Papers by Siddeswara Mayura Guru
Australia's TERN: Advancing Ecosystem Data Management in Australia
AGU Fall Meeting Abstracts, Dec 1, 2013
ANU Press eBooks, Feb 19, 2018
LAND USE IN AUSTRALIA 254 • The establishment of a land use and land resources centre-a virtual o... more LAND USE IN AUSTRALIA 254 • The establishment of a land use and land resources centre-a virtual organisation operating on a collaborative basis and drawing on the expertise of Australian agencies and research institutions with allied interests and objectives-would be an excellent way of securing the institutional capabilities to deliver on this vision.
Electronic Journal of Structural Engineering
Deployment of a large number of sensors across the world has provided several opportunities and c... more Deployment of a large number of sensors across the world has provided several opportunities and challenges. One of the opportunities is the ability to conduct macro-scale experiments using heterogeneous data with wider temporal and spatial variability. This has potential to drastically increase the scientific outcomes and discover new knowledge about our environment. Challenges include dealing with heterogeneity of data for distribution in a seamless environment and management of tasks and processes that manipulate disparate data to discover new knowledge. In this paper, we have adopted Open Geospatial Consortium – Sensor Web Enablement (OGC-SWE) framework to standardise the description and access of hydrometeorological phenomena. This will ease the seamless discovery and sharing of data. We have also proposed Kepler inspired scientific workflow based hydrology workbench to compose heterogeneous hydrometeorological data services and processes for knowledge discovery. These concepts ...
The Environmental and Earth sciences are faced with complex and dynamic challenges: they cannot b... more The Environmental and Earth sciences are faced with complex and dynamic challenges: they cannot be solved in isolation from each other or from other sciences, such as the social and health sciences. Researchers who tackle real world challenges must have data that are easy to use and understandable in a variety of contexts. An important element of understanding these data is the use of well-organised, community-accepted terminology for data. With the increasing uptake of the semantic web and the demand for open data, data descriptors of varying quality and technical maturity are proliferating (e.g. ESIP/RDA Earth, Space and Environmental Sciences Interest Group (ESES-IG), Semantic Resource Catalogue, 2021). These range from simple lists, through thesauri and taxonomies, to formalised ontologies. This proliferation can be extremely confusing for the practitioner (data creator or re-user), as there are no agreed criteria to support a selection decision. In addition, the variety of desc...
Conservation Science and Practice, 2020
Quantifying species population trends is crucial for monitoring progress towards global conservat... more Quantifying species population trends is crucial for monitoring progress towards global conservation targets, justifying investments, planning targeted responses and raising awareness about threatened species. Many global indicators are slow in response and report on common species, not on those at greatest risk of extinction. Here we develop a Threatened Species Index as a dynamic tool for tracking annual changes in Australia's imperiled birds. Based on the Living Planet Index method and containing more than 17,000 time series for 65 bird taxa surveyed systematically, the index at its second iteration shows an average reduction of 59% between 1985 and 2016, and 44% between 2000 and 2016. Decreases seem most severe for shorebirds and terrestrial birds and least severe for seabirds. The index provides a potential means for measuring performance against the Convention on Biological Diversity's Aichi Target 12, enabling governments, agencies and the public to observe changes in...
This session was organized as a co-located meeting during RDS Plenary 17 in support of the PARSEC... more This session was organized as a co-located meeting during RDS Plenary 17 in support of the PARSEC project. To maximize semantic interoperability of our data the use of shared or harmonized terminology is essential, particularly where the data comes from multiple communities and from many countries. The term 'vocabulary' is used to denote any semantic asset containing terms and information about those terms, including value sets (i.e., bag of terms, term list), controlled-vocabularies, glossaries, thesauri, and taxonomies, and potentially even concept maps, ontologies, and knowledge graphs. With the increasing uptake of the semantic web, vocabularies and other semantic resources are proliferating. Researchers are becoming confused as to which one they should use, and more importantly, which ones they can trust. And where it can be shown that a vocabulary does not exist, what is best practice in developing, maintaining and sustaining one. RDA Session Information Notes (Google)...
