Introduction to the Scientific Web Space
January 22, 2004
Your SIMR-hosted Web Site
The primary purpose of your Stowers Institute website is to enable your
communication with the research community on the matters directly relevant to
the Institute’s mission, i.e. scientific research and education. Many people would
like to add a few personal touches to their websites; this is acceptable as long as
the considerations of research excellence, professional appearance, and good
taste are kept in mind. Some of the Institute policies, for example those covering
Intellectual Property, Open Source Software, and others, may be directly
applicable to the contents of your web pages. Please consult your supervisor or
Research Operations if in doubt.
Requesting an Account
To request an account, email the Unix Administrator with the desired
account name and password. Accounts on the web server are separate from
other computer accounts at the Institute. The name of an account dictates how
the account is accessed. For example, all pages for the “test” account would be
found under the URL http://research.stowers-institute.org/test/. Graduate
students, post-docs, and technicians should consult their PI before requesting an
account.
Web Server Overview
Web Server
The web server, http://research.stowers-institute.org/ runs on a Linux
platform and has been configured to provide the following services.
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Authentication – Passwords protect the web pages.
Authorization
o Local – Only users inside the Institute can see the web pages.
o Global – Anyone can see the web pages.
Scripting – Dynamic web page content generated by server side scripts.
Content Development
Content will be created and maintained by each individual team or user. This
includes development of all text and graphics. In specific cases, the Institute’s
Web Programmer is available to answer web development questions.
Web users are free to develop content with any Web authoring software.
Dreamweaver is the recommended editing tool as it allows for beginners and
advanced users alike to develop content in a simple and rapid manner and can
be ordered through the IT Request Form. Free Web authoring tools such as
Mozilla or a text editor also can be used to develop web content.
A default web page that can be edited or removed is provided as a starting
point for web development. Several template styles that include a predefined
table structure and a Stowers Institute graphics motif are available in the files
named template. To use a template, copy the “images” directory along with a
template file to your workspace. The screenshot details the files present by
default in a web account. The default web page is called index.html.
Directory Structure
Directory translation is performed automatically by the web server.
Documents placed in a user’s public_html directory are visible to a web browser
as shown in the table. The previous screenshot is of the test user’s public_html
directory.
Physical Directory
URL
/home/test/public_html/index.html
http://research.stowersinstitute.org/test/index.html
/home/test/public_html/images/picture.gif http://research.stowersinstitute.org/test/images/picture.gif
Transferring Files to the Web Server
Windows – DreamWeaver
DreamWeaver can interface with the web server by creating a Site entry.
To define a new site, select the Manage Sites option from the Site menu. Then
select New. Under the Local Info Category name your site and select a local
folder for web development files. Next, enter the following information under the
Remote Info Category.
Access : FTP
FTP Host: research.stowers-institute.org.
Home Directory: public_html/
Login: Your Web Username
Password: Your Web Password
After saving the site, use the Get and Put arrows in the Site menu to transfer files
back and forth between the Local View and the Remote View. The Remote View
is the web site on the web server, and the Local View is the local copy of your
web site. Usually, the local copy is edited before transferring the files to the web
server.
Macromedia provides a detailed description of configuring DreamWeaver
to transfer data using FTP.
Windows – FTP
Files can be published via FTP by either using an FTP client or the built-in
FTP feature of Internet Explorer. When using Internet Explorer, type the URL
ftp://user:password@research.stowers-institute.org/ into the Address bar,
substituting user with your web server user name and password with your web
server password. For an example, see the previous screenshot that was taken
when the user test with the password happy connected via FTP using Internet
Explorer. Web site files are placed in the public_html directory.
UNIX – Secure Copy (scp)
Files can be securely copied (over an encrypted connection) to the web
server using the scp command in UNIX. To copy a file to the public_html
directory, use this command:
scp –pr public_html user@research.stowers-institute.org:~/public_html/
For more information, look at the man page for scp by entering `man scp` at a
UNIX command prompt.
UNIX – FTP
The UNIX FTP client is called ftp. For information on this command, refer
to the man page by typing man ftp at a UNIX command prompt. The basic
connection method for ftp is started by entering the command `ftp
research.stowers-institute.org` at a UNIX command prompt. Once the FTP
program has connected, prompts for your user name and password will be
shown. After authenticating, files should be put in your public_html directory.
Software Applications
Software applications written by Institute members or a third party can be
hosted on the web server. A variety of programming languages are supported
including Perl, PHP, and others. When hosting an application, users are
encouraged to contact the Bioinformatics Group for code review, application
verification, or any related questions.
Some applications require SQL database services for data storage and
retrieval. Two major open database platforms are supported on the web server,
namely MySQL and PostgreSQL. Both are open source databases, and only
PostgreSQL, under the BSD license, can be used without restriction. MySQL is
under the GPL and can only be used by applications under the GPL unless a
commercial license is purchased. Consult the Institute’s Open Source policy or
Research Operations if licensing questions arise. Contact the Unix Administrator
to request a database account.