The South African National Bioinformatics Institute is partnering Bika Lab Systems in customising an Open Source Bika LIMS branch for genomic lab disciplines and biobanking, including the management of sample and data distribution. The current Bika branch for health care laboratories, Bika Health 3.1, which already fulfils clinical subject requirements, is the starting point for this venture.
Central to achieving its long term goal of specimen management in a multi-country exchange, remains the challenge of interoperability and applying open standards. It is expected that a variety of different LIMS, EMR and specimen management systems will be used to build and query regional genetic databases.
Initial integration will be with OpenSpecimen, to facilitate multi-site sample storage, orders, shipping, tracking and protocol management.
LIMS for Bioinformatics
Bika Health workflow will be customised for sample preparation, extraction and amplification, and expanding sample partitioning to dynamic aliquot taking. The system already ticks the biobank boxes for clinical LIMS, version controlled document management of SOPs and patient consent forms, billing, supplies and ERP interfacing. These functions will be customised to fit biobank integration, which will benefit the Bika Health and universal LIMS branches too.
Biospecimen sampling kit assembly will be the first new feature in an expanded biobank configuration, modelled on work carried out by Dr Carmen Swanepoel and Prof Akin Abayomi at the University of Stellenbosch’s faculty of Medicine and Health Sciences Tygerberg campus where the system will be piloted. Much work has gone into requirements analysis and contingency planning – the continent represents unique challenges – and a manual run successfully completed.
The project participants came together through the Human Heredity and Health in Africa (H3Africa) initiative, and are inspired to be part of the historic project contributing to the exploration of African genetics. Further implementations are foreseen in botanical and zoological applications in the many local projects having similar requirements.
Through the University of Western Cape, SANBI has committed masters computer science student Toluwaleke Ademuyiwa to the project who will soon be joining the Bika code house in Pringle Bay. Jordi Puiggené and the Barcelona Naralabs team, and OpenSpecimen specialists Krishagni will be providing additional capacity.
Organisations and individuals interested in participating in the project, be it through sharing requirements and wish lists, testing, contributing code or cattle, are invited to contact Lemoene at email@example.com, or SANBI’s Prof Alan Christoffels, firstname.lastname@example.org.
The South African National Bioinformatics Institute (SANBI)
In addition to developing upcoming scientists in these fields, SANBI does cutting edge bioinformatics and computational biology research relevant to South African, African and global populations, often through international collaboration with partner organisations. This provides an ideal environment for stimulating the development of its students and encourages them to strive for excellence.
The Stellenbosch University Medicine and Health Sciences faculty
A dynamic, people-centred and inclusive environment, internationally recognised for its excellence in research, education and clinical training in medicine and health sciences, and for the contribution it makes to improving health and health care in South Africa, the African continent and beyond.
The Human Heredity and Health in Africa Initiative
The H3Africa initiative aims to facilitate a contemporary research approach to the study of genomics and environmental determinants of common diseases with the goal of improving the health of African populations.
OpenSpecimen, formerly caTissue Plus, is a Free and Open Source biospecimen management system, used in some of the most respected global biobanks. The system manages sample collection, patient consent, QC, request and distribution protocols in highly configurable implementations. Krishagni provides professional implementation services, user and technical support, data migration, customisations, integration and training.
Naralabs specialises in Laboratory Information Management Systems (LIMS) and offers professional technology and engineering services such as consulting, implementation, training, system maintenance and technical support. Naralabs actively participates in the Bika LIMS project, both in software design and development tasks, and also offers technical support to the community of users and developers.
Bika Lab Systems
Bika Lab Systems provides full LIMS implementation life cycle support or any part thereof – requirements analysis, design, customisation and testing, development, installation and configuration, project management and quality control, documentation, systems integration, administration, hosting, user and technical training and support
Bika Lab Systems sponsors and co-ordinates the Bika open source LIMS project, committed to keep the Bika code free and available and to maintain effective organisational support.