Perspectives on Data Reproducibility
- 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
The basics of computational reproducibility: version control, documentation, automation
Instructor: Dr. Shaun Mahony
Schedule and additional information: Day 2: Software Carpentry
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
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:
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)