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

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.de

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?