací a statistiky ČR produkuje dlouhodobě velké množství hodnotných analýz, reportů a publikací, které jsou zaměřeny na širokou veřejnost, zástupce krajské správy a poskytovatele zdravotní péče. Primárním cílem sdělení je přehledově představit sadu nově implementovaných interaktivních webových portálů, které prezentují klíčové výstupy vybraných projektů a aktivit.
Institute of Health Information and Statistics of the Czech Republic has been producing many valuable analyses, reports and publications, which are focused mainly on the public, regional representatives and healthcare providers. The primary goal of this contribution is to introduce a set of developed and implemented web-based platforms representing key outputs of selected projects and activities under the umbrella of Institute of Health Information and Statistics.
BACKGROUND: Structural biomolecular data are commonly stored in the PDB format. The PDB format is widely supported by software vendors because of its simplicity and readability. However, the PDB format cannot fully address many informatics challenges related to the growing amount of structural data. To overcome the limitations of the PDB format, a new textual format mmCIF was released in June 1997 in its version 1.0. mmCIF provides extra information which has the advantage of being in a computer readable form. However, this advantage becomes a disadvantage if a human must read and understand the stored data. While software tools exist to help to prepare mmCIF files, the number of available systems simplifying the comprehension and interpretation of the mmCIF files is limited. FINDINGS: In this paper we present mmView - a cross-platform web-based application that allows to explore comfortably the structural data of biomacromolecules stored in the mmCIF format. The mmCIF categories can be easily browsed in a tree-like structure, and the corresponding data are presented in a well arranged tabular form. The application also allows to display and investigate biomolecular structures via an integrated Java application Jmol. CONCLUSIONS: The mmView software system is primarily intended for educational purposes, but it can also serve as a useful research tool. The mmView application is offered in two flavors: as an open-source stand-alone application (available from http://sourceforge.net/projects/mmview) that can be installed on the user's computer, and as a publicly available web server.
- Publication type
- Journal Article MeSH
PURPOSE: Rapid identification and characterization of multidrug-resistant Klebsiella pneumoniae strains is necessary due to the increasing frequency of severe infections in patients. The decreasing cost of next-generation sequencing enables us to obtain a comprehensive overview of genetic information in one step. The aim of this study is to demonstrate and evaluate the utility and scope of the application of web-based databases to next-generation sequenced (NGS) data. METHODOLOGY: The whole genomes of 11 clinical Klebsiella pneumoniae isolates were sequenced using Illumina MiSeq. Selected web-based tools were used to identify a variety of genetic characteristics, such as acquired antimicrobial resistance genes, multilocus sequence types, plasmid replicons, and identify virulence factors, such as virulence genes, cps clusters, urease-nickel clusters and efflux systems. RESULTS: Using web-based tools hosted by the Center for Genomic Epidemiology, we detected resistance to 8 main antimicrobial groups with at least 11 acquired resistance genes. The isolates were divided into eight sequence types (ST11, 23, 37, 323, 433, 495 and 562, and a new one, ST1646). All of the isolates carried replicons of large plasmids. Capsular types, virulence factors and genes coding AcrAB and OqxAB efflux pumps were detected using BIGSdb-Kp, whereas the selected virulence genes, identified in almost all of the isolates, were detected using CLC Genomic Workbench software. CONCLUSION: Applying appropriate web-based online tools to NGS data enables the rapid extraction of comprehensive information that can be used for more efficient diagnosis and treatment of patients, while data processing is free of charge, easy and time-efficient.
- MeSH
- Anti-Bacterial Agents pharmacology MeSH
- Databases, Genetic MeSH
- DNA, Bacterial genetics MeSH
- Genome, Bacterial * MeSH
- Internet MeSH
- Klebsiella pneumoniae genetics MeSH
- Drug Resistance, Multiple, Bacterial genetics MeSH
- Multilocus Sequence Typing MeSH
- Plasmids MeSH
- Base Sequence MeSH
- Publication type
- Journal Article MeSH
Biomolecular channels play important roles in many biological systems, e.g. enzymes, ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of (bio)macromolecular channels, tunnels and pores. Results are presented in a clear manner, making their interpretation easy. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The users can tune advanced parameters when performing a channel search to direct the search according to their needs. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz.
- MeSH
- Cytochrome P-450 CYP3A chemistry MeSH
- Enzymes chemistry MeSH
- Internet MeSH
- Ion Channels chemistry MeSH
- Protein Conformation MeSH
- Models, Molecular MeSH
- Computer Graphics MeSH
- Ribosomes chemistry MeSH
- Software MeSH
- User-Computer Interface MeSH
- Ribosome Subunits, Large, Archaeal chemistry MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The phenomenon of treatment and social rehabilitation of people with addiction is inherently based on the cooperation and collaboration of many disciplines. These are mainly: psychiatry, addictionology, special pedagogy, andragogy, psychology and social work. The knowledge and experience of experts from the above mentioned fields and from the described institutions in the context of cooperation with information technology experts is reflected in the main result of the product discussed in the article. This is the software: a web application for mobile phones and other devices. The Five Ways to Wellbeing method is a powerful tool for promoting mental health and wellbeing that has been developed by the UK NHS. This method focuses on five key areas that can help maintain good mental health and prevent relapse. These are 1. keeping in touch with other people, 2. regular exercise, 3. maintaining mindfulness, 4. learning new things, and 5. altruism. This article presents part of the results of an evaluation study conducted within the framework of the TAČR project ÉTA: Application for the development of social competences of people with addiction in the context of indications for special education and therapeutic intervention, reg. no.: TL05000482. The project is guaranteed by Palacký University in Olomouc. The research was conducted at P-Centrum z.s., non-profit organization focused on addictology services, which is the application guaranty of the project. The aim of the paper is to present how the research implemented the Five Ways to Wellbeing methods into a web-based application for E-health. The methodological design of the study is based on qualitative research, specifically an evaluation study. The results suggest that the Five ways to wellbeing method is suitable for implementation in this web-based application and offers further potential in addiction treatment and relapse prevention.
SUMMARY: We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.
E-photosynthesis framework is a web-based platform for modeling and analysis of photosynthetic processes. Compared to its earlier version, the present platform employs advanced software methods and technologies to support an effective implementation of vastly diverse kinetic models of photosynthesis. We report on the first phase implementation of the tool new version and demonstrate the functionalities of model visualization, presentation of model components, rate constants, initial conditions and of model annotation. The demonstration also includes export of a model to the Systems Biology Markup Language format and remote numerical simulation of the model.
