Free software helps to manage neuroscience experimental data

The program is being developed by a team at the Research, Innovation and Dissemination Center for Neuromathematics, which is supported by FAPESP. The first module is available for download.

By Karina Toledo

Agência FAPESP – The Research, Innovation and Dissemination Center for Neuromathematics (Neuromat), one of the Research, Innovation & Diffusion Centers (CEPIDs) supported by FAPESP, has just launched the first module of a free software program called Neuroscience Experiments System (NES). This program helps to organize, control and manage neurophysiological data from patients and experiments.

This first version of the open-source software tool, available for download at https://github.com/neuromat/nes, is designed to offer a user-friendly interface for the storage of clinical data and medical assessments of patients and volunteers in experiments. In addition, the tool has an interface for managing the online questionnaires used in surveys for research purposes.

“The software is part of a project to build a public neurophysiological database organized by Neuromat, a pioneering initiative in neuroscience. We also expect these initiatives to facilitate cooperation among researchers,” said Kelly Rosa Braghetto, a professor in the Mathematics & Statistics Institute’s Department of Computer Science at the University of São Paulo (IME-USP) and a member of the group responsible for developing NES.

Set up in 2013 at the University of São Paulo, Neuromat is staffed by some 50 researchers from Brazilian and foreign universities in areas such as mathematics, computer science, statistics, neuroscience, biology, physics and communication. The group’s aim is to integrate mathematical modeling and neuroscience in pursuit of a better understanding of how the human brain works.

According to Braghetto, the first module of NES is modeled on experiments conducted at the Federal University of Rio de Janeiro’s Deolindo Couto Institute of Neurology (INDC-UFRJ) under the coordination of Professor Claudia Vargas, one of Neuromat’s principal researchers.

“The research group at the Federal University of Rio de Janeiro studies the rehabilitation of patients with brachial plexus injury [a type of neurological lesion that impairs arm and hand movement]. This first module was developed to register outpatient data,” Braghetto told Agência FAPESP.

Also being implemented is a module to register information on experimental protocols and on physiological measurements collected in surveys.

“Researchers often fail to register the full details of the protocol used in an experiment, such as specific equipment configuration parameters. These details may have an impact on data analysis. The software will prevent this kind of situation from happening,” said Braghetto.

Open-source software

According to Braghetto, because of the open source code of the software, users can download the program and adapt it to meet their research needs.

The next module to be developed will be designed to manage data collected during neuroimaging examinations, such as magnetic resonance imaging (MRI) scans. There will also be a module dedicated to the management of data obtained from animal experiments.

The sequence of implementation of the NES data acquisition modules will be prioritized in accordance with demand from the laboratories associated with Neuromat. The Neuromat team expects that in the future it will be possible for scientists to share databases of neuroscience experiments.

“We take great care to preserve the privacy of the volunteers and patients from whom data are collected. This is a key aspect of our approach to developing the technology. Databases are fairly frequently made available for sharing in other sciences but this is still unusual in neuroscience,” said Braghetto.

More information: http://neuromat.numec.prp.usp.br.