G4120: Introduction to Computational Biology: G4120: Introduction to Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology Lecture 1 January 23, 2003 Copyright © 2003 Oliver Jovanovic, All Rights Reserved.


Growth of GenBank: Growth of GenBank


A History of Computing: A History of Computing 30,000 BC Tally systems Africa & Europe 8,500 BC Prime system Africa 1000 BC Abacus China & Babylon 1500 Mechanical calculator Leonardo da Vinci 1621 Slide rule William Oughtred 1642 Arithmetic Machine Blaise Pascal 1822 Difference Engine Charles Babbage 1830 Analytical Engine Charles Babbage 1831 Computer program Lady Ada Lovelace 1936 Z1 Computer Konrad Zuse 1936 Turing Machine Alan Turing 1938 Boolean Circuits Claude Shannon 1943 COLOSSUS Alan Turing 1945 von Neumann Machine John von Neumann 1946 ENIAC J. Presper Eckert & John W. Mauchly, University of Pennsylvania 1947 Transistor William Shockley, John Bardeen & Walter Brattain, Bell Laboratories 1951 UNIVAC Remington Rand Corporation 1953 IBM 701 EDPM IBM Corporation 1954 FORTRAN John Backus 1958 Integrated Circuit Jack Kilby & Robert Noyce, Texas Instruments 1964 Mouse & Graphical User Interface Douglas Engelbart, Stanford University


A History of Computing: A History of Computing 1969 ARPAnet UCLA, Stanford, UC Santa Barbara & University of Utah 1969 UNIX Ken Thompson & Dennis Ritchie, Bell Laboratories 1971 Email Roy Tomlinson, BBN 1972 Telnet Jon Postel, BBN 1973 C Dennis Ritchie & Brian Kernighan, Bell Laboratories 1973 Ethernet Robert Metcalfe, Harvard University/Xerox PARC 1973 FTP Alex McKenzie, BBN 1974 TCP Vint Cerf & Robert Kahn 1975 Microsoft Corporation Bill Gates & Paul Allen 1976 Apple Computer Steve Wozniak & Steve Jobs 1976 Apple I Apple Computer 1978 Usenet Tom Truscott, Jim Ellis & Steve Bellovin 1981 IBM PC IBM Corporation 1981 MS-DOS Microsoft Corporation 1982 TCP/IP ARPA 1983 Lisa Apple Computer 1984 DNS Jon Postel 1984 Macintosh Apple Computer 1985 Windows Microsoft Corporation 1986 NeXT Computer Steve Jobs 1987 Perl Larry Wall 1989 BSD NR1 University of California at Berkeley


A History of Computing: A History of Computing 1989 HTTP & HTML Tim Breners-Lee, CERN 1991 Linux Linus Torvald 1991 Python Guido van Rossum 1993 Mosaic Marc Andreessen 1994 Netscape Corporation Marc Andreessen & Jim Clarke 1999 G4 Apple Computer 2001 OS X Apple Computer


A History of Computational Biology: A History of Computational Biology 1869 DNA Johann Friedrich Miescher 1924 Chromosomal DNA Robert Feulgen 1928 Transforming principle Franklin Griffith 1936 Turing Machine Alan Turing 1944 DNA transformation Oswald Avery, Maclyn McCarty & Colin MacLeod 1948 Information Theory Claude Shannon 1949 Chargaff's Rule Erwin Chargaff 1951 Alpha-helix & beta-sheet Linus Pauling & Robert Corey 1952 Developmental gradients Alan Turing 1953 Double helix James Watson & Francis Crick 1955 Protein sequence Fred Sanger 1961 Codons Sidney Brenner & Francis Crick 1965 Atlas of Protein Sequences Margaret Dayhoff 1966 Genetic code Marshall Nirenberg, Robert Holley & Har Gobind Khorana 1970 Restriction enzyme Hamilton Smith, Johns Hopkins 1970 Needleman-Wunsch S. Needleman & C. Wunsch 1971 MEDLINE NIH/NLM 1973 Brookhaven Protein Data Bank Brookhaven National Laboratory 1972 Recombinant DNA Stanley Cohen & Herbert Boyer 1977 DNA Sequencing Allan Maxam & Walter Gilbert/Frederick Sanger 1977 Staden programs Roger Staden 1980 øX174 (5,386 bp)


