scholarly journals Ecotaxonomy: Linking traits, taxa, individuals and samples in a flexible virtual research environment for ecological studies

2019 ◽  
Vol 3 ◽  
Author(s):  
Anton Potapov ◽  
Dorothee Sandmann ◽  
Stefan Scheu
Keyword(s):  
Large Scale ◽  
Research Progress ◽  
Global Biodiversity Information Facility ◽  
Research Environment ◽  
Data Interoperability ◽  
Initial Stage ◽  
Darwin Core ◽  
Virtual Research Environment ◽  
Public Output ◽  
Beta Testing

Major research progress in ecology is being achieved through large-scale collaborations across people, groups and countries. In large-scale projects harmonization of data is tedious and time-consuming, but needs to be done reliably and rapidly. This is especially true if projects investigate under-explored organism groups such as tropical invertebrates. To link taxa to their role in ecosystems, functional traits of the taxa need to be considered. However, despite the urgent need for a common database for invertebrate traits, this is yet to be established. We developed an open web platform, Ecotaxonomy (ecotaxonomy.org), that allows traits, taxa, individuals and samples to be linked within research projects. Ecotaxonomy includes a virtual research environment, allowing project members to work jointly online on the data input, integration and retrieval. The taxonomic system of Ecotaxonomy is based on the Global Biodiversity Information Facility (gbif.org), but may be complemented by morphospecies, pictures, literature and other parameters. Any parameters can be customized inside the system and attached either to taxa, individuals, or environmental samples (Fig. 1). As public output, the system provides interactive identification keys and web catalogs of traits and taxa. Ecotaxonomy is implemented on GCore platform, that is being developed by Complex Cloud Solutions (http://ccs.msk.ru/en/). The GCore is based on Node.js, allowing for fast and efficient standardised programming. Thus, custom modules can be implemented in the future by external developers in the framework of the platform. Ecotaxonomy is now open for beta-testing. After a public release (presumably in 2020), our goal is to keep the system and the code open and ensure data interoperability via Darwin core standards. The initial stage of Ecotaxonomy development (2016-2023) is funded in the framework of a DFG-funded project (SFB 990). To ensure long-term sustainability, we are involving ecological laboratories around the world and ultimately seek to establish a permanent funding by governmental or non-governmental organisations. Using and developing Ecotaxonomy, and linking it to existing open repositories will greatly improve the efficiency and integration of research in trait-based ecology.

Old habits, new dynamics: a case study of Web 2.0 in collaborative humanities and arts research

2011 ◽  
Vol 5 (2) ◽  
pp. 147-157
Author(s):  
Dan Goren
Keyword(s):  
Web 2.0 ◽  
Digital Technology ◽  
Large Scale ◽  
Web 2.0 Technologies ◽  
Research Project ◽  
Research Practices ◽  
Research Environment ◽  
Arts And Humanities ◽  
Virtual Research Environment

Whilst the application of online multimedia digital technology within arts and humanities research has burgeoned over the last decade, the practice of openly conducting collaborative and in particular discursive research publicly online remains one of the most unfamiliar and conceptually problematic areas for many academics in the field. Based on user surveys, blog posts, and forum discussions, this article provides both an account and assessment of Web 2.0 technologies in use on a large-scale arts and humanities research project. Examining usage by and impressions of both the project team and the wider community of users, it investigates both the advantages gained and problems faced through the use of a virtual research environment (VRE). It also pays special attention to the use of video and its implications for research practices.

scholarly journals Interoperable and scalable data analysis with microservices: applications in metabolomics

2019 ◽  
Vol 35 (19) ◽  
pp. 3752-3760 ◽  
Author(s):  
Payam Emami Khoonsari ◽  
Pablo Moreno ◽  
Sven Bergmann ◽  
Joachim Burman ◽  
Marco Capuccini ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
Large Scale ◽  
Scientific Discipline ◽  
Supplementary Information ◽  
Resonance Spectroscopy ◽  
Research Environment ◽  
Metabolomics Data ◽  
Analysis Workflow ◽  
Virtual Research Environment

