1. Computational Biology Dr. Jens Allmer Lecture Slides Week 1 Week 1

2. Your Instructor (Me) Education –BSc: University of Münster –MSc: University of Münster –PhD: University of Münster Worked at –Izmir Institute of Technology (since Sept 2008) –Izmir University of Economics, Turkey (Feb 2007 – Aug 2008) –University of Muenster, Germany (Jan 2006 – Feb 2007) –University of Pennsylvania, USA (Jan 2004 – Dec 2005) –University of Jena, Germany (Nov 2002 – Dec 2003)

3. Course Rules Attendance –Is essential and will be monitored strictly –if( absence > 12h) NA; Make-up –No make-up for project –Quiz can only be taken for grade once It must be finished within 30 minutes after starting It can be retaken for practice –Midterm and Final need medical report

4. Course Rules Lecture starts on time –if late enter QUIETLY –if more then 5 min late DO NOT ENTER wait for break Breaks are 10 to 15 min max –if late after break enter QUIETLY –if more then 5 min late DO NOT ENTER wait for next break Early leave –Announce before course starts or in break In your own interest –Don’t come late you will have problems following the course –Don’t miss a class since you will have problems in the following weeks

5. Course Rules Quiz –Represents 10% of your overall grade –Can only be taken online –Can only be taken once for grading purposes (first try) –Must be finished and submitted within 30 min –Can be taken multiple times for study purposes You will only learn your overall score not the correct individal answers –Generally 10 questions (mostly multiple choice)

6. Course Rules Project (group of 3) –See website for a general description –Involves 5 deadlines (see calendar) –No extention –No make-up –No extras –Must be electronicly submitted to jensallmer.iyte@analysis.urkund.com jensallmer.iyte@analysis.urkund.com –Formats include: doc, ppt, odx (use template!) –Not allowed are formats that may not be edited by me and pdf, docx, and similar formats that are not widespread –Must be significantly different from other groups Otherwise all involved will obtain zero for that assignment –Additional files need to be send to mbg404@allmer.dembg404@allmer.de

7. Grading All information available on class website Grading individualized – Quizzes15% – Mind Maps10% –Project (inc. Presentation) 25% –Midterm125% –Midterm225%

8. Website http://mbg404.allmer.dehttp://mbg404.allmer.de Lecture Notes Slides Additional materials and challenges Quizzes Grades Attendance

9. Website To see your grades you need to login Some material may need login as well Currently –UserID = StudentID –Password = StudentID Change now –UserID = working email address –Password = whatever you will remember If you already have a login you can still use it

10. Course Times The course will take place every Tuesday (check website calendar or subscribe to it) –Start 13:30 lasting for 2-4 hours –Mixed lecture and practice Location –Computer lab Z10

11. Course Structure Lecture –45 min lecture –05 min mind mapping –10 min break Practice –45 min practice –15 min break Repeat until 4h

12. BREAK?

13. Mind Mapping Have you ever studied a subject or brainstormed an idea, only to find yourself with pages of information, but no clear view of how pieces fit together?  Mind mapping –Learn more effectively –Improves memorization –Enhances creativity –Speeds up analyses –Gives structure to complex ideas –Records information for future use Source: http://www.mindtools.com/pages/article/newISS_01.htm

14. An Example Mind Map for MicroRNAs

15. How to Mind Map 1.Identify the central topic write in center 2.Write major parts of the topic on lines in all directions 3.Repeat 2. with ever finer level of detail until satisfied Source: http://www.mindtools.com/pages/article/newISS_01.htm

16. Note Taking with Mind Maps Capture ideas organized into topics –What if the central topic which I chose is not the central topic? –Make a new mind map which captures the topic correctly Uses Cases –Note taking in class –Recapitulization after lecture –Analysis of a new topic –Structuring of any intended writing When –During acquisition of new knowledge (faster than writing) –For review 5m, 1h, 6h, 1d, 7d, 1m after note taking

17. Mind Mapping Tips 1.Use single words or very short phrases 2.Write clearly and readable 3.Use color! 4.Seperate ideas (color, lines, shading) 5.Draw symbols and images 6.Draw links among elements

18. A More Elaborate Mind Map Source: http://www.mindtools.com/pages/article/newISS_01.htm

19. What is a computer? What is a program?

20. Four operations computers perform: input of data processing of data output of data storage of data Computers do not rate data; they manipulate it Garbage in = garbage out A manipulator of data What is a Computer?

