Image: Keith Edkins [CC BY-SA 2.0], via geograph
Baobab LIMS hoped for support from South Africa after its European grant ran out
An open-source bioinformatics software system developed as a Europe-Africa collaboration is struggling financially after the support it had counted on from the South African government failed to materialise.
The Baobab Laboratory Information Management System (Baobab LIMS) was set up to help biobanks track the collection, processing and storage of human biospecimens. It was developed by African and European researchers as part of B3Africa, a project funded by the European Union.
That core support ended in September 2018. Since then, those who manage the project have struggled to secure funding to develop it further—including broadening its functionalities and making it more user-friendly.
European partners may have offered to support the project had the South African government not indicated at a meeting in Kenya in 2018 that it would support its development after the B3Africa grant ran out, says Alan Christoffels, director of the South African National Bioinformatics Institute based at the University of the Western Cape and one of the leaders of the Baobab LIMS project.
“We had a small group discussion about what to do with innovations that came out of the [European Union] grant. The answer from the Department of Science and Technology [now innovation] was that they would fund the Africa-driven projects,” Christoffels told Research Professional News. “This commitment, albeit verbal, left EU participants with the assumption that continuity had been achieved.”
That assumption proved wrong. Although there has been funding from South Africa’s Technology Innovation Agency to build a business model, which also included some funding for development, the project has struggled since the EU grant ended to find money to pay the salaries of its two developers.
For the past 18 months, Baobab LIMS has relied on a handful of contracts to customise the system for clients outside South Africa. One of the system’s business sustainability options is paid-for customisation. The system is used in Uganda, and is about to be implemented in Côte d’Ivoire and Nigeria.
South Africa’s Department of Science and Innovation did not respond to questions for this report.
Meanwhile, several research labs in South Africa have opted for solutions other than Baobab LIMS. Diplomics, a network of academic, commercial and industrial labs in South Africa funded by the DSI through the South African Research Infrastructure Roadmap, has collectively agreed to use the commercial software LabWare.
“The choice of LabWare over alternative open-source programmes was based mainly on its better fit for purpose, its broader functionality and better reported user experience,” said Diplomics director Tim Newman.
Tulio de Oliveria, director of the KwaZulu-Natal Research Innovation and Sequencing Platform in Durban, which is part of Diplomics, said it had opted for LabWare after trialling Baobab LIMS for more than a year. “We spent a lot of time trying to make [Baobab LIMS] work for the lab. It’s not that the software doesn’t work: it’s great. But a lot of the time people in the lab want something off the shelf,” he says, adding that if and when suitable modules from Baobab LIMS become available it will be happy to switch back.
Christoffels says he understands laboratories might opt for alternative systems that suit them better. But he would like decision-making about such investments to become more transparent, especially when it is public money that is being spent—and since the government says it wants to support local innovation.