A History of Computational Biology: A History of Computational Biology 1980 IntelliGenetics, Inc. 1981 Smith-Waterman Temple Smith & Michael Waterman 1981 Sequence motif Russell Doolittle 1982 GenBank LANL/EMBL/NCBI 1982 GCG University of Wisconsin 1983 Rapid similarity searches W.J. Wilbur and David Lipman 1985 FASTP David Lipman & William Pearson 1985 PCR Kary Mullis 1986 SWISS-PROT University of Geneva/EMBL 1988 NCBI NIH/NLM 1988 FASTA William Pearson & David Lipman 1988 DNA Strider Christian Marck 1988 EndNote Niles & Associates. 1989 Oxford Molecular Group, Ltd. 1990 BLAST Stephen Altschul & David Lipman, NCBI 1990 Human Genome Project NIH/DOE 1992 The Institute for Genomic Research Craig Venter 1994 DNA computer Leonard Adelman 1995 Haemophilus influenzae (1.8 Mb) / TIGR Mycoplasma genitalium (0.58 Mb) 1995 BioPerl Jong Park 1996 Saccharomyces cerevisiae (12.1 Mb)


A History of Computational Biology: A History of Computational Biology 1996 PROSITE Amos Bairoch 1997 PubMed NCBI 1997 Escherichia coli (4.7 Mb) 1998 Swiss Institute of Bioinformatics 1998 Celera, Inc. Craig Venter 1998 Caenorhabditis elegans (97 Mb) 2000 Drosophila melanogaster (180 Mb) Celera, Inc. 2001 Homo sapiens (2.9 Gb) Celera, Inc./Human Genome Project.


Evolution of Operating Systems: Evolution of Operating Systems UNIX Microsoft Apple


Macintosh OS X Frameworks: Macintosh OS X Frameworks


Macintosh OS X Startup: Macintosh OS X Startup Startup Sequence BootROM, Open Firmware, Startup Manager, BootX, Kernel extensions, System and kernel initialization, StartupItems, Log in Useful Startup Keys Hold X key at startup: boots into OS X (if set to boot from OS 9) Hold C key at startup: boots from CD drive (if a bootable CD is in it) Hold Option key at startup: boots into Startup Manager mode (can select OS) Hold Command and S keys at startup: boots into Single-user Mode Single-user Mode Can run file-system consistency check (fsck) UNIX utility by typing “fsck -y” and pressing Return. If it gives an OK message, all is well. If it gives a FILE SYSTEM WAS MODIFIED message, run fsck again until it gives an OK message. When done, type “reboot” and press Return to restart in normal mode. This works just as well, and is more convenient than running Apple’s Disk First Aid, which requires rebooting from a CD. Run fsck or Disk First Aid at least once a month, more often if you use your computer heavily.


The Macintosh OS X Finder: The Macintosh OS X Finder Finder Finder Preferences… in the Finder menu lets you alter the Finder’s behavior: recommend Always open folders in a new window, Always show file extensions Applications folder: install all applications here only – has Toolbar shortcut Home folder: save all other files here – has Toolbar shortcut (otherwise it is in the Users folder) Useful Finder Key Combinations Hold Option key while dragging a file to duplicate it Hold Command key while dragging a file to move it Hold Command and Option keys down while dragging a file to create an alias Hold Option while double clicking a folder to close the previous window when you open the new one Press Shift while clicking to select more than one item (in List view, press Command while clicking for discontinuous selection) Press Control while clicking to get a contextual menu Press Shift and Command and N to create a new folder Press Command and I with an item selected to Show Info Press Command and K to connect to a server Press Command and ? to get Mac Help, which has extensive documentation on OS X, your computer, and various applications. See the Shortcuts section in the List of Topics for other useful key combinations.


