PSU Bootcamp on Reproducible Research

PSU Bootcamp on Reproducible Research

June 6-10, 2016

Day 1: Perspectives on Data Reproducibility

Presentations by

  • Dr. Cooduvali Shashikant
  • Dr. Ross Hardison
  • Dr. Qunhua Li
  • Dr. James Broach
  • Dr. George Perry

Day 2: Software Carpentry

The basics of computational reproducibility: version control, documentation, automation


  • Dr. Istvan Albert

Day 3: Statistical Analysis

Reproducible statistical inference, simulations, RNA-Seq bootcamp


  • Dr. Naomi Altman

Day 4: Reproducible research with Galaxy

Introduction to Galaxy and Variant Calling, Jupyter Notebooks, RNA-Seq with Galaxy


  • Dr. Anton Nekrutenko

Day 5: Summaries and Reviews

  • Topics based on suggestions from students.
  • Making custom galaxy tools.
  • Best practices in research computing.
  • Plotting with plotly and shiny.

Software Installation

  • How to install the software used in the bootcamp

General Information

Course location, hours, requirements

  • Boot camp will be held Jun 6-10; 9-5PM in 011 Life Science Building
  • Breakfasts and lunches are planned. Participants are on their own for most dinners.

Funding and Support

The bootcamp is funded by the Administrative Supplement to NIGMS Predoctoral Training Grants (PA-15-136)

The boot camp is organized by the Computation, Bioinformatics and Statistics Predoctoral Training Program at Penn State supported by the NIH T32 program.

See the Photo Album

Penn State • 2016 • bootcamp-central via pyblue