Broadscale ecology assessments require combination of data from many sources. The Australian Terr... more Broadscale ecology assessments require combination of data from many sources. The Australian Terrestrial Ecosystems Research Network (TERN) aggregates data collected by multiple statutory agencies and research organizations. This data is structured according to a variety of schemas. We have developed a system to harmonize the site-based observation data following the ISO/OGC Observations and Measurements model. This is implemented using (i) the W3C SSN ontology, with extensions for (ii) the TERN Sites domain, (iii) homogeneous observation collections. This implementation also depends on use of (iv) controlled-vocabularies for observable-properties, and (v) for the value-spaces of these, as well as other elements of the observation descriptions. For use in this platform, all published as linked-data, with a distinct persistent URI for each vocabulary item). Each data provider has its own set of vocabularies, so while the core ontology has enabled structural harmonization, full semant...
Weber, T., McPhee, M.J. and Anderssen, R.S. (eds) MODSIM2015, 21st International Congress on Modelling and Simulation, 2015
In order to perform complex scientific data analysis, multiple software and skillsets are general... more In order to perform complex scientific data analysis, multiple software and skillsets are generally required. These analyses can involve collaborations between scientific and technical communities, with expertise in problem formulation and the use of tools and programming languages. While such collaborations are useful for solving a given problem, transferability and productivity of the approach is low and requires considerable assistance from the original tool developers. Any complex scientific data analysis involves accessing and refining large volumes of data, running simulations and algorithms, and visualising results. These steps can incorporate a variety of tools and programming languages, and can be constructed as a series of activities to achieve a desired outcome. This is where scientific workflows are very useful. Scientific workflows abstract complex analyses into a series of interdependent computational steps that lead to a solution for a scientific problem. Once constructed, the workflow can be executed repeatedly and the results reproduced with minimal assistance from the original tool developers. This improves transferability, repeatability and productivity, and reduces costs by reusing workflow components for similar problems but using different datasets. Kepler is a popular open-source scientific workflow tool for designing, executing, archiving and sharing workflows. It has the ability to couple disparate execution environments on a single platform. For example, users can run analysis steps written in Python, R and Matlab on a single platform as part of a single analysis and synthesis experiment. Kepler provides a wide variety of reusable components that perform various tasks, including data access from databases, remote system, file system and web services, and data servers, and executes these processes in a local or distributed environment. Together these functionalities provide greater flexibility for researchers to undertake complex scientific analyses compared with traditional homogeneous environments. In this paper, we will describe a new scientific workflow based on Kepler that automates data analysis tasks for Marxan, a widely used conservation planning software. Marxan is used by over 4,200 active users in more than 180 countries to identify gaps in biodiversity protection, identify cost effective areas for conservation investment and inform multiple-use zoning. Its use is expanding rapidly and this new functionality will improve the application of Marxan to various conservation planning problems. A Kepler workbench has been extended to provide functionality to invoke Marxan and execute it within a distributed environment using Nimrod/K. Our aim was to develop a reproducible, reusable workflow to generate conservation planning scenarios on the Kepler platform. The workflow components include data acquisition and pre-processing, construction of planning scenarios, generation of efficient solutions to the complex problem formulations and visualization of outputs. The workflow components are shared for reuse and reconfigured to design and simulate other conservation planning applications. We also present a use case to demonstrate a Kepler Marxan workflow to design and implement conservation planning computational simulation experiments.
CoESRA: From virtual desktop to science gateway
The Collaborative Environment for Ecosystem Science Research and Analysis (CoESRA) is a Web-based... more The Collaborative Environment for Ecosystem Science Research and Analysis (CoESRA) is a Web-based virtual desktop environment that integrates existing eResearch infrastructure in Australia for synthesis and analysis of scientific data for the ecological science community. Data synthesis and analysis is performed through scientific workflows. Even though this is powerful, it has a large learning curve for novice users. We have implemented a Web layer on top of an existing virtual desktop layer to hide this complexity from users. This new layer allows users to execute scientific workflows without requiring a desktop, and thus reduces the learning curve. The virtual desktop is still accessible for more advanced users.
