Mark Servilla

Cyberinfrastructure for the analysis of ecological acoustic sensor data: a use case study in grid deployment

Abstract The LTER Grid Pilot Study was conducted by the National Center for Supercomputing Applications, the University of New Mexico, and Michigan State University, to design and build a prototype grid for the ecological community. The featured grid application, the Biophony Grid Portal, manages acoustic data from field sensors and allows researchers to conduct real-time digital signal processing analysis on high-performance systems via a web-based portal. Important characteristics addressed during the study include the management, access, and analysis of a large set of field collected acoustic observations from microphone sensors, single signon, and data provenance. During the development phase of this project, new features were added to standard grid middleware software and have already been successfully leveraged by other, unrelated grid projects. This paper provides an overview of the Biophony Grid Portal application and requirements, discusses considerations regarding grid architecture and design, details the technical implementation, and summarizes key experiences and lessons learned that are generally applicable to all developers and administrators in a grid environment.

Defining linkages between the GSC and NSF's LTER program: How the Ecological Metadata Language (EML) relates to GCDML and other outcomes

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designers tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTERs experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected.

The contribution and reuse of LTER data in the Provenance Aware Synthesis Tracking Architecture (PASTA) data repository

Abstract Sites in the Long Term Ecological Research (LTER) Network have now contributed greater than 5000 data packages into the LTER Network Information System (NIS). This corpus of data and metadata allows us to analyze characteristics of data from the LTER program, including temporal coverage, data format, rate of submission, volume of data, and ecological characteristics of the data (e.g., ecosystems, processes, organisms). In addition, data/metadata congruence checks included in the Provenance Aware Synthesis Tracking Architecture (PASTA) underlying the NIS allow us to examine the quality of metadata submitted. Initial records of data use and citation provide the means to evaluate the efficacy of this repository in disseminating data throughout a broader community – 89 citations of data packages found in 52 articles have been documented to date.

Ensuring the quality of data packages in the LTER network data management system

Abstract Considerable data analyses use automated workflows to ingest data from public repositories, and rely on data packages of high structural quality. The Long Term Ecological Research (LTER) Network now screens all packages entering its long-term archive to ensure completeness and quality, and to ascertain that metadata and data are structurally congruent, i.e., that the data typing and formats expressed in metadata agree with that found in data entities. The EML Congruence Checker (ECC) system is a component of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA), and operates on data tables in packages described with Ecological Metadata Language using the EML Data Manager Library, written in Java. Checking is extensible for other data types and customizable via a template. Reports are retained as part of the submitted data package, and summaries here reflect the general usability of LTER data for a variety of purposes. On average in 2015, site-contributed data in the LTER catalog were 95% compliant (valid) with the current suite of checks.

CyberInfrastructure for the analysis of ecological acoustic sensor data: a use case study in grid deployment

The LTER grid pilot study was conducted by the National Center for Supercomputing Applications, the University of New Mexico, and Michigan State University, to design and build a prototype grid for the ecological community. The featured grid application, the Biophony Grid Portal, manages acoustic data from field sensors and allows researchers to conduct real-time digital signal processing analysis on high-performance systems via a Web-based portal. Important characteristics addressed during the study include the management, access, and analysis of a large set of field collected acoustic observations from microphone sensors, single signon, and data provenance. During the development phase of this project new features were added to standard grid middleware software and have already been successfully leveraged by other, unrelated grid projects. This paper provides an overview of the Biophony Grid Portal application and requirements, discusses considerations regarding grid architecture and design, details the technical implementation, and summarizes key experiences and lessons learned that are generally applicable to all developers and administrators in a grid environment.