So lets start! 8/26/16. Did you register your clicker? Key concept: The COMPUTER does the recipe! Make it as hard, tedious, complex as you want!

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Did you register your clicker? Theresa McCracken @McHumor.

1-1:50 (40305), 2-2:50 (40306) Find your lab! TA: Vahid Noroozi Mon 3-5pm 4030 SEL 2 So lets start! Key concept: The COMPUTER does the recipe! Make it as hard, tedious, complex as you want!

1 Did you register your clicker? Theresa CSE 111 Bio: Program Design I Lecture 2: What is Computer Science Intro to Bio Tanya Berger- Wolf (CS) & Boris Igić (Bio) University of Illinois, Chicago August 25, 2016 Labs: Monday 2249F SEL 1-1:50 (40305), 2-2:50 (40306) Find your lab! TA: Vahid Noroozi Mon 3-5pm 4030 SEL 2 So lets start! Key concept: The COMPUTER does the recipe! Make it as hard, tedious, complex as you want! Crank through a million genomes? No problem! Look through 100,000 documents in a lawsuit to pick out the 17 or the 42,000 containing a par_cular phrase? Easy- peasy! (What the cs111 law course will do) Find one person in a 30,000 student campus? Yawn! Process a million dots on the screen or a bazillion sound samples? (What the media computa_on course will do) 3 1

2 What computers understand It s not text, numbers, mul_media at all. It s unimedia (Nicholas Negroponte) Everything is 0 s and 1 s Computers are exceedingly stupid The only data they understand is 0 s and 1 s They can only do the most simple things with those 0 s and 1 s Move this value here Add, mul_ply, subtract, divide these values Compare these values, and if one is less than the other, go follow this step rather than that one. Key Concept: Encodings But we can interpret these numbers any way we want. We can encode informa_on in those numbers Even the no_on that the computer understands numbers is an interpreta_on We encode the voltages on wires as 0 s and 1 s Which we can, in turn, interpret as a decimal number Tiny detour: Useful terminology The 8 bit byte is the basic unit of memory today. In some sense, a really _ny unit. You more oden see: 1 kilobyte = 1 KB = 1K = 2 10 = 1,024 bytes 1 megabyte = 1 MB = 1M = 2 20 = 1,048,576 bytes 1 gigabyte = 1 GB = 1G = 2 30 = 1,073,741,824 bytes What is a computer? A device that executes a stored program (sequence of instruc_ons). A program is a par_cular wri_ng of a recipe in some par_cular language. (Recipe is likely to be in English or French or Arabic or Hindi; program in a programming language such as C, Java, Visual Basic, or Python) 2

All computers consist of 3 components Memory stores program and data (informa_on) Primary: RAM Secondary: hard drive Central Processing Unit (CPU) Control fetch next instruc_on, decode it, execute it

3 All computers consist of 3 components Memory stores program and data (informa_on) Primary: RAM Secondary: hard drive Central Processing Unit (CPU) Control fetch next instruc_on, decode it, execute it ArithmeOc Logic Unit perform simple opera_ons on data (add, compare two for equality, etc.) Input/Output Detour: Specs for a computer Ads for computers typically give: Speed of the CPU (in GHz, say ; recent past in MHz, where 1,000 MHz = 1.0 GHz) Amount of RAM in MB Size of hard drive in GB Which fancy I/O devices (e.g., DVD burner?) Interes_ngly, perceived speed today oden depends mainly on amount of RAM. Moore s Law Heading to Python Programs? Gordon Moore, one of the founders of Intel, made the claim that (essen_ally) computer power doubles for the same dollar every 18 months. This has held true for over 30 years. (Note: some think the end is finally near.) Go ahead! Make your computer do the same thing to all 2.9 billion base pairs of your DNA! It doesn t care! And it won t take much _me either! 2 eggs 1 c milk 1 c sided flour ½ t vanilla extract 12 oz. farmer's cheese 4 oz. cream cheese, sodened ⅓ c sugar 1 t lemon juice 1 t vanilla extract 1 egg yolk Bauer: Combine eggs, milk, salt and vanilla and blend well. Gradually add flour. Beat well. Filling: Combine cheeses, sugar, juice, vanilla and egg yolk in a bowl and mix together un_l smooth. Repeat un_l all the bauer is used: Put a ladleful of bauer into heated greased skillet. Tilt pan to swirl the bauer so it covers the bouom of the skillet. Fry on one side un_l bubbles form, the top is set, and bouom is golden brown. Carefully loosen edges of the crepe and slip it out of the skillet onto a plate. Fill each fried crepe: Place 1 tablespoon of filling on one edge. Roll once to cover filling. Fold sides into the center and con_nue rolling un_l completely closed. Ader all are assembled, heat 2 tablespoons of buuer in the skillet and place each crepe, seam side down, in the skillet and fry 2 minutes on each side, turning once. 3

8/26/16 Features of recipe How do you put a giraﬀe into a fridge?

