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Software and hardware infracstructure for research in electrophysiology

MOUČEK, R., JEŽEK, P., VAŘEKA, L., ŘONDÍK, T., BRŮHA, P., PAPEŽ, V., MAUTNER, P., NOVOTNÝ, J., PROKOP, T., ŠTĚBETÁK, J. Software and hardware infracstructure for research in electrophysiology. Frontiers in Neuroinformatics, 2014, roč. 8, č. 20, s. 1-15. ISSN: 1662-5196
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As in other areas of experimental science, operation of electrophysiological laboratory, design and performance of electrophysiological experiments, collection, storage and sharing of experimental data and metadata, analysis and interpretation of these data, and publication of results are time consuming activities. If these activities are well organized and supported by a suitable infrastructure, work efficiency of researchers increases significantly. This article deals with the main concepts, design, and development of software and hardware infrastructure for research in electrophysiology. The described infrastructure has been primarily developed for the needs of neuroinformatics laboratory at the University of West Bohemia, the Czech Republic. However, from the beginning it has been also designed and developed to be open and applicable in laboratories that do similar research. After introducing the laboratory and the whole architectural concept the individual parts of the infrastructure are described. The central element of the software infrastructure is a web-based portal that enables community researchers to store, share, download and search data and metadata from electrophysiological experiments. The data model, domain ontology and usage of semantic web languages and technologies are described. Current data publication policy used in the portal is briefly introduced. The registration of the portal within Neuroscience Information Framework is described. Then the methods used for processing of electrophysiological signals are presented. The specific modifications of these methods introduced by laboratory researches are summarized; the methods are organized into a laboratory workflow. Other parts of the software infrastructure include mobile and offline solutions for data/metadata storing and a hardware stimulator communicating with an EEG amplifier and recording software.

Event-related potential datasets based on a three-stimulus paradigm

VAŘEKA, L., BRŮHA, P., MOUČEK, R. Event-related potential datasets based on a three-stimulus paradigm. GigaScience, 2014, roč. 3, č. 1, s. 1-5. ISSN: 2047-217X
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The event-related potentials technique is widely used in cognitive neuroscience research. The P300 waveform has been explored in many research articles because of its wide applications, such as lie detection or brain-computer interfaces (BCI). However, very few datasets are publicly available. Therefore, most researchers use only their private datasets for their analysis. This leads to minimally comparable results, particularly in brain-computer research interfaces. Here we present electroencephalography/event-related potentials (EEG/ERP) data. The data were obtained from 20 healthy subjects and was acquired using an odd-ball hardware stimulator. The visual stimulation was based on a three-stimulus paradigm and included target, non-target and distracter stimuli. The data and collected metadata are shared in the EEG/ERP Portal

P300 data validator

VAŘEKA, L., BRŮHA, P., MOUČEK, R. P300 data validator. 2014.
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The P300 validator contains multiple Matlab scripts that are used for calculating quality measure (typically accuracy) for common odd-ball paradigm data. The Windowed means paradigm was used for feature extraction and linear discriminant analysis was used for classification. The project is also available on: https://github.com/INCF/p3-validator The P300 validator was also used for data validation in the following publication: Vařeka, L.; Brůha, P.; Mouček, R. Event-related potential datasets based on a three-stimulus paradigm. Gigascience 2014, 3. This work was supported by the UWB grant SGS-2013-039 Methods and Applications of Bio- and Medical Informatics.

TSD 2015

Konopík, M., Ekštein, K., Matoušek, V., Král, P., Mouček, R. TSD 2015. Plzeň, 14.09.2015 - 17.09.2015.
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TSD conference has evolved as a prime forum for interaction between researchers in both spoken and written language processing from all over the world. Proceedings of TSD formed a book published by Springer-Verlag in their Lecture Notes in Artificial Intelligence (LNAI) series. The TSD proceedings are regularly indexed by Thomson Reuters Conference Proceedings Citation Index. LNAI series are listed in all major citation databases such as DBLP, SCOPUS, EI, INSPEC, or COMPENDEX. Totally 5 invited speakers, 51 participants from the whole world and 25 participants from the Czech Republic visited the TSD Conference in the middle of September 2015. The conference was organized by 9 organizers form the University of West Bohemia in Pilsen.

Development and usage of odML based OpenEHR archetypes in electroencephalography

PAPEŽ, V., MOUČEK, R. Development and usage of odML based OpenEHR archetypes in electroencephalography. Cairns, 2015.
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The work describes a development of the openEHR archetypes in electrophysiology domain. These archetypes are based on internationally respected odML terminology. The goal is to prepare a set of archetypes suitable for a publication process into odML repositories.

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