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• Technical and Specialized Skills
  * Remote login, file transfer, etc.: [[Secure Shell|SSH]] (+scp), [[Rsync (command)|rsync]], FTP * [http://www.sagemath.org/ Sage] (System for Algebra and Geometry Experimentation)
  6 KB (773 words) - 11:35, 5 February 2020
• Bash
  ...xt output. Because of the nature of Linux, some functions of the operating system have to be implemented as shell builtins. The most notable example is cd, w |'''$ ~2T''' || All Present Users on system from "<tt>/etc/passwd</tt>"
  34 KB (5,354 words) - 19:04, 9 May 2023
• Shebang
  ...]) causing Unix-like operating systems to execute the commands in the text file using a specified interpreter (program) when executed. ...require an interpreter program start with other magic combinations. (See [[File format]] for more details of magic numbers.)
  5 KB (755 words) - 23:20, 25 May 2006
• GeSHi/Java
  System.out.println("\tUnrecognized command " + line); else System.out.println("\tUnrecognized command " + line);
  6 KB (738 words) - 17:32, 17 December 2005
• Database Systems (academic course)
  ...ctured and stored asking for more powerful tools than the use of files and file systems. On the other hand database systems offer basic mechanisms to struc Several exercises using different database system are given during the course period.
  2 KB (273 words) - 23:35, 25 May 2006
• Bayesian Phylogenetic Analysis
  The [[NEXUS file format|NEXUS files needed]] in this tutorial are the following: ...where you can enter commands. The next set of commands will load the data file, specify <tt>outgroup</tt>, request that the program should not prompt you
  28 KB (4,371 words) - 03:28, 14 April 2008
• NJplot
  ...Perriere1996">Perrière G, Gouy M (1996). "WWW-Query: An on-line retrieval system for biological sequence banks". ''Biochimie'' '''78''':364-369. {{doi|10.10 ''note: taken from the <tt>njplot.help</tt> file.''
  4 KB (587 words) - 02:42, 13 July 2012
• LaTeX
  .../sub>X''', written as '''LaTeX''' in plain text, is a document preparation system for the [[TeX]] typesetting program. \usepackage{epsfig} % place at top of .tex file
  13 KB (1,882 words) - 01:17, 24 June 2008
• AWS/DevOps
  ...mate maintenance activities without having to manage a separate scheduling system. With regard to information security, events can provide notifications of c ...cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -c file:cloudwatchconfig.cfg -s
  28 KB (3,792 words) - 17:56, 26 February 2021
• Linux
  '''Linux''' is a computer operating system and its kernel. It is one of the most prominent examples of free software a The kernel is the core piece of the Linux operating system.
  7 KB (1,028 words) - 20:06, 24 October 2014
• Python
  ...&mdash; a Python library for symbolic mathematics (aka a computer algebra system (CAS)) ...org/ PyMedia] &mdash; module for wav, mp3, ogg, avi, divx, dvd, cdda, etc. file manipulations.
  11 KB (1,639 words) - 21:59, 9 September 2022
• MySQL
  ...ithreaded, multi-user, SQL (Structured Query Language) Database Management System (DBMS). $ file $(which mysql_secure_installation)
  15 KB (2,259 words) - 00:21, 10 February 2021
• CHARMm
  ...ual name of the program (or script which runs the program) on the computer system being used. ; <tt>filename.inp</tt> : A text file which contains the CHARMM commands. It starts by loading the molecular topo
  4 KB (546 words) - 00:49, 3 April 2009
• Agrep
  ...ommand Line Tools|command line tool]] for use with the [[Linux]] operating system. ...ken directly from the agrep [ftp://ftp.cs.arizona.edu/agrep/README README] file.''
