Solving biological problems with MATLAB Lecturer: Chen Keasar, e-mail: chen@cs.bgu.ac.il

1. Solving biological problems with MATLAB Lecturer: Chen Keasar, e-mail: chen@cs.bgu.ac.il 08-6477875 Office hours: 37/102 Sunday, 14:00-16:00 Tutors: Mor Ben-Tov (Life Sciences) E-mail: morbentov@gmail.com Office hours: 40/310 Wednesday 15:00-16:00 Yonatan Natan (Sde-Boker) E-mail: flyingjony@gmail.com Office hours: Sunday 15:00-16:00 • Web page URL: http://lhttp://moodle.bgu.ac.il/moodle/

2. What will you learn in the course? • Algorithms • Building blocks for writing a MATLAB program • Using MATLAB for mathematical applications • Handling graphics in MATLAB

3. The rules of this course • No formal pre-requisite • Math course ( מתמטיקה של מערכות or equivalent) is assumed • lecture notes on web - print and bring • Tutorials – central role in the course • Start in class, complete at home, submit every week (through the web site) • Each student submits own independent work • The use of the Forum of course is allowed, but no code • Missing tutorials (e.g., Miluim), can be exempt but it’s your interest to submit even if later3

4. The rules of the game (cont.) • • Students from SedeBoqer campus will have tutorial there • • The tutors will instruct you exactly how tom submit tutorial – MUST follow instructions • • Tutorials not submitted accordingly – will not be accepted ! • Final project – selected from a list - or request your own project (no tater than week 5 of the semenster). • • After project submission – an oral exam in front of computer on the project • • Final grade – 35% tutorials, 65% final exam

5. What do I do with MATLAB?

6. CLUSTERING

21. Generation of energy function

26. What is MATLAB • MATLAB is a language • MATLAB is an interpreter • MATLAB is an integrated environment • MATLAB is a product of MathWorks

27. What is MATLAB • MATLAB is a language • popSize=23 • is a statement in this language. • It means: • 1. Allocate some space in the computer memory. • 2. Tag this space “popSize”. • 3. Store the number 23 in that space. • MATLAB is an interpreter • MATLAB is an integrated environment

28. What is MATLAB • MATLAB is a language • popSize=23 • MATLAB is an interpreter • A program that: • 1. reads MATLAB statements • 2. Translates them to machine language • 3. Executes them. • MATLAB is an integrated environment

29. What is MATLAB • MATLAB is a language • popSize=23 • MATLAB is an interpreter (command window) • >> • popSize = • 23 • MATLAB is an integrated environment popSize=23

30. What is MATLAB • MATLAB is a language • popSize=23 • MATLAB is an interpreter (command window) • MATLAB is an integrated environment

31. What is MATLAB • MATLAB is an integrated environment

32. Programming with MATLAB Basic components in computer program takes input -> operates on it -> gets output Various Input/Output methods – later simplest input: Allocating a value to a variable, e.g.,: a=2 popSize=23

33. Variable Names • Variables start with a letter • Can continue with more letters, digits etc. • Not longer than 31 characters • Make names easy to remember • make sure no typos • MATLAB is case sensitive • popSizeis different from PopSizeor popSize1

34. Non-recommended variable names a b1 gc initialpopulationsize

35. Functions extend the language Specific Syntax: functionoutput=functionName(input) …. the function itself … end Words of MATLAB language

36. functionoutput=functionName(input) …. the function itself … end Any word you want. Becomes a new word in the language

37. functionoutput=functionName(input) …. the function itself … end Any word you want. Known only within the function

38. functionoutput=functionName(input) …. the function itself … end MATLAB code (may include function calls)

39. Our first function Motivation: populations parthenogenetic aphids

40. Our first function functionpopSize2 = popDynam(popSize1) birthRate = 0.2 deathRate = 0.1 birth = popSize1 * birthRate death = popSize1 * deathRate change = birth - death popSize2 = popSize1 + change end We will save it in a file popDynam.m

42. What had happened? The MATLAB interpreter replaced popSize1 by 23 and executed the lines one by one. functionpopSize2 = popDynam(popSize1) birthRate = 0.2 deathRate = 0.1 birth = popSize1* birthRate death = popSize1* deathRate change = birth - death popSize2 = popSize1 + change end 23 23 23 23

43. This is a bit too verbose

44. Our first function (fixed) function popSize2 = popDynam(popSize1) birthRate = 0.2; deathRate = 0.1; birth = popSize1 * birthRate; death = popSize1 * deathRate; change = birth – death; popSize2 = popSize1 + change; end Is this the shortest way I could write the function?

48. The function’s value may be assigned to a variable (actually it is always assigned)

49. Variables defined in the command window are kept in memory.

50. You can see them all in the “Workspace” window