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MendeLIMS: a web-based laboratory information management system for clinical genome sequencing

Susan M Grimes1 and Hanlee P Ji12*

Author Affiliations

1 Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA

2 Division of Oncology, Stanford University School of Medicine, Palo Alto, CA 94304, USA

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BMC Bioinformatics 2014, 15:290  doi:10.1186/1471-2105-15-290

Published: 27 August 2014



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.


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.


We maintain a publicly available demonstration version of the application for evaluation purposes at webcite. 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 webcite.

Next generation sequencing; Clinical studies; Laboratory information management; Pathology; Genomics; Genetics