Future internet enablers for VGI applications

This paper presents the authors experiences with the development of mobile Volunteered Geographic Information (VGI) applications in the context of the ENVIROFI project and Future Internet Public Private Partnership (FI-PPP) FP7 research programme.FI-PPP has an ambitious goal of developing a set of Generic FI Enablers (GEs) - software and hardware tools that will simplify development of thematic future internet applications. Our role in the programme was to provide requirements and assess the usability of the GEs from the point of view of the environmental usage area, In addition, we specified and developed three proof of concept implementations of environmental FI applications, and a set of specific environmental enablers (SEs) complementing the functionality offered by GEs. Rather than trying to rebuild the whole infrastructure of the Environmental Information Space (EIS), we concentrated on two aspects: (1) how to assure the existing and future EIS services and applications can be integrated and reused in FI context; and (2) how to profit from the GEs in future environmental applications.This paper concentrates on the GEs and SEs which were used in two of the ENVIROFI pilots which are representative for the emerging class of Volunteered Geographic Information (VGI) use-cases: one of them is pertinent to biodiversity and another to influence of weather and airborne pollution on users’ wellbeing. In VGI applications, the EIS and SensorWeb overlap with the Social web and potentially huge amounts of information from mobile citizens needs to be assessed and fused with the observations from official sources. On the whole, the authors are confident that the FI-PPP programme will greatly influence the EIS, but the paper also warns of the shortcomings in the current GE implementations and provides recommendations for further developments

Environmental metabolomics : databases and tools for data analysis

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Marine Chemistry 177 (2015): 366–373, doi:10.1016/j.marchem.2015.06.012.Metabolomics is the study of small molecules, or ‘metabolites’, that are the end products of biological processes. While -omics technologies such as genomics, transcriptomics, and proteomics measure the metabolic potential of organisms, metabolomics provides detailed information on the organic compounds produced during metabolism and found within cells and in the environment. Improvements in analytical techniques have expanded our understanding of metabolomics and developments in computational tools have made metabolomics data accessible to a broad segment of the scientific community. Yet, metabolomics methods have only been applied to a limited number of projects in the marine environment. Here, we review analysis techniques for mass spectrometry data and summarize the current state of metabolomics databases. We then describe a boutique database developed in our laboratory for efficient data analysis and selection of mass spectral targets for metabolite identification. The code to implement the database is freely available on GitHub (https://github.com/joefutrelle/domdb). Data organization and analysis are critical, but often under-appreciated, components of metabolomics research. Future advances in environmental metabolomics will take advantage of continued development of new tools that facilitate analysis of large metabolomics datasets.The field data populating the database comes from scientific cruises funded by grants from the National Science Foundation to EBK and KL (Atlantic Ocean, OCE-1154320) and E.V. Armbrust (Pacific Ocean, OCE-1205233). The laboratory experiment with coastal seawater was funded by a grant from the Gulf of Mexico Research Initiative to EBK and H.K. White. The laboratory experiments with microbial isolates and the database development are funded by the Gordon and Betty Moore Foundation through Grant GBMF3304 to EBK

EcoGIS – GIS tools for ecosystem approaches to fisheries management

Executive Summary: The EcoGIS project was launched in September 2004 to investigate how Geographic Information Systems (GIS), marine data, and custom analysis tools can better enable fisheries scientists and managers to adopt Ecosystem Approaches to Fisheries Management (EAFM). EcoGIS is a collaborative effort between NOAA’s National Ocean Service (NOS) and National Marine Fisheries Service (NMFS), and four regional Fishery Management Councils. The project has focused on four priority areas: Fishing Catch and Effort Analysis, Area Characterization, Bycatch Analysis, and Habitat Interactions. Of these four functional areas, the project team first focused on developing a working prototype for catch and effort analysis: the Fishery Mapper Tool. This ArcGIS extension creates time-and-area summarized maps of fishing catch and effort from logbook, observer, or fishery-independent survey data sets. Source data may come from Oracle, Microsoft Access, or other file formats. Feedback from beta-testers of the Fishery Mapper was used to debug the prototype, enhance performance, and add features. This report describes the four priority functional areas, the development of the Fishery Mapper tool, and several themes that emerged through the parallel evolution of the EcoGIS project, the concept and implementation of the broader field of Ecosystem Approaches to Management (EAM), data management practices, and other EAM toolsets. In addition, a set of six succinct recommendations are proposed on page 29. One major conclusion from this work is that there is no single “super-tool” to enable Ecosystem Approaches to Management; as such, tools should be developed for specific purposes with attention given to interoperability and automation. Future work should be coordinated with other GIS development projects in order to provide “value added” and minimize duplication of efforts. In addition to custom tools, the development of cross-cutting Regional Ecosystem Spatial Databases will enable access to quality data to support the analyses required by EAM. GIS tools will be useful in developing Integrated Ecosystem Assessments (IEAs) and providing pre- and post-processing capabilities for spatially-explicit ecosystem models. Continued funding will enable the EcoGIS project to develop GIS tools that are immediately applicable to today’s needs. These tools will enable simplified and efficient data query, the ability to visualize data over time, and ways to synthesize multidimensional data from diverse sources. These capabilities will provide new information for analyzing issues from an ecosystem perspective, which will ultimately result in better understanding of fisheries and better support for decision-making. (PDF file contains 45 pages.

