02asep17i1

02asep17i1 - Bphys/Biol E-101 = HST 508 = GEN224 Your grade...

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Bphys/Biol E-101 = HST 508 = GEN224 Your grade is based on six problem sets and a course project, with emphasis on collaboration across disciplines. Open to: upper level undergraduates, and all graduate students. The prerequisites are basic knowledge of molecular biology, statistics, & computing. Please hand in your questionnaire after this class. First problem set is due before Lecture 3 starts via email or paper depending on your section TF. Harvard-MIT Division of Health Sciences and Technology 1 HST.508: Genomics and Computational Biology
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Bio 101: Genomics & Computational Biology Week#1 Intro 1: Computing, Statistics, Perl, Mathematica Week#2 Intro 2: Biology, comparative genomics, models & evidence, applications Week#3 DNA 1: Polymorphisms, populations, statistics, pharmacogenomics, databases Week#4 DNA 2: Dynamic programming, Blast, multi-alignment, H idden M arkov M odels Week#5 RNA 1: 3D-structure, microarrays, library sequencing & quantitation concepts Week#6 RNA 2: Clustering by gene or condition, DNA/RNA motifs. Week#7 Protein 1: 3D structural genomics, homology, dynamics, function & drug design Week#8 Protein 2: Mass spectrometry, modifications, quantitation of interactions Week#9 Network 1: Metabolic kinetic & flux balance optimization methods Week#10 Network 2: Molecular computing, self-assembly, genetic algorithms, neural-nets Week#11 Network 3: Cellular, developmental, social, ecological & commercial models Week#12 Project presentations Week#13 Project Presentations Week#14 Project Presentations 2
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Intro 1: Today's story, logic & g oals Life & computers : Self-assembly required Discrete & continuous models Minimal life & programs Catalysis & Replication Differential equations Directed graphs & pedigrees Mutation & the Single Molecules models Bell curve statistics Selection & optimality 3
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4 101 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 4
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5 acgt 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1 1 0 1
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gggatttagc tcagtt ggg agagcgcca gact gaa ga t ttg gag g tcctgtgtt cgatcc ac agaattc gcacca Post- 300 genomes & 3D structures
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Discrete Continuous a sequence a weight matrix of sequences lattice molecular coordinates digital analog (16 bit A2D converters) Σ∆ x ± dx neural/regulatory on/off gradients & graded responses sum of black & white gray essential/neutral conditional mutation alive/not probability of replication 7
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Bits (discrete) bit = binary digit 1 base >= 2 bits 1 byte = 8 bits + Kilo Mega Giga Tera Peta Exa Zetta Yotta + 3 6 9 12 15 18 21 24 - milli micro nano pico femto atto
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02asep17i1 - Bphys/Biol E-101 = HST 508 = GEN224 Your grade...

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