SOFTWARE INFRASTRUCTURE FOR EEG/ERP RESEARCH

Roman Mouček, Petr Jaroš, Petr Ježek and Václav Papež

Department of Computer Science and Engineering, University of West Bohemia

Univerzitní 8, 306 14, Pilsen, Czech Republic

Keywords: EEG, ERP, INCF, EEG/ERP Portal, JERPA, Software infrastructure, Semantic web, RDF, OWL, Signal

processing methods, Statistical methods, Data conversions.

Abstract: This paper deals with the software infrastructure for EEG/ERP (electroencephalography, event related

potentials) research. The requirements for building this infrastructure have arisen from laboratory needs,

unavailability of appropriate software tools and incompatibility of previously used commercial solutions.

The standardization of EEG/ERP data formats and construction of complex and publicly open software

infrastructure is also supported by International Neuroinformatics Coordinating Facility (INCF) since these

efforts can significantly accelerate brain research. The presented software infrastructure includes the web

based EEG/ERP portal as the central data storage for data/metadata obtained in EEG/ERP experiments and

JERPA software as the desktop software tool for computationally demanding operations. Supporting

libraries (e.g. library of signal processing methods) developed and integrated to EEG/ERP portal and/or

JERPA software are briefly described.

1 INTRODUCTION

Our research group at Department of Computer

Science and Engineering, University of West

Bohemia in cooperation with other partner

institutions specializes in EEG/ERP research

(electroencephalography, event related potentials).

Within our partner network we are responsible,

except performing experiments, for EEG/ERP

laboratory operation, development of advanced

software tools for EEG/ERP research, proposal and

modification of signal processing methods,

development of hardware for subjects’ stimulation

during EEG/ERP experiments and integration of

software tools and hardware devices into general

solution for EEG/ERP research.

EEG/ERP experiments take usually long time

and produce extensive data. Since we had had

difficulties with long-term storage and management

of these data and we have not found any suitable

data store for them we started to design and

implement a software tool for EEG/ERP

data/metadata storage and management. The

resulting EEG/ERP portal (Ježek, 2010) together

with necessary hardware and software laboratory

equipment became the basic building blocks for the

next development of software tools and hardware

devices for EEG/ERP research.

As the members of International

Neuroinformatics Coordinating Facility (INCF)

(INCF, 2011) we develop software tools for

EEG/ERP research in coordination with other

member countries. For example, EEG/ERP portal is

currently registered within Neuroscience

Information Framework (NIF) (NIF, 2011).

Moreover, we are involved in INCF program for

standards in electrophysiological data sharing.

The aim of this paper is to emphasize the

importance of data and software tools

standardization in EEG/ERP research and briefly

introduce the proposed and partly implemented

software infrastructure for EEG/ERP research.

The paper is organized as follows. At first the

existing and complex software solutions for data and

tools organization are briefly introduced by focusing

on neuroinformatics portals of INCF member

countries. Then EEG/ERP domain is shortly

described. The fourth section deals with proposal,

description and realization of software infrastructure

for EEG/ERP research. The essential parts of this

infrastructure are briefly described. The concluding

remarks include the next vision of described

infrastructure and the forthcoming tasks.

478

Mou

cek R., Jaroš P., Ježek P. and Papež V..

SOFTWARE INFRASTRUCTURE FOR EEG/ERP RESEARCH.

DOI: 10.5220/0003692204780481

In Proceedings of the International Conference on Knowledge Engineering and Ontology Development (KEOD-2011), pages 478-481

ISBN: 978-989-8425-80-5

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

2 PORTAL SOLUTIONS IN

NEUROINFORMATICS

As INCF members we coordinate our efforts with

other INCF member countries. Their software

solutions for neuroinformatics research serve also as

an inspiration for our approaches. This section

provides basic information about activities of the

selected INCF member countries and their

neuroinformatics portal solutions.

CARMEN (CARMEN, 2011) is a virtual

laboratory for neurophysiology, which is developed

at eleven UK universities. It enables sharing and

collaborative exploitation of data, analysis code and

expertise. The complete lifecycle of

neurophysiology data is addressed. The primary data

types are neural activity recordings (signals and

image series).

The infrastructure for brain science information

and neuroinformatics within INCF Japan Node

(JNODE, 2011) includes developing and publishing

brain science databases under so-called platforms.