21. What is a computer? The Basics Input of dataProcessing of data Storage of data Output of data

22. Hardware: physical components of a computer; what you can touch and feel Software: instructions the hardware uses Some hardware includes software (drivers, firmware) Program: a set of instructions Operating system: a program that allows applications to communicate with the computer; the interface between the human and the computer Applications: program that runs cooperatively with an operating system. What we use to “compute” Terminology: The Basics

23. Operating Systems Interprets input from mouse and keyboard Creates the Graphical User Interface (GUI) Finds files and directories on the hard disk (HDD) Creates the monitor images Gives meanings to the buttons Knows where components are and sends information to the right place OS: software for your computer What is an Operating System?

24. Operating Systems What an operating system does: Applications “Programs” You Your Computer’s Hardware Operating System

25. Primary piece is called the kernel Buttons in applications are objects “I must know my part of the process” A program is a collection of pieces: How the OS Works Linux OpenOffice Writer Save

26. Typically stored in C:\Program Files An application is in pieces: kernel and supporting Microsoft Office: 8 applications, 3,286 files Loaded software: Installing Applications Microsoft Office Program Files

27. Terminology Program Application Software Operating System

28. Programs in Biology Sequence Alignment –BLAST –FASTA –CUSTALW –TEACOFFEE –... MS/MS Proteomics –MASCOT –OMSSA –Sequest –PEAKS –... Other more Targeted Purposes –Too many to list

29. Servers and Websites Example: NCBI Provide processing power (many computing nodes) Provide programs for you to use Provide GUI Is shared with other users (Queue)

30. Locally Run Programs Example: BLAST Only your PC computes Programs available on your computer (downloaded installed) Some with some without GUI Not shared Additional features may be activated different environment variables (e.g.: sequence db) may be used

31. RapidMiner || Orange Datamining Data visualization Data analysis Machine Learing

32. Microsoft Access or Open Office Base Databases Store and manipulate large amount of data Organize and relate data Create reports

33. BREAK?

34. Console Programs Input –Typing (responding to questions) –Files –Parameters Control –Switches –Parameters –INI files Output –Echoed to screen –Files –Redirection

35. Console Programs Program path/Program Title.Program Extention –C:\test.exe –C:/test.bat –C:\folder1\folder2\test.exe Giving information to the program –Any input on the command line follows the program –C:/test.bat input goes here –Input is separated by spaces –Input can consist of parameters switches and switches with parameter

36. Input / Control Parameters –Separated by spaces –Following the program name –C:\test.exe param1 param2 –May be anything –Can contain file paths C:\test.exe c:\input.txt –Paths with spaces need to be escaped C:\test.exe “c:\document and settings\input.txt” Some operating systems or programs want to receive switches before parameters are given

37. Control Switches –Separated by spaces –Often introduced with a prefix (/,-) –Example C:\test.exe /?(This could display help information) –/X –X (/?, -?, -h, -help) –Example C:\test.exe -s1 -s2 (test.exe should take s1 and s2 into account)

38. Console Familiarity Dr. Jens Allmer Practice Slides 1

39. Bring up Console Start – Run ‘cmd’ – OK Start – Programs – Accessories – Command Prompt

40. Console Commands X: + Enter –Changes to the specified drive cdpath.. || \ ||../ ||..\ –Changes the current directory copy from to –Copies a file to a different location –From may be a list of files concatenated by + –Copy f1+f2+f3 destination

41. Console Commands dir –Lists files and directories –Switches A[DHSRA-], B,C,D,L,N,O[N,E,S,E,D,G,-], P,Q,S,T[C,A,W],W,X,4 Playtime –Sort the directory listing by time latest one first

42. Console Commands md title –Creates a directory named ‘title’ del file_path –Deletes the file specified by the path deltree folder_path || rmdir folder_path –Deletes the directory specified in folder path

43. Playtime Create a new directory Delete the newly created directory

44. Console Commands fc || comp –What does it do? –How can you use it? find –How does it work? –How can you control it?