Music Information Retrieval in Live Coding: A Theoretical Framework

The work presented in this article has been partly conducted while the first author was at Georgia Tech from 2015–2017 with the support of the School of Music, the Center for Music Technology and Women in Music Tech at Georgia Tech. Another part of this research has been conducted while the first author was at Queen Mary University of London from 2017–2019 with the support of the AudioCommons project, funded by the European Commission through the Horizon 2020 programme, research and innovation grant 688382. The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Music information retrieval (MIR) has a great potential in musical live coding because it can help the musician–programmer to make musical decisions based on audio content analysis and explore new sonorities by means of MIR techniques. The use of real-time MIR techniques can be computationally demanding and thus they have been rarely used in live coding; when they have been used, it has been with a focus on low-level feature extraction. This article surveys and discusses the potential of MIR applied to live coding at a higher musical level. We propose a conceptual framework of three categories: (1) audio repurposing, (2) audio rewiring, and (3) audio remixing. We explored the three categories in live performance through an application programming interface library written in SuperCollider, MIRLC. We found that it is still a technical challenge to use high-level features in real time, yet using rhythmic and tonal properties (midlevel features) in combination with text-based information (e.g., tags) helps to achieve a closer perceptual level centered on pitch and rhythm when using MIR in live coding. We discuss challenges and future directions of utilizing MIR approaches in the computer music field

Web-based Remote Sensing Applications and Java Tools for Environmental Monitoring

This paper introduces a web-based remote sensing application which can provide advanced image comparison and processing functions for natural habitat conservation and environmental monitoring. This project is one of several NASA Affiliated Research Center (ARC) projects being developed at San Diego State University in response to NASA\u27s Earth Science Enterprise (ESE) Focus Area program. This project utilized Java programming and commercial Internet Map Server technology to provide integrated web-based analytical capabilities to regional government agencies and park services. A prototype website (http://map.sdsu.edu/arc) was established to demonstrate the on-line analytical functions and potential operational applications for environmental monitoring and habitat managers. The web-based prototype was tested and evaluated by several user groups, including park rangers, graduate students, and GIS professionals. Users\u27 feedback indicated that the Java-based tools and Internet Map Servers can provide a flexible way to access both remote sensing data and geospatial analytical tools for environmental monitoring tasks

Designing Improved Sediment Transport Visualizations

Monitoring, or more commonly, modeling of sediment transport in the coastal environment is a critical task with relevance to coastline stability, beach erosion, tracking environmental contaminants, and safety of navigation. Increased intensity and regularity of storms such as Superstorm Sandy heighten the importance of our understanding of sediment transport processes. A weakness of current modeling capabilities is the ability to easily visualize the result in an intuitive manner. Many of the available visualization software packages display only a single variable at once, usually as a two-dimensional, plan-view cross-section. With such limited display capabilities, sophisticated 3D models are undermined in both the interpretation of results and dissemination of information to the public. Here we explore a subset of existing modeling capabilities (specifically, modeling scour around man-made structures) and visualization solutions, examine their shortcomings and present a design for a 4D visualization for sediment transport studies that is based on perceptually-focused data visualization research and recent and ongoing developments in multivariate displays. Vector and scalar fields are co-displayed, yet kept independently identifiable utilizing human perception\u27s separation of color, texture, and motion. Bathymetry, sediment grain-size distribution, and forcing hydrodynamics are a subset of the variables investigated for simultaneous representation. Direct interaction with field data is tested to support rapid validation of sediment transport model results. Our goal is a tight integration of both simulated data and real world observations to support analysis and simulation of the impact of major sediment transport events such as hurricanes. We unite modeled results and field observations within a geodatabase designed as an application schema of the Arc Marine Data Model. Our real-world focus is on the Redbird Artificial Reef Site, roughly 18 nautical miles offshor- Delaware Bay, Delaware, where repeated surveys have identified active scour and bedform migration in 27 m water depth amongst the more than 900 deliberately sunken subway cars and vessels. Coincidently collected high-resolution multibeam bathymetry, backscatter, and side-scan sonar data from surface and autonomous underwater vehicle (AUV) systems along with complementary sub-bottom, grab sample, bottom imagery, and wave and current (via ADCP) datasets provide the basis for analysis. This site is particularly attractive due to overlap with the Delaware Bay Operational Forecast System (DBOFS), a model that provides historical and forecast oceanographic data that can be tested in hindcast against significant changes observed at the site during Superstorm Sandy and in predicting future changes through small-scale modeling around the individual reef objects

5th Data Science Symposium [Book of Abstracts]

Modern digital scientific workflows - often implying Big Data challenges - require data infrastructures and innovative data science methods across disciplines and technologies. Diverse activities within and outside HGF deal with these challenges, on all levels. The series of Data Science Symposia fosters knowledge exchange and collaboration in the Earth and Environment research community

BioMeT and algorithm challenges: A proposed digital standardized evaluation framework

Technology is advancing at an extraordinary rate. Continuous flows of novel data are being generated with the potential to revolutionize how we better identify, treat, manage, and prevent disease across therapeutic areas. However, lack of security of confidence in digital health technologies is hampering adoption, particularly for biometric monitoring technologies (BioMeTs) where frontline healthcare professionals are struggling to determine which BioMeTs are fit-for-purpose and in which context. Here, we discuss the challenges to adoption and offer pragmatic guidance regarding BioMeTs, cumulating in a proposed framework to advance their development and deployment in healthcare, health research, and health promotion. Furthermore, the framework proposes a process to establish an audit trail of BioMeTs (hardware and algorithms), to instill trust amongst multidisciplinary users