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MendeLIMS: a web-based laboratory information management system for clinical genome sequencing
BACKGROUND: Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155081/ https://www.ncbi.nlm.nih.gov/pubmed/25159034 http://dx.doi.org/10.1186/1471-2105-15-290 |
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author | Grimes, Susan M Ji, Hanlee P |
author_facet | Grimes, Susan M Ji, Hanlee P |
author_sort | Grimes, Susan M |
collection | PubMed |
description | BACKGROUND: Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. RESULTS: To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. CONCLUSIONS: We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-290) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4155081 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41550812014-09-06 MendeLIMS: a web-based laboratory information management system for clinical genome sequencing Grimes, Susan M Ji, Hanlee P BMC Bioinformatics Software BACKGROUND: Large clinical genomics studies using next generation DNA sequencing require the ability to select and track samples from a large population of patients through many experimental steps. With the number of clinical genome sequencing studies increasing, it is critical to maintain adequate laboratory information management systems to manage the thousands of patient samples that are subject to this type of genetic analysis. RESULTS: To meet the needs of clinical population studies using genome sequencing, we developed a web-based laboratory information management system (LIMS) with a flexible configuration that is adaptable to continuously evolving experimental protocols of next generation DNA sequencing technologies. Our system is referred to as MendeLIMS, is easily implemented with open source tools and is also highly configurable and extensible. MendeLIMS has been invaluable in the management of our clinical genome sequencing studies. CONCLUSIONS: We maintain a publicly available demonstration version of the application for evaluation purposes at http://mendelims.stanford.edu. MendeLIMS is programmed in Ruby on Rails (RoR) and accesses data stored in SQL-compliant relational databases. Software is freely available for non-commercial use at http://dna-discovery.stanford.edu/software/mendelims/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2105-15-290) contains supplementary material, which is available to authorized users. BioMed Central 2014-08-27 /pmc/articles/PMC4155081/ /pubmed/25159034 http://dx.doi.org/10.1186/1471-2105-15-290 Text en © Grimes and Ji; licensee BioMed Central Ltd. 2014 This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. |
spellingShingle | Software Grimes, Susan M Ji, Hanlee P MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title | MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title_full | MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title_fullStr | MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title_full_unstemmed | MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title_short | MendeLIMS: a web-based laboratory information management system for clinical genome sequencing |
title_sort | mendelims: a web-based laboratory information management system for clinical genome sequencing |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155081/ https://www.ncbi.nlm.nih.gov/pubmed/25159034 http://dx.doi.org/10.1186/1471-2105-15-290 |
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