The overall goal of the software development and core facilities section is to make the new methodologies, algorithms, and models developed in the MIDAS Center's research projects more accessible to both the research and public health communities. To do so, we 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, we propose to develop and to 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 the software developments are: i) Develop an MCP capable of integrating large scale stochastic modeling approaches working at different scales of resolution. We will start by creating a multiscale hybrid model based on combining the global individual-based metapopulation 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, ii) 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. iii) 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

Public Health Relevance

To extend the results of the MIDAS Center's research projects beyond academia, the Software Development team will help translate the research into products that can be used by external researchers and public health officials. The scope of work includes dissemination of the Center's research tools, updating computational tools to suit the needs of users, and integrating multiple tools into coherent, usable platforms.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Specialized Center--Cooperative Agreements (U54)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-BBCB-5 (MI))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Fred Hutchinson Cancer Research Center
United States
Zip Code
Feldstein, Leora R; Matrajt, Laura; Elizabeth Halloran, M et al. (2016) Extrapolating theoretical efficacy of inactivated influenza A/H5N1 virus vaccine from human immunogenicity studies. Vaccine 34:3796-802
Bento, Ana I; Rohani, Pejman (2016) Forecasting Epidemiological Consequences of Maternal Immunization. Clin Infect Dis 63:S205-S212
Xue, Katherine S; Hooper, Kathryn A; Ollodart, Anja R et al. (2016) Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture. Elife 5:e13974
Koepke, Amanda A; Longini Jr, Ira M; Halloran, M Elizabeth et al. (2016) PREDICTIVE MODELING OF CHOLERA OUTBREAKS IN BANGLADESH. Ann Appl Stat 10:575-595
Ngwa, Moise C; Liang, Song; Kracalik, Ian T et al. (2016) Cholera in Cameroon, 2000-2012: Spatial and Temporal Analysis at the Operational (Health District) and Sub Climate Levels. PLoS Negl Trop Dis 10:e0005105
Chao, Dennis L; Dimitrov, Dobromir T (2016) Seasonality and the effectiveness of mass vaccination. Math Biosci Eng 13:249-59
Neher, Richard A; Bedford, Trevor; Daniels, Rodney S et al. (2016) Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proc Natl Acad Sci U S A 113:E1701-9
Chen, Wan-Jun; Lai, Sheng-Jie; Yang, Yang et al. (2016) Mapping the Distribution of Anthrax in Mainland China, 2005-2013. PLoS Negl Trop Dis 10:e0004637
Fang, Li-Qun; Yang, Yang; Jiang, Jia-Fu et al. (2016) Transmission dynamics of Ebola virus disease and intervention effectiveness in Sierra Leone. Proc Natl Acad Sci U S A 113:4488-93
Magpantay, F M G; Domenech DE Cellès, M; Rohani, P et al. (2016) Pertussis immunity and epidemiology: mode and duration of vaccine-induced immunity. Parasitology 143:835-49

Showing the most recent 10 out of 63 publications