Materials for the Data Applications 1 workshop of the Programming Bootcamp hosted by the Predictive Plant Phenomics (P3) NRT program on August 13-19, 2019. The other workshops in this bootcamp are:
- August 13: Introduction to R taught by Paul Villanueva
- August 14: Introduction to Python taught by Paul Villanueva
- August 15: Introduction to UNIX taught by Shane Dooley
- August 16: Data Applications 1 taught by Paul Villanueva
- August 19: Data Applications 2 (this page) taught by Paul Villanueva
This workshop is an introduction to network analysis in R using the iGraph package. There are two parts to this workshop:
- iGraph basics, which demonstrates some basics of using
iGraphin R - PPI network of Saccharomyces, which is a small case study in using network analysis to look at a protein-protein interaction network in Saccharomyches.
The Predictive Plant Phenomics NRT is an interdisciplinary program combining plant biology, engineering, and data science. However, since most of the P3 students have backgrounds in the biological sciences, they likely haven't had substantial programming training. These workshops are the annual Programming Bootcamps are an introduction for the incoming class of P3 students (and anyone else that would like to attend) to programming basics.
From the P3 website:
"New methods to increase crop productivity are required to meet anticipated demands for food, feed, fiber, and fuel. Using modern sensors and data analysis techniques, it is now feasible to develop methods to predict plant growth and productivity based on information about their genome and environment. However, doing so requires expertise in plant sciences as well as computational sciences and engineering.
Through the Predictive Plant Phenomics (P3) Program, we bring together students with diverse backgrounds, including plant sciences, data sciences, and engineering, and provide them with data-enabled science and engineering training. The collaborative spirit required for students to thrive in this unique intellectual environment will be strengthened through the establishment of a community of practice to support collective learning.
The National Science Foundation Research Traineeship (NRT) is the Foundation's new traineeship program designed to encourage the development and implementation of bold, new, potentially transformative, and scalable models for STEM graduate education training. The NRT prougram also seeks to catalyze and advance cutting-edge interdisciplinary research, and prepare STEM graduate students more effectively for multiple research and research-related career paths."
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