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Computational Methods in Biophysics and Genomics Analysis

Explore the intersection of biophysics, genomics, computing, and economics. Dive into quantitative exercises, communication tools, project discussions, and more for a comprehensive understanding of the subjects.

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Computational Methods in Biophysics and Genomics Analysis

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  1. Biophysics 101, Tue 8-Sep-2009Genomics, Computing, Economics Thanks to: RBH Azco

  2. Class outline (1) Topic priorities for homework since last class (2) Quantitative exercise (3) Discuss communication/presentation tools (4) Topic priorities, homework for next class (5) Project tools discussion

  3. (1) Topic priorities for homework since last class (a) Your notes (b) Followup on the "experiment" from Tue: Tversky & Kahneman (1974) Judgement under Uncertainty: Heuristics and Biases. Science 185:1124). (c) Exponential growth Spreadsheet & Python examples

  4. 1. Estimate 8 x 7 x 6 x 5 x 4 x 3 x 2 x 1 2. From a group "of 70 engineers and 30 lawyers: Dick is a 30 year old man. He is married with no children. A man of high motivation, he promises to be quite successful in his field. He is well liked by his colleagues." What is the probability that Dick is an engineer? Human subject experimentation7 questions. 5 seconds each 3. Write down a string of 10 random H & T characters. 4. From 10 people, how many different committees of 2 members? 8 members? 5. One person draws 4 red balls & 1 white. Another 12 red & 8 white. What odds should each individual give that the source is 2/3 red (rather than 2/3 white)? 6. Estimate 1 x 2 x 3 x 4 x 5 x 6 x 7 x 8

  5. Human experiment results 1 (& 6): 8 x 7 x 6 x 5 x 4 x 3 x 2 x 1 (& rev) Actual: 40320 1974 median: 2250 descending; 512 ascending 2: The probability that Dick is an engineer should be 70:30 in one case and 30:70 in the other with odds ratio = (70/30)/(30/70) = 5.44 1974: observed ratio was close to 1.0. 3: n=2,3,4,5,6 in a row are quite likely (.998, .9, .61, .32, .14) 1974: more than two in row (HH or TT) were rarely chosen. 4: 10 people, # committees of 2 or 8 members? Actual: C(10,2)=C(10,8)=45 1974 median for 2 was 70; for 8 was 20. C(n,i)= n!/[i!(n-i)!]

  6. Human experiment results 5: 4/5 vs 12/20 -- which better supports 2/3 red rather than 2/3 white? 1974: Most people felt 4/5 (80%) is better evidence than 12/20 (60%) Actual: [C(5,4)(2/3)^4 (1/3) / C(5,1)(2/3)(1/3)^4]= 8 odds ratio [C(20,12)(2/3)^12 (1/3)^8 / C(20,8)(2/3)^8(1/3)^12]= 16

  7. Hence, programming in statistics & economics Mechanical-Analog: slide rule (1620) Mechanical-Digital: Babbage (1837), DigiComp (1963) Electronic-Analog: 1940s Electronic Digital -- Procedural, imperative languages: Basic(’63), Lisp(’58), Algol, Cobol(’59), Fortran(’54), C(‘72), IBM360-Assembly(’64), FORMAC, APL, PL/I Dynamic languages: Perl(‘87), Python(‘91). Spreadsheets: double-entry bookkeeping (12th Century) Electronic Mattessich (’61). PC:Bricklin’s Visicalc (’79), Excel(’85), public spreadsheets (’70) Wikicalc etc. http://www.meccano.us/analytical_engine/P1010006.MOV

  8. Exp.py # File: Exp.py # http://www.python.org/download/ # http://matplotlib.sourceforge.net/users/installing.html (EPD) # http://matplotlib.sourceforge.net/users/pyplot_tutorial.html import numpy as np import matplotlib.pyplot as plt t1 = np.arange(0.0, 5.0, 0.1) plt.plot(t1, np.exp(t1), 'ro') plt.show()

  9. Exp.xls A3 =k*A2 A3 =k*A2*(1-A2) A3 =MAX(k*A2*(1-A2),0)

  10. Vertebratebrain size evolution Human-chimp 1.2% Human-human 0.1% Genome: 2x 3Gbp Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiensScience 2005 Bond et al 2002 ASPM is a major determinant of cerebral cortical size. Nat Genet. 32(2):316-20. Jerison, Paleoneurology & the Evolution of Mind, Scientific Amer. 1976

  11. The Future of Human Naturehttp://www.bu.edu/pardee/events/conferences/2003/nature-program.html The Law of Accelerating Returns  Ray Kurzweil(The Singularity Is Near : When Humans Transcend Biology) An analysis of the history of technology shows that technological change is exponential, contrary to the common-sense "intuitive linear" view. So we won't experience 100 years of progress in the 21st century -- it will be more like 20,000 years of progress (at today's rate). .. ultra-high levels of intelligence that expand outward in the universe at the speed of light. http://www.kurzweilai.net/articles/art0134.html?printable=1 Bill Joy Wired 8.04 | Apr 2000 Our most powerful 21st-century technologies - robotics, genetic engineering, and nanotech - are threatening to make humans an endangered species.

  12. Inheritance is not just DNA

  13. Inheritance is not just DNA Past Locomotion 50 km/h Ocean depth 75 m Visible l .4-.7 m Temperature 275-370 Memory time 20 yr Memory 1E9 bits Compute speed 1E14 ops Compute energy5E12 op/J Current 26720 km/h 10,912 m pm-Mm 3-1900oK 5000 yr 1E17 bits 1E14 ops 5E12 op/J http://www.techworld.com/opsys/features/index.cfm?fuseaction=displayfeatures&featureid=467&page=1&pagepos=5 http://www.merkle.com/humanMemory.html

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