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• DNA Microarray Analysis (academic course)/Dimension reduction
  ...tp://cran.r-project.org/doc/manuals/R-intro.pdf An Introduction to R] (PDF file). library(MASS) # function for writing to file is used
  6 KB (974 words) - 18:11, 27 March 2012
• GNU Privacy Guard
  ===Encrypt a file=== * Encrypt a file named <code>filename.txt</code> for a single individual (i.e., specify that
  3 KB (504 words) - 00:08, 25 August 2020
• AWS/DevOps
  ...cloudwatch-agent/bin/amazon-cloudwatch-agent-ctl -a fetch-config -m ec2 -c file:cloudwatchconfig.cfg -s * Amazon Elastic File System
  28 KB (3,792 words) - 17:56, 26 February 2021
• Linux
  * File management
  7 KB (1,028 words) - 20:06, 24 October 2014
• Python
  ...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
  $ file $(which mysql_secure_installation) ...n the <tt>/etc</tt> directory). You can also have your own personal config file by creating a <tt>~/.my.cnf</tt> in your home directory.
  15 KB (2,259 words) - 00:21, 10 February 2021
• FASTA format
  In [[:Category:Bioinformatics|bioinformatics]], '''FASTA format''' is a file format used to exchange information between genetic sequence databases. FASTA format files often have file extensions like .fa, .fasta, or .fsa.
  7 KB (982 words) - 23:02, 13 July 2012
• Formatdb
  ...ource for other formats such as the GenBank report. Once a source database file has been formatted by <tt>formatdb</tt> it is not needed by BLAST. Please n -t Title for database file [String]
  7 KB (1,145 words) - 01:29, 24 July 2008
• Blastall
  ...e to perform a <tt>blastn</tt> search (nucleotide ''vs.'' nucleotide) of a file called <code>QUERY</code> would be: The output is placed into the output file <code>out.QUERY</code> and the search is performed against the "<code>nr</c
  8 KB (1,298 words) - 00:45, 17 August 2007
• Abstracts
  ...t]], and the output is emailed back to the user in three files: one output file, and the two processed proteins. Besides the electrostatic and desolvation
  15 KB (2,140 words) - 00:25, 24 August 2007
• Skittles
  ...plotting with programs such as [[gnuplot]]. It generates a "SKTTLS Report" file. ...SKTOUT file is given, a copy of this SKTTLS report is also written to that file. Three residuals are calculated for each bond between protein or nucleic ac
  6 KB (965 words) - 20:57, 2 March 2015
• Linux 101
  |'''file''' ''filename'' || display file type of file with name ''filename''
  1 KB (180 words) - 05:21, 18 May 2007
• Jmol
  ...o longer supported by some browsers. It supports a wide range of molecular file formats.
  2 KB (306 words) - 01:09, 17 August 2007
• Comm (command)
  ...between the two files; lines are either shown in the "from file #1", "from file #2", or "in both" columns. This feature can be especially useful when you * The <tt>foo</tt> file has the following lines:
  1 KB (250 words) - 21:58, 25 May 2006
• CHARMm
  ; <tt>filename.inp</tt> : A text file which contains the CHARMM commands. It starts by loading the molecular topo ; <tt>filename.out</tt> : The log file for the CHARMM run, containing echoed commands, and various amounts of comm
  4 KB (546 words) - 00:49, 3 April 2009
• Curl
  ...cation (Basic, Digest, NTLM and Negotiate for HTTP and kerberos4 for FTP), file transfer resume, HTTP proxy tunnelling, and many other features. cURL is op The main purpose and use for cURL is to automate unattended file transfers or sequences of operations. It is for example a good tool for sim
  10 KB (1,538 words) - 04:37, 21 April 2023
• Agrep
  ...ken directly from the agrep [ftp://ftp.cs.arizona.edu/agrep/README README] file.'' ...e> (or in uncompressed form as <code>agrep/agrep-2.04.tar</code>). The tar file contains
  13 KB (1,944 words) - 06:33, 20 April 2012
• Wget
  * Download a file and store it locally using a different file name: * Resume large file download:
  5 KB (719 words) - 07:18, 13 September 2021
• Replace (command)
  replace from to [from to] ... -- file [file] ... replace from to [from to] ... < file
  2 KB (371 words) - 05:59, 8 February 2007
• FAST Alignment and Search Tool
  -o|--out fn output file name [stdout]
  1 KB (196 words) - 01:54, 10 February 2007
• Rsync
  ...rts of the source file which are identical to some part of the destination file, and only sends those parts which cannot be matched in this way. Effectivel *optionally preserves symbolic links, hard links, file ownership, permissions, devices and times
  13 KB (2,005 words) - 21:34, 11 July 2015
• Sudo
  ...y errors, in which case it will offer to reject the changes or re-edit the file.
