The emergence of vibrant research communities of computer scientists in Kenya and Uganda has occurred in the context of neoliberal privatization, commercialization, and transnational capital flows from donors and corporations. We explore how this funding environment configures research culture and research practices, which are conceptualized as two main components of a research community. Data come from a three-year longitudinal study utilizing interview, ethnographic and survey data collected in Nairobi and Kampala. We document how administrators shape research culture by building academic programs and training growing numbers of PhDs, and analyze how this is linked to complicated interactions between political economy, the epistemic nature of computer science and sociocultural factors like entrepreneurial leadership of key actors and distinctive cultures of innovation. In a donor-driven funding environment, research practice involves scientists constructing their own localized research priorities by adopting distinctive professional identities and creatively structuring projects. The neoliberal political economic context thus clearly influenced research communities, but did not debilitate computing research capacity nor leave researchers without any agency to carry out research programs. The cases illustrate how sites of knowledge production in Africa can gain some measure of research autonomy, some degree of global competency in a central arena of scientific and technological activity, and some expression of their regional cultural priorities and aspirations. Furthermore, the cases suggest that social analysts must balance structure with culture, place and agency in their approaches to understanding how funding and political economy shape scientific knowledge.