  13 KB (1,944 words) - 06:33, 20 April 2012
• Sudo
  ...to run programs in the guise of another user (normally in the guise of the system's [[superuser]]). It is currently maintained by Todd C. Miller. ...risk of any unattended terminals. Once authentication has taken place, the system updates a [[timestamp]] and the user may then use <code>sudo</code> without
  3 KB (472 words) - 02:01, 26 April 2007
• Miscellaneous commands
  ...[[ISO Images|ISO]] files in Linux. Linux users can easily convert the NRG file using the [[dd]] command in the following way: ==Selecting random lines from a file==
  20 KB (3,106 words) - 23:38, 10 September 2021
• Sed/scripts
  == File spacing == * double space a file
  30 KB (4,929 words) - 22:47, 21 August 2019
• Coreutils
  ; Formatting file contents : <code>fmt pr fold</code> ; Special file types : <code>ln mkdir rmdir mkfifo mknod</code>
  9 KB (1,324 words) - 23:35, 6 February 2013
• Named pipe
  ...longer being used. Processes generally attach to the named pipe (usually a file) to perform inter-process communication. cat file > pipe
  1 KB (218 words) - 06:54, 19 August 2006
• PyMOL
  '''PyMOL''' is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC *[[Protein Data Bank (file format)]]
  1 KB (158 words) - 04:18, 24 April 2007
• Netpbm program directory
  ;jpegtopnm : convert JFIF/JPEG/EXIF file to Netpbm format ;bmptopnm : convert Windows or OS/2 Bitmap file to PPM or PGM
  17 KB (2,636 words) - 06:49, 1 September 2006
• LAMP on Mandriva
  ...that you do '''not''' set your MySQL root password to be the same as your system root password!''). ...de> file has been removed, this is now set in the <code>/etc/my.cnf</code> file.
  7 KB (1,074 words) - 01:52, 3 May 2007
• Expect (command)
  # Exit the telnet session, and wait for a special end-of-file character. # Exit the ftp session, and wait for a special end-of-file character.
  7 KB (1,064 words) - 03:05, 13 April 2008
• Secure Shell
  * Step 3: Set directory/file permissions (if not already set): ...r remote server without entering a password. This is useful for automating file transfers. However, it ''must'' be used with care. If not executed properly
  10 KB (1,480 words) - 18:24, 6 February 2024
• Urpmi
  urpmf <file> # Find package that contains a file urpmi --auto-select # Update your system
  3 KB (499 words) - 05:50, 17 July 2009
• Linux directory structure
  ...system as they depend on whether certain subsystems, such as the X Window System, are installed. |Essential [[device file|'''dev'''ices]] (e.g., [[:/dev/null]])
  7 KB (974 words) - 20:12, 19 April 2022
• Shell colour codes
  ...de>.dir_colors</code> in your <code>$HOME</code> directory to override the system defaults. Below are the colour init strings for the basic file types. A colour init string consists of one or more of the following numeri
  1 KB (236 words) - 02:08, 9 October 2006
• Make
  ...make all the files and other tools involved in generating the final output file (or files). ...nk]] file and would only want the [[fasta]] sequence of the genome. If the file is named "foo.gbk", then one could use gmake to get the fasta sequence: exe
  6 KB (1,015 words) - 03:38, 1 October 2009
• TAB file format
  A '''tab file''' is file format proposed by Rasmus Wernersson for annotating biological sequences.<r ...st/bioperl/Bio/SeqIO/tab.pm Bio::SeqIO::tab]). It is a nearly raw sequence file input/output stream.
  11 KB (1,628 words) - 01:05, 13 July 2012
• PostScript
  ;pstops : shuffle pages in a PostScript file (see manpage for details) ...t.html ''First Guide to PostScript''] is an introduction to the PostScript system.
  3 KB (469 words) - 01:21, 8 February 2009
• Rdate
  ...and time from a host or hosts on the network and optionally set the local system time. ; -s : Set the local system time from the host; must be specified by root.
  783 bytes (126 words) - 02:08, 26 April 2007
• Findutils
  ...n with other programs to provide modular and powerful directory search and file locating capabilities to other commands. * <tt>updatedb</tt> - update a file name database
  10 KB (1,695 words) - 23:28, 21 May 2015
• Bioinformatics resource list
  ; R : A statistical computation and graphics system. (''License: GNU'') ; openbabel : A free, open-source version of the Babel chemistry file translation program. (''License: GPL'')
  13 KB (1,598 words) - 06:08, 20 May 2008
• Mt
  $ tar --index-file=foo.log -jcvf /dev/nst0 /data /home * Or, list files to exclude in a file (one filename per line):
  6 KB (1,008 words) - 08:58, 17 February 2016
• ISO Images
  This results in a file called <code>cd.iso</code> in folder <code>/tmp</code> which contains all t ...s-NT or Windows-95 machines). The <code>-r</code> is for the directory and file permissions, user/group IDs, etc.