Each platform is being developed to organize

specific neuroinformatics databases (e.g. cerebellar

or brain machine interface platform). The research

results can be shared with the public.

German neuroinformatics node (GNODE, 2011)

focuses on the development and free distribution of

tools for handling and analysing neurophysiological

data. Especially software and hardware

infrastructure that eases the acquisition, storage and

analysis of experimental data in cellular and systems

neurophysiology is developed. Standardization of

data formats and analysis tools is encouraged.

Neuroscience Information Framework (NIF)

(NIF, 2011) developed within INCF national node of

the USA is a dynamic inventory of web-based

neuroscience resources: data, materials, and tools. It

advances neuroscience research by enabling

discovery and access to public research data and

tools worldwide through an open source, networked

environment. NIF offers e.g. a search portal looking

for neuroscience information, tools, data or

materials, access to content normally not indexed by

search engines, tools for resource providers to make

resources more discoverable (e.g. ontologies),

standards for data annotation, etc.

3 RESEARCH IN EEG/ERP

DOMAIN

EEG and ERP techniques are widely used in

research of brain processes. These techniques

include design and realization of EEG/ERP

experiments, recording and collection of EEG/ERP

data/metadata, long-term management and sharing

of these data, and data analysis and interpretation

(signal processing methods and statistical methods).

All these activities are currently partly covered

by commercial or open-source software tools and

hardware devices. However, especially commercial

recording tools are based on proprietary data formats

and include limited and closed-source software tools

for data processing. This situation seriously

complicates the access, storage, management,

analysis and public sharing of neuroscience data and

metadata and finally slows down brain research.

As the reaction to this situation and laboratory

needs, and in accordance with INCF efforts our

research group started to develop open source

software infrastructure and hardware devices for

electrophysiology research. The software

infrastructure is described in the following section.

4 INFASTRUCTURE IN EEG/ERP

RESEARCH

The software tools for EEG/ERP data and metadata

management, EEG/ERP signal analysis and

processing, and design of EEG/ERP experiments are

developed. The simplified component model of

EEG/ERP infrastructure is given in Figure 1. Details

and dependencies of components within EEG/ERP

portal were omitted to maintain the model

readability.

4.1 EEG/ERP Portal

EEG/ERP portal is the main building block of the

presented infrastructure. It serves as a system for

storage and management of EEG/ERP resources -

data, metadata, scenarios, tools and materials related

to EEG/ERP experiments. Thus EEG/ERP portal

advances electrophysiology research by enabling

access to public data, tools and results of research

groups. The main features provided by the system

include:

 Management of EEG/ERP data/metadata

 Management of EEG/ERP experimental

scenarios

 Management of data related to testing subjects

 Sharing of knowledge and working within

groups

 Signal processing methods

 Content management system

 Full text search

SOFTWARE INFRASTRUCTURE FOR EEG/ERP RESEARCH

479

Figure 1: Component model of EEG/ERP infrastructure.

The system is developed as a standalone

software product; the access to resources stored in

the database is available through a web interface. It

uses the layered architecture (MVC pattern)

consisting of persistent layer (relational database),

the application layer (object oriented model, ORM

provided by Hibernate) and presentation layer (JSP).

Spring security framework is used to introduce user

roles. Users’ authentication and authorized access to

data resources and signal processing tools are

ensured. Facebook can be also used as an external

authentication authority.

To register the EEG/ERP portal as

a recognizable source of neuroscientific data and

metadata the representation of portal structure in

semantic web languages and technologies is often

required. Two possible mappings from common data

structures to RDF/OWL are currently possible to

perform.

DbTransformer library (extended with its

graphical user interface) (Mouček, 2011) provides

an automatic mapping from the relational database

to RDF graph and to RDF/OWL output.

Transformational library provides a mapping from

object oriented model again to RDF/OWL output. It

processes POJO objects and serializes them into

output OWL structure. This processing includes

parsing Java classes, their methods and attributes

using Java Reflection API. The advantage of this

approach is that the internal ontology model can be

enriched by Java annotations added to classes, their

attributes and methods (Annotation library with its

graphical user interface in Figure 1).

