Semantic Framework - Because the Semantic Web uses its technologies for presenting data/metadata on the web and common systems are based on object-oriented languages a need for suitable mapping is emerging. This software solves the difficulties during transformation of data layer represented by object-oriented code into the semantic web structures (OWL, RDF). Since there is difference between semantic expressivity of these data representations it is necessary to fill this semantic gap. The software solves these differences in semantics and provide a possibility to add missing semantics into the Java code using Java annotations. These annotations are consequently processed by the proposed framework. Download
EEG Data Processor – Framework for Running Signal Processing Methods - This software solves difficulties related to running of signal processing methods. Although several systems that implement signal processing methods exist, their sharing and remote calling is not satisfactorily solved. This software is a custom server-side approach that provides a powerful plug-in engine for integration of signal processing methods. The plug-in engine ensures high modularity and flexibility of the system. Since the implemented methods are accessible via the SOAP Web Service, integration with another system is available. There is also possible to use the system locally via a web browser. The set of basic methods is already implemented. Download
EEG/ERP Data Clustering Tool - C++ software tool allows clustering of features obtained by processing the EEG/ERP data. The features are any waveforms that correspond to significant EEG signal changes (e.g. ERP components or artifacts). Clustering and evaluation of its results can separate possible ERP components from artifacts and noise. The method was tested for the P300 component and the results were presented in the following paper: Vařeka L., Mautner P.: The Event-Related Potential Data Processing Using ART 2 Network, BMEI 2012, 16 – 18 October, 2012, Chongqing, China, pp. 467-471. The work was supported by SGS-2010-038 Methods and Applications of Biomedical Informatics. Download
Stimulation protocol and data for diagnosing developmental coordination disorder – The stimulation protocol of the experiment (type: ignored protocol) has been used in research of structure and diagnosis of developmental coordination disorders in children at preschool and primary school age. It is based on sound stimulation and written in the programming language of the Presentation software. Enclosed anonymized experimental data obtained from 16 subjects fulfill the conditions imposed on the quality of such data (number of artifacts, presence of components). Download
ExtendedJenaBean – Tool for transformation of OO code into OWL Download
Annotation tool for data classes - The tool for annotating POJO data classes adds annotations to translated POJO classes, from which the tool Jenabean generates output in the language of the Semantic Web. The tool offers through a graphical user interface a customizable list of available annotations. The user selects the appropriate set of annotations, decides on their location to POJO objects and adds their values. The annotation tool and its importance in the process of transformation of semantic description of object-oriented code into the expressive means of Semantic Web was presented in the paper Ježek, Peter; Mouček Roman. EEG / ERP portal – Extending object oriented code for the missing semantics using Java annotation, 4th Congress of Neuroinformatics 2011, Boston, USA. The user manual for the product is in the attached file manual.pdf. Download
Library of statistical methods for EEG/ERP experiments - The sample product enables users to statistically process data from EEG/ERP experiments. It is implemented as java library and apart from refactored one way analysis of variance (ANOVA) it contains three newly implemented statistical methods – a two way analysis of variance (ANOVA), a one way multivariate ANOVA (MANOVA) and a two way MANOVA. The MANOVA is implemented with all MANOVA significant statistical tests – Pillai- Bartlett trace, Wilk’s lambda, Hotelling Lawley trace and Roy’s greatest characteristic root. The library was presented in the paper Roman Mouček, Petr Jaroš, Petr Ježek, Václav Papež: Software infrastructure for EEG/ERP research, Proceedings of the International Conference on Knowledge Enginering and Ontology Development, Paris, 2011. The user manual for the product is in the attached file manual.pdf. Download
EEG data formats converting tool - The sample product enables mutual conversion of the following EEG data formats – EDF, Brain Vision and KIV. The software, implemented in Java, is used as a standalone product and as a library suitable for integration into the EEG signal processing software. Conversion and mutual compatibility of EEG data formats is one of the solutions to standardize electrophysiological data that is addressed in the INCF (International Neuroinformatics Coordinating Facility) electrophysiology Task Force – http://datasharing.incf.org/ep/Converters. The software was presented in the paper Roman Mouček, Petr Ježek: Overview of neuroinformatics infrastucture in Pilsen, CZ, 4th Congress of Neuroinfomatics, 2011, Boston, USA. The user manuals for the product are in the attached files manual.pdf and manual_en.pdf (english version). Download
