At the Bio-IT World Conference and Expo 2023, a presentation moderated by BioTeam CEO Dr. Ari Berman discussed the computing challenges facing bioinformatics researchers on the African continent.
Access to high performance computing (HPC) plays a key role in the success of any bioinformatics study. The field simply involves too much data to regularly perform research on a traditional computer.
However, regions of the world such as Uganda and Mali, Africa often struggle to implement HPC infrastructure. From a lack of reliable power and internet access to a deficit of trained HPC professionals, a variety of factors have made African supercomputing work difficult.
This is the exact problem the African Centers of Excellence in Bioinformatics and Data Intensive Sciences (ACE) was formed to solve. The discussion hosted by Berman highlighted some of ACE’s successes, as well as what organizations like BioTeam can do to assist ACE’s growth into a self-sustaining bioinformatics ecosystem.
This presentation featured remarkable individuals dedicated to addressing this challenge, including Mike Tartakovsky, the Chief Information Officer of the National Institute of Allergy and Infectious Diseases (NIAID), who delivered a speech, along with NIAID International Program Manager Chris Whalen. They were joined by other BioTeam experts, as well as ACE Director Daudi Jjingo.
“Biomedical research, especially here, has over the last couple of decades undergone a lot of changes,” said Jjingo during his talk at the presentation. “(ACE) has several objectives, but one of those is to provide an HPC platform that researchers from our ecosystem here, but also students, can use to either learn or to perform research that they would otherwise not be able to perform on their desktops and laptops.”
During the talk, as well as during private interviews, Jjingo along with BioTeam Senior Scientific Consultants Shane Corder and Laura Boykin Okalebo expanded on BioTeam’s efforts to connect ACE to the HPC resources the organization needs to succeed.
African bioinformatics is necessary, not easy
Although there are many systemic issues facing bioinformatics work in African countries like Uganda and Mali, there are three main challenges to overcome: the reliability of power and internet in the region, a lack of proper HPC hardware, and a shortage in trained professionals with HPC skills.
To begin, computing in general simply isn’t possible without reliable power and internet. But, HPC is especially vulnerable because of the long periods of time devoted to completing a task.
Whalen of NIAID had some interesting points about this challenge. He stated that he once went on a tour of laboratories in Burkina Faso, Mali, Senegal, and Guinea. During this trip, he plugged a device into outlets at the laboratories to check if clean, reliable power was coming out. He didn’t find a single plug with sufficient power.
“We see a growth in the need for the right infrastructure,” said Jjingo. “Right in terms of capacity, but also right in terms of operational mode ¬– by which I mean energy efficient. Obviously, because power and sustainability around this is an issue. Because of BioTeam’s competencies and BioTeam’s previous experiences, we feel that BioTeam is definitely going to be an important partner for us in the next decade or so.”
On top of simple power needs, countries like Uganda and Mali are also working with partners to acquire the specific HPC hardware needed to perform bioinformatics supercomputing tasks. Jjingo mentions that in addition to providing ACE with state-of-the-art hardware, BioTeam has also given a lot of strategic advisory services on how ACE can position itself to manage certain technical barricades.
Outside of the physical systems necessary for HPC, ACE also faces a lack of access to HPC training opportunities. Computer science is difficult enough when dealing with traditional machines, and trained HPC professionals are in high demand and low supply even outside of Africa. As such, BioTeam strives to spread HPC knowledge to ACE members.
“You can’t learn high performance computing, really, at a college setting,” said Corder. “A lot of that stuff is passed down from experts such as myself to the new crop. And we try to give them the information that they need to actually take care of these clusters themselves.”
That last bit from Corder seems to be the guiding principle of BioTeam’s work with ACE – self-sufficiency. This work is meant to foster a community of resilient HPC professionals on a continent that – for systemic and imperialistic reasons – currently lacks certain skills and infrastructure to make it happen.
Continuing to build a better compute infrastructure in Africa
While the presentation made sure not to underestimate the challenges ahead for ACE, there was also much talk about currently implemented solutions as well as potential future ones. Partnerships with BioTeam and NIAID has brought much compute infrastructure to Uganda.
Whalen discussed the rack of donated BiocompACe servers, as well as donated uninterruptible power supply units that can keep a machine working despite a temporary loss of power. He mentioned donated storage infrastructure through NetAPp, as well as virtual machines.
He again mentioned the need for local support teams that are trained on how to support these systems. Thankfully, BioTeam is working hard with ACE to make sure locals have the tools they need and deserve.
Boykin Okalebo brought up how important virtual engagements are with ACE members.
“We conduct office hours every two weeks,” said Boykin Okalebo in an interview. “And this is all about building relationships with the students, making them feel comfortable to ask questions, providing a space for them to bring issues with their code, things they’re interested in with data science – all of those types of things. We let the students drive the agenda.”
These meetings generally take the form of a video chat where BioTeam experts will share their screen with ACE researchers and work through whatever issue they may have. Boykin-Okalebo mentioned one student who is working with cattle genetics to look for disease tolerance with ticks. When he has a problem – maybe his code is running inefficiently or just not working at all – he contacts BioTeam and pulls up his script for them to look over.
Boykin Okalebo also discussed pushing students toward Figshare, which is an open access online repository where researchers can preserve and share their research outputs. She stated that Figshare allows African scientists to get credit for research they may have performed for collaborators outside Africa who might otherwise get all the credit for publishing the work.
On top of the knowledge base that BioTeam provides, there is also a sense of comradery.
“These meetings have spawned other interactions, too,” said Corder. “There’s a handful of students that have my BioTeam phone number. And I literally get texts from them, even on the weekends where they’ll be like ‘I can’t do X, Y or Z’. And, I’m like, ‘All right, hold on. Let me log on.’ It’s a human connection, right? We’re building friendships and trust.”
One thing Boykin Okalebo made abundantly clear, both in the presentation and in a private interview, is that this is not charity – it is a collaboration. The whole world improves with access to knowledge and technology, and there are clear and brutal historic reasons as to why Africa doesn’t have what certain Western countries do.
“We’re all donating our time and equipment, and at the end of the day, we all just care about equalizing the global playing field,” said Boykin Okalebo. “And to do that, you have to come to a partnership with people and empower people to do their own thing.”