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Baobab LIMS for Biobanking
BIOREPOSITORIES use laboratory information management systems (LIMS) to track and manage the collection, processing and storage of biological specimens and associated metadata for research. In many low and middle-income (LMIC) countries, particularly in Africa, exorbitant commercial LIMS licensing fees make it difficult for scientists to properly manage large study cohorts or ‘biobanks’ of specimens by employing database technology.
This could cause researchers to question the processing and storage procedures as well as the quality or integrity of the biobank’s specimen collection.
The South African National Bioinformatics Institute (SANBI) at the University of the Western Cape has developed Baobab LIMS, an open-source software resource that research facilities can access to help manage biospecimens.
“On the African continent, several users and test sites have employed the software, a number of training and engagement events have taken place and the Baobab LIMS team has customised the software for specific projects,” says Dr Dominique Anderson, a SANBI senior researcher.
Baobab LIMS was funded by the EU Horizon 2020 programme through the B3Africa consortium as one of “a suite of tools” developed “to harmonise e-infrastructure for biobanking” in LMIC countries.
Prof Alan Christoffels, the Director of SANBI and DST/NRF Research Chair in Bioinformatics and Health Genomics, originally co-developed Baobab LIMS with Dr Hocine Bendou. The system has been enhanced and is managed by Dr Anderson, working with developers Ziphozakhe Mashologu, Quinton Coert and Lunga Baliwe, among others. Throughout the project, Dr Anderson, who has a background in biotechnology and bioinformatics and prior experience in quality management and accreditation, worked closely with researchers and the developers to ensure that the final interface matched what users needed.
International best practice recommends that biobanks implement quality management systems (QMS). The LIMS forms one component of the QMS processes and enhances quality and compliance and accurate record-keeping. The system enables scientists and researchers to manage the life-cycle of biospecimens, including tracking where the biospecimens were sourced and shipped, the sample type and quantity received, minimal associated metadata, where the biospecimens are stored in the laboratory, and whether specific laboratory analysis has been performed on the biospecimens.
“There are many commercial LIM systems that can be used as part of the quality management in biobanking, biorepositories or biocollections, but these systems are expensive. The annual licensing fees for these systems, as well as training and any modification requirements, may not be sustainable for resource-limited laboratories. So, while a pharmaceutical company, for example, will be able to afford a commercial LIMS, other researchers who are doing very valuable research, especially in the low and middle-income countries, cannot afford these fees,” says Dr Anderson.
The fact that commercial LIMS are built with proprietary software means that the source code cannot be altered except by the company that developed it. Because Baobab LIMS is built with open-source code, the code is publicly available and can be customised and made fit for purpose.
Baobab was built using Bika LIMS, which was initially developed for the wine biotechnology industry. With Bika’s approval, SANBI collaborated with Prof Akin Abayomi and Dr Carmen Swanepoel from NSB, a small academic biobank in the Division of Haematology, NHLS and Stellenbosch University, and used their working systems to build various modules to transform Bika LIMS into a human biospecimen LIMS.
The current version of Baobab LIMS is a feature-rich system with a number of functionalities geared toward sample management. It allows scientists to not only capture detailed information about samples but to share this information with clients through system-generated reports.
“It is fully configurable and allows scientists in the biobanks to actually set up the features on the LIMS to reflect, for example, what their freezer looks like,” says Dr Anderson.
“Because we are working with very sensitive information, scientists have to actually install the software code onto their secure servers. Once it is installed, it belongs to that person or facility and that facility then configures the system to its needs.”
The system is accessible via any web browser, but only to individuals who have authorised access.