Java2SemanticWeb – Tool for transforming data and metadata to the Semantic Web resources - The tool is used for transforming POJO objects to Semantic Web (RDF and OWL). There are used libraries Jena and OWL API for transformation. The tool was presented in the paper Štěbeták J. Brůha P., R. meal.”Neuroinformatics – Data Management and Analytic Tools for EEG / ERP Research”, The International Conference: Beyond AI 2011, December 08, Pilsen, Czech Republic, no. 91-96. Description of used tools and libraries is located at http://eeg-semantic-web.origo.ethz.ch/wiki/doc. Solved within grants: Ministry of Education, Youth and Sports of theCzech Republic under the grant ME 949 and SGS-UWB Grant 2010-038 Methods and Applications of Biomedical Informatics. Download
eegdsp – library for EEG signal processing - eegdsp is a library for EEG/ERP signal processing. It allows user to access fast fourier transform, wavelet transform (both discrete and continuous), and matching pursuit algorithm via unified interface. Results are stored into colections (our own design) which allow their efficient processing. Download
Software modules for design and run of EEG/ERP experiments - Software modules for design and run of EEG/ERP experiments allows displaying of parallel stimuli in ERP experiments and creation of sound stimuli. XNA library is used for stimuli drawing. Delay of displaying of stimuli was minimalized, so this tool fulfilled higly demanding requirements on synchronisation of the stimuli and parallel communication with EEG signal measuring system. Software was presented in an article Jaroš Petr, Háka Petr, Mouček Roman: PRESTI Neuroscience Stimuli Presetation Software, Knowledge Management and Information Sharing, Paris, 2011. Software installation and user manual is provided in document manual.pdf. Download
Mobile agents for processing EEG/ERP signals - Mobile agents for EEG/ERP (electroencephalography, event related potentials) processing are a set of software tools such that the methods of EEG/ERP signal processing are easily transferred and executed on a remote computer where the EEG / ERP data repository is located. The presented set of software tools includes the implementation of methods for artifacts detection in EEG / ERP signals and conversion of EEG/ERP data formats in the form of mobile agents. A user is able to extend this set easily. A result of mobile agent work is notified to users by e-mail message. The importance of the system of mobile agents for processing EEG/ERP signals and testing results of implemented mobile agents were published in the paper Using Mobile Agents in EEG Signal Processing, 2nd International Conference on Agents and Artificial Intelligence, Valencia, Spain, 2010. Description of installation and user manual are in the attached file manual.pdf. Download
Portal of EEG experiments - The system unifies storage, download and interchange of EEG/ERP data and metadata. Various user roles are defined. The system is web based portal available through internet. It ensures platform independence and it is easy to use.
Project was supported by grants E 949 and 2C06009 Cot-Sewing and presented at Healthinf 2010, INCF 2008, INCF 2009 and INCF 2010 conferences. Download
Jerpa – Integration of signal processing methods - Jerpa is a desktop application, allowing the run methods for signal processing. The program provides a graphical interface for signals visualization, execute methods, work with projects. Methods for processing in the system can be added as plug-ins.
The system development was supported by grant ME 949. Download
Tool for automatic transfer of relational database into semantic web resources DBTransformer - The described software tool allows automatic transfer of structure of relational database into semantic web resources (e.g. RDF, OWL etc.). Its functionality is based on D2RQ libraries (Freie Universität Berlin) and OWL API (University of Manchester). This cross-platform tool is created in JAVA. The tool (its importance and applicability) is described in the paper “Neuroinformatics database and Semantic Web”, 10th Conference on Cognition and Artificial Life. Description of installation and user manual are in the attached file DBTransformerDocumentation.pdf. Download
Tool for stimuli presentation in neuroinformatics experiments PreSti - The software is used to design test scenarios and present visual stimuli. These stimuli are used in experiments, where evoked potentials (electrical brain responses to sensory stimuli) measured on subjects are examined. The program allows design test scenarios to users without any programming knowledge, since the design of test scenarios is done in a graphical environment by creating flowcharts. Software functionality can be extended by additional modules that add new symbols suitable for the design of test scenarios in the graphical environment. The software can communicate over parallel port with the device for measuring brain waves. The program is capable of running on Windows operating systems from XP version. The software tool was presented in the paper “PreSti – Software for presentation of stimuli” published in the proceedings of the 10th Conference on Cognition and Artificial Life. Description of installation and user manual are in the attached file presti.pdf. Download
Tool for visualization and processing of EEG signals BrainStudio - The authorized application is a tool for design of processing and visualization of biomedical signals. Application features include their mutual comparison, tagging and manual segmentation, and synchronized playback of experiment video and brain activity recording. The signals can be processed with external modules. The data exchange between modules is provided by the application. Detailed description of the application including user guide can be found in the attached diploma thesis “Software for EEG Data Processing”. The program was presented at the conference Transtec 2007. Download