Some_mes, a repe on of a part Assumed knowledge about context An expected result (yum!) 25 Why use computers for biology?

detailed informa_on is available diﬀerent ques_ons can be asked (models of evolu_on) => requires new math Computer science

4 8/26/16 Features of recipe How do you put a giraﬀe into a fridge? Fixed vocab of words, abbrevia_ons, symbols Syntax: Rules about what can be said & where Sequence of opera_ons to be done in order Some_mes, a repe on of a part Assumed knowledge about context An expected result (yum!) 25 Why use computers for biology? Biology perspecove More and more biological informa_on is available => need for eﬀec_vely accessing and using the informa_on As more detailed informa_on is available diﬀerent ques_ons can be asked (models of evolu_on) => requires new math Computer science perspecove Excellent applica_on domain Poses special computa_onal challenges Brings computer science closer to scien_ﬁc discovery Currently growing (computa_onal biology, bioinforma_cs, computa_onal ecology, medicine 4

VARIABLES STRINGS Theresa McCracken @McHumor.

com/1513/ Introduc_ons: Python Richer syntax allows greater

def alifesim(numgens,popsize,numtoselect,network,inhibitorl): """Do an

$"" fitd={} # get ini_al pop and create popl of (fitness,org) tuples$ = org.getfitness() popl.

numtoselect) # get top orgs for i in range(numgens): popl=[] for j in

replicate() # get fitness if hash(neworg) in fitd:

5 VARIABLES STRINGS Theresa Randall Munroe, XKCD xkcd.com/1513/ Introduc_ons: Python Richer syntax allows greater expressiveness! def alifesim(numgens,popsize,numtoselect,network,inhibitorl): """Do an ar_ficial life simula_on for numgens genera_ons with popsize organisms."" fitd={} # get ini_al pop and create popl of (fitness,org) tuples popl=[] for org in createini_alpop(popsize,network,inhibitorl): fitness = org.getfitness() popl.append((fitness,org)) fitd[hash(org)]=fitness topl = gettoporgs(popl, numtoselect) # get top orgs for i in range(numgens): popl=[] for j in range(popsize): toreplicate=random.choice(topl) neworg = toreplicate[1].replicate() # get fitness if hash(neworg) in fitd: fitness=fitd[hash(neworg)] else: fitness=neworg.getfitness() fitd[hash(neworg)]=fitness popl.append((fitness,neworg)) topl = gettoporgs(popl, numtoselect) print "gen:",i,":",topl[0] if i%50==0: fitd.clear() return topl[0] Learning to program is a bit like learning a foreign language! 31 5

8/26/16 Ader all, there are thousands of

Hello World Rela_vely nice syntax Emerging as

graphics, audio, scien_ﬁc compu_ng, Python:

$Java: class HelloWorld { sta_c public void main($ println( "Hello World!

6 8/26/16 Ader all, there are thousands of languages to choose from! Why? Hello World Rela_vely nice syntax Emerging as language of choice in many ﬁelds Packages for graphics, audio, scien_ﬁc compu_ng, Python: print Hello World! Java: class HelloWorld { sta_c public void main( String args[] ) { System.out.println( "Hello World!" ); } } C++: #include <iostream.h> main() { cout << "Hello World!" << endl; return 0; } Ook: Befunge: Image: University of Florida Python Demo 34 6

Genome Sizes Carsonella ruddii, 160,000 base pairs (bp) porcine (pig) circovirus 1.7Kbp, ssdna cowpea mosaic virus, 9.

Largest genome: (A) Human, (B) Fish, (C) Amoeba, (D) Flowering plant, (E) Don t know 4Kbp, ssrna phi29 (Bacillus phage) 19Kbp, dsdna Paris

Write first programs (first assignment yippee!) Read the textbook: 0.1-0.8 Post something on PIazza 39 7

7 Genome Sizes Carsonella ruddii, 160,000 base pairs (bp) porcine (pig) circovirus 1.7Kbp, ssdna cowpea mosaic virus, 9.4Kbp, ssrna phi29 (Bacillus phage) 19Kbp, dsdna humans? Genome Sizes Carsonella ruddii, 160,000 base pairs (bp) porcine (pig) circovirus 1.7Kbp, ssdna cowpea mosaic virus, 9.4Kbp, ssrna phi29 (Bacillus phage) 19Kbp, dsdna humans? Largest genome: (A) Human, (B) Fish, (C) Amoeba, (D) Flowering plant, (E) Don t know Genome Sizes Carsonella ruddii, 160,000 base pairs (bp) porcine (pig) circovirus 1.7Kbp, ssdna cowpea mosaic virus, 9.4Kbp, ssrna phi29 (Bacillus phage) 19Kbp, dsdna Paris japonica, 150Gbp Protopterus aethiopicus, 130Gbp Amoeba dubia, 670Gbp Come to the lab: Install Python+VC Learn to use it For next class Write first programs (first assignment yippee!) Read the textbook: Post something on PIazza 39 7

Chapter 1: Introduction to Computer Science and Media Computation

Chapter 1: Introduction to Computer Science and Media Computation Story What is computer science about? What computers really understand, and where Programming Languages fit in Media Computation: Why digitize