4.2 JERPA and JUIGLE

Because of large EEG/ERP data, computationally

demanding signal processing methods and the need

to visualize and process EEG/ERP signal off line

a desktop software tool for visualization and basic

processing of EEG/ERP records was developed.

JERPA (Java Event Related Potential Analysis) as

the main component of this software was built using

the layered architecture. It includes:

 GUI framework (JUIGLE) that provides

support for creating graphical components for

signal visualization and output of signal

processing methods

 Plugin engine for installing new methods as

plugins into the system

 Data store engine (connection to EEG/ERP

portal, data management)

4.3 Library of Signal Processing

Methods

Data from EEG/ERP experiments are processed

KEOD 2011 - International Conference on Knowledge Engineering and Ontology Development

480

using signal processing methods. The developed

library is intended for processing of EEG/ERP

signals and includes wavelet transform, matching

pursuit algorithm, FastICA algorithm and Hilbert-

Huang transform. The wavelet transform and

matching pursuit algorithm are integrated into

EEG/ERP portal, FastICA algorithm is integrated as

plug-in into JERPA software.

4.4 Library of Statistical Methods

The library of statistical methods includes Java

implementations of the following statistical

methods:

 One way and two way analysis of variance

(ANOVA)

 One way and two way multivariate analysis of

variance (MANOVA)

While one way ANOVA, implemented in the

math library, was refactored, the other methods were

newly implemented. MANOVA was implemented

with all MANOVA significant statistical tests –

Pillai-Bartlett trace, Wilk’s lambda, Hotelling

Lawley trace and Roy’s greatest characteristic root.

4.5 Data Conversion Library

There exists a variety of data formats for storing

EEG/ERP data. Data conversion library provides

conversion methods between European Data Format

(EDF), Vision Data Exchange Format (VDEF) and

KIV format. The further library extension

(conversions from/to SignalML and odML data

format) is planned.

4.6 Presti

Presti is a software tool for presenting stimuli in

ERP experiments. It aims at users without

knowledge of programming. The concept of the

program is taking advantage of visual programming

methodology. The users could easily edit, create and

run test scenarios in a simple and intuitive graphical

interface.

5 CONCLUSIONS

This paper described the software infrastructure for

EEG/ERP research. The requirements for building

such infrastructure have arisen from laboratory

needs, unavailability of appropriate software tools

and incompatibility of used commercial solutions.

Moreover, the standardization of data formats and

construction of complex and publicly open software

infrastructure is supported by INCF since these

efforts can significantly accelerate brain research.

The presented software infrastructure includes

the web based EEG/ERP portal as the central data

storage for data/ metadata obtained in EEG/ERP

experiments and JERPA software as the desktop

software tool for computationally demanding

operations. Supporting libraries are developed and

integrated to EEG/ERP portal and/or JERPA

software.

In near future we plan to perform an extensive

testing of online communication module, which will

mainly serve for brain computer interface tasks, and

continue on EEG/ERP data format standardization

task.

ACKNOWLEDGEMENTS

The work was supported by the UWB grant SGS-

2010-038 Methods and Applications of Bio- and

Medical Informatics and by the SPAV project

CZ 1.07/2.3.00/09.0050.

REFERENCES

CARMEN portal (CARMEN). (2011). Retrieved June 20,

2011, from https://portal.carmen.org.uk/

German Neuroinformatics Node (GNODE), (2011).

Retrieved June 10, 2011http://www.g-node.org/

International Neuroinformatics Coordinating Facility

(INCF), (2011). Retrieved May 9, 2011, from

http://www.incf.org/

INCF Japan Node (JNODE), (2011). Retrieved June 16,

2011, from http://www.neuroinf.jp/jnode

Neuroscience Information Framework (NIF). (2011).

Retrieved May 9, 2011, from http://www.neuinfo.org/

Ježek, P., Mouček, R., 2010. Database of EEG/ERP

experiments. In HEALTHINF 2010 - Proceedings of

the Third International Conference on Health

Informatics. Valencia, Spain (pp. 222-227).

Mouček, R., Ježek, P., Papež, V., 2011. Semantic web

technologies in EEG/ERP domain – software solution.

In HEALTHINF 2011 - Proceedings of the 4th

International Conference on Health Informatics.

Rome. Italy (pp. 618-621).

SOFTWARE INFRASTRUCTURE FOR EEG/ERP RESEARCH

481