G4120: Introduction to Computational Biology

Transcription

1 ICB Fall 2006 G4120: Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology Copyright 2006 Oliver Jovanovic, All Rights Reserved.

2 The Binary Language of Computers Computers are digital machines, which means their most basic level of function involves using discrete symbols from a finite set, most commonly on (1) or off (0). A signal that can carry one of two possible messages (0 or 1) is called a binary signal, or a bit. In 1936, Alan Turing proved that a finite state machine (FSM) moving up or down a tape of symbols, reading or writing one symbol at a time, could solve any computable problem, and serve as a universal machine. = Universal Turing Machine 0 or 1 = 1 bit 8 bits = 1 byte 1,024 bits = 1 kilobit 1,024 bytes (approximately 1 thousand bytes) = 1 kilobyte (K) 1,024 kilobytes (approximately 1 million bytes) = 1 megabyte (M) 1,024 megabytes (approximately 1 billion bytes) = 1 gigabyte (G) 1,024 gigabytes (approximately 1 trillion bytes) = 1 terabyte (T)

3 Architecture

4 Components Darwin The core open source Unix operating system, consisting of the Mach 3.0 kernel (protected memory, virtual memory, preemptive multitasking, symmetric multiprocessing), BSD 4.4 (free, stable, secure), I/O, file system. Quartz and Quartz Extreme Apple s 2D display layer, based on the PDF format, and capable of sophisticated transparency and antialiasing. OpenGL (Open Graphics Language) The industry standard application programming interface (API) created by SGI for 3D graphics display. QuickTime Multimedia layer and API for handling various graphic and video formats. Audio Sound and MIDI layer. Cocoa A sophisticated rapid API based on NeXT s OpenStep. Java A full version of Sun s Java 2 cross-platform API. Carbon An API and set of libraries which allow applications developed them to run under both OS 9 and OS X. Classic An environment that runs older OS 9 only applications (such as DNA Strider). Aqua The graphical user interface for OS X. AppleScript Provides easy but powerful system and application level scripting and automation.

5 The Internet Overview In 1981, there were 213 computers acting as Internet hosts, in 2005, there are over 350 million Internet hosts. Computational biology uses applications with Internet connectivity (EndNote, MacVector), Internet applications (DNA Artist), Web applications (BLAST, GenMark) and Web databases (GenBank, PubMed), among other Internet host resources.

6 Internet Protocols TCP/IP (Transmission Control Protocol/Internet Protocol) A multilayered protocol architecture that allows for the transmission of data over networks. Datagram Packets of data containing the IP addressing information needed to switch them from one network to another until they arrive at their final destination. TCP (Transmission Control Protocol) Provides reliable delivery of datagrams using connection oriented streaming with error detection and correction. UDP (User Datagram Protocol) Provides low overhead connectionless datagram delivery. DHCP (Dynamic Host Configuration Protocol) Automates the configuration of computers that use TCP/IP by automatically assigning Internet addressing information from a network DHCP server.

7 Internet Addressing IP Address (Internet Protocol Address) An IP address is a 32 bit number, written in the form of four decimal numbers in the range that are separated by dots (e.g ). Columbia University Medical Center (CUMC) IP addresses will always have the format x.x or x.x. Subnet Mask A subnet mask allows for defining a local network, called a subnet, within a larger network. CUMC subnet masks will always have the format Router A device that routes packets of data between networks. A router sits between your computer and local area network and the networks beyond it. CUMC router IP addresses will always have the format x.1 or x.1. DNS (Domain Name Server) These specialized servers automatically translate an easy to remember domain name (e.g. microbiology.columbia.edu) into the appropriate IP address (e.g ). CUMC DNS IP addresses are and Ethernet Address A unique 48 bit number, usually written in the form of 12 hexadecimal digits separated by colons in groups of two (e.g. 00:03:93:bc:3c:18), which is assigned to every piece of network hardware, including Ethernet cards and AirPort cards. It is also called a MAC (media access control) address. Search Domains This optional information is automatically appended to names you type in Internet applications. If you have defined a search domain of columbia.edu, typing www will take you to

8 File Transfer Protocols FTP (File Transfer Protocol) Allows you to transfer files to or from a remote machine running FTP. Recommend using Fetch or Safari. Fetch is available for free to students at: SFTP (Secure File Transfer) Allows you to securely transfer files with all data encrypted. Recommend Fugu, available free at: SMB (Server Message Block) Allows you to transfer files to or from a PC. WebDAV (Web-based Distributed Authoring and Versioning) Allows you to collaborate with others on remote editing of documents. Used by ical and iphoto. Macintosh File Structure Macintosh files can have an unusual structure, consisting of two pieces, a resource fork and a data fork. Most files have only a data fork, but those with both a resource and data fork may not transfer smoothly across other files systems (e.g., Windows, Linux). Thus, Macintosh files are often best transferred in a compressed format (e.g.,.sit,.gz or.zip) which converts them into a compressed data only file, and preserves their structure when they are again expanded on another Macintosh. Stuffit Expander is a utility that expands various compressed files. You can create a compressed.zip archive of any file or folder in OS X 10.4 by Control clicking on it and selecting Create Archive of... from the contextual menu that appears. A.zip archive can be uncompressed by double-clicking on it.

