Research Assistant/Software Developer

Project: Open-source software to improve SARS-CoV-2 surveillance
Job Title: Research Assistant/Software Developer
Positions Available: 2
Hours Commitment: 5 hours per week
Position Duration: 18 weeks
Hourly Rate: $20-25 depending on experience
Start date: Flexible May/June 2021

Dr. James Hay, PhD, a postdoctoral research fellow at the Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health, is hiring two students to develop statistical software tools to analyze epidemiological surveillance data with applications to the SARS-CoV-2 pandemic. Students will be part of the Michael Mina lab, a group focused on developing mathematical and epidemiological models using serological and virological data to better understand the population epidemiology and immunology of infectious diseases.

Project description
Testing to find infections and track the spread of the virus is central to tackling the COVID-19 pandemic, helping decision makers know when and what interventions to put in place. While most people think of
COVID-19 tests as being only positive or negative, most routine tests (RT-PCR) quantify how much virus genetic material there is in each sample. Through our research, we have developed a new statistical method to harness this information, which is otherwise discarded, to generate unbiased, accurate estimates of the epidemic trajectory (see This project aims to develop an open-source software tool with a user interface to make this method accessible to non-specialist users, adding a much-needed method to the public health surveillance toolkit. The primary output will be a well-documented R package and accompanying Shiny app to estimate epidemiological patterns from routinely collected RT-qPCR testing. A secondary output will be a journal publication, depending on progress.

Job description
We are looking for two students: one will take responsibility for developing the R package, documentation, and communication materials, and one will be responsible for developing the user interface and improving the inference algorithms. This is an ideal opportunity for students with a strong interest in developing analytical tools for public health surveillance and collaborating across computational and epidemiological disciplines. This is also a great opportunity to gain experience working in a leading infectious disease epidemiology department and research group. Work hours are flexible, but regular weekly and later biweekly meetings will be arranged. Both graduate and undergraduate students will be considered. All work and meetings will be held remotely, and therefore applicants are encouraged to apply regardless of location.


  • Test, tidy and document existing R code (Research Assistant)
  • Write vignettes and example analyses (Research Assistant)
  • Add new functions and epidemiological tools to the package (Research Assistant)
  • Optimize underlying algorithms and code to improve speed (Software Developer)
  • Develop a point-and-click interface for non-specialist users (Software Developer)
  • Extend models and inference framework for new use cases and data types (Software Developer)


  • (Required) Demonstrate excellent written and verbal communication skills.
  • (Required) Ability to work collaboratively as part of a team.
  • (Required) Enrolled in an undergraduate or graduate degree in the biological sciences, physical sciences, computer science, mathematics, or statistics.
  • (Required) Experience coding in R or a demonstrated ability and willingness to learn quickly.
  • (Required) Prior experience or courses in applied statistics, Bayesian statistics, or mathematical modeling.
  • (Required) Equipment will not be provided, so the applicant must have access to a laptop or personal computer.
  • (Desired) Experience in applying mathematical or statistics models to answer epidemiological questions.
  • (Desired) Experience coding in C++ is a bonus but not necessary.
  • (Desired) Experience developing and distributing software packages (Software Developer).
  • (Desired) Experience developing statistical tools to estimate model parameters.

Please also feel free to reach out with any questions before applying.

Job Type: Part-time

Pay: $20.00 - $25.00 per hour

COVID-19 considerations:
This is a remote working position.


  • High school or equivalent (Preferred)


  • undergraduate education or research: 1 year (Preferred)

Work Location:

  • Fully Remote

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