EasyGDB: a low-maintenance and highly customizable system to develop genomics portals.

EasyGDB is an easy-to-implement low-maintenance tool developed to create genomic data management web platforms. It can be used for any species, group of species, or multiple genome or annotation versions. EasyGDB provides a framework to develop a web portal that includes the general information about species, projects and members, and bioinformatics tools such as file downloads, BLAST, genome browser, annotation search, gene expression visualization, annotation and sequence download, and gene ids and orthologs lookup. The code of EasyGDB facilitates data maintenance and update for non-experienced bioinformaticians, using BLAST databases to store and retrieve sequence data in gene annotation pages and bioinformatics tools, and JSON files to customize metadata. EasyGDB is a highly customizable tool. Any section and tool can be enabled or disabled like a switch through a single configuration file. This tool aims to simplify the development of genomics portals in non-model species, providing a modern web style with embedded interactive bioinformatics tools to cover all the common needs derived from genomics projects. The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb. © The Author(s) 2022. Published by Oxford University Press.

Citation

Noe Fernandez-Pozo, Aureliano Bombarely. EasyGDB: a low-maintenance and highly customizable system to develop genomics portals. Bioinformatics (Oxford, England). 2022 Aug 10;38(16):4048-4050

Mesh Tags

PMID: 35748710

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