Day 1: Perspectives on Data Reproducibility

SCHEDULE

• 8:45 - 9:00 - Coffee and light breakfast
• 9:00 - 9:45 - Introductions and opening remarks by Dr. Cooduvali Shashikant
• 9:45 - 9:55 - Lecture by Dr. Frank Pugh
• 9:45 - 10:30 - Lecture by Dr. Ross Hardison
• 10:30 - 11:00 - Coffee break
• 11:00 - 11:45 - Lecture by Dr. Qunhua Li
• 12:00 - 1:30 - Lunch (provided)
• 1:30 - 2:15 - Lecture by Dr. George Perry
• 2:15 - 3:00 - Lecture by Dr. James Broach
• 3:00 - 3:30 - Coffee break
• 3:30 - 4:15 - Watch the Baggerly video
• 4:15 - 5:00 - Software review and installation
• 6:00 - 7:30 - Dinner (not provided)
• 7:30 - 9:00 - R tutorials by Dr. Naomi Altman

MATERIALS

Presentations

1. Introduction to the PSU BootCamp by Dr. Cooduvalli Shashikant
2. It can happen to you. Sources and proximity of lack of reproducibility by Dr. Ross Hardison
3. Statistical issues in reproducible research by Dr. Qunhua Li
4. Data management / archiving across the biological sciences by Dr. George Perry

Publications

1. Challenges in irreproducibile research a special section in Nature
2. Is there a reproducibility crisis? in Nature, 2016
3. Why Most Published Research Findings Are False in PLOS Medicine, 2005
4. Improving Validation Practices in ''Omics'' Research in Science, 2011
5. Six red flags for suspect work in Nature, 2013
6. Raise the standard for preclinical cancer research in Nature, 2012

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, 2010

2. Intro R Videos by Naomi Altman, Penn State, 2016

PRACTICE

• Install the required software
• Get to know thy neighbor