2019 PSU Bootcamp on Reproducible Research

June 3-7, 2019

INFORMATION TOP

The first day of the boot camp will be held in 108 Business Building. On Monday we begin with coffee and light breakfast at 8:45 AM.

Day 2-5 will be in 107 Business Building with the following program:

Day 5 ends at noon, lunch provided.

Please bring your laptop. You may need to install new software instructions.

Teaching Assistants

Hillary Koch, hillary.koch01@gmail.com, Graduate Student, Statistics Program CBIOS Trainee

Molly Rathbun, molly.rathbun@gmail.com, Graduate Student, BMMB Program CBIOS Trainee

Funding and Support

The boot camp is organized by theĀ Computation, Bioinformatics and Statistics Predoctoral Training Program at Penn StateĀ 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 theĀ Administrative Supplement to NIGMS Predoctoral Training Grants (PA-15-136)

DAY 1 TOP

Day 1: Perspectives on Data Reproducibility - Monday June 3, 2019

Rm 108 Business Building

Coordinator: Cooduvalli Shashikant

DAY 2 TOP

Day 2: Software Carpentry and Data Analysis - Tuesday June 4, 2019

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

Rm 107 Business Building
Instructors:

Schedule

Class Material

Install software

Presentation

Lesson

Best Practices for Scientific Computing

Shell scripting

Markdown

Git

Additional Reading Materials

Running scripts on Penn State clusters (ICS-ACI)

Advanced Bash scripting

Make

Alternatives to Git/GitHub

Alternatives to Markdown

DAY 3 TOP

Day 3: Essential Pieces of Reproducibility - Wednesday Jun 5, 2019

Rm 107 Business Building

Instructor: Anton Nekrutenko

Agenda

DAY 4 TOP

Day 4: Proper Statistical Interference, effective plotting and reproducible reporting - Thursday, Jun 6, 2019

Rm 108 Business Building

Instructor: Qunhua Li

Schedule:

Materials:

DAY 5 TOP

Day 5: Reproducibility Issues - Friday, Jun 7, 2019

Rm 108 Business Building

Coordinators: Hillary Koch & Molly Rathbun

ARCHIVES TOP

Penn State • generated from bootcamp-central via pyblue