Briefing to the Dept. of Biochemistry on the availability and possible uses of personal web pages.    02/27/01

This document will be indexed with other documents about bioinformatics accumulated for the use of the Biochemistry Dept. at http://biochem.uthscsa.edu/~hs_lab/bioinfo.html

Note to non-Biochemistry viewers:  The information here was taylored to specific hardware and software available in the Dept. of  Biochemistry.  The degree to which it applies in other computing environments may vary.

Disclaimer: Any opinion expressed or implied represents that of the author and is not necessarily shared by the University.

Summary

This is a summary for the Biochemistry faculty of the capabilities we currently have to use web pages in our work. There are examples given and accompanying technical information. The emphasis here is on what you can do with existing software, at no additional cost, and with little or no technical knowledge.

There are two documents: this one [http://biochem.uthscsa.edu/~hs_lab/deptshow.html] has examples, and the other has a compendium of technical information [http://biochem.uthscsa.edu/~hs_lab/techdoc.html].
 

Contents - links jump to headings within this page.

• Posting a document to a web page.
• Converting files to html.
• Adding hyperlinks to a document.
• Broadcasting a document to a selected group.
• Updating files after posting.
• Limiting access with passwords.

Posting a document to a web page for easy retrieval.

• What?
• Typically documents that you would need while working at a computer.  Could be data sets, instructions for using programs, documents frequently referred to while writing papers or grants, etc.
• Why?
• If you work at more than one computer, this makes sure the document is easily retrievable from each of them.
• It's less likely to get lost.
• If the document is sometimes updated, retrieval by a browser always retrieves the most recent version.
• What do you need?
• A username and password on a computer with a web server.  If you have a directory on biochem.uthscsa.edu (the departmental linux system that Bo maintains) you already have the necessary login information. [details] PIs in the dept. that have unix machines usually have installed web servers.  It is also possible to install a web server on any  Windows NT or Mac platform, although I don't know if anyone in the department has done so.  The technical instructions assume that you get a username and password from Bo Demeler.
• Netscape navigator and composer (2 parts of the free Netscape Communicator package); or Microsoft  Internet Explorer plus Microsoft Word 97 or above; or some other browser and some other html editor.  If you want to learn html, then any text editor will do, but an html editor saves you from having to learn any html.  The technical instructions will initially cover Netscape Composer or Microsoft Word.
• An ssh/scp client.  This is a more secure way to log into remote computers and exchange files than ftp/telnet/fetch clients.  Support for the latter is being dropped most places throughout the university.
• What you need to do:
• If you don't have a username and password, get it by e-mail from Bo.
• Verify username and password by telnet to your web directory.  Change the password. (takes a minute or 2 once you find your telnet program.
• If you don't have a home page, make one and ftp it to your web directory (takes less than 5 minutes) [making a home page; details][making a new page with Composer]

[making a new page with Word]
• Ftp the page you want to post to the web directory (less than a minute).  The page can be in any format.  If it is in plain text or html, browsers will directly display it.  For other formats, you can download it from any browser, but you need the program installed that reads the format if you want to look at it.
• Add a link to the home page pointing to the new page (takes a few mouse clicks, see below).  Links from the home page to the other pages are not strictly necessary, but they greatly simplify finding the documents later.  The home page itself is necessary, but it doesn't actually require any content. [adding hyperlinks; details]
• Example:
• Here's a text file with a summary of instructions for the unix vi editor that I posted for my own use  http://biochem.uthscsa.edu/~hs_lab/frames/vi.

Converting files to html

• What?
• Any text file, or any document that Microsoft Word can read.  Microsoft Powerpoint and Excel also can directly output html versions.  I presