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					Computers & Internet

Operating Systems
• Windows • Unix • Linux

Directories and files
• Root – (e.g. c: or d: in windows)

directories D:\My Documents\articles root

Internet
Browsers: • Internet explorer (IE) • Mozilla

Online computations
• Submit a job and wait for the results

Download the executable
• An executable file (*.exe) – a file that executes commands • Several websites offer a program that can be downloaded and be run locally from your computer

Why run locally?
• Automatize (run 100 runs one after another) • Run large jobs (>100 sequences) – many websites do not allow this

Command-line programs
• Command line = DOS (in windows) • Startruncmd (enter)

Using DOS – basic commands
• c: , d: - to switch between drives • cd – change directory example: cd adi\data • Use tab to fill in the rest • cd .. – moves one directory up • cd\ - moves to the root directory (c: or d: )

Running a command-line program
• In DOS: Type the name of the executable followed by the arguments • Each program has its required arguments and format (read manual) • Example: clustalw.exe myfile.txt myfile.aln
executable Input file arguments Output file

Local path vs. full path

Local path: pdb1a6q.aln Full path: D:\My Documents\data and results\pp2c\msa\pdb1a6q.aln

Running a command-line
• If you’re not sure – best to work with full path!

Some tricks and tips
Right-click on the command window

Text files
• Most biological data is represented as a text file. • Thus, most data files you download should be viewed in Notepad.

Important Note
• There is a difference between the way newline (“enter”) is represented in Windows and UNIX • Therefore text files downloaded from UNIX may sometimes appear as one line (no “enters”) – esp. when viewing with Notepad • Opening with WORD will usually enable viewing the newlines.

Bioedit
• Useful tool for viewing sequences • http://www.mbio.ncsu.edu/BioEdit/p age2.html

ALGORITHMICS
• When building an algorithm, two main considerations:  Time  Memory (storage place)

Time Complexity
• The time, or number of steps it will take to perform a computation as a function of n (n can be – length of sequence, number of sequences, etc.) • Notation: O(log n) - logarithmic Very Good O(n) – linear Good O(nm) – polynomial Bad O(cn) – exponential Bad

Memory
• Make sure that during the computation we do not exceed the amount of storage available on harddisk.


				
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