Software

  • Democratizing uncertainty quantification

    Uncertainty Quantification (UQ) is vital to safety-critical model-based analyses, but the widespread adoption of sophisticated UQ methods is limited by technical complexity. In this paper, we introduce UM-Bridge (the UQ and Modeling Bridge), a high-level abstraction and software protocol that facilitates universal interoperability of UQ software with simulation codes. It breaks down the technical complexity…

  • Computational models for improving surveillance for the early detection of direct introduction of cassava brown streak disease in Nigeria

    Cassava is a key source of calories for smallholder farmers in sub-Saharan Africa but its role as a food security crop is threatened by the cross-continental spread of cassava brown streak disease (CBSD) that causes high yield losses. In order to mitigate the impact of CBSD, it is important to minimise the delay in first…

  • Using phylogenetic summary statistics for epidemiological inference

    Since the coining of the term phylodynamics, the use of phylogenies to understand infectious disease dynamics has steadily increased. As methods for phylodynamics and genomic epidemiology have proliferated and grown more computationally expensive, the epidemiological information they extract has also evolved to better complement what can be learned through traditional epidemiological data. However, for genomic…

  • HPVsim: An agent-based model of HPV transmission and cervical disease

    In 2020, the WHO launched its first global strategy to accelerate the elimination of cervical cancer, outlining an ambitious set of targets for countries to achieve over the next decade. At the same time, new tools, technologies, and strategies are in the pipeline that may improve screening performance, expand the reach of prophylactic vaccines, and…

  • Implementation and applications of PACE-HRH, a stochastic workload model of human resources for health

    Background Effective healthcare systems need adequate numbers of well-trained human resources for health (HRH). To support evidence-based strategic planning, modeling is sometimes used to estimate the number of required health workers and to allocate them appropriately. However, despite the demonstrated utility of models, there are several limitations to existing tools, including the inability to reflect…

  • Modeling COVID-19 vaccination strategies in LMICs considering uncertainty in viral evolution and immunity

    Vaccines against the SARS-CoV-2 virus were developed in record time, but their distribution has been highly unequal. With demand saturating in high-income countries, many low- and middle-income countries (LMIC) finally have an opportunity to acquire COVID-19 vaccines. But the pandemic has taken its toll, and a majority of LMIC populations have partial immunity to COVID-19…

  • One size does not fit all: an application of stochastic modeling to estimating primary healthcare needs in Ethiopia at the sub-national level

    Background: Primary healthcare systems require adequate staffing to meet the needs of their local population. Guidelines typically use population ratio targets for healthcare workers, such as Ethiopia’s goal of two health extension workers for every five thousand people. However, fixed ratios do not reflect local demographics, fertility rates, disease burden (e.g., malaria endemicity), or trends…

  • The changing health impact of vaccines in the COVID-19 pandemic: a modeling study

    Much of the world’s population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a global imprinting of immunity that changed the COVID-19 landscape.…

  • Preventing a cluster from becoming a new wave in settings with zero community COVID-19 cases

    Background In settings with zero community transmission, any new SARS-CoV-2 outbreaks are likely to be the result of random incursions. The level of restrictions in place at the time of the incursion is likely to considerably affect possible outbreak trajectories, but the probability that a large outbreak eventuates is not known. Methods We used an…

  • The changing value of vaccines in the COVID-19 pandemic

    The Omicron wave has left a global imprinting of immunity which changes the COVID landscape. In this study, we simulate six hypothetical variants emerging over the next year and evaluate the impact of existing and improved vaccines. We base our study on South Africa’s infection- and vaccination-derived immunity. Our findings illustrate that variant-chasing vaccines will…