warm-up exercise Representing Data Digitally goals for today proteins example from nature

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1 Representing Data Digitally Anne Condon September 6, 007 warm-up exercise pick two examples of in your everyday life* in what media are the is represented? is the converted from one representation to another, as you use the? How? how does a particular representation of the influence what you can do with the? might any errors arise when you use the? *one example should be computer-related, one not...try for examples no-one else might think of goals for today be able to define a representation scheme understand, and start working on, course learning goals on representation let s start with two examples example from nature proteins are critical to life organisms need ways to store and transmit descriptions of proteins proteins beads on a necklace, with 0 different bead types (amino acids) what medium, and what representation scheme does nature use? news/science_ed/structlife/

2 DNA storage medium in the cell a (double-stranded) bead necklace with four different kinds of beads (bases, nucleotides): A,C,G, T genes to keep our body functioning, proteins are constantly manufactured in our cells genes segments of our DNA store descriptions for proteins the genetic code specifies how a protein (sequence of amino acids) can be represented as DNA (sequence of bases) the genetic code the genetic code: example TTC phenylalanine TTA leucine TTG leucine CTT leucine CTC leucine CTA leucine CTG leucine ATT isoleucine ATA isoleucine GTT valine GTA valine TCC serine TCA serine TCG serine CCT proline CCC proline CCA proline CCG proline ACT threonine ACA threonine GCT alanine GCA alanine TAC tyrosine TAA stop TAG stop CAT histidine CAC histidine CAA glutamine CAG glutamine AAT asparagine AAA lysine GAT aspartic acid GAA glutamic acid TGC cysteine TGA stop TGG tryptophan CGT arginine CGC arginine CGA arginine CGG arginine AGT serine AGA arginine GGT glycine GGA glycine one code for methionine isoleucine phenelalanine aspartic acid glycine is... (partial table needed for example) the genetic code: example one code for methionine isoleucine phenelalanine aspartic acid glycine is... ATGATCTTTGACGGG (partial table needed for example)

3 suppose you have no paper, and need to describe a connect-the-dots representation using your voice. How could you do it? dimension of the grid (in cm),,,,,,,,,, first dot third dot fifth dot second dot fourth dot 0 0,,,,,,,,,, a continuous-line drawing can be represented as a sequence of dots drawn on a page a sequence of numbers, which lists the coordinates of the dots on a D grid (preceded by dimension of grid in cm) activity make a continuous-line drawing on a piece of paper, and represent it as best you can using a sequence of dots how did you decide on the number of dots to use? where to position the dots? what principles would you suggest in general, for selecting the dots to represent a picture?

4 a representation scheme a description of how of one type (source ) can be represented using of another type (encoded ) source representation scheme encoded why study representation schemes? central to CS: designing representation schemes to balance engineering (e.g. errors) with usability (e.g. aesthetic) considerations is major activity useful: facility with helps in other fields, and in everyday life fun: designing and critiquing representation schemes is creative, and a new lens with which you view your world example: representation schemes in CS polygonal representation of surfaces (see work of Alla Sheffer in CS) this is the D version of connect-the-dots! course learning goals on describe properties of representation schemes that can be found in many contexts of the world around you critique properties of representation schemes, from the stand-point of usability and engineering considerations, given information about the context in which the scheme is used course learning goals on engage in design of schemes, for example by proposing modifications that address shortcomings of given representation schemes put your knowledge to practical use, for example, in making decisions about representing your own, or deciding you want to go into CS, or applying the knowledge in your own field

5 scheme property : digital vs not digital digital scheme: encoded is digital (source may be digital or analog) digital : comprised of symbols over a finite alphabet analog : not digital, e.g. continuous line scheme property : lossless vs lossy lossless: source can be reconstructed exactly from encoded lossy: not lossless scheme property : robustness in the face of errors this one is easiest to explain in context... let s go back to one example the genetic code: robustness in the face of errors what if a DNA base is copied incorrectly? ATGATCTTTGACGGG ATGATCTCTGACGGG what if a DNA base is deleted? ATGATCTTTGACGGG ATGATCTTGACGGG critique: what might this tell us about the cell s translation machinery? summary: some properties of schemes digital or not lossless or lossy robustness in the face of errors recall: goals for today be able to define a representation scheme understand, and start working on, course learning goals on representation do you remember the goals?

6 a representation scheme a description of how of one type (source ) can be represented using of another type (encoded ) source representation scheme encoded course learning goals on describe properties of representation schemes that can be found in many contexts of the world around you critique properties of representation schemes, from the stand-point of usability and engineering considerations, given information about the context in which the scheme is used course learning goals on engage in design of schemes, for example by proposing modifications that address shortcomings of given representation schemes put your knowledge to practical use, for example, in making decisions about representing your own, or deciding you want to go into CS, or applying the knowledge in your own field