MOTIVATION: Expanding research highlights the importance of guanine quadruplex structures. Therefore, easy-accessible tools for quadruplex analyses in DNA and RNA molecules are important for the scientific community. RESULTS: We developed a web version of the G4Hunter application. This new web-based server is a platform-independent and user-friendly application for quadruplex analyses. It allows retrieval of gene/nucleotide sequence entries from NCBI databases and provides complete characterization of localization and quadruplex propensity of quadruplex-forming sequences. The G4Hunter web application includes an interactive graphical data representation with many useful options including visualization, sorting, data storage and export. AVAILABILITY AND IMPLEMENTATION: G4Hunter web application can be accessed at: http://bioinformatics.ibp.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- DNA MeSH
- G-Quadruplexes * MeSH
- Guanine MeSH
- Internet MeSH
- Computers MeSH
- Sequence Analysis, DNA MeSH
- Software MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Využití metod průzkumové analýzy dat (exploratory data analysis, EDA) je při hodnocení klinických dat v medicíně klíčovou fází. Vizualizační principy, modely poukazující na trendy vývoje či např. znázornění potenciálních závislostí, pomáhají k lepší interpretaci měření a v diagnostickém rozhodování. Počet dostupných moderních EDA balíků pro vývojáře v posledních letech roste v souvislosti s rozvojem oboru Data Science. NeuroEDA je interaktivní webová aplikace pro hodnocení biomedicínských dat. Aplikace byla naprogramována ve statistickém jazyce R, v rámci reaktivního paradigmatu frameworku Shiny. Je dále rozvíjena a využívána Katedrou biomedicínské informatiky FBMI ČVUT ve spolupráci s Neurologickou klinikou 1. LF UK a VFN v Praze, především pro hodnocení pacientů s dystoniemi a Parkinsonovou nemocí. Zpracování uživatelských dat v tabulkové formě (.csv, excel) probíhá v serverové části. Kromě základních popisných statistik, průzkumových grafů a shlukové analýzy, které jsou vhodné i pro hodnocení velkých dat, nabízí aplikace metody pro robustní a neparametrickou analýzu. Ty jsou v neurologii obzvlášť vhodné. Typicky z důvodu malých počtů a vlivných pozorování. Dále kvůli častému nesplnění dalších statistických předpokladů. Mezi její výhody patří snadná rozšiřitelnost o nové R balíky a rychlá odezva ve webových prohlížečích. Uživatelské interaktivní prostředí umožňuje práci s funkcemi jazyka R bez znalosti skriptování.
Usage of methods for exploratory data analysis (EDA) plays an important role in assessment of clinical medical data. Visualizations, models and illustration of dependency can help for better understanding of measurements in the diagnostics and making decision. The number of available modern EDA packages for developers is increasing as well as the development of the Data Science field. NeuroEDA is an interactive web application for biomedical data assessment. The application was programmed in the R statistical language, based on reactive paradigm framework called Shiny. It is further developed and used by the Department of Biomedical Informatics FBME CTU in cooperation with the Neurological Clinic of the 1st Medical Faculty, Charles University in Prague. Especially for the patients with dystonia and Parkinson's disease. Computations and processing of user data are executed on the server side. Basic descriptive statistics, interactive graphs, clustering, robust and LOESS regression were implemented and are suitable for analytics of big data. Robust regression is especially suitable in neurology. Typically, due to the small numbers of measured observations and failure to prove other statistical assumptions. Among its advantages we can consider easy expandability of new R packages and quick response in web browsers. User interface allows to work with the R language features without any scripting knowledge.
