CSE 111 Bio: Program Design I Lecture 1: Introduction. Robert Sloan (CS) & Rachel Poretsky (Bio) University of Illinois, Chicago August 30, 2017

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1 CSE 111 Bio: Program Design I Lecture 1: Introduction Robert Sloan (CS) & Rachel Poretsky (Bio) University of Illinois, Chicago August 30, 2017

2 Randall Munroe, XKCD, FIRST: WHICH COMPUTER SCIENCE CLASS?

3 UIC CS Classes CS 100, Discovering Computer Science: CS for fun, no credit if in College of Engineering CS 111, Program Design I (This course!) Students with little to no programming experience who Are CS majors or minors, or CoE students planning to use CS , or any student wanting to learn more Now in three flavors! (This is the bio flavor) CS 141, Program Design II: If you already have programming experience

4 Two Versions of CS 111 this semester Green (Bio themed): 12:30-1:45pm, LC C3. Team taught by Profs. Robert Sloan (CS) and Rachel Poretsky (BioS) Traditional (media manipulation themed): 12:30-1:45pm, 250 BSB. CS Prof. Cynthia Taylor

5 What will everybody do in CS 111? Learn the basics of programming in Python Very popular programming language, commonly used Easy to read and understand More about Why Python soon And

6 One of (based on section) Use media computation Draw pictures, manipulate images, manipulate sound files Solve biological problems (learn some biology) e.g., DNA analysis, finding genes, cell function

7 What if I already have programming experience? CS 111 Proficiency Exam: ugrad@cs.uic.edu Write single, complete program (Online) Language should be C-derivative (Python, C, C++, Java, PHP, etc.) Should show you understand: Variables, loops, if statements, arrays (or perhaps lists if Python), function calls

8 NEXT: SOME BORING SYLLABUS STUFF

9 Instructors: Robert Sloan and Rachel Poretsky Sloan: UIC CS Prof. Current Research: (1) Computer security and privacy, especially public policy and legal issues; (2) CS education Poretsky: UIC BioS Prof. Research: Microbial ecology, i.e., the interactions, functions, and assembly of microorganisms (bacteria and archaea you ll hear more about this soon) in their environments (which range from humans to oceans to sewage and more).

10 Office Hours Sloan 1112 SEO Tue 2:30 4:00 And by appointment Poretsky SEL 4100 Thu 2:30 3:30 And by appointment

11 (Grad) TAs Zhu (Ellen) Wang and Mao Li Labs: Mon 12-12:50pm, 1-1:50pm, 2-2:50pm, 3-3:50pm Office hours: Ellen, Mon. 4:30 6:30; Mao Wed. 1 3 Piazza!

12 Undergrad TAs Joseph Torres Daisy Arellano Funmilola Akintoye Office hours to be announced in next 24 hours 12

13 Everything is on some website Blackboard: grades, assignments blackboard.uic.edu Course website: Syllabus, schedule, readings, lecture slides Piazza: Forum (more next slide)

14 Use Piazza instead of ing piazza.com/uic/fall2017/cs111green/home For public questions (lab and project questions) Your classmates benefit from your questions Your classmates can answer your questions We will check the forum frequently For personal questions (grades) Can ask questions to instructors only Means any of us (Profs & TAs) can answer your question All CS 111 communication is in one place

15 Clickers! Lets you vote on multiple choice questions in real time. Like pub trivia, except the subject is always CS 111 Register on Blackboard before next class!

16 This class uses Python Randall Munroe, XKCD 25

17 Course Textbooks

18 Sign in or create an account at learn.zybooks.com Enter zybook code UICCS111Fall2017 Subscribe A subscription is $38 and will last until Dec 29,

19 Good news: your biology textbook for this class is available for free online! If you prefer, you can also get a print version at a very low cost. 28

20 Optional book Computing for Biologists Python Programming and Principles Ran Libeskind-Hadas, Eliot Bush (Harvey Mudd College) Paperback ISBN:

21 Weekly Lab Assignments Give you a chance to practice what we re learning, with TAs to answer questions and help you out Short weekly lab assignment, put up Monday morning, work on it in lab Monday, due Wednesday by midnight. (Week 1 only: Thursday by midnight, to accommodate people switching classes) You should be able to complete most of it in lab Submit via Blackboard

22 Collaboration Policy Please do Post on the forum Talk with classmates about assignments Please don t Copy someone s code Show someone else your code Good rule of thumb: Wait half an hour after discussing, write code/do problem

23 Welcome to UIC CS CS Student Affairs Office (905 SEO) Visit with any questions. If they can t answer, they can tell you who can. Director of Undergraduate Studies Joe Hummel (908 SEO) Cody Cranch will be holding open undergraduate advising sessions, in CS lounge, during first two weeks of semester. Dates and times: Tues, Aug 29: 10-12p (already over) Wed, Aug 30: 12 2pm Thurs, Aug 31: 3 5pm Tues, Sept 5: 10 1pm Thurs, Sept 7: 4 7pm 39

24 Questions? All of this info on class website

25 Register for Piazza For Next Class Register your clicker on Blackboard Do posted reading in both Zybooks Python and Concepts in Biology! Optional but recommended: Install Python on your own computer (details on course website under Additional Materials and at end of lecture)

