Center for Statistics and Quantitative Infectious Diseases – Software Development & Core Facilities
Lead PI
Abstract
The Center for Statistics and Quantitative Infectious Diseases (CSQUID) is a multi-institutional MIDAS Center of Excellence with a multi-disciplinary approach to computational, statistical, and mathematical modeling of important infectious diseases. Research is motivated by multi-scale problems such as immunologic, epidemiologic, and environmental drivers of the spread of infectious diseases with the goal of understanding and communicating the implications for public health policy.
To extend the results of the MIDAS Center’s research projects beyond academia, the Software Development team, led by Northeastern professor Alessandro Vespignani, will help translate the research into products that can be used by external researchers and public health officials. To do so, the team will integrate some of the independently developed tools to create a coherent computational infrastructure that is more than the sum of its methodological parts. In particular, the Software Development team will develop and maintain a suite of computational tools for infectious disease modeling and analysis centered around a multi-scale modeling computational platform (MCP), optimized for cloud deployment.
The major aims of these software developments are:
- Develop an MCP capable of integrating large scale stochastic modeling approaches working at different scales of resolution. We will start by creating a multi-scale hybrid model based on combining the global individual-based meta-population model GLEAM with the US scale agent-based influenza model FluTE. The MCP architecture will be designed around the existing GLEAMviz client-server architecture. It will be expanded with the development of Application Programming Interfaces (APIs) for the plug-in of models developed by the MIDAS research community. The MCP will consist of computationally intensive tools, so we plan to design and to deploy a cloud computing environment with elastic capabilities.
- Develop new features and graphical user interfaces (GUIs) for statistical tools developed in the context of the research activities of the Center such as extensions of pomp, TranStat, among others. We will develop integrated workflows aimed at allowing those programs to exchange data and parameter estimates with the MCP in an automated way.
- Develop a website that will act as a sharing repository for the software developed in this MIDAS Center, with training materials, manuals, and workflow examples. We aim to provide the best accessibility and to foster adoption of the developed software by MIDAS, the research community, and public health agencies by using best practices and public repositories.