Abstract Motivation Developing a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator. Results We developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science. Availability and implementation The PhenoMeNal consortium maintains a web portal (https://portal.phenomenal-h2020.eu) providing a GUI for launching the Virtual Research Environment. The GitHub repository https://github.com/phnmnl/ hosts the source code of all projects. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Recent Advances in Unmanned Aerial Vehicles Forest Remote Sensing—A Systematic Review. Part II: Research Applications

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 397
Author(s):  
Riccardo Dainelli ◽  
Piero Toscano ◽  
Salvatore Filippo Di Gennaro ◽  
Alessandro Matese
Keyword(s):  
Remote Sensing ◽  
Unmanned Aerial Vehicle ◽  
Sustainable Management ◽  
Large Scale ◽  
Spectral Signature ◽  
Accurate Information ◽  
Data Interoperability ◽  
Critical Issues ◽  
Management Context ◽  
Aerial Vehicle

Forest sustainable management aims to maintain the income of woody goods for companies, together with preserving non-productive functions as a benefit for the community. Due to the progress in platforms and sensors and the opening of the dedicated market, unmanned aerial vehicle–remote sensing (UAV–RS) is improving its key role in the forestry sector as a tool for sustainable management. The use of UAV (Unmanned Aerial Vehicle) in precision forestry has exponentially increased in recent years, as demonstrated by more than 600 references published from 2018 until mid-2020 that were found in the Web of Science database by searching for “UAV”+“forest”. This result is even more surprising when compared with similar research for “UAV”+“agriculture”, from which emerge about 470 references. This shows how UAV–RS research forestry is gaining increasing popularity. In Part II of this review, analyzing the main findings of the reviewed papers (227), numerous strengths emerge concerning research technical issues. UAV–RS is fully applicated for obtaining accurate information from practical parameters (height, diameter at breast height (DBH), and biomass). Research effectiveness and soundness demonstrate that UAV–RS is now ready to be applied in a real management context. Some critical issues and barriers in transferring research products are also evident, namely,(1) hyperspectral sensors are poorly used, and their novel applications should be based on the capability of acquiring tree spectral signature especially for pest and diseases detection, (2) automatic processes for image analysis are poorly flexible or based on proprietary software at the expense of flexible and open-source tools that can foster researcher activities and support technology transfer among all forestry stakeholders, and (3) a clear lack exist in sensors and platforms interoperability for large-scale applications and for enabling data interoperability.

scholarly journals Research progress of carbon-assisted etching of silicon nanostructures

2021 ◽  
Vol 2076 (1) ◽  
pp. 012060
Author(s):  
Xiaoyu Yang ◽  
Ling Tong ◽  
Lin Wu ◽  
Baoguo Zhang ◽  
Zhiyuan Liao ◽  
...  
Keyword(s):  
Large Scale ◽  
Low Cost ◽  
Lithium Ion ◽  
Development Trend ◽  
Research Progress ◽  
Silicon Nanostructures ◽  
Storage Devices ◽  
Existing Problems ◽  
Energy Conversion And Storage ◽  
Silicon Based

Abstract Silicon nanostructures are attracting growing attention due to their properties and promising application prospects in solar energy conversion and storage devices, thermoelectric devices, lithium-ion batteries, and biosensing technologies. The large-scale and low-cost preparation of silicon nanostructures is critical for silicon-based advanced functional devices commercialization. In this paper, the feasibility and mechanism of silicon nanostructure fabricated by non-metallic carbon catalytic etching, as well as the currently existing problems and future development trend are reviewed.