26 FINALLY: WHAT IS COMPUTER SCIENCE? Randall Munroe, XKCD,

27 What is computer science? Biology = study of living things Chemistry = study of structure and composition of matter What is computer science the study of? Computer Science ¹ study of computers! Computer Science is the study of: Processes» Algorithms» Programs» Recipes What is doable using computation and how

28 Some Pioneers 1967 Vision of CS The theory and design of computers, as well as the study of all the phenomena arising from them Allen Newell, Alan Perlis, Herb Simon, Science, 1967 Only really big difference today: Design of computers is its own field: Computer Engineering

29 CS s Disciplinary Roots today Natural! Sciences! Philosophy" Math" Operations" Research" Biology" Computational" Biology" Programming" Languages" Algorithms" Statistics" Machine" Learning" Natural" Language" Linguistics" Learning" Science" Human-" Computer" Interaction" Social! Sciences! Psychology" Computer" Systems" Computer" Eng." Engineering! Robotics" Biomed." Eng." Software" Engineering" Mechanical" Eng." Additional connections to Additional digital connections media, to law arts & entertainment, public policy, business, public business, policy, " the arts.

30 What about programming? Computer science ¹ programming! But scientists, lawyers, business executives, computer scientists, etc., all study writing to communicate for at least 13 years Programming is other main way computer scientists communicate; requires extensive study Computer scientist -> programmer Composer -> musician Almost all computer scientists spend some of their working time programming

31 If Computer Science is the study of computation, meaning Processes» Algorithms» Programs» Recipes Then the next question is:

32 What s computation good for Computer science is the study of recipes Computer scientists study How the recipes are written (algorithms, software engineering) The units used in the recipes (data structures, databases) What can recipes be written for (systems, intelligent systems, theory) How well the recipes work (human-computer interfaces)

33 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 particular phrase? Easy-peasy! (What the spring 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 computation course will do)

34 Key concept: The COMPUTER does the recipe! Make it as hard, tedious, complex as you want! Look through 100,000 documents in a lawsuit to pick out the 17 or the 42,000 containing a particular phrase? Easy-peasy! Crank through a million genomes? No problem! Find one person on UIC s 29,000 student campus? Yawn! Process a million dots on a screen or a bazillion sound samples? (What the media computation course will do)

35 Heading to Python Programs? 2 eggs 1 c milk 1 c sifted flour ½ t vanilla extract 12 oz. farmer's cheese 4 oz. cream cheese, softened ⅓ c sugar 1 t lemon juice 1 t vanilla extract 1 egg yolk Batter: 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 until smooth. Repeat until all the batter is used: Put a ladleful of batter into heated greased skillet. Tilt pan to swirl the batter so it covers the bottom of the skillet. Fry on one side until bubbles form, the top is set, and bottom 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 continue rolling until completely closed. After all are assembled, heat 2 tablespoons of butter in the skillet and place each crepe, seam side down, in the skillet and fry 2 minutes on each side, turning once.

36 Features of recipe Fixed vocab of words, abbreviations, symbols Syntax: Rules about what can be said & where Sequence of operations to be done in order Sometimes, a repetition of a part Assumed knowledge about context An expected result (yum!)

37 Additional feature of recipes And other common analogies, such as Knitting patterns for knitting Sheet music for playing music If you go to a great restaurant, one with a fancy table in the kitchen where you can watch the chefs all night long, and you go there twice a week for 15 weeks, then: You must make more money than professors! And You won t learn how to cook!

38 Why computer science + biology? Biology is the science that studies life. What exactly is life? This may sound like a silly question with an obvious answer, but it is not easy to define life (e.g., viruses). From its earliest beginnings, biology has wrestled with four questions: 1. What are the shared properties that make something alive? 2. How do those various living things function? 3. When faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better understand them? 4. How did this diversity arise and how is it continuing? Computer science helps biologists answer these questions 56

39 Why use computers for biology? Biology perspective More and more biological information is available => need for effectively accessing and using the information As more detailed information is available different questions can be asked (models of evolution) => requires new math Computer science perspective Excellent application domain Poses special computational challenges Brings computer science closer to scientific discovery Currently growing (computational biology, bioinformatics, computational ecology, medicine

40 Figure 1.19 The Human Genome Project was a 13-year collaborative effort among researchers working in several different fields of science. The project was completed in (credit: the U.S. Department of Energy Genome Programs) 58

41 INSTALLING PYTHON ON YOUR OWN COMPUTER 59

42 Getting Python 3: Anaconda We re using Python 3, specifically Anaconda distribution of Python 3.6. To get it: Go to Choose whichever of Mac or Windows you have (or Linux if applicable) Click the download button for the Graphical Installer for Python 3.6 version. (The Graphical Installer and the Command-Line installer install exactly the same thing, but the Graphical Installer is much easier to use.) Open the downloaded file, and click Agree/Continue to do the install 60

43 Using Python We strongly recommend using Spyder: Integrated Development Environment for Python, meaning it has both Place to write Python programs Place to run (or execute) Python programs Demo next. Directions also on class website under Additional Materials 61

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