Development of Open source Laboratory Information Management System (LIMS) For Human Biobanking

Abstract

Biobanks are collections of biological samples and associated data for future use. The day to day activities in a biobank laboratory is underpinned by a laboratory information management system (LIMS). For example, the LIMS manages the execution of tests on biospecimens and track their movement and processing through the laboratory. There are a range of commercially available Biobank LIMS systems on the market but their costs are prohibitive in a resource limited setting. The cost of Commercial off-the-shelf software includes the initial cost of acquiring the system, as well as the cost of maintenance and support throughout the software's life cycle. The Bika LIMS system on the other hand is Free and open source software (FOSS) with decreased license cost, used routinely in non-medical laboratories. Ideally, if Bika LIMS could be customised to handle human biospecimens, then both biobanks and genetics laboratories could benefit. Central to any biobank functionality in Bika LIMS is the ability to import information from routine biomedical equipment. We identified two instruments that are key to human biobanking and are lacking in Bika LIMS namely BioDrop ?LITE and the Qubit Fluorometric instrument. Import interfaces for importing DNA/RNA concentration analyses from these instruments and management of the results with associated sample information would add value to the LIMS. The aim of the thesis was to customise Bika LIMS for utility in a biomedical laboratory. In collaboration with colleagues at Tygerberg medical school, the Bika LIMS software was customised to accommodate the DNA and RNA concentration analyses results for a pathology laboratory and the LIMS workflows customised for use at Tygerberg medical school. In this process the manual operations of Tygerberg medical school laboratory would migrate to the use of Bika LIMS. The analytical module in Bika LIMS was implemented using PYTHON, by using logic that allows importing of specific analyses. A template was created for the BioDrop ?LITE and Qubit Fluorometric instruments used for developing the interface for an analysis import form. The instruments generate results in CSV file format. A parser was created to read and parse the files uploaded from the import form, by splitting them into parts, extracting the data, and populating key-value pairs. The controller manages the submission of the form by initialising the parser that imports the specific file into the LIMS where it is managed by the configured Bika LIMS workflow.