  3 KB (472 words) - 02:01, 26 April 2007
• Sudosh
  ...line history then you can still find the commands called in the shell in a file such as <code>.sh_history</code> but if you use a shell such as [[C shell|c
  1 KB (254 words) - 02:03, 26 April 2007
• Visudo
  ...its the '''[[sudoers]]''' file in a safe fashion. The <code>sudoers</code> file (typically found at <code>/etc/sudoers</code>) allows listed users access t
  503 bytes (79 words) - 02:04, 26 April 2007
• Sudoers
  '''sudoers''' is a [[:Category:Linux Files|file]] (typically located at <code>/etc/sudoers</code>) containing a list of whi The <code>sudoers</code> file is composed of two types of entries: aliases (basically variables) and user
  2 KB (352 words) - 11:29, 7 July 2014
• GnuPlot
  ===Running from a file of commands=== ...en a third shell running ghostview to view the eps file. To load a command file:
  15 KB (2,365 words) - 07:16, 20 April 2012
• Sed
  ...h one to the whole text file in memory, sed iterates once through the text file applying the whole list of edit commands to each line. Because only one lin ...and then be applied using the ''-f'' option to read the commands from the file:
  11 KB (1,730 words) - 00:56, 18 May 2015
• Chcase
  ...recursing, change files matching this mask to all upper case, overwrite if file exists:
  2 KB (329 words) - 00:47, 14 December 2012
• 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
• Fdupes
  ...n. That is, it ignores filenames and locations; if the ''contents'' of the file are identical, it will find these files to be identical. It was written by ; <tt>-f --omitfirst</tt> : omit the first file in each set of matches
  3 KB (442 words) - 01:43, 26 April 2007
• FastContact
  ...at, and the output is e-mailed back to the user in three files: One output file, and the two processed proteins. Besides the electrostatic and desolvation ...to 1500. The email address is where the output/results will be sent (as a file attachment). Hydrogen bonds and missing atoms are built and optimized on th
  13 KB (1,540 words) - 18:05, 18 February 2012
• Dr. Rasmus Nielsen Laboratory/Notes
  ** [[NEXUS file format]]
  3 KB (524 words) - 00:48, 26 July 2006
• Robots Exclusion Standard
  ...rmation specifying the parts that should not be accessed is specified in a file called '''robots.txt''' in the top-level directory of the website.
  4 KB (662 words) - 23:40, 30 May 2012
• .htaccess
  ...ty to customize configuration directives defined in the main configuration file. The configuration directives need to be in <code>.htaccess</code> context :In this case you would need another <code>.htaccess</code> file in <code>/public</code>, containing these lines:
  7 KB (1,064 words) - 21:41, 15 April 2015
• Regular expression
  / </font># identify URLs within a text file<font color="blue">
  13 KB (2,034 words) - 21:46, 9 March 2009
• Sed/scripts
  == File spacing == * double space a file
  30 KB (4,929 words) - 22:47, 21 August 2019
• Sed/manpage
  sed [OPTION]... {script-only-if-no-other-script} [input-file]... ...editor is used to perform basic text transformations on an input stream (a file or input from a pipeline). While in some ways similar to an editor which pe
  8 KB (1,304 words) - 05:58, 7 August 2006
• 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
• Redirection (Linux)
  ...stitution) part creates a FIFO and lets tee listen on it. Then, it uses > (file redirection) to redirect the STDOUT of command to the FIFO that your first ...am reads the output from another with no need for an explicit intermediate file:
  12 KB (1,905 words) - 20:29, 22 September 2020
• Nohup
  ...ground as daemons. Output that would normally go to the terminal goes to a file called <tt>nohup.out</tt> if it has not already been redirected. ...the command is not run. Any <tt>nohup.out</tt> or <tt>$HOME/nohup.out</tt> file created by <tt>nohup</tt> is made readable and writable only to the user, r
  3 KB (473 words) - 03:11, 14 April 2008
• Curl/manual
  <pre>curl ftp://name:passwd@machine.domain:port/full/path/to/file</pre> <pre>curl -u name:passwd ftp://machine.domain:port/full/path/to/file</pre>
  29 KB (4,993 words) - 01:53, 26 April 2007
• PyMOL
  *[[Protein Data Bank (file format)]]
  1 KB (158 words) - 04:18, 24 April 2007
• ImageMagick
  ...port] : saves any visible window on an X server and outputs it as an image file. You can capture a single window, the entire screen, or any rectangular por ...ites the original image file, whereas, convert writes to a different image file.
