Difference between revisions of "Philosophy of Biology Graduate Programs:About"

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Published on Nov. 19, 2014, [http://philbio.net PhilBio.net] was created by [http://shamiller.net Shawn A. Miller], a [http://philosophy.ucdavis.edu/people/shamille Ph.D. candidate] in the Department of Philosophy and the Science & Technology Studies Program at UC Davis. It is the basis of the Creative Commons template available at [http://philwiki.net PhilWiki.net] that allows anyone to essentially clone this site.
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Though there isn't any bleeding-edge technology running behind the scenes of PhilBio.net, the software is still a big part of the equation. Particularly notable is that all of the essential pieces running the server are open-source software. Nothing of what follows is necessary for using the site, but everyone who visits here and finds it useful owes a big debt of gratitude to those who wrote the software, and then gave it away for free.
 
  
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== What Server? ==
 
  
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PhilBio.net runs on a server in San Francisco hosted by [http://digitalocean.com DigitalOcean] for a modest cost. PhilBio.net is actually a so-called ''virtual machine'', which means that it is an autonomous software entity that exists with other such entities on the same piece of hardware. Through software, the virtual machine is made to look like, and functions as, its very own computer. In this way, DigitalOcean and other cloud hosting services such as [https://www.linode.com/ linode] differ from web hosting services such as GoDaddy or Hostgator, where one basically rents hard drive space on a web server but does not have access to additional software programs.
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The following are the key open-source software pieces of the PhilBio.net virtual machine:
 
  
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=== [http://www.mediawiki.org/wiki/MediaWiki MediaWiki v1.24.0] ===
 
  
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This is the software that users and editors interact with most directly; it is the wiki server software. It is what you are looking at right now. MediaWiki was originally developed for use on Wikipedia and is available under a [https://gnu.org/licenses/gpl.html GNU General Public License (GPL)]. The software is written in PHP, and the installation file is a mere 20 MB.
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=== [http://ubuntu.com Ubuntu v14.04] ===
 
  
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The operating system running PhilBio.net is Ubuntu [http://releases.ubuntu.com/14.04/ 14.04]. Ubuntu is a version of Linux, though 'GNU/Linux' is a more [https://www.gnu.org/gnu/gnu-linux-faq.html accurate term]. Operating systems are enormously complex and contain thousands of individual software programs. There are a variety of versions of Ubuntu, and they are all ''mostly'' open source. Even versions of Ubuntu that do not package free-standing propriety software programs—such as the version running this server—still contain proprietary software drivers, which are necessary for accessing the underlying proprietary hardware. This simply can't be helped.
 
  
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=== [http://httpd.apache.org/ Apache v2.4.7] ===
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Apache is web server—or HTTP server—software. It makes the resources of a computer visible and available to the outside world and is, thus, essential. Apache software is open source and available via its own [http://www.apache.org/licenses/ license]. [http://wiki.nginx.org/Main Nginx] is also open source server software.
 
  
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=== [http://www.mysql.com/ MySQL v5.5.40] ===
 
  
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MySQL is database software. It is pronounced "My S-Q-L," not "My Sequel." The SQL stands for structure query language. When you save a wiki edit, create a page, or start an account, that information is stored in a MySQL database. [https://wordpress.org/ WordPress] blog posts are usually saved into MySQL databases, as well. The software is available under both open-source and proprietary licenses, though PhilBio.net obviously runs the open source variety.
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=== [http://php.net/ PHP v5.5.9] ===
 
  
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PHP—which stands for PHP: Hypertext Preprocessor—is a programming language that was created by Rasmus Lerdorf in 1994. Much of the software running PhilBio.net is written in PHP, including MediaWiki. The server is able to execute PHP programs because the engine required to do this is open source. PHP is available under its own [http://php.net/license/ license].
 
  
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=== Other Tools ===
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Since PhilBio.net is a virtual machine located miles away from its [http://shamiller.net administrator], additional software tools are needed to connect to, maintain, and modify the server. Those, too, are open source, and include:
 
  
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* '''[http://www.openssh.com/ OpenSSH (Secure Shell)]''' allows users to connect to remote computers securely.
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* '''[http://rsync.samba.org/ rsync]''' allows users to transfer files over, e.g., SSH.
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* '''[http://gnometerminator.blogspot.com/p/introduction.html Terminator]''' is a terminal, that is, a program that users interact with by typing in commands.
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* '''[http://tmux.sourceforge.net/ tmux]''' is a terminal multiplexer that allows users to run multiple programs inside one, e.g., Terminator terminal running OpenSSH.
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* '''[http://www.vim.org/ vim]''' is a text editor. A great deal of the server maintenance done to PhilBio.net is simply editing text files.
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Revision as of 18:24, 1 October 2018

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