G4120: Introduction to Computational Biology

Transcription

1 ICB Fall 2003 G4120: Computational Biology Oliver Jovanovic, Ph.D. Columbia University Department of Microbiology Copyright 2003 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 1937, Alan Turing proved that a finite state machine 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. 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 v.3 kernel (protected memory, virtual memory, preemptive multitasking, symmetric multiprocessing), BSD 4.4 (free, stable, secure), 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 2003, there are over 170 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 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 ). Health Sciences 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. Health Sciences 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. Health Science 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. cancercenter.columbia.edu) into the appropriate IP address (e.g ). Health Sciences 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. 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 typing cumicro2 with a search domain of cpmc.columbia.edu also defined will take you to cumicro2.cpmc.columbia.edu.

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 Internet Explorer. Fetch is available for free to students at SFTP (Secure File Transfer) Allows you to securely transfer files with all data encrypted. Recommend using Fugu, available at for free to students. 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. These often do not transfer smoothly across other files systems (e.g., Windows, Linux). Thus, Macintosh files will often be transferred in a compressed format (e.g.,.sit,.gz or.zip) which converts them into a data only file, and preserves their structure when they are again expanded on another Macintosh. Stuffit Expander is a utility that expands compressed files.

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 Microsoft s Internet Explorer and Apple s Safari 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. Rendezvous 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 > Show All Headers to check the origin of suspicious Edit > Add Bcc Header 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 > 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 icons 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 ichat Chat, video chat, file transfer, chat rooms Internet Connect Virtual Private Network/Point-to-Point Tunneling Protocol client

11 Web Browsing Safari Apple s web browser, meant to replace Internet Explorer, which is no longer being developed for the Macintosh Command click on a link to open it in a new window 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) Has internal shortcuts.html page inside package Command click title bar to see all pages visited in the current site Option click back or forward arrow to see URLs visited recently Control click (or hold click) 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

12 Useful Applications 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. If you do this sort of work, you may want to upgrade to QuickTime Pro, or get Final Cut Express. itunes Manages a digital music collection. ical Calendering application, allows for sharing of schedules using a WebDAV server. Use Option Return to create a line break in an entry. Additional calenders for import (e.g. U.S. holidays) are available at 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 BBEdit or TextWrangler will work better. Excel The spreadsheet standard. Capable of producing excellent graphs and charts with some effort. PowerPoint The standard for doing presentations. Apple s Keynote provides an easier to use alternative, with fewer features, but better, although demanding, graphics.

13 Useful Utilities Disk Utility Can verify and repair permissions on your hard drive. Worth checking once a month Can erase CD-RWs and DVD-RWs Can verify and repair your hard drive if booted from the Mac OS X Install CD (or use fsck -y) Disk Copy 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, drag to trash to eject (if refuses to eject, logout) Can copy CDs and DVDs, erase CD-RWs and DVD-RWs, and burn multisession CD-ROMs (select Burn Image from File menu, Burn, click on triangle and select Allow additional burns) Print Center Add new printers here (any OS X application can print to PDF format by selecting File > Print and clicking on Save As PDF...) Keychain Access Allows you to store and automatically access different passwords in a safe, encrypted file. Preview Allows for some image file format conversion (Adobe Acrobat is better for viewing PDFs) Calculator Has Convert menu for scientific conversions. Grab Useful for doing screen captures (Snapz Pro X gives even more options)