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• 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

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