2020 PSU Bioinformatics Data Reproducibility Bootcamp
INFORMATION TOP
Welcome to the first virtual offering of the PSU Bioinformatics Data Reproducibility Bootcamp!
Important resources:
Instructor
Teaching Assistants
Organizers
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 the Huck Institutes of the Life Sciences and participating colleges at Penn State. The computational resources are provided by The Institute for Computational and Data Sciences (ICDS).
The boot camp was first conceived and supported in Jun 2016 by the Administrative Supplement to NIGMS Predoctoral Training Grants (PA-15-136)
DAY 1 TOP
Day 1: Wednesday August 12, 2020
All times below are listed in US Eastern time (America/New_York). Click on any of the times to convert it to your local timezone.
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08:30 Welcome, Overview of Day 1
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09:00 Presentation by István Albert
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10:00 Presentation by Justin Petucci - An Overview of ICDS Research Computing Services
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10:30 Break
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11:00 Automate with the shell
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12:30 Lunch
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01:30 Automate with the shell (cont)
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03:00 Break
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03:30 Ice breaker
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04:30 Presentation by Kate Stankiewicz - 'Data is available online': the challenges of reanalyzing published data
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05:00 Done for the day!
DAY 2 TOP
Day 2: Thursday August 13, 2020
All times below are listed in US Eastern time (America/New_York). Click on any of the times to convert it to your local timezone.
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08:30 Overview of Day 2
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09:00 Presentation by Paul Medvedev - Understanding how bioinformatics work is published and incentivized: a computer science perspective
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10:00 Presentation by Arun Srinivasan - Out of Tune: Tuning Parameters and Reproducible Machine Learning
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10:30 Break
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11:00 RNA-seq
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12:30 Lunch
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01:30 RNA-seq (cont)
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03:00 Break
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03:30 Presentation by Qunhua Li - Statistical issues on reproducibility in genomic research
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04:30 Presentation by Matthew Jensen - Constructing and maintaining reproducible bioinformatics pipelines in your research
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05:00 Done for the day!
DAY 3 TOP
Day 3: Friday August 14, 2020
All times below are listed in US Eastern time (America/New_York). Click on any of the times to convert it to your local timezone.
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08:30 Overview of Day 3
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09:00 Record with version control
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10:30 Break
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11:00 Record with version control (cont)
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12:30 Lunch
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01:30 Differential expression analysis
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03:00 Break
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03:30 Verify with workflowr
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05:00 Done for the day!