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20190712-iqbio.pdf

Patrick Kimes
July 12, 2019
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 20190712-iqbio.pdf

Patrick Kimes

July 12, 2019
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  1. Replicability Hackathon 2019 IQ BIO REU, UPR-RP Data Sciences, Dana-Farber

    Cancer Institute Biostatistics, Harvard TH Chan School of Public Health Patrick Kimes, PhD Kelly Street, PhD
  2. I’d like to thank the Academy… Keegan Korthauer, PhD Alejandro

    Reyes, PhD for making this Patricia Ordóñez, PhD Juan S. Ramírez-Lugo, PhD Rafael Irizarry, PhD for making this possible
  3. Code of Conduct https://github.com/pkimes/PR2019replicathon/blob/master/code_of_conduct.md Assume competence in the people you

    interact with. There are no stupid questions. Be considerate in speech and actions, and actively seek to acknowledge and respect the boundaries of fellow community members. Take care of each other. Alert one of the organizers or facilitators if you notice a dangerous situation, someone in distress, or a potential violation of this Code of Conduct, even if it seems inconsequential. We do not tolerate harassment in any form.
  4. Replicability Hackathon 2019 IQ BIO REU, UPR-RP Data Sciences, Dana-Farber

    Cancer Institute Biostatistics, Harvard TH Chan School of Public Health Patrick Kimes, PhD Kelly Street, PhD
  5. “39% of effects were subjectively rated to have replicated the

    original results.” “… replications of 100 experimental and correlational studies …” https://www.ncbi.nlm.nih.gov/pubmed/26315443
  6. let’s clarify some language reproducibility replicability the ability to take

    the original data and the computer code used to analyze the data and reproduce all of the numerical findings from the study https://simplystatistics.org/2016/08/24/replication-crisis/
  7. let’s clarify some language reproducibility replicability the ability to take

    the original data and the computer code used to analyze the data and reproduce all of the numerical findings from the study https://simplystatistics.org/2016/08/24/replication-crisis/
  8. let’s clarify some language reproducibility replicability the ability to repeat

    an entire study, independent of the original investigator without the use of original data https://simplystatistics.org/2016/08/24/replication-crisis/
  9. let’s clarify some language reproducibility replicability the ability to repeat

    an entire study, independent of the original investigator without the use of original data https://simplystatistics.org/2016/08/24/replication-crisis/
  10. https://simplystatistics.org/2016/08/24/replication-crisis/ “the replication crisis in science is largely attributable to

    a mismatch in our expectations of how often findings should replicate and how difficult it is to actually discover true findings in certain fields.”
  11. https://simplystatistics.org/2013/08/01/the-roc-curves-of-science/ “…I argue that the rate of discoveries is higher

    in biomedical research than in physics. But, to achieve this higher true positive rate, biomedical research has to tolerate a higher false positive rate.”
  12. drug sensitivity in cancer cell lines cell line cell culture

    from a single cell that can grow indefinitely given appropriate conditions • easily grown • relatively inexpensive • amenable to high- throughput testing https://www.ncbi.nlm.nih.gov/pubmed/26248648
  13. drug sensitivity in cancer cell lines dose response curve model

    fit to viability as a function of drug concentration
  14. “Upon careful analysis of the same data, we have come

    to quite different and much more positive conclusions.” https://www.ncbi.nlm.nih.gov/pubmed/27905415