Control Web je distribuované objektové prostředí pro vývoj aplikací reálného času, vizualizaci procesů a simulací s využitím platformy Windows, vyvíjená více než 20 let. V průmyslových aplikacích se Control Web stal v ČR de facto velmi rozšířeným standardem. Pro tvorbu biomedicínských přístrojů nabízí možnosti snadného vizuálního návrhu jednotlivých řídících a vizualizačních komponent biotechnologických přístrojů. Jednou z dalších možností je i využití systému pro vizualizaci výukových simulací. Předchozí verzi tohoto systému byla např. využita pro realizaci simulátoru Golem nebo a tvorbu interaktivního simulátoru ledviny. Současná verze systému mimo jiné umožňuje využívat 3D komponenty a nástroje počítačového vidění. Pro tuto verzi je vyvíjena simulační komponenta, která umožní využít vizualizaci výstupů simulačního modelu běžícího na pozadí systému. Práce na tvorbě výukových lékařských simulátorů je mimo jiné podporována projektem MPO FR—TI3/869.
Control Web is a distributed object-oriented environment designed for the development of real-time applications, and process visualization and simulation using the Windows platform. This environment has been developed for more than 20 years until now; in fact, in industrial applications, Control Web has become a widely spread standard in the Czech Republic. In the field of biomedical instruments development, Control Web offers easy visual design of individual control and visualizing components of biotechnological devices. Another of its capabilities is the possibility of using the system for visualization of educational simulations. For example, a previous version of this system was used to implement the Golem simulator or to design an interactive kidney simulator. Besides others, the current version of the system supports 3D components and computer vision tools. A simulation component is being developed for this version, which will make it possible to use visualization of the outputs of a simulation model running in the background. Besides others, the development of medical training simulators has been supported by the project FR-TI3/869 of the Ministry of Industry and Trade of the Czech Republic.
Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a unique query language with Python-like syntax to define the patterns that will be extracted from datasets provided by the user, or from the entire Protein Data Bank (PDB). Moreover, the database-wide search can be restricted using a variety of criteria, such as PDB ID, resolution, and organism of origin, to provide only relevant data. The extraction generally takes a few seconds for several hundreds of entries, up to approximately one hour for the whole PDB. The detected patterns are made available for download to enable further processing, as well as presented in a clear tabular and graphical form directly in the browser. The unique design of the language and the provided service could pave the way towards novel PDB-wide analyses, which were either difficult or unfeasible in the past. The application is available free of charge at http://ncbr.muni.cz/PatternQuery.
- MeSH
- Databases, Protein * MeSH
- Internet MeSH
- Protein Conformation MeSH
- Lectins chemistry MeSH
- Macromolecular Substances chemistry MeSH
- Molecular Conformation * MeSH
- Models, Molecular MeSH
- Software * MeSH
- Binding Sites MeSH
- Zinc Fingers MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple information transfer molecule. Understanding the architecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n(2)) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algorithm are freely accessible at http://siret.cz/setter.
- MeSH
- Algorithms MeSH
- Internet MeSH
- Nucleic Acid Conformation MeSH
- RNA chemistry MeSH
- Software MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- MeSH
- Feedback, Psychological MeSH
- Internet utilization MeSH
- Humans MeSH
- Anorexia Nervosa psychology therapy MeSH
- Therapy, Computer-Assisted instrumentation MeSH
- Psychotherapy methods instrumentation MeSH
- Check Tag
- Humans MeSH
- Publication type
- Meeting Abstract MeSH
With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals. Database URL: : http://cetaf.org/cetaf-stable-identifiers.
- MeSH
- Biodiversity * MeSH
- Databases, Factual * MeSH
- Semantic Web * MeSH
- Software * MeSH
- Natural Language Processing * MeSH
- Publication type
- Journal Article MeSH
When parasites invade paired structures of their host non-randomly, the resulting asymmetry may have both pathological and ecological significance. To facilitate the detection and visualisation of asymmetric infections we have developed a free software tool, Analysis of Symmetry of Parasitic Infections (ASPI). This tool has been implemented as an R package (https://cran.r-project.org/package=aspi) and a web application (https://wayland.shinyapps.io/aspi). ASPI can detect both consistent bias towards one side, and inconsistent bias in which the left side is favoured in some hosts and the right in others. Application of ASPI is demonstrated using previously unpublished data on the distribution of metacercariae of species of Diplostomum von Nordmann, 1832 in the eyes of ruffe Gymnocephalus cernua (Linnaeus). Invasion of the lenses appeared to be random, with the proportion of metacercariae in the left and right lenses showing the pattern expected by chance. However, analysis of counts of metacercariae from the humors, choroid and retina revealed asymmetry between eyes in 38% of host fish.
