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20200626-iqbio-intro.pdf

 20200626-iqbio-intro.pdf

E1a375fbe8cc71e23307a519eb4848e9?s=128

Patrick Kimes

June 26, 2020
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  1. Healthcare Innovation Replicathon 2020 IQ BIO REU, UPR-RP Data Sciences,

    Dana-Farber Cancer Institute Biostatistics, Harvard TH Chan School of Public Health Patrick Kimes, Kelly Street, Jill Lundell, Mercedeh Movassagh Luli Zou, Ana Betty Villaseñor-Altamirano
  2. HEALTHCARE INNOVATION REPLICATHON 12 y 13 de julio de 2019

  3. Hi! Ana Betty Patrick Jill Mercedeh Kelly Luli

  4. 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
  5. Code of Conduct https://www.pkimes.com/PR2020replicathon/code_of_conduct 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.
  6. part I. the crisis

  7. http://jtleek.com/talks.html

  8. None
  9. “many scientific studies are difficult or impossible to replicate or

    reproduce.”
  10. https://doi.org/10.1371/journal.pmed.0020124

  11. https://doi.org/10.1371/journal.pmed.0020124 “Simulations show that for most study designs and settings,

    it is more likely for a research claim to be false than true.”
  12. “… replications of 100 experimental and correlational studies …” https://www.ncbi.nlm.nih.gov/pubmed/26315443

  13. “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
  14. 39%?? https://www.ncbi.nlm.nih.gov/pubmed/26315443

  15. http://jtleek.com/talks.html

  16. http://jtleek.com/talks.html

  17. http://jtleek.com/talks.html

  18. http://jtleek.com/talks.html

  19. http://jtleek.com/talks.html

  20. http://jtleek.com/talks.html

  21. http://jtleek.com/talks.html

  22. what’s going on?

  23. let’s clarify some language reproducibility replicability

  24. 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/
  25. 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/
  26. 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/
  27. 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/
  28. let’s clarify some language reproducibility replicability

  29. replicability

  30. what’s going on? replicability

  31. crisis: experiments are replicated. results not so much. replicability

  32. should we expect scientific results to always replicate? replicability

  33. Psychology studies reproducibility 2 https://www.nytimes.com/2015/09/01/opinion/psychology-is-not-in-crisis.html? “But the failure to replicate

    is not a cause for alarm; in fact, it is a normal part of how science works.”
  34. 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.”
  35. 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.”
  36. should we expect scientific results to always replicate? not always

    replicability
  37. crisis: experiments are replicated. results not so much. or maybe

    that’s science? replicability
  38. 39%??

  39. replicability crisis opportunity

  40. part II. the question

  41. our question https://www.ncbi.nlm.nih.gov/pubmed/22460902 https://www.ncbi.nlm.nih.gov/pubmed/22460905

  42. https://www.ncbi.nlm.nih.gov/pubmed/22460902 https://www.ncbi.nlm.nih.gov/pubmed/22460905 our question

  43. drug sensitivity in cancer cell lines

  44. drug sensitivity in cancer cell lines what is a cell

    line?
  45. 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
  46. drug sensitivity in cancer cell lines what do we mean

    by drug sensitivity?
  47. drug sensitivity in cancer cell lines viability relative measure of

    cell line abundance after treatment
  48. drug sensitivity in cancer cell lines dose response curve model

    fit to viability as a function of drug concentration
  49. drug sensitivity in cancer cell lines IC50 IC50 concentration at

    which cell growth is inhibited 50%
  50. drug sensitivity in cancer cell lines AUC area under the

    activity curve AUC
  51. drug sensitivity in cancer cell lines got it! … but

    why?
  52. drug sensitivity in cancer cell lines clinical https://www.ncbi.nlm.nih.gov/pubmed/26248648

  53. drug sensitivity in cancer cell lines important, impactful research!

  54. https://www.ncbi.nlm.nih.gov/pubmed/22460902 https://www.ncbi.nlm.nih.gov/pubmed/22460905 our question

  55. https://www.ncbi.nlm.nih.gov/pubmed/24284626

  56. https://www.ncbi.nlm.nih.gov/pubmed/24284626

  57. https://www.ncbi.nlm.nih.gov/pubmed/27905415

  58. None
  59. part III. the opportunity

  60. crisis: experiments are replicated. results not so much. replicability opportunity

  61. what does it mean for results to “replicate”? replicability

  62. what does it mean for results to “replicate”? good question!!

    replicability
  63. None
  64. crisis: experiments are replicated. results not so much. replicability opportunity

  65. crisis: experiments are replicated. results not so much. or maybe

    yes? opportunity replicability
  66. Healthcare Innovation Replicathon 2020 IQ BIO REU, UPR-RP Data Sciences,

    Dana-Farber Cancer Institute Biostatistics, Harvard TH Chan School of Public Health Patrick Kimes, Kelly Street, Jill Lundell, Mercedeh Movassagh Luli Zou, Ana Betty Villaseñor-Altamirano