What Insects and Openness Have in Common
A spotlight on OpenScienceKE, a Mozilla mini-grant recipient
To the casual observer, insect bioinformatics and open source may not seem to have much in common. One concerns mosquito or tsetse DNA; the other is often associated with software development.
But for Caleb Kibet, the two are a perfect match. So much so that he’s devoting part of his career to integrating them.
Caleb is a Nairobi, Kenya-based scientist with a PhD in Bioinformatics. He is currently a bioinformatician at the International Centre of Insect Physiology and Ecology (ICIPE), and teaches bioinformatics at Jomo Kenyatta University of Agriculture and Technology.
Additionally, Caleb leads OpenScienceKE, an initiative that promotes open approaches to bioinformatics research in Kenya. OpenScienceKE recently received a Mozilla mini-grant: $4,000 in funding, made possible by the Alfred P. Sloan Foundation.
“We received a mini-grant to explore where we are as a country in terms of the implementation and adoption of open science,” Caleb told Mozilla.
“Open science” means handling research and data in more transparent and accessible ways. Open science can accelerate breakthroughs and progress in research.
(Caleb himself starting working open when pursuing his PhD. “I wanted to ensure that the research I conducted was accessible,” he says.)
Caleb and team started by examining the state of open science at three Kenyan universities: Jomo Kenyatta University of Agriculture and Technology, University of Nairobi, and The Technical University. In this first stage, they made the students and researchers aware of open science through seminars.
“The next stage of the project was to enable students to practice open science,” Caleb explains. “We did this through workshops where we trained students on open science tools, starting with collaboration tools like GitHub and Jupyter Notebook for literate programming. We also introduced them to the Linux command line.”
In all, Caleb and team provided in-depth training to more than two dozen bioinformatics students and researchers. (Nearly 70 applied to participate in the workshops, but OpenScienceKE could only accommodate 30.)
The training was followed by hackathons, so those individuals newly introduced to open science could practice their new skills. Caleb was happily surprised: “You could see the students’ enthusiasm after the workshops and hackathons,” he says. “We usually work from around 9:30 a.m. until 5 p.m., but by 5 p.m., we almost had to force some of them out of the venue because they kept hacking and trying to learn more.”
Caleb notes his initiative has obstacles: In May, a country-wide lecturer strike closed down university classes. And in some cases, Caleb and team had a hard time getting through to some institutions.
Despite challenges, Caleb is eager to expand OpenScienceKE in the months and years ahead: “In the short term, we are working to share the collaborative work that we have done from the hackathon and workshops. In the long term, we want to build a community around open science within the country.”
If you’d like to learn more, you can read Caleb’s full interview about his project. If you’d like to get involved, you can reach Caleb on his Twitter feed or through the GitHub repository for his project.