Baobab LIMS to enhance ISO 9001:2015 certified quality management system for sample and data tracking, logistics and work scheduling
Oct. 18, 2017 —Cape Town, South Africa—The Centre for Proteomic and Genomic Research (CPGR) today announced plans to implement the Baobab LIMS (Laboratory Information Management System), an open-source platform developed with a view to make state-of-the-art tracking of samples, data and lab reagents feasible in resource-constrained settings.
Baobab LIMS was funded by the European Union Horizon2020 programme as part of an integrated approach to building IT infrastructure to bridge biobanking activities between Europe and Africa (www.b3africa.org).
The project, published in the Biobanking and Biopreservation Journal in April 2017, is a culmination of 5 years of work with multinational academic partners in South Africa, Kenya, Nigeria, Uganda, Austria, France and Sweden. The South African effort was led by The South African National Bioinformatics Institute (SANBI) at the University of the Western Cape (UWC).
CPGR is a non-profit organization dedicated to providing state-of-the-art ‘omics’ services to South Africa’s life sciences and biotech communities, originating from an initiative by the South Africa Department of Science and Technology (DST). The organization deals with a diversity of samples, and concomitant logistics, in research projects as well as for routine molecular testing in Sub-Saharan Africa. It has chosen Baobab LIMS owing to its ability to integrate sample and data tracking, as well as management of lab reagents, among other features.
‘We expect that Baobab will allow us to develop a fit-for-purpose LIMS solution in a cost-effective manner through access to local expertise’, said Dr Lindsay Petersen, Genomics Manager. ‘Previous trials with alternative systems have always pointed to the need for extensive customization, something that we will be able to achieve faster with Baobab. We envisage that the LIMS will form a strong backbone in our efforts to provide high-quality services on a diversity of ‘omics’ platforms in (South) Africa’, said Dr Petersen.
The Baobab LIMS forms part of the Biobank-in-a-Box suite of tools that has been released by the African-European consortium in 2017 as a standalone application called eB3kit. Users locally and as far afield as Ghana, Nigeria, Tunis, Uganda and Poland are piloting the software as an alternative LIMS in their genetics laboratories.
‘Commercial LIMS alternatives are currently available but do not cater to resource-limited settings where researchers cannot afford licensing fees,’ says Professor Alan Christoffels, Director at the SAMRC’s Bioinformatics Research Unit based at the University of the Western Cape. ‘This new software is available for free download allowing more researchers across the globe to have access to an essential tool that will facilitate biospecimen management’, added Professor Christoffels.
‘We view Baobab LIMS as a platform that will allow CPGR to more effectively integrate work done across sites in different African countries, such as in the MADCaP project, said Reinhard Hiller, Ph.D., Managing Director at CPGR. ‘In addition, the platform may also facilitate inter-laboratory collaboration in large-scale infrastructure initiatives, such as DIPLOMICS. Overall, we envisage that it will boost ‘omics’ productivity significantly’, noted Dr Hiller.
The Centre for Proteomic and Genomic Research (CPGR) is one of Africa’s first fully integrated ‘omics’ service providers, built to leapfrog South Africa’s ability to conduct information-rich biomedical research onto a globally competitive level. Amongst others, the organization offers the following ‘omics’ capacity: Next-Generation Sequencing: NextSeq500 (1x), MiSeq (1x), MiniSeq (1x), IonTorrent PGM (2x), IonProton (1x), for sequencing projects; Microarrays: Affymetrix GS 3000 and Affymetrix GeneTitan for genotyping and gene-expression analysis; Mass spectrometry: Thermo Q Exactive, Waters Xevo TQS triple quadrupole, SCIEX API4000 triple quadrupole and ABI 4800 MALDI-ToF/ToF for MS-Proteomics; High-throughput PCR: QuantStudio 12K Flex Real-Time PCR System, QuantStudio 3D Digital PCR System and ABI 7900 for qRT-PCR and genotyping applications; Automated DNA/RNA QC, library handling and sample processing; dedicated IT infrastructure and bioinformatic applications for data analysis and interpretation.
The CPGR is a non-profit company located in Cape Town, South Africa, based on an initiative by the Department of Science and Technology (DST), and financially supported by the Technology Innovation Agency (TIA). The CPGR combines state-of-the-art information rich genomic and proteomic (‘omics’) technologies with bio-computational pipelines to render services and support projects in the life science and biomedical arena in (South) Africa, all run in an ISO 9001:2015 certified and ISO 17025 compliant quality management system. Among others, the CPGR has recently launched an accelerator program to stimulate the creation of South African start-ups based on ‘omics’ technologies and set up Artisan Biomed to develop and implement Precision Medicine solutions in (South) Africa.
The South African National Bioinformatics Institute (SANBI) is situated at the University of the Western Cape in Cape Town and has been established in 1996. As of 2001, SANBI obtained its Medical Research Council Bioinformatics Unit status. Bioinformatics is a specialist discipline straddling the fields of biology and computer science and is integral to modern biological research. This interdisciplinary space provides the impetus for SANBI’s primary focus to develop and implement computational methodologies that allow biomedical researchers to accelerate their genomics data analyses. SANBI aims to heighten awareness of bioinformatics in South Africa and to assist the country in making optimal use of this technology. As the leading bioinformatics entity on the African continent, we continue to foster local and regional collaborations on health-related topics that cover both communicable and non-communicable diseases.
The research profile at SANBI includes research teams focusing on HIV dynamics, Mycobacterial genomics, Evolutionary dynamics of Plant Viruses, Biomarker Discovery, Rooibos Genomics, and Computational Infrastructure Development.
Linda de Waal