The Toolbar and Dock: The Toolbar and Dock Toolbar Red to close, Yellow to dock, Green to resize, Clear to hide/show Toolbar The Toolbar normally holds: Back/Forward, Views (Icon, List, Column), Shortcuts (Home, Applications, etc.), and Search Drag items to the Toolbar to add them (hold Command while dragging to rearrange or remove an item) Customize Toolbar… from the Finder View menu lets you freely rearrange and add special items to the Toolbar Dock Drag items on to add, off to remove, or left or right to rearrange Can add a folder or folders with aliases to your favorite applications Click and hold to get application options, or hierarchical submenus for a folder or hard drive item Press Command and click an item to open a window showing the item Press Command and Option and click an item to bring it forward and hide everything except it (click on an item in the dock to make it visible again, or select Show All from the Finder menu to make everything visible again) Click the Dock, press and hold Command, then press Tab to cycle through all open applications To hide the Dock, press Command and Option and D. Press the same keys to fully show it again To change the Dock, hold the mouse pointer over the separation line in the Dock, when it changes, click and drag to resize the Dock (down smaller, up larger), or hold the Control key and click while holding the pointer over the separation line to get various Dock preferences (can also select Dock from System Preferences)


System Preferences: System Preferences Setting System Preferences Use Show All to view all preference panes, or drag commonly used Preferences to top Dock: set Dock preferences General: recommend Font smoothing style Medium, can adjust interface appearance and behavior Energy Saver: lets you adjust when your computer goes to sleep (don’t need to turn it off) Mouse: allows you to adjust double click and tracking speed Internet: set Web defaults (can ignore Email, .Mac and iDisk) Network: set TCP/IP settings. Can create multiple settings for different locations from the popup Location menu (select New Location or Edit Locations) Sharing: turn various file sharing options on or off, activate/deactivate Firewall Software Update: check at least once a month for critical updates Classic: controls OS 9 emulation (Classic mode) Startup Disk: controls the system you will start up with (OS X or OS 9)


Email Preferences: Email Preferences Email Setup for Columbia University Accounts 1) Open Mail 2) Select Preferences from the Mail menu 3) Select Accounts, click Add Account 4) Select IMAP Account Type, enter Email Address and Full Name, Incoming Mail Server: imap.columbia.edu, Username: UNI only, Password: leave blank 5) Select Add Server from Outgoing Mail Server 6) Enter Outgoing Mail Server: send.columbia.edu, check Use Secure Sockets Layer (SSL), select Password Authentication, Username: UNI only, Password: leave blank 7) Click OK 8) Click on Advanced tab, check Use SSL, port should change to 993 9) Select Password Authentication and click OK. 10) Select Composing in Mail Preferences, click Configure LDAP… 11) Click Add 12) Enter Name: Columbia LDAP, Server: ldap.columbia.edu 13) Click Save 14) Click Close


Macintosh OS X Resources: Macintosh OS X Resources Recommended Books Mac OS X Unleashed, Second Edition by John Ray & William C. Ray Mac OS X: The Missing Manual, Second Edition by David Pogue Mac OS X Killer Tips by Scott Kelby Macintosh OS X troubleshooting and help sites http://www.apple.com http://www.macosxhints.com http://www.macfixit.com http://www.macosxfaq.com Macintosh OS X software and hardware sites http://www.versiontracker.com http://www.dealmac.com Macintosh OS X news sites http://www.macslash.com http://www.slashdot.com http://www.macintouch.com http://www.macminute.com


Assignments: Assignments 1) Software Update Run Software Update from System Preferences. Download and install any new updates that are available. 2) EndNote a) Download and install EndNote 6.01 for OS X from Columbia University: http://www.columbia.edu/acis/software/endnote/ b) Download and install the EndNote 6.02 update from Niles & Associates: http://www.endnote.com/support/EN602_Mac_updater.asp c) Run the updated EndNote, create a new EndNote library named ICB in the Documents folder of your Home folder, select New Reference from the Reference menu, then enter the following reference into the appropriate fields: Turing, A. M. 1936. On computable numbers, with an application to the Entscheidungsproblem. Proceedings of the London Mathematical Society. 42:230-265. d) Quit EndNote and email the database file as an email attachment to jovanovic@cancercenter.columbia.edu using Mail. 3) Backup Copy your Home folder onto a blank CD-R. Use the Mac Help function to learn how, if you’re unsure.