Bootcamp

Perspectives on Data Reproducibility

Schedule

8:30 – 8:45 - Coffee and light breakfast
8:45 - 9:15 - Dr. Cooduvalli Shashikant: Introductions and opening remarks
9:15 – 10:00 - Dr. Kenneth Weiss: How we make scientific inference and its relation to reproducibility from an evolutionary perspective
10:45 - 10:45 - Dr. Ross Hardison: It can happen to you: Sources and proximity of lack of reproducibility
10:45 - 11:05 - Coffee break
11:05 - 11:50 - Dr. Rick Gilmore: The reproducibility “crisis” in psychology and neuroscience
12:00 - 1:30 - Lunch (provided)
1:30 - 2:15 - Dr. Vasant Honavar: Computational reproducibility and data sharing
2:15 - 3:00 - * Dr. James Rosenberger: Issues that are important from a publication perspective and re-producing the analysis from the source data from an experiment
3:00 - 3:20 - Coffee break
3:20 - 4:05 - Dr. Cheryl Keller: Metadata madness: Lessons from Encode
4:05 – 5:00 – Software review and installation: TA’s and Instructors

Videos

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

Reading Materials

Software installation

Install the required software

Install software

Install the required software

Presentation

Software carpentry and reproducible data analysis by Shaun Mahony

Software Carpentry

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

Instructor: Dr. Shaun Mahony

Schedule and additional information: Day 2: Software Carpentry

Statistical Analysis

Proper statistical inference, effective plotting and reproducible reporting

Instructor: Dr. Qunhua Li

Reproducible research with Galaxy

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

Instructor: Anton Nekrutenko

Summaries and Reviews

Topics based on suggestions from students.

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

8:45 - 9:00 - Coffee and light breakfast
9:00 - 10:30 – Presentations by Instructors and TAs
10:30 - 10:50 - Coffee break
10:50 - 12:30 – Best Practices and Q & A: Presentations by past boot camp attendees: Anurag Verma, Matthew Jensen and Di (Bruce) Chen
12:30 - Boot camp ends

Organizers

Course location, hours, requirements

Boot camp will be held July 10-14; 8:45-5PM in 107 Business Buildings
Breakfasts and lunches are planned. Participants are on their own for dinners.
Boot camp ends on Friday July 14 before lunch.

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

Dr. Cooduvalli Shashikant, Co-Director, Bioinformatics and Genomics Program Option: css13@psu.edu

Instructors:

Shaun Mahony mahony@psu.edu
Qunhua Li qunhua.li@psu.edu
Anton Nekrutenko anton@bx.psu.edu

Teaching Assistants

Wilfried Guiblet wmg133@psu.edu,
Yafei Lyu yul@psu.edu,

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)

2017 PSU Bootcamp on Reproducible Research

July 10-14, 2017

DAY 1 TOP