  3 KB (533 words) - 15:04, 26 February 2011
• Netpbm
  == File formats and programs == * The [[Portable pixmap (file format)|portable pixmap/greymap/bitmap formats]] PPM, PGM, PBM. They are co
  2 KB (245 words) - 06:49, 1 September 2006
• 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
• Portable pixmap (file format)
  ...'''portable graymap file format''' ('''PGM''') and the '''portable bitmap file format''' ('''PBM''') specify rules for exchanging graphics files. They pro ...essive conversion programs to turn this code into a [[Windows bitmap|bmp]] file:
  5 KB (761 words) - 04:02, 14 April 2008
• LAMP on Mandriva
  ...de> file has been removed, this is now set in the <code>/etc/my.cnf</code> file. ...<code>use_mysqld_safe="1"</code> in the <code>/etc/sysconfig/mysqld</code> file to use the old <tt>mysqld_safe</tt> script.
  7 KB (1,074 words) - 01:52, 3 May 2007
• Axel
  ...wget]]. The difference is that it is both an accelerator and it splits the file into multiple pieces. --output=f -o f Specify local output file
  2 KB (258 words) - 01:54, 26 April 2007
• .netrc
  ...'''.netrc''' file contains configuration and autologin information for the File Transfer Protocol client ftp. (''note: It is usually located in your home d The .netrc file contains login and initialization information used by the auto-login proces
  3 KB (524 words) - 01:04, 5 September 2006
• 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
• Sgrep
  ...s from C or make complex queries to SGML files based on the [[DTD]] of the file. * Step 1: Create a file called '<code>query</code>' containing the following:
  3 KB (464 words) - 01:55, 26 April 2007
• Fish protocol
  ...'''FISH''' requires nothing more than a working shell, and doesn't require file transfer to be enabled on the SSH server. Optionally, there can be a specia ...o be mounted clientside, which reduces hassle when only using FISH for one file.
  1 KB (170 words) - 05:25, 7 September 2006
• 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
• Units (command)
  ...e data file that comes with this program, or you can provide your own data file to suit your needs. -f, --file specify units data files (-f '' loads default file)
  4 KB (615 words) - 22:12, 16 April 2007
• Urpmi
  urpmf <file> # Find package that contains a file
  3 KB (499 words) - 05:50, 17 July 2009
• Xmerge
  ;<code>-o</code>:set output file for final image, if written (default test.ppm) ;<code>-O</code>:set output file for mapping data, if written
  3 KB (581 words) - 06:49, 20 April 2007
• Linux directory structure
  |Essential [[device file|'''dev'''ices]] (e.g., [[:/dev/null]]) |Host-specific system-wide [[configuration file]]s.
  7 KB (974 words) - 20:12, 19 April 2022
• Shell colour codes
  ...colour <tt>ls</tt> utility <code>/etc/DIR_COLORS</code>. You can copy this file to <code>.dir_colors</code> in your <code>$HOME</code> directory to overrid 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
• Matrix2png
  ;<code>-data <file></code> : (required) ;<code>-desctext <file></code> : (optional)
  5 KB (794 words) - 20:19, 11 July 2012
• Tab
  #REDIRECT [[Tab file format]]
  29 bytes (4 words) - 01:14, 17 October 2006
• PostScript
  ;pstops : shuffle pages in a PostScript file (see manpage for details)
  3 KB (469 words) - 01:21, 8 February 2009
• Perl
  lines printed. If a file named by an argument cannot be opened for some reason, Perl warns you about it, and moves on to the next file.
  5 KB (746 words) - 04:15, 31 March 2008
• RSvgDevice
  ...programming language|R]]. It allows you to output your data to an [[SVG]] file. devSVG(file = "Rplots.svg", width = 10, height = 8,
  715 bytes (95 words) - 01:08, 29 October 2006
• Rdate
  * e.g. add the following to a file in your <tt>/etc/cron.hourly/</tt> dir (after choosing an NTP):
  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
• Ramachandran plot
  ...in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-c ...r more residues, and of which at least 10% are outliers are listed in this file: http://xray.bmc.uu.se/gerard/rama/ramathisweek.txt (Note that this list ma
  27 KB (3,212 words) - 18:52, 26 July 2012
• WikiSH
  To make a HTML file from a wiki file call <tt>wiki.sh</tt> with the wiki file as parameter: This creates a HTML file called <code>MyWiki.html</code>.
