Provision of an integrated data analysis platform for computational neuroscience experiments

© Emerald Group Publishing Limited. Purpose – The purpose of this paper is to provide an integrated analysis base to facilitate computational neuroscience experiments, following a user-led approach to provide access to the integrated neuroscience data and to enable the analyses demanded by the biomedical research community. Design/methodology/approach – The design and development of the N4U analysis base and related information services addresses the existing research and practical challenges by offering an integrated medical data analysis environment with the necessary building blocks for neuroscientists to optimally exploit neuroscience workflows, large image data sets and algorithms to conduct analyses. Findings – The provision of an integrated e-science environment of computational neuroimaging can enhance the prospects, speed and utility of the data analysis process for neurodegenerative diseases. Originality/value – The N4U analysis base enables conducting biomedical data analyses by indexing and interlinking the neuroimaging and clinical study data sets stored on the grid infrastructure, algorithms and scientific workflow definitions along with their associated provenance information

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

INCF Lithuanian Workshop on Neuroscience and Information Technology

The aim of this workshop was to give a current overview of neuroscience and informatics research in Lithuania, and to discuss the strategies for forming the Lithuanian Neuroinformatics Node and becoming a member of INCF. The workshop was organized by Dr. Aušra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF.
The workshop was attended by 15 invited speakers, among them 4 guests and 11 Lithuanian neuroscientists, and over 20 participants. The workshop was organized into three main sessions: overview of the INCF activities including the Swedish and UK nodes of INCF; presentations on Neuroscience research carried out in Lithuania; discussion about the strategies for forming an INCF national node, and the benefits of having such a node in Lithuania (Appendix A: Program; Appendix B: Abstracts)

The Automation of Electrophysiological Experiments and Data Analysis

The role of computation in science is continually growing and neuroscience is no exception. Despite this, a severe lack of scientific software infrastructure persists, slowing progress in many domains. In this thesis, we will see how the combination of neuroscience and software engineering can build infrastructure that enables discovery. The first chapter discusses the Turtle Electrophysiology Project, or TEP, an experiment-automation and data-management system. This system has allowed us to automate away some of the most tedious tasks involved in conducting experiments. As a result, we can collect more data in less time, and with fewer errors related to the loss of metadata: information about how the data were collected). Also, since all of the metadata is automatically digitized during the experiment we can now completely automate our analyses. Chapters two and three are examples of research conducted using the ever-evolving TEP system. In the first instance, we used TEP to deliver visual stimuli and handle data-management. In chapter three, the experiments involved delivering electrical stimuli instead of visual stimuli, and much more rigorous analysis. And even though TEP was not specifically designed to handle collecting data this way, the flexible tags system enabled us to do so. Finally, chapter four details the construction of a robust analysis tool called Spikepy. Whereas TEP is specially designed for the turtle preparation we have, Spikepy is a general-purpose spike-sorting application and framework. Spikepy takes flexibility to the extreme by being a plugin-based framework, yet maintaining a very easy to use interface

Responsible Data Governance of Neuroscience Big Data

Open access article.Current discussions of the ethical aspects of big data are shaped by concerns regarding the social consequences of both the widespread adoption of machine learning and the ways in which biases in data can be replicated and perpetuated. We instead focus here on the ethical issues arising from the use of big data in international neuroscience collaborations. Neuroscience innovation relies upon neuroinformatics, large-scale data collection and analysis enabled by novel and emergent technologies. Each step of this work involves aspects of ethics, ranging from concerns for adherence to informed consent or animal protection principles and issues of data re-use at the stage of data collection, to data protection and privacy during data processing and analysis, and issues of attribution and intellectual property at the data-sharing and publication stages. Significant dilemmas and challenges with far-reaching implications are also inherent, including reconciling the ethical imperative for openness and validation with data protection compliance and considering future innovation trajectories or the potential for misuse of research results. Furthermore, these issues are subject to local interpretations within different ethical cultures applying diverse legal systems emphasising different aspects. Neuroscience big data require a concerted approach to research across boundaries, wherein ethical aspects are integrated within a transparent, dialogical data governance process. We address this by developing the concept of “responsible data governance,” applying the principles of Responsible Research and Innovation (RRI) to the challenges presented by the governance of neuroscience big data in the Human Brain Project (HBP)

Ethical Reflections of Human Brain Research and Smart Information Systems

open access journalThis case study explores ethical issues that relate to the use of Smart Infor-mation Systems (SIS) in human brain research. The case study is based on the Human Brain Project (HBP), which is a European Union funded project. The project uses SIS to build a research infrastructure aimed at the advancement of neuroscience, medicine and computing. The case study was conducted to assess how the HBP recognises and deal with ethical concerns relating to the use of SIS in human brain research. To under-stand some of the ethical implications of using SIS in human brain research, data was collected through a document review and three semi-structured interviews with partic-ipants from the HBP. Results from the case study indicate that the main ethical concerns with the use of SIS in human brain research include privacy and confidentiality, the security of personal data, discrimination that arises from bias and access to the SIS and their outcomes. Furthermore, there is an issue with the transparency of the processes that are involved in human brain research. In response to these issues, the HBP has put in place different mechanisms to ensure responsible research and innovation through a dedicated pro-gram. The paper provides lessons for the responsible implementation of SIS in research, including human brain research and extends some of the mechanisms that could be employed by researchers and developers of SIS for research in addressing such issues

1st INCF Workshop on Global Portal Services for Neuroscience

The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated portal services

Beyond Research Ethics: Dialogues in Neuro-ICT Research

open access articleThe increasing use of information and communication technologies (ICTs) to help facilitate neuroscience adds a new level of complexity to the question of how ethical issues of such research can be identified and addressed. Current research ethics practice, based on ethics reviews by institutional review boards (IRB) and underpinned by ethical principlism, has been widely criticized. In this article, we develop an alternative way of approaching ethics in neuro-ICT research, based on discourse ethics, which implements Responsible Research and Innovation (RRI) through dialogues. We draw on our work in Ethics Support, using the Human Brain Project (HBP) as empirical evidence of the viability of this approach