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) • Startruncmd (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.