scholarly journals Data Quality Task Group 2: Tests and Assertions

2018 ◽  
Vol 2 ◽  
pp. e25608 ◽  
Author(s):  
Lee Belbin ◽  
Arthur Chapman ◽  
John Wieczorek ◽  
Paula Zermoglio ◽  
Alex Thompson ◽  
...  
Keyword(s):  
Data Quality ◽  
Task Group ◽  
Global Biodiversity Information Facility ◽  
Unique Identifier ◽  
Project Completion ◽  
Darwin Core ◽  
Resource Type ◽  
Valuable Product ◽  
Group 2 ◽  
Validation Tests

Task Group 2 of the TDWG Data Quality Interest Group aims to provide a standard suite of tests and resulting assertions that can assist with filtering occurrence records for as many applications as possible. Currently ‘data aggregators’ such as the Global Biodiversity Information Facility (GBIF), the Atlas of Living Australia (ALA) and iDigBio run their own suite of tests over records received and report the results of these tests (the assertions): there is, however, no standard reporting mechanisms. We reasoned that the availability of an internationally agreed set of tests would encourage implementations by the aggregators, and at the data sources (museums, herbaria and others) so that issues could be detected and corrected early in the process. All the tests are limited to Darwin Core terms. The ~95 tests refined from over 250 in use around the world, were classified into four output types: validations, notifications, amendments and measures. Validations test one of more Darwin Core terms, for example, that dwc:decimalLatitude is in a valid range (i.e. between -90 and +90 inclusive). Notifications report a status that a user of the record should know about, for example, if there is a user-annotation associated with the record. Amendments are made to one or more Darwin Core terms when the information across the record can be improved, for example, if there is no value for dwc:scientificName, it can be filled in from a valid dwc:taxonID. Measures report values that may be useful for assessing the overall quality of a record, for example, the number of validation tests passed. Evaluation of the tests was complex and time-consuming, but the important parameters of each test have been consistently documented. Each test has a globally unique identifier, a label, an output type, a resource type, the Darwin Core terms used, a description, a dimension (from the Framework on Data Quality from TG1), an example, references, implementations (if any), test-prerequisites and notes. For each test, generic code is being written that should be easy for institutions to implement – be they aggregators or data custodians. A valuable product of the work of TG2 has been a set of general principles. One example is “Darwin Core terms are either: literal verbatim (e.g., dwc:verbatimLocality) and cannot be assumed capable of validation, open-ended (e.g., dwc:behavior) and cannot be assumed capable of validation, or bounded by an agreed vocabulary or extents, and therefore capable of validation (e.g., dwc:countryCode)”. Another is “criteria for including tests is that they are informative, relatively simple to implement, mandatory for amendments and have power in that they will not likely result in 0% or 100% of all record hits.” A third: “Do not ascribe precision where it is unknown.” GBIF, the ALA and iDigBio have committed to implementing the tests once they have been finalized. We are confident that many museums and herbaria will also implement the tests over time. We anticipate that demonstration code and a test dataset that will validate the code will be available on project completion.

scholarly journals Best practices for connecting genetic records with specimen data

2018 ◽  
Vol 2 ◽  
pp. e26369
Author(s):  
Michael Trizna
Keyword(s):  
Best Practices ◽  
Good News ◽  
Sequencing Technology ◽  
Global Biodiversity Information Facility ◽  
A Value ◽  
Darwin Core ◽  
High Quality Sequence ◽  
Voucher Specimens ◽  
Tight Connection ◽  
Biodiversity Information

As rapid advances in sequencing technology result in more branches of the tree of life being illuminated, there has actually been a decrease in the percentage of sequence records that are backed by voucher specimens Trizna 2018b. The good news is that there are tools Trizna (2017), NCBI (2005), Biocode LLC (2014) to enable well-databased museum vouchers to automatically validate and format specimen and collection metadata for high quality sequence records. Another problem is that there are millions of existing sequence records that are known to contain either incorrect or incomplete specimen data. I will show an end-to-end example of sequencing specimens from a museum, depositing their sequence records in NCBI's (National Center for Biotechnology Information) GenBank database, and then providing updates to GenBank as the museum database revises identifications. I will also talk about linking records from specimen databases as well. Over one million records in the Global Biodiversity Information Facility (GBIF) Trizna (2018a) contain a value in the Darwin Core term "associatedSequences", and I will examine what is currently contained in these entries, and how best to format them to ensure that a tight connection is made to sequence records.

