SLIMS—a user-friendly sample operations and inventory management system for genotyping labs

• Published in: Bioinformatics Vol. 26; no. 14; pp. 1808 - 1810
• Main Authors: Van Rossum, Thea, Tripp, Ben, Daley, Denise
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.07.2010
• Subjects: Applications Note; Biological and medical sciences; Database Management Systems; Databases, Factual; Diseases; Fundamental and applied biological sciences. Psychology; General aspects; Genotype; Inventory management; Java (programming language); LIMS; Manuals; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Searching; Software; Source code; User-Computer Interface; Genotype; Typing; Management; Sample
• ISSN: 1367-4803; 1367-4811; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btq271

We present the Sample-based Laboratory Information Management System (SLIMS), a powerful and user-friendly open source web application that provides all members of a laboratory with an interface to view, edit and create sample information. SLIMS aims to simplify common laboratory tasks with tools such as a user-friendly shopping cart for subjects, samples and containers that easily generates reports, shareable lists and plate designs for genotyping. Further key features include customizable data views, database change-logging and dynamically filled pre-formatted reports. Along with being feature-rich, SLIMS' power comes from being able to handle longitudinal data from multiple time-points and biological sources. This type of data is increasingly common from studies searching for susceptibility genes for common complex diseases that collect thousands of samples generating millions of genotypes and overwhelming amounts of data. LIMSs provide an efficient way to deal with this data while increasing accessibility and reducing laboratory errors; however, professional LIMS are often too costly to be practical. SLIMS gives labs a feasible alternative that is easily accessible, user-centrically designed and feature-rich. To facilitate system customization, and utilization for other groups, manuals have been written for users and developers. Availability: Documentation, source code and manuals are available at http://genapha.icapture.ubc.ca/SLIMS/index.jsp. SLIMS was developed using Java 1.6.0, JSPs, Hibernate 3.3.1.GA, DB2 and mySQL, Apache Tomcat 6.0.18, NetBeans IDE 6.5, Jasper Reports 3.5.1 and JasperSoft's iReport 3.5.1. Contact: denise.daley@hli.ubc.ca