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

Mammal predator and prey species richness are strongly linked at macroscales

Predator-prey interactions play an important role for species composition and community dynamics at local scales, but their importance in shaping large-scale gradients of species richness remains unexplored. Here, we use global range maps, structural equation models (SEM), and comprehensive databases of dietary preferences and body masses of all terrestrial, non-volant mammals worldwide, to test whether (1) prey bottom-up or predator top-down relationships are important drivers of broad-scale species richness gradients once the environment and human influence have been accounted for, (2) predator-prey richness associations vary among biogeographic regions, and (3) body size influences large-scale covariation between predators and prey. SEMs including only productivity, climate, and human factors explained a high proportion of variance in prey richness (R2 = 0.56) but considerably less in predator richness (R2 = 0.13). Adding predator-to-prey or prey-topredator paths strongly increased the explained variance in both cases (prey R2 = 0.79, predator R2 = 0.57), suggesting that predator-prey interactions play an important role in driving global diversity gradients. Prey bottom-up effects prevailed over productivity, climate, and human influence to explain predator richness, whereas productivity and climate were more important than predator top-down effects for explaining prey richness, although predator top-down effects were still significant. Global predator-prey associations were not reproduced in all regions, indicating that distinct paleoclimate and evolutionary histories (Africa and Australia) may alter species interactions across trophic levels. Stronger crosstrophic- level associations were recorded within categories of similar body size (e.g., large prey to large predators) than between them (e.g., large prey to small predators), suggesting that mass-related energetic and physiological constraints influence broad-scale richness links, especially for large-bodied mammals. Overall, our results support the idea that trophic interactions can be important drivers of large-scale species richness gradients in combination with environmental effects. © 2013 by the Ecological Society of America

Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges--management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu

Observations on the relationship between verbal explicit and implicit memory and neuronal density in the left and right hippocampus in temporal lobectomy patients.

The relationship between neuronal density and verbal memory in left and right hippocampal subfields was investigated in patients who underwent surgery for alleviation of temporal lobe epilepsy. The surgery consisted of unilateral partial removal of the hippocampus along with the anterior temporal lobe and amygdala. Study 1 looked at post-surgical explicit versus implicit verbal memory for lists of words while Study 2 looked at pre- and post-surgical explicit memory for word pairs. Left subfield CA1 appeared to be the most consistently involved in explicit and implicit memory. The results of the two studies confirm presence of hemispheric asymmetry in verbal memory. The notion that hippocampal control of memory is most apparent in post-surgical performance is discussed

e-Science Infrastructure for the Social Sciences

When the term „e-Science“ became popular, it frequently was referred to as “enhanced science” or “electronic science”. More telling is the definition ‘e-Science is about global collaboration in key areas of science and the next generation of infrastructure that will enable it’ (Taylor, 2001). The question arises to what extent can the social sciences profit from recent developments in e- Science infrastructure? While computing, storage and network capacities so far were sufficient to accommodate and access social science data bases, new capacities and technologies support new types of research, e.g. linking and analysing transactional or audio-visual data. Increasingly collaborative working by researchers in distributed networks is efficiently supported and new resources are available for e-learning. Whether these new developments become transformative or just helpful will very much depend on whether their full potential is recognized and creatively integrated into new research designs by theoretically innovative scientists. Progress in e-Science was very much linked to the vision of the Grid as “a software infrastructure that enables flexible, secure, coordinated resource sharing among dynamic collections of individuals, institutions and resources’ and virtually unlimited computing capacities (Foster et al. 2000). In the Social Sciences there has been considerable progress in using modern IT- technologies for multilingual access to virtual distributed research databases across Europe and beyond (e.g. NESSTAR, CESSDA – Portal), data portals for access to statistical offices and for linking access to data, literature, project, expert and other data bases (e.g. Digital Libraries, VASCODA/SOWIPORT). Whether future developments will need GRID enabling of social science databases or can be further developed using WEB 2.0 support is currently an open question. The challenges here are seamless integration and interoperability of data bases, a requirement that is also stipulated by internationalisation and trans-disciplinary research. This goes along with the need for standards and harmonisation of data and metadata. Progress powered by e- infrastructure is, among others, dependent on regulatory frameworks and human capital well trained in both, data science and research methods. It is also dependent on sufficient critical mass of the institutional infrastructure to efficiently support a dynamic research community that wants to “take the lead without catching up”.

Provenance-based trust for grid computing: Position Paper

Current evolutions of Internet technology such as Web Services, ebXML, peer-to-peer and Grid computing all point to the development of large-scale open networks of diverse computing systems interacting with one another to perform tasks. Grid systems (and Web Services) are exemplary in this respect and are perhaps some of the first large-scale open computing systems to see widespread use - making them an important testing ground for problems in trust management which are likely to arise. From this perspective, today's grid architectures suffer from limitations, such as lack of a mechanism to trace results and lack of infrastructure to build up trust networks. These are important concerns in open grids, in which "community resources" are owned and managed by multiple stakeholders, and are dynamically organised in virtual organisations. Provenance enables users to trace how a particular result has been arrived at by identifying the individual services and the aggregation of services that produced such a particular output. Against this background, we present a research agenda to design, conceive and implement an industrial-strength open provenance architecture for grid systems. We motivate its use with three complex grid applications, namely aerospace engineering, organ transplant management and bioinformatics. Industrial-strength provenance support includes a scalable and secure architecture, an open proposal for standardising the protocols and data structures, a set of tools for configuring and using the provenance architecture, an open source reference implementation, and a deployment and validation in industrial context. The provision of such facilities will enrich grid capabilities by including new functionalities required for solving complex problems such as provenance data to provide complete audit trails of process execution and third-party analysis and auditing. As a result, we anticipate that a larger uptake of grid technology is likely to occur, since unprecedented possibilities will be offered to users and will give them a competitive edge

Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset

CRU TS (Climatic Research Unit gridded Time Series) is a widely used climate dataset on a 0.5 degrees latitude by 0.5 degrees longitude grid over all land domains of the world except Antarctica. It is derived by the interpolation of monthly climate anomalies from extensive networks of weather station observations. Here we describe the construction of a major new version, CRU TS v4. It is updated to span 1901-2018 by the inclusion of additional station observations, and it will be updated annually. The interpolation process has been changed to use angular-distance weighting (ADW), and the production of secondary variables has been revised to better suit this approach. This implementation of ADW provides improved traceability between each gridded value and the input observations, and allows more informative diagnostics that dataset users can utilise to assess how dataset quality might vary geographically