2017 PSU Bootcamp on Reproducible Research

July 10-14, 2017

DAY 1

Perspectives on Data Reproducibility

Schedule

Videos

  1. The Importance of Reproducible Research in High-Throughput Biology: Case Studies in Forensic Bioinformatics by Keith Baggerly, UT M.D. Anderson Cancer Center, 201
  2. Intro R Videos by Naomi Altman, Penn State, 2016

Reading Materials

Software installation

DAY 2

Install software

Presentation

Software Carpentry

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

Instructor: Dr. Shaun Mahony

Schedule and additional information: Day 2: Software Carpentry

DAY 3

Statistical Analysis

Proper statistical inference, effective plotting and reproducible reporting

Instructor: Dr. Qunhua Li

DAY 4

Reproducible research with Galaxy

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

Instructor: Anton Nekrutenko

DAY 5

Summaries and Reviews

Topics based on suggestions from students.

Best Practices: Presentations by former boot camp attendees followed by Q & A

GENERAL INFO

Organizers

Course location, hours, requirements

Please contact the organizers for registration or other bootcamp related issues:

Instructors:

Teaching Assistants

Funding and Support

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

The boot camp was first conceived and supported in Jun 2016 by the Administrative Supplement to NIGMS Predoctoral Training Grants (PA-15-136)

ARCHIVE

Website content for the previous years:

Penn State • 2017 • bootcamp-central via pyblue