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Research Plan

The project development is divided into three steps

AIM 1 will focus on the development of scripts (in UNIX shell, Python, and R) to connect the separate steps of a typical population genomics project. Python will serve as our central pipeline scripting language.

The goal of AIM 2 is to incorporate PPP tools into the Galaxy Project by building a GUI for all steps of the pipeline A publicly available server instance of PPP will be created and hosted for (a) running population genomic analyses, (b) demonstrating the utility of different pipelines, and (c) to obtain suggestions, and feedback on continued development. This server will be listed among Galaxy’s growing list of public servers, and will provide a unique resource for model-based analyses for population geneticists.

Apart from the server, a standalone version of PPP on the Galaxy project will be released for users to implement on their own machines. This will allow users to (a) reproduce PPP’s functionality, (b) preserve confidential/pre-release data integrity, and (c) develop their own pipelines for PPP to be shared with the community.

AIM 3 will focus on a second major release of PPP that incorporates additional programs and functionality. Many of the decisions about priorities under AIM 3, in termsof which kinds of functionality to add, and which specific tools to include in the platform, will hinge on what has been learned during AIMS 1 and 2 and from feedback from users.

New scripts will be written to expand the visualization options, such as for more kinds of genome-wide scans, and figures of demographic models. Corresponding modules will be added to both the standalone, and public server instances of PPP’s Galaxy GUI.