  11 KB (1,842 words) - 14:44, 14 July 2014
• Ptx
  ...x Command Line Tools|command-line]] utility to produce a permuted index of file contents similar to a '''[[KWIC]]''' (keywords in their context). It is par -G, --traditional behave more like System V `ptx'
  15 KB (2,341 words) - 02:00, 26 April 2007
• Dbacl
  Suppose a file document.txt contains English text lines interspersed with noise lines. To ...and filled with appropriate sample emails. A [[Crontab (command)|crontab]] file can be used to learn the three categories once a day, e.g.
  7 KB (1,190 words) - 08:53, 22 February 2007
• Dd (command)
  ; '''if'''=''file'' : Input File: Read from ''file'' instead from [[Redirection (Linux)|standard input]]. ; '''of'''=''file'' : Output File: Write to ''file'' instead to standard output. See also the keyword '''notrunc'''.
  10 KB (1,656 words) - 01:46, 7 May 2018
• Shred
  ...o hide its contents, and optionally delete it. It overwrites the specified FILE(s) repeatedly, in order to make it harder for even very expensive hardware * <tt>shred [OPTIONS] FILE [...]</tt>
  4 KB (623 words) - 02:39, 13 February 2007
• Linux HDD
  ...machine, you must add the appropriate line to your <code>/etc/fstab</code> file. Something ''like'' the following should work for most uses: Then mount it using the information in your <code>/etc/fstab</code> file:
  7 KB (1,275 words) - 03:45, 1 December 2015
• Pax
  ...read and write file archives and copy directory hierarchies. A POSIX File System Archiver. It supports the two most common forms of standard Unix archive (b ...<code>a.pax</code> which are owned by root with group bin and preserve all file permissions:
  1 KB (251 words) - 04:20, 6 July 2012
• Update timezone files for earlier Daylight Savings Time
  ...load the [ftp://elsie.nci.nih.gov/pub/ patch from here]. You will need the file <code>tzdata2007c.tar.gz</code> (this may have changed since writing this). ...that tell us we have successfully updated our <code>/etc/localtime</code> file.
  5 KB (705 words) - 01:44, 14 May 2015
• Flash motherboard BIOS
  ...dos.org FreeDOS] as an example. FreeDOS is a free DOS-compatible operating system. ...ents in a human-readable format. This table contains a description of the system's hardware components, as well as other useful pieces of information such a
  3 KB (497 words) - 21:04, 11 March 2007
• Iftab
  '''iftab''' - static information about the network interfaces. The file <code>/etc/iftab</code> contains descriptive information about the various ...electors allow <tt>ifrename</tt> to identify each network interface on the system. If a network interface matches all descriptors of a mapping, <tt>ifrename<
  6 KB (856 words) - 17:23, 3 January 2014
• Crontab
  ...eads a series of commands from [[standard input]] and collects them into a file also known as a "crontab" which is later read and whose instructions are ca export EDITOR=vi # to specify a editor to open crontab file.
  8 KB (1,304 words) - 08:49, 18 September 2021
• Linux kernel
  The '''kernel''' is the core piece of the [[Linux]] operating system. * File management
  6 KB (897 words) - 10:20, 17 November 2014
• RPM Package Manager
  ...ly Red Hat Package Manager, abbreviated '''RPM''') is a package management system. NOTE: RPM file names normally have the following format:
  8 KB (1,064 words) - 22:36, 19 April 2023
• Recovery Is Possible
  ...the author takes time to compile and quickly test the build. The operating system's X11-capable version does not require X11 to be started at bootup, and can ...leted files, by ignoring the filesystem and checking disk blocks for known file types
  3 KB (481 words) - 05:17, 2 April 2007
• Fstab
  ...they are to be used or otherwise integrated into the overall system's file system. The following is an example of a fstab file on a Red Hat [[Linux]] system:
  6 KB (838 words) - 01:45, 3 April 2007
• Common Unix Printing System
  The '''Common Unix Printing System''' ('''CUPS''') is a modular printing system for Unix-like computer operating systems that allows a computer to act as a For example, a generic PPD file for all models of HP Color LaserJet contains:
  6 KB (795 words) - 22:59, 23 January 2008

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