1. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu How to Write a Program Yannick Pouliot, PhD Bioresearch Informationist lanebioresearch@stanford.edu © 2009 The Board of Trustees of The Leland Stanford Junior University

2. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 2 The Bioresearch Informationist: At Your Service Yannick Pouliot, PhD, Lane Medical Library & Knowledge Management Center Bioresearch Informationist ≈ computational biologist in residence Role: Support laboratory researchers regarding biocomputational resources and their use …especially postdocs Contact: lanebioresearch@stanford.edulanebioresearch@stanford.edu

3. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 3 Objectives Understanding the thinking process behind writing a program.

4. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Check Point Q: Do you have Perl installed? 4

5. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu So What’s Needed for Writing a Program? Need knowledge of: 1. Language instructions (FOR loop, CASE, IF, etc) 2. Syntax: correctly invoking instructions Having a (very) clear strategy  Programming is giving instructions to an idiot savant Must be complete Must work in every aspect  We’ll use a simple method can greatly facilitate the process and increase quality of your work 5

6. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Our Example: Writing a Program that Prints “Hello World” Applying “Ten Steps to Write a Program Without Tears” to print text 6

7. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Step 1: Start With The End: What is the Outcome? Visualize what the end result of your program will be  Be highly specific, e.g. Silly: print “hello” whenever the program runs Real: calculate the average frequency of CpG islands in human genes known to code for interleukins  Definition of interleukin  protein exists?  Everywhere in the genome?  What about pseudogenes? Do they count? Useful to create flowchart diagram of process 7

8. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Flowcharting to Understand the Process Lots of tools, some free  I use MS Visio (Win only)MS Visio 8

9. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Step 3: Breakdown Tasks into Chunks ( = “Subroutines”) For us, we want to print a single word: “hello”  Chunk = print whatever word is requested Use individual subroutines to handle chunks Subroutines used whenever a complex and/or repetitive step is involved Why? Because subs simplify writing and reading of code because they subsume set of instructions under a human- understandable sentence, e.g.  “PrintText()”  “QueryDB()” 9

10. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Step 6: How is Our Data Stored? 10 We’ll store text to be printed in a string variable Q: what should it be called? $TextToPrint = ‘Hello World’; @HumanGeneList = (‘Gene1’,’Gene2’,’Gene3’,’Gene4’);

11. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Putting it Practice 11

12. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Step 7: Update Generic Program to Put Everything Together 1. Download and save “GenericProgram.pl” under a new name, e.g., “printtext.pl” 2. Open in vanilla flavor text editor (NOT MS Word) 1. Windows: Use NotePad 2. Mac: Use Applications/TextEdit  Use Format/Make Plain Text to ensure … plain text 3. Save file If Mac user, remove first line of text (“#!c:/…”) 12

13. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Updating printtext.pl 13 PrintText printtext.pl

14. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu Run The Program Type perl –f “printtext.pl” 14

15. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu In Summary… Think in great detail about what the outcome looks like Think in terms of chunks Think about your variables (“data structures”) 15

16. Lane Medical Library & Knowledge Management Center http://lane.stanford.edu 16