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EasyGDB: a low-maintenance and highly customizable system to develop genomics portals
SUMMARY: 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 informa...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9364376/ https://www.ncbi.nlm.nih.gov/pubmed/35748710 http://dx.doi.org/10.1093/bioinformatics/btac412 |
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author | Fernandez-Pozo, Noe Bombarely, Aureliano |
author_facet | Fernandez-Pozo, Noe Bombarely, Aureliano |
author_sort | Fernandez-Pozo, Noe |
collection | PubMed |
description | SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb. |
format | Online Article Text |
id | pubmed-9364376 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-93643762022-08-11 EasyGDB: a low-maintenance and highly customizable system to develop genomics portals Fernandez-Pozo, Noe Bombarely, Aureliano Bioinformatics Applications Notes SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: The code and manual to use EasyGDB can be found at https://github.com/noefp/easy_gdb. Oxford University Press 2022-06-24 /pmc/articles/PMC9364376/ /pubmed/35748710 http://dx.doi.org/10.1093/bioinformatics/btac412 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Notes Fernandez-Pozo, Noe Bombarely, Aureliano EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title | EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title_full | EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title_fullStr | EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title_full_unstemmed | EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title_short | EasyGDB: a low-maintenance and highly customizable system to develop genomics portals |
title_sort | easygdb: a low-maintenance and highly customizable system to develop genomics portals |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9364376/ https://www.ncbi.nlm.nih.gov/pubmed/35748710 http://dx.doi.org/10.1093/bioinformatics/btac412 |
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