In defense of public scientific-data sharing: a NeuroMat op-ed
by Claudia Domingues Vargas and Fabio Kon
In recent years, much of the international scientific community, with the support of governmental agencies, such as the National Science Foundation (NSF) from the United States, the European Commission and the São Paulo Research Foundation (FAPESP) in Brazil, have advocated for what has been called "open science." Aspects of this new model of sharing scientific information are threefold. Firstly, scientific results are to be spread out through “open-access” vehicles, so that any scientist and citizen could be granted an easy access to discoveries , regardless of their background or financial situation. Secondly, tools used in the scientific process should also be shared openly; since much of science today depends on computational tools, this indicates that they should be made available as “free software.” Lastly, research data must be shared as "open data:" not only should the raw and processed data be openly available, but also format descriptions and meanings of such data (what we may called metadata) should be widely distributed. When such information is collected from humans, special caution is required in the distributing, respecting the privacy and anonymity of those involved. One of the pillars of experimental science is its reproducibility. And science only becomes reproducible if the data and tools used in the experiments, simulations and analysis are also openly and freely provided.
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NeuroMat’s open science initiatives
Neuroscience Experiments System (NES)
NES (neuromat.numec.prp.usp.br/nes) is a web-based system that provides neuroscience experiments data and metadata record facilities in a secure and user-friendly platform. It was designed to provide a single repository for the experimental data of an entire research laboratory, group, or project. NES is a free software tool, developed using open technologies and tools that can be easily installed and used in any research laboratory. Its modular structure and web interface provide an intuitive use of its data management functionalities. NES was developed to combine experimental data with its provenance information. The system also allows recording of additional data for experimental volunteers, such as information on clinical history and socio-demographic data. NES requires the experimenter to record in detail each step involved in the experimental protocol before storing collected primary data. The experimental protocol is described as a workflow, which can contain both sequential and parallel steps. NES uses a standardized data model in neuroscience, enabling interoperability with other initiatives for data representation standardization. NES is licensed under Mozilla Public License version 2.0 and its source code and documentation are available at github.com/neuromat/nes.
The Goalkeeper Game
The Goalkeeper Game is a computer game being developed by the NeuroMat team since June 2015, associated to the experimental protocol being developed with plasticity in brachial plexus avulsion. In this game, brain signatures are evaluated through the performance of the participant in guessing the next direction chosen by the penalty-taker. The system records the sequence of guesses of the player, who must identify the context tree model used by a virtual penalty-taker.
In this way, the game allows for cheap and large-scale reaction time and error rate data collection, offering an alternative and complementary means to infer about brain functioning. The game’s source code is open, and the beta version is freely available at game.numec.prp.usp.br.
Open Database for neuroscience data
An open database for neuroscientific data is being implemented with the data generated and collected through NeuroMat’s initiatives such as with brachial plexus avulsion and Parkinson’s disease. The data is anonymized for sensitive information and feed a database that will be made publicly available via NeuroMat’s Web portal. Currently, the new Web portal project is being developed to restructure NeuroMat’s actual homepage to harbor this database.
Lectures about open science
- Data Management in NeuroMat and the Neuroscience Experiments System (NES) - Kelly Rosa Braghetto, IME-USP
- NeuroMAT Technology Transfer with Open Source Software and Open Data - Fabio Kon, IME-USP
- NeuroMat technology transfer, open source software, and open data – Fabio Kon, IME-USP
- Development of NeuroMat open databases – Kelly Rosa Braghetto, IME-USP
- General issues and the experience of constructing a clinical database in a university hospital – Cláudia Domingues Vargas, UFRJ