02bsep24i2

02bsep24i2 - Intro 1: Last week's take home lessons Life...

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Unformatted text preview: Intro 1: Last week's take home lessons Life & computers : Self-assembly Math: be wary of approximations Catalysis & Replication Differential equations: dy/dt=ky(1-y) Mutation & the single molecule: Noise is overcome Directed graphs & pedigrees Bell curve statistics: Binomial, Poisson, Normal Selection & optimality Harvard-MIT Division of Health Sciences and Technology HST.508: Genomics and Computational Biology 1 Intro 2: Today's story, logic & goals Biological side of Computational Biology Elements & Purification Systems Biology & Applications of Models Life Components & Interconnections Continuity of Life & Central Dogma Qualitative Models & Evidence Functional Genomics & Quantitative models Mutations & Selection 2 3 For most NA & protein backbones: C,H,N,O,P,S 6+13 Useful for many species: Na, K, Fe, Cl, Ca, Mg, Mo, Mn, Se, Cu, Ni, Co, Si Elements ---- From atoms to (bio)molecules H 2 O H 2 , O 2 H + , OH- CH 4 C 60 CO 3 - NH 3 N 2 NO 3 - H 2 S S n SO 4 Mg ++ PH 3 K + PO 4 Na + Gas Elemental Salt 4 Purify Elements, molecules, Clonal growth assemblies, organelles, cells, organisms chromatography 5 Purified history Pre 1970s: Column/gel purification revolution Mid-1970s: Recombinant DNA brings clonal (single-step) purity. 1984-2002: Sequencing genomes & automation aids return to whole systems. 6 Intro 2: Today's story, logic & goals Biological side of Computational Biology Elements & Purification Systems Biology & Applications of Models Life Components & Interconnections Continuity of Life & Central Dogma Qualitative Models & Evidence Functional Genomics & Quantitative models Mutations & Selection 7 "A New Approach To Decoding Life: Systems Biology" Ideker et al 2001 (http://arep.med.harvard.edu/pdf/Ideker01b.pdf) 1. Define all components of the system. 2. Systematically perturb and monitor components of the system (genetically or environmentally). 3. Refine the model such that its predictions most closely agree with observations. 4. New perturbation experiments to distinguish among model hypotheses. 8 Systems biology critique An old approach. New spins: 1. all components 2. Systematically perturb Unstated opportunities? 3. Refine the model without overfitting. Methods to recapture unautomated data. Explicit(automatic?) logical connections. 4. Optimization of new perturbation experiments & technologies. Automation, ultimate applications , & synthetics as 9 standards for: search, merge, check 10 Transistors > inverters > registers > binary adders > compilers > application programs pice simulation of a CMOS inverter (figures) (http://et.nmsu.edu/~etti/spring97/electronics/cmos/cmostran.html) Why? #0. Why sequence the genome(s)? To allow #1,2,3 below....
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This note was uploaded on 01/24/2010 for the course HST. 508 taught by Professor Dr.georgechurch during the Fall '02 term at MIT.

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02bsep24i2 - Intro 1: Last week's take home lessons Life...

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