IBIOMES: managing and sharing biomolecular simulation data in a distributed environment.
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ABSTRACT:
SUBMITTER: Thibault JC
PROVIDER: S-EPMC8489555 | biostudies-literature | 2013 Mar
REPOSITORIES: biostudies-literature
Publications
iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.
Thibault Julien C JC Facelli Julio C JC Cheatham Thomas E TE
Journal of chemical information and modeling 20130305 3
Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from thei ...[more]
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Project description:BackgroundFew environments have been developed or deployed to widely share biomolecular simulation data or to enable collaborative networks to facilitate data exploration and reuse. As the amount and complexity of data generated by these simulations is dramatically increasing and the methods are being more widely applied, the need for new tools to manage and share this data has become obvious. In this paper we present the results of a process aimed at assessing the needs of the community for data representation standards to guide the implementation of future repositories for biomolecular simulations.ResultsWe introduce a list of common data elements, inspired by previous work, and updated according to feedback from the community collected through a survey and personal interviews. These data elements integrate the concepts for multiple types of computational methods, including quantum chemistry and molecular dynamics. The identified core data elements were organized into a logical model to guide the design of new databases and application programming interfaces. Finally a set of dictionaries was implemented to be used via SQL queries or locally via a Java API built upon the Apache Lucene text-search engine.ConclusionsThe model and its associated dictionaries provide a simple yet rich representation of the concepts related to biomolecular simulations, which should guide future developments of repositories and more complex terminologies and ontologies. The model still remains extensible through the decomposition of virtual experiments into tasks and parameter sets, and via the use of extended attributes. The benefits of a common logical model for biomolecular simulations was illustrated through various use cases, including data storage, indexing, and presentation. All the models and dictionaries introduced in this paper are available for download at http://ibiomes.chpc.utah.edu/mediawiki/index.php/Downloads.
| S-EPMC3915074 | biostudies-literature
Project description:MotivationTechnical advances have revolutionized the life sciences and researchers commonly face challenges associated with handling large amounts of heterogeneous digital data. The Findable, Accessible, Interoperable and Reusable (FAIR) principles provide a framework to support effective data management. However, implementing this framework is beyond the means of most researchers in terms of resources and expertise, requiring awareness of metadata, policies, community agreements, and other factors such as vocabularies and ontologies.ResultsWe have developed the Globally Accessible Distributed Data Sharing (GADDS) platform to facilitate FAIR-like data-sharing in cross-disciplinary research collaborations. The platform consists of (i) a blockchain based metadata quality control system, (ii) a private cloud-like storage system and (iii) a version control system. GADDS is built with containerized technologies, providing minimal hardware standards and easing scalability, and offers decentralized trust via transparency of metadata, facilitating data exchange and collaboration. As a use case, we provide an example implementation in engineered living material technology within the Hybrid Technology Hub at the University of Oslo.AvailabilityDemo version available at https://github.com/pavelvazquez/GADDS.Supplementary informationSupplementary data are available at Bioinformatics online.
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