There is a large amount of plot-based ecological data collected by different agencies and at diff... more There is a large amount of plot-based ecological data collected by different agencies and at different jurisdictions. Often, data are collected using varying survey methods and procedures, even though observed properties are similar. Typically, use of these data for analysis is confined to a jurisdiction from where the data was collected. However, integration of these datasets would enable their use at a larger scale for analysis and synthesis. In this paper, we will describe a Semantic Web approach to integrate plot-based ecological data from different agencies in Australia. We will also discuss some of the initial implementation progress.
A Computational Pipeline for the IUCN Risk Assessment for Meso-American Reef Ecosystem
2017 IEEE 13th International Conference on e-Science (e-Science), 2017
Coral reefs are of global economic and biological significance but are subject to increasing thre... more Coral reefs are of global economic and biological significance but are subject to increasing threats. As a result, it is essential to understand the risk of coral reef ecosystem collapse and to develop assessment process for those ecosystems. The International Union for Conservation of Nature (IUCN) Red List of Ecosystem (RLE) is a framework to assess the vulnerability of an ecosystem. Importantly, the assessment processes need to be repeatable as new monitoring data arises. The repeatability will also enhance transparency. In this paper, we discuss the evolution of a computational pipeline for risk assessment of the Meso-American reef ecosystem, a diverse reef ecosystem located in the Caribbean, with the focus on improving the execution time starting from sequential and parallel implementation and finally using Apache Spark. The final form of the pipeline is a scientific workflow to improve its repeatability and reproducibility.
Essential Environmental Measures Native Vegetation Information Model and Data Exchange
• The impacts of human-forced climate change will continue to be felt for millennia, irrespective... more • The impacts of human-forced climate change will continue to be felt for millennia, irrespective of our success or failure to mitigate greenhouse gas emissions. • Therefore, climate change adaptation must be understood as a 'forever' activity and mainstreamed in policy, planning and decision-making. • In parallel, we are witnessing unprecedented land use change in terms of extent and intensification that is transforming the land surface, together with subsurface processes, in ways as profound as climate change. • Policies and programs that aim to reduce emissions of greenhouse gases from the land sector will continue to be a key component of Australia's response to its Paris Agreement commitments. • We have the data and information to address these emerging pressures; however, we lack the public understanding, political will and national policy to require their use. LAND USE IN AUSTRALIA 242 • State and territory governments must take the necessary step change. There is a need for national leadership by the Australian Government if the new generation of data, knowledge products and decision support tools are to be developed, and the policies that drive their application in support of agreed national land use goals put in place.
Building Australia’s Scalable Drone Cloud
<p>Remotely Piloted Aircraft (RPA), commonly known as drones, provi... more <p>Remotely Piloted Aircraft (RPA), commonly known as drones, provide sensing capabilities that address the critical scale-gap between ground- and satellite-based observations. Their versatility allows researchers to deliver near-real-time information for society.</p><p>Key to delivering RPA information is the capacity to enable researchers to systematically collect, process, manage and share RPA-borne sensor data. Importantly, this should allow vertical integration across scales and horizontal integration across different RPA deployments. However, as an emerging technology, the best practice and standards are still developing and the large data volumes collected during RPA missions can be challenging.</p><p>Australia’s Scalable Drone Cloud (ASDC) aims to coordinate and standardise how scientists from across earth, environmental and agricultural research manage, process and analyse data collected by RPA-borne sensors, by establishing best practices in managing 3D-geospatial data and aligned with the FAIR data principles.</p><p>The ASDC is building a cloud-native platform for research drone data management and analytics, driven by exemplar data management practices, data-processing pipelines, and search and discovery of drone data. The aim of the platform is to integrate sensing capabilities with easy-to-use storage, processing, visualisation and data analysis tools (including computer vision / deep learning techniques) to establish a national ecosystem for drone data management.</p><p>The ASDC is a partnership of the Monash Drone Discovery Platform, CSIRO and key National Collaborative Research Infrastructure (NCRIS) capabilities including the Australian Research Data Commons (ARDC), Australian Plant Phenomics Facility (APPF), Terrestrial Ecosystem Research Network (TERN), and AuScope.</p><p>This presentation outlines the roadmap and first proof-of-concept implementation of the ASDC.</p>
