2018 PSU Bootcamp on Reproducible Research

June 18-21, 2018

DAY 1

Day 1: Perspectives on Data Reproducibility

Schedule

8:45 - COFFEE AND LIGHT BREAKFAST

9:00-9:30 - Wilfried Guiblet and Monika Cechova: Introductions.

9:30-10:15 - Cooduvalli Shashikant: Is there a reproducibility crisis?

10:15-10:35 - COFFEE BREAK

10:35-11:20 - James Broach: “10% of the time, it works every time” - Recognizing sloppy science

11:20-12:05 - Keith Baggerly: http://videolectures.net/cancerbioinformatics2010_baggerly_irrh/

12:05-1:15 - LUNCH

1:15-2:00 - Cheryl Keller: It’s a Mad, Mad, Metadata World

2:00-2:45 - Molly Hall: Quality control is essential to ensuring reproducibility in genotype and non-genetic data

2:45-3:30 - Vasant Honavar: Computational reproducibility and data sharing

3:30-3:50 - BREAK

3:50-4:05 - Aswathy Sebastian: An example of reproducibility incident

4:05-4:50 - Instructions by Shaun Mahony and TAs to Tuesday's sessions

Videos

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Reading Materials

Some shell basics

Software Installation

Bootcamp softwares

Putty - for Windows users

DAY 2

Day 2: Software carpentry and reproducible data analysis

Schedule

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

Instructor: Dr. Shaun Mahony, Assistant Professor, Biochemistry & Molecular Biology

Class Material

Install software

Presentation

Lesson

Best Practices for Scientific Computing

Shell scripting

Markdown

Git

Additional Reading Materials

Advanced Bash scripting

Make

Alternatives to Git/GitHub

Alternatives to Markdown

DAY 3

Day 3: Proper statistical inference, effective plotting and reproducible reporting

Schedule

Proper statistical inference, effective plotting and reproducible reporting

Instructor: Dr. Qunhua Li

Videos

Reading Materials

DAY 4

Day 4: Essential pieces of reproducibility - Conda, Jupyter, Galaxy, Blogs

Monika Cechova, Anton Nekrutenko | biomonika@psu.edu, anton@nekrut.org

Python!

Agenda

Tutorials and Reading

DAY 5

Workshop on emerging methods for sequence analysis

For those that registered for the workshop, information is available at

GENERAL INFORMATION

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)

ARCHIVES

Penn State • 2018 • bootcamp-central via pyblue