scholarly journals How to improve quality of care in overcrowded emergency departments? Development and evaluation of a virtual research environment. (Preprint)

2019 ◽  
Author(s):  
Charles-Henri Houze Cerfon ◽  
Christine Vaissié ◽  
Laurent Gout ◽  
Bruno Bastiani ◽  
Sandrine Charpentier ◽  
...  
Keyword(s):  
Emergency Department ◽  
Emergency Medicine ◽  
Quality Of Care ◽  
Simulated Patients ◽  
Emergency Physicians ◽  
Research Environment ◽  
Significant Difference ◽  
Ed Overcrowding ◽  
Virtual Research Environment

BACKGROUND Despite wide literature on ED overcrowding, scientific knowledge on emergency physicians’ cognitive processes coping with overcrowding is limited. OBJECTIVE We sought to develop and evaluate a virtual research environment that will allow us to study the effect of physicians’ strategies and behaviours on quality of care in the context of emergency department overcrowding. METHODS A simulation-based observational study was conducted over two stages: the development of a simulation model and its evaluation. A research environment in Emergency Medicine combining virtual reality and simulated patients has been designed and developed. Then, twelve emergency physicians took part in simulation scenarios and had to manage thirteen patients during a 2-hour period. The study outcome was the authenticity of the environment through realism, consistency and mastering. The realism was the resemblance perceived by the participants between virtual and real Emergency Department. The consistency of the scenario and the participants’ mastering of the environment was expected for 90% of the participants. RESULTS The virtual emergency department was considered realistic with no significant difference from the real world concerning facilities and resources except for the length of time of procedures that was perceived to be shorter. 100% of participants deemed that patient information, decision-making and managing patient flow were similar to real clinical practice. The virtual environment was well-mastered by all participants over the course of the scenarios. CONCLUSIONS The new simulation tool, Virtual Research Environment in Emergency Medicine has been successfully designed and developed. It has been assessed as perfectly authentic by emergency physicians compared to real EDs and thus offers another way to study human factors, quality of care and patient safety in the context of ED overcrowding.

VirES for Swarm & Virtual Research Environment: Software, guides & infrastructure to boost accessibility of Swarm

2021 ◽  
Author(s):  
Ashley Smith ◽  
Martin Pačes
Keyword(s):  
Community Involvement ◽  
Geomagnetic Field ◽  
Data Retrieval ◽  
Product Portfolio ◽  
It Services ◽  
Research Environment ◽  
Wide Range ◽  
Geomagnetic Field Models ◽  
Virtual Research Environment ◽  
Model Residuals

<p>ESA's Swarm mission continues to deliver excellent data providing insight into a wide range of geophysical phenomena. The mission is an important asset whose data are used within a number of critical resources, from geomagnetic field models to space weather services. As the product portfolio grows to better deliver on the mission's scientific goals, we face increasing complexity in accessing, processing, and visualising the data and models. ESA provides “VirES for Swarm” [1] (developed by EOX IT Services) to help solve this problem. VirES is a web-based data retrieval and visualisation tool where the majority of Swarm products are available. VirES has a graphical interface but also a machine-to-machine interface (API) for programmable use (a Python client is provided). The VirES API also provides access to geomagnetic ground observatory data, as well as forwards evaluation of geomagnetic field models to give data-model residuals. The "Virtual Research Environment" (VRE) adds utility to VirES with a free cloud-based JupyterLab interface allowing scientists to immediately program their own analysis of Swarm products using the Python ecosystem. We are augmenting this with a suite of Jupyter notebooks and dashboards, each targeting a specific use case, and seek community involvement to grow this resource.</p><p>[1] https://vires.services</p>

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