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Kratov S, Zybarev Y. To the question of the digital platform "bioinformatics" creating and its system-forming solutions. J Integr Bioinform 2020; 17:/j/jib.ahead-of-print/jib-2020-0029/jib-2020-0029.xml. [PMID: 33141107 DOI: 10.1515/jib-2020-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/28/2020] [Indexed: 11/15/2022] Open
Abstract
The article reports the main provisions of the concept and solutions for creating the digital platform in the field of bioinformatics and the formation of the thematically oriented and industrial digital ecosystems on its basis. The composition and structure of the digital platform are discussed: information repositories, data and knowledge bases, thematically oriented software repository, task-oriented services for various target groups of users. Within the framework of the platform, it is also planned to organize a system of high-quality access to specialized data centres and high-performance computing infrastructure. Particular attention is devoted to one of the components of such platform - the project office for bioresource collections management. The project office has registered such types of collections as animal collections: wild and laboratory animals, live breeding, museum zoological animal collections, farm animals; plant collections: herbarium funds of plants biological diversity, living collections of natural flora, agricultural plants. Collection types such as collections of human biomaterials, cell culture collections, microorganism collections are important for medical research.
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Affiliation(s)
- Sergey Kratov
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
- Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia
| | - Yurii Zybarev
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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McCluskey K, Barker KB, Barton HA, Boundy-Mills K, Brown DR, Coddington JA, Cook K, Desmeth P, Geiser D, Glaeser JA, Greene S, Kang S, Lomas MW, Melcher U, Miller SE, Nobles DR, Owens KJ, Reichman JH, da Silva M, Wertz J, Whitworth C, Smith D. The U.S. Culture Collection Network Responding to the Requirements of the Nagoya Protocol on Access and Benefit Sharing. mBio 2017; 8:e00982-17. [PMID: 28811341 PMCID: PMC5559631 DOI: 10.1128/mbio.00982-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The U.S. Culture Collection Network held a meeting to share information about how culture collections are responding to the requirements of the recently enacted Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (CBD). The meeting included representatives of many culture collections and other biological collections, the U.S. Department of State, U.S. Department of Agriculture, Secretariat of the CBD, interested scientific societies, and collection groups, including Scientific Collections International and the Global Genome Biodiversity Network. The participants learned about the policies of the United States and other countries regarding access to genetic resources, the definition of genetic resources, and the status of historical materials and genetic sequence information. Key topics included what constitutes access and how the CBD Access and Benefit-Sharing Clearing-House can help guide researchers through the process of obtaining Prior Informed Consent on Mutually Agreed Terms. U.S. scientists and their international collaborators are required to follow the regulations of other countries when working with microbes originally isolated outside the United States, and the local regulations required by the Nagoya Protocol vary by the country of origin of the genetic resource. Managers of diverse living collections in the United States described their holdings and their efforts to provide access to genetic resources. This meeting laid the foundation for cooperation in establishing a set of standard operating procedures for U.S. and international culture collections in response to the Nagoya Protocol.
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Affiliation(s)
- Kevin McCluskey
- Fungal Genetic Stock Center, Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Katharine B Barker
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, Ohio, USA
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science, University of California, Davis, Davis, California, USA
| | - Daniel R Brown
- Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, Florida, USA
| | - Jonathan A Coddington
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Kevin Cook
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University, Bloomington, Indiana, USA
| | | | - David Geiser
- The Fusarium Research Center, Penn State University, State College, Pennsylvania, USA
| | - Jessie A Glaeser
- U.S. Forest Service, Northern Research Station, Center for Forest Mycology Research, Madison, Wisconsin, USA
| | - Stephanie Greene
- USDA National Laboratory for Genetic Resources Preservation, Fort Collins, Colorado, USA
| | - Seogchan Kang
- Penn State University, State College, Pennsylvania, USA
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, East Boothbay Harbor, Maine, USA
| | | | | | | | | | | | | | - John Wertz
- E. coli Stock Center, Yale University, New Haven, Connecticut, USA
| | - Cale Whitworth
- Bloomington Drosophila Stock Center, Department of Biology, Indiana University Bloomington, Indiana, USA
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