ToMaTo a Virtual Research Environment for Large Scale Distributed Systems Research

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.

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Interoperable and scalable data analysis with microservices: applications in metabolomics

Bioinformatics ◽

10.1093/bioinformatics/btz160 ◽

2019 ◽

Vol 35 (19) ◽

pp. 3752-3760 ◽

Cited By ~ 10

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.

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GENI: Large-scale distributed infrastructure for networking and distributed systems research

2014 IEEE Fifth International Conference on Communications and Electronics (ICCE) ◽

10.1109/cce.2014.6916696 ◽

2014 ◽

Cited By ~ 3

Author(s):

Mark Berman ◽

Chip Elliott ◽

Lawrence Landweber

Keyword(s):

Distributed Systems ◽

Large Scale ◽

Systems Research ◽

Distributed Infrastructure

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

Biodiversity Information Science and Standards ◽

10.3897/biss.3.37166 ◽

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.

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An Integrated Specification and Verification Environment for Component-Based Architectures of Large-Scale Distributed Systems

10.21236/ada501823 ◽

2009 ◽

Cited By ~ 1

Author(s):

John Hatcliff ◽

Torben Amtoft ◽

Anindya Banerjee

Keyword(s):

Distributed Systems ◽

Large Scale ◽

Specification And Verification

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A Bridge Too Far?

10.1093/oso/9780198733249.003.0006 ◽

2018 ◽

Author(s):

Charlotte P. Lee ◽

Kjeld Schmidt

Keyword(s):

Information Systems ◽

Science And Technology Studies ◽

Large Scale ◽

Cooperative Work ◽

Computer Supported Cooperative Work ◽

Practical Action ◽

Systems Research ◽

Information Infrastructures ◽

Information Systems Research ◽

Critical Investigation

The study of computing infrastructures has grown significantly due to the rapid proliferation and ubiquity of large-scale IT-based installations. At the same time, recognition has also grown of the usefulness of such studies as a means for understanding computing infrastructures as material complements of practical action. Subsequently the concept of “infrastructure” (or “information infrastructures,” “cyberinfrastructures,” and “infrastructuring”) has gained increasing importance in the area of Computer-Supported Cooperative Work (CSCW) as well as in neighboring areas such as Information Systems research (IS) and Science and Technology Studies (STS). However, as such studies have unfolded, the very concept of “infrastructure” is being applied in different discourses, for different purposes, in myriad different senses. Consequently, the concept of “infrastructure” has become increasingly muddled and needs clarification. The chapter presents a critical investigation of the vicissitudes of the concept of “infrastructure” over the last 35 years.

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