Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

Record number 539516
Title A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository : Prospects for research-based educational experiences
Author(s) Epstein, Samuel C.; Charkoudian, Louise K.; Medema, Marnix H.
Source Standards in Genomic Sciences 13 (2018)1. - ISSN 1944-3277
DOI https://doi.org/10.1186/s40793-018-0318-y
Department(s) Bioinformatics
EPS
Publication type Refereed Article in a scientific journal
Publication year 2018
Keyword(s) Biosynthetic gene cluster - Course-based undergraduate research experience - MIBiG - Natural product - Specialized metabolism
Abstract

Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.

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