- MeSH
- Trematode Infections parasitology pathology MeSH
- Data Interpretation, Statistical MeSH
- Metacercariae physiology MeSH
- Fish Diseases parasitology pathology MeSH
- Perches parasitology MeSH
- Software * MeSH
- Trematoda physiology MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
Large biomolecules-proteins and nucleic acids-are composed of building blocks which define their identity, properties and binding capabilities. In order to shed light on the energetic side of interactions of amino acids between themselves and with deoxyribonucleotides, we present the Amino Acid Interaction web server (http://bioinfo.uochb.cas.cz/INTAA/). INTAA offers the calculation of the residue Interaction Energy Matrix for any protein structure (deposited in Protein Data Bank or submitted by the user) and a comprehensive analysis of the interfaces in protein-DNA complexes. The Interaction Energy Matrix web application aims to identify key residues within protein structures which contribute significantly to the stability of the protein. The application provides an interactive user interface enhanced by 3D structure viewer for efficient visualization of pairwise and net interaction energies of individual amino acids, side chains and backbones. The protein-DNA interaction analysis part of the web server allows the user to view the relative abundance of various configurations of amino acid-deoxyribonucleotide pairs found at the protein-DNA interface and the interaction energies corresponding to these configurations calculated using a molecular mechanical force field. The effects of the sugar-phosphate moiety and of the dielectric properties of the solvent on the interaction energies can be studied for the various configurations.
V rámci projektu FRVŠ jsme připravili webovou e-learningovou aplikaci, která je implementována v jazyce Java v rozšířené verzi Java EE 6. Aplikace je navržena tak, aby bylo možné studijní materiály doplňovat, upravovat a dále rozšiřovat o další oblasti výuky. Tímto krokem se nám podařilo vytvořit multimediální e-learningový systém, který bude snadno udržitelný i v dalším časovém horizontu. Aplikace se automaticky přizpůsobuje jazykové preferenci studenta. Obsahuje administrátorské rozhraní pro vytváření nových studijních modulů a jejich rozšiřování a jednoduchý testovací modul, který dává uživateli zpětnou vazbu z právě nastudované látky. V aplikaci jsme vytvořili studijní modul zabývající se metodou elektrických analogií, což je jedna z hojně využívaných metod modelování živých organismů. Tuto metodu vysvětlujeme na problematice měření tělesného složení. Materiál obsahuje také informační video znázorňující klinický experiment, který probíhá na cvičení předmětu vyučovaného v rámci studia biomedicínského inženýrství na Fakultě elektrotechnické ČVUT v Praze. Video je vhodný způsob domácí přípravy a ukázka experimentálního měření pro studenty, kteří se nemohou výuky zúčastnit. Doufáme, že systém pomůže zatraktivnit nejen biomedicínské inženýrství vyučované na ČVUT, ale poskytne také cenné informace budoucím odborníkům na tomto poli.
A web-based e-learning application has been prepared within the realm of a Higher Education Development Fund (FRVŠ) project, implemented in Java in the extended version Java EE 6. The application was designed to support additions, modifications of study materials, and their expansions with courses in additional fields. This step enabled us to created a multimedia e-learning system that can be easily maintained also in respect to a further time horizon. The application adapts automatically to the student’s language preference. It includes an administrator’s interface used to create new study modules and to expand them, as well as a simple testing module providing the user with feedback regarding the content studied right at the given time. A study module was created in the application on the electric analogy method, which is one of amply used modelling methods of living organisms. This method is explained using body composition measurement as an example. An informative video is also included in the material, which shows a clinical experiment done at the seminar of a subject taught as part of the biomedical engineering study at the Faculty of Electrical Engineering, Czech Technical University in Prague. The video provides a suitable way of home study and an illustration of an experimental measurement for students who cannot be present. We hope that the system will help to make more attractive not only biomedical engineering taught at the Czech Technical University, but also to provide precious information to future specialists in this field.