9 Telecommunications Protocols SMTP (Simple Mail Transfer Protocol) Used by . Recommend using Apple s Mail, which does a good job of preserving Macintosh file structure when sending attached files, without requiring an additional compression step. NNTP (Network News Transfer Protocol) The newsgroup protocol used by Usenet, a world-wide distributed discussion system organized into newsgroups (e.g., bionet.biology.computational, sci.bio.evolution or sci.med.informatics). Recommend using groups.google.com to search or browse Usenet. HTTP (HyperText Transfer Protocol) The protocol behind the World Wide Web. Recommend Apple s Safari or Mozilla s Firefox for browsing, for searching. URL (Uniform Resource Locator) Used to locate resources on the WWW: ftp://ftp.ncbi.nlm.nih.gov file://macintosh%20hd/documents/read%20me.pdf (a blank space is replaced by a %20 ) SSH (Secure Shell) Can use to securely login remotely, or securely forward outgoing . AppleTalk An older Apple networking protocol still often used for printing and filesharing. Bonjour An Apple protocol that allows software and networkable devices to automatically discover each other on all available networks (Internet, local Ethernet, local wireless network, AirPort card, etc.).

10 Telecommunications Applications Mail Apple s client, features sophisticated sorting and junk mail filtering capabilities, works with IMAP (Internet Message Access Protocol) or POP (Post Office Protocol) mail servers ~/Library/Mail stores most mail files ~/Library/Mail/LSMMap file stores junk mail training ~/Library/Mail/Mailboxes stores mail (can also drag self created folders from Mail to desktop to create backups) ~/Library/Preferences/com.apple.mail.plist stores mail preferences View > Message > Long Headers to check the origin of suspicious View > Message > Raw Source to check the content and links of suspicious View > Bcc Address Field to send blind carbon copies Mark junk mail as such, and correct mistakes to improve the accuracy of the junk mail filter, then set Mail > Preferences > Junk Mail to Automatic to automatically sort it out Address Book Stores contact information, linked to Mail To quickly create groups, select members by Command clicking, then select New Group From Selection command in File menu Can bring up maps from the home or work labels Can import from Palm by selecting all contacts, dragging to temporary folder on desktop, then dragging all from folder into Address Book Backup by backing up entire Address Book application (File > Back up Address Book...) ichat Chat, audio chat, video chat, file transfer, chat rooms Internet Connect Virtual Private Network/Point-to-Point Tunneling Protocol (VPN/PPTP) client

11 Web Browsing Safari Apple s web browser, meant to replace Internet Explorer, which is no longer being developed for the Macintosh. Another good alternative is Mozilla s Firefox. Command click on a link to open it in a new window (or tab) Has a tabbed browsing mode which can be activated from Safari > Preferences > Tabs Can select entire URL by clicking on its favorites icon (favicon.ico) Can drag a URL to the Desktop or folder to create an Internet Shortcut Has internal Shortcuts.html page inside Safari package (file:///applications/safari.app/contents/ Resources/Shortcuts.html) Command click on the title bar to see all pages visited in the current site Option click on the back or forward arrow to see URLs visited recently Control click (or hold click) on the back or forward arrow to see names of sites visited recently Command 1 to 9 is links 1 to 9 on Bookmarks Bar Can create a Bookmark Bar folder for web downloads (file:///pathname) Can search bookmarks (click book icon on left of Bookmark Bar, then Command F) View, Status Bar to see URLs (Command Backslash) Can open all bookmarks in a folder in the Bookmark Bar by Command clicking on it Command clicking on a link in the Bookmark Bar opens it in a new tab behind your current view Can activate a Debug menu in Safari which has many useful options (including letting Safari appear to be Internet Explorer) by typing the following commands in Terminal (after quitting Safari): defaults write com.apple.safari IncludeDebugMenu 1 exit

12 Useful Applications Dictionary Built in dictionary and thesaurus. Can activate by Command Control D (can hover and activate). Excel The spreadsheet standard. Capable of producing excellent graphs and charts with some effort. iphoto Can do limited file format conversion, can create libraries and custom albums useful for storing and organizing gel photos and other scientific data. Try to keep each library under 650 MB so you can easily back it up to a CD-R. imovie Useful for simple film editing, including time lapse photography, which can be useful for scientific presentations. More advanced users can upgrade to QuickTime Pro, or get Final Cut Express. ical Calendering application, allows for sharing of schedules using a WebDAV server. Use Option Return to create a line break in an entry. The Department of Microbiology has an ical at webcal://microbiology.columbia.edu/calendar/micro.ics and additional calendars for import (e.g. U.S. holidays) are available at Keynote and PowerPoint Apple s Keynote provides an easier to use alternative to the presentation standard, Microsoft s PowerPoint. Keynote has fewer features but far better graphics and templates. Word The standard for word processing. Works well with EndNote to manage references in publications. If you are doing a lot of text or sequence manipulation, an application such as TextWrangler or BBEdit is better.

13 Useful Utilities Disk Utility Can verify and repair permissions on your hard drive. Worth checking once a month Can verify your hard drive (and repair it if booted from another drive or CD). Check monthly Allows you to create disk images and encrypted disk images, which are virtual disks. It is one of the best ways to securely store or distribute Macintosh files To dismount a mounted disk image, click eject icon, or drag to trash (if refuses to eject, logout) Can copy CDs and DVDs, erase CD-RWs and DVD-RWs, and burn multisession CD-Rs (select Burn... from Images menu, click on triangle and select Leave disc appendable) Print Center and PDF Printing Add new printers here, and select default printers Any OS X application can print to PDF file format by selecting File > Print and clicking on Save As PDF... To reduce the size of an image-heavy PDF select Compress PDF instead Keychain Access Allows you to store and automatically access different passwords in a safe, encrypted file Preview Allows for image file viewing and conversion (Adobe Acrobat is also good for viewing PDFs) Calculator Has Convert menu for scientific conversions and Scientific Calculator mode. Grab Useful for doing screen captures (can also use Command-Shift-3 and Command-Shift-4)

14 References Introductory Books Take Control of Tiger by Adam Engst, et al. Mac OS X Tiger Pocket Guide by Chuck Toporek Mac OS X Tiger Timesaving Techniques by Larry Ullman & Mark Liyange