Magister Scientiae - MSc (Bioinformatics) / 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.
| Identifer | oai:union.ndltd.org:netd.ac.za/oai:union.ndltd.org:uwc/oai:etd.uwc.ac.za:11394/6326 |
| Date | January 2018 |
| Creators | Ademuyiwa, Toluwaleke |
| Contributors | Christoffels, Alan |
| Publisher | University of the Western Cape |
| Source Sets | South African National ETD Portal |
| Language | English |
| Detected Language | English |
| Rights | University of the Western Cape |
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