POSE: Phase I: Evolving RevBayes into an Open-Source Ecosystem for Phylogenetics

Iowa State University, Ames IA

Investigators

Abstract

Evolutionary trees provide information about the relationships among lineages of emerging pathogens and cancer cells, as well as plants, animals and other organisms. To study evolution and the diversity of life on Earth, researchers need high-quality software for constructing evolutionary trees from DNA sequence data. RevBayes is a freely available and popular software package for constructing evolutionary trees. It achieves high flexibility through the use of an interpreted programming language that allows users to construct evolutionary trees from a variety of different types of data under many different scenarios. The community of scientists currently using and developing RevBayes is distributed across many different universities and countries. The RevBayes community develops and maintains a variety of resources, including inference software, visualization tools, and detailed user tutorials. As an open-source project, RevBayes benefits from free contributions from users and developers around the world. A major goal for this Pathways to Enable Open-Source Ecosystems (POSE) project is to assess how to transition this community into a self-sustaining and self-governing ecosystem that can ensure continued growth and stability by making use of free contributions from an increasing number of users and developers. These efforts and experiences will help inform other teams in the field. Training opportunities for junior researchers to learn transferable software development skills will be offered. Junior researchers will also be provided with networking opportunities both within and outside the RevBayes team. This project will investigate and test strategies to improve the experience of community members at all levels (user, contributor, developer) in order to increase the rate at which people join the community and transition to higher levels of involvement. The OSE will facilitate this collaboration by establishing a deliberate dialog with potential, new, and veteran developers to identify where the project is succeeding and where it can be improved. The team will organize an in-person meeting to obtain feedback from community members and discuss community organization. They will also conduct a poll to incorporate feedback from community members from a variety of backgrounds and career stages. Based on this feedback, the OSE will improve the clarity and depth of existing RevBayes user tutorials and developer documentation, which will ultimately empower RevBayes users to make new biological discoveries and RevBayes developers to innovate new models and methods. A comparative database of software for estimating evolutionary trees and a review how RevBayes is used in published scientific studies will be conducted. These assessments will provide a multifaceted view of the breadth of the RevBayes community, as well as their research interests and needs. These activities will be combined with efforts to understand and improve the current governance structure of the RevBayes project and create new venues for communication between users and developers. By establishing the foundation for RevBayes to function as an open-source ecosystem, the team will ensure that the RevBayes project and its products are viable for long-term stability and growth. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.