Ecological Informatics, 2020
Background: The optimal duration of triple anti-platelet therapy (DTAP) remains unclear in patien... more Background: The optimal duration of triple anti-platelet therapy (DTAP) remains unclear in patients with acute myocardial infarction (AMI). Methods: We retrospectively analyzed 716 AMI patients who received TAP (aspirin, clopidogrel, and cilostazol) after drug-eluting stent (DES) implantation from November 2005 to May 2008. Mean age was 61.9 ± 11.70 years (male gender 74.1%) and mean duration of TAP was 98.1 ± 115.34 days. We compared the major adverse cardiovascular events [MACE, defined as the composite of cardiac death, non-fatal AMI, stent thrombosis, and target vessel revascularization (TVR)] between the group of DTAP ≥3 months (n = 497) and those of <3 months (n = 219). Results: There were no significant differences in the incidences of cardiac death, non-fatal AMI, stent thrombosis, and TVR at 1-year follow-up between the two groups. However, the group of DTAP ≥3 months had lower incidence of MACE than those <3 months (5.9% vs. 10.7%, p = 0.044). The rate of bleeding complications was similar between the two groups. By Cox regression analysis with propensity score adjustment, Killip class IV and DTAP ≥3 months were
Conservation Biology, 2019
The optimal design of reserve networks and fisheries closures depends on species occurrence infor... more The optimal design of reserve networks and fisheries closures depends on species occurrence information and knowledge of how anthropogenic impacts interact with the species concerned. However, challenges in surveying mobile and cryptic species over adequate spatial and temporal scales can mask the importance of particular habitats, leading to uncertainty about which areas to protect to optimize conservation efforts. We investigated how telemetry‐derived locations can help guide the scale and timing of fisheries closures with the aim of reducing threatened species bycatch. Forty juvenile speartooth sharks (Glyphis glyphis) were monitored over 22 months with implanted acoustic transmitters and an array of hydrophone receivers. Using the decision‐support tool Marxan, we formulated a permanent fisheries closure that prioritized areas used more frequently by tagged sharks and considered areas perceived as having high value to fisheries. To explore how the size of the permanent closure co...
BioScience, 2017
DISCLAIMER: This draft manuscript is distributed solely for purposes of scientific peer review. I... more DISCLAIMER: This draft manuscript is distributed solely for purposes of scientific peer review. Its content is deliberative and predecisional, so it must not be disclosed or released by reviewers. Because the manuscript has not yet been approved for publication by the U.S. Geological Survey (USGS), it does not represent any official USGS finding or policy. Non disclosure prior to publication. In agreeing to be a peer reviewer for a USGS information product, reviewers must agree to be bound by the strictest scientific ethics in ensuring confidentiality of the science that is being reviewed and to not disclose or divulge any results or conclusions, or to make any public statements regarding the science before it is published and released.
Collaborative Environment for Ecosystem Science Research and Analysis
UQ eSpace
The objective of the project is to demonstrate the value in better connecting eResearch infrastru... more The objective of the project is to demonstrate the value in better connecting eResearch infrastructure by bringing ecosystem science data streams closer to the tools in a common environment for further analysis tasks, and by supporting data publishing of the results.
The Science of the total environment, Jan 6, 2015
Mitigating the environmental effects of global population growth, climatic change and increasing ... more Mitigating the environmental effects of global population growth, climatic change and increasing socio-ecological complexity is a daunting challenge. To tackle this requires synthesis: the integration of disparate information to generate novel insights from heterogeneous, complex situations where there are diverse perspectives. Since 1995, a structured approach to inter-, multi- and trans-disciplinary(1) collaboration around big science questions has been supported through synthesis centres around the world. These centres are finding an expanding role due to ever-accumulating data and the need for more and better opportunities to develop transdisciplinary and holistic approaches to solve real-world problems. The Australian Centre for Ecological Analysis and Synthesis (ACEAS <http://www.aceas.org.au>) has been the pioneering ecosystem science synthesis centre in the Southern Hemisphere. Such centres provide analysis and synthesis opportunities for time-pressed scientists, polic...
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Papers by Siddeswara Mayura Guru