Computational Biology
Dr. Jens Allmer
Week 1
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)
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
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
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)
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
[email protected]– 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 [email protected]
Grading
• All information available on class website
• Grading individualized– Quizzes 15%– Mind Maps 10%– Project (inc. Presentation) 25%– Midterm1 25%– Midterm2 25%
Website
• http://mbg404.allmer.de
• Lecture Notes• Slides• Additional materials and challenges• Quizzes
• Grades• Attendance
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
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
Course Structure
• Lecture– 45 min lecture– 05 min mind mapping– 10 min break
• Practice– 45 min practice– 15 min break
• Repeat until 4h
BREAK?
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
An Example Mind Map for MicroRNAs
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
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
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
A More Elaborate Mind Map
Source: http://www.mindtools.com/pages/article/newISS_01.htm
What is a computer? What is a program?
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?
What is a computer?
The Basics
Input of data Processing of data
Storage of data Output of data
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
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?
Operating Systems
What an operating system does:
Applications“Programs”You
YourComputer’sHardware
Operating System
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
OpenOfficeWriter
Save
Save
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
MicrosoftOffice
ProgramFiles
Terminology
• Program• Application• Software• Operating System
Programs in Biology
• Sequence Alignment– BLAST– FASTA– CUSTALW– TEACOFFEE– ...
• MS/MS Proteomics– MASCOT– OMSSA– Sequest– PEAKS– ...
• Other more Targeted Purposes– Too many to list
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)
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
RapidMiner || Orange
• Datamining
• Data visualization
• Data analysis
• Machine Learing
Microsoft Access or Open Office Base
• Databases
• Store and manipulate large amount of data
• Organize and relate data
• Create reports
BREAK?
Console Programs
• Input– Typing (responding to questions)– Files– Parameters
• Control– Switches– Parameters– INI files
• Output– Echoed to screen– Files– Redirection
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
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
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)
Console Familiarity
Dr. Jens Allmer
Practice Slides 1
Bring up Console
• Start – Run ‘cmd’ – OK
• Start – Programs – Accessories – Command Prompt
Console Commands
• X: + Enter– Changes to the specified drive
• cd path .. || \ || ../ || ..\ – 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
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
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
Playtime
• Create a new directory
• Delete the newly created directory
Console Commands
• fc || comp– What does it do?– How can you use it?
• find– How does it work?– How can you control it?