  2 KB (278 words) - 22:31, 2 January 2015
• Bioinformatics resource list
  ; openbabel : A free, open-source version of the Babel chemistry file translation program. (''License: GPL'') ; pine : University of Washington Pine mail user agent. (''License: see file CPYRIGHT'')
  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
• LFasta
  ...be handled by using the <code>gff</code> option. This specifies a [[GFF]] file that is read from or written to depending on the which way the formatting g ...ript adds a prediction track to LFasta (lfa) entries as specified by a GFF file. This is useful for comparing predictions.
  7 KB (870 words) - 01:39, 13 July 2012
• 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
• Zimg
  Create a file called <code>my.dat</code> containing the following (128x128 matrix):
  453 bytes (60 words) - 00:11, 1 January 2007
• Xls2csv
  ...that is in the WINDOWS-1252 character set (WinLatin1) and save it as a csv file in the UTF-8 character set. -c : the filename to save the generated csv file as
  2 KB (364 words) - 05:00, 17 May 2007
• Firefox
  *You can work offline in Firefox just go to File>Work Offline. This means that you can browse your previously visited pages Note: In JRE 1.4.2, this file was in <code>plugin/i386/ns610-gcc32</code>
  7 KB (1,193 words) - 07:15, 30 April 2010
• 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 -b, --break-file=FILE word break characters in this FILE
  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
• MSMS
  ''Note: The input file must have four columns: x, y, z (from a PDB structure) and r (radius).''
  3 KB (480 words) - 04:43, 17 July 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
• Tex2im
  The content of input file should be plain latex mathmode code. Alternatively, a string containing the ;<code>-o file</code> : specifies output filename, default is inputfile with new extension
  5 KB (868 words) - 07:48, 25 December 2008
• Awk/scripts
  ...<code>$1</code>, on the foo <code>foo1</code>, and the second field on the file <code>foo2</code>: *Append the output to the file <code>foo</code>:
  18 KB (2,772 words) - 22:57, 26 October 2021
• Glob()
  '''glob()''' is a Unix library function that expands file names using a pattern matching notation reminiscent of [[regular expression *[http://perldoc.perl.org/File/Glob.html Perl 'File::Glob' module]
  4 KB (646 words) - 01:43, 16 June 2012
• 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 arc ...<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
  ...sure that you have support for the <code>vfat</code> and <code>loop</code> file systems in the kernel. Or you can have those features compiled as modules. Consult <code>/proc/fileystems</code> to see if you have the needed file systems supported. If you do, you should be able to "loop mount" the floppy
  3 KB (497 words) - 21:04, 11 March 2007
• Samba
  ...sername and password in a text file that anyone can read, you can create a file in, for an example, <code>/etc/samba/smbpasswd</code> with the following tw It is possible to set the mount uid, gid, and umasks for file/directory create/deletion/overwrite with the following set of options:
  5 KB (785 words) - 17:57, 8 May 2014
• PDB Validation Suite
  ''Note: The majority of this article was taken directly from the README file.'' For example, to create reports for a file in mmCIF format named <code>1xyz.cif</code> type:
  6 KB (895 words) - 02:37, 24 March 2007
• Iftab
  '''iftab''' - static information about the network interfaces. The file <code>/etc/iftab</code> contains descriptive information about the various ...s use <code>/etc/iftab</code>. For an example, openSUSE uses the following file.''
  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
• Binutils
  ...t code in various object file formats. The current versions use the Binary File Descriptor library (libbfd). They are typically used in conjunction with GN *<code>addr2line</code> &mdash; convert address to file and line
  2 KB (285 words) - 03:57, 1 April 2007
• Linux kernel
  * File management $ file /sbin/init
  6 KB (897 words) - 10:20, 17 November 2014
• RPM Package Manager
  NOTE: RPM file names normally have the following format: ...automatically compiled and installed, following instructions in the .spec file included in the SRPM.
  8 KB (1,064 words) - 22:36, 19 April 2023
• Recovery Is Possible
  ...leted files, by ignoring the filesystem and checking disk blocks for known file types
  3 KB (481 words) - 05:17, 2 April 2007
• Fstab
  ...how 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
  For example, a generic PPD file for all models of HP Color LaserJet contains: ...rators Manual, [http://www.cups.org/doc-1.1/sam.html#FILE_TYPING_FILTERING File Typing and Filtering]. (accessed 2007-01-09).</ref>
  6 KB (795 words) - 22:59, 23 January 2008
• List of GNU packages
  | [[File Transfer Protocol|ftp]], [[telnet]], [[rsh]], [[rlogin]], [[tftp]] | Archiver able to creates and handles file archives in various formats
  8 KB (1,101 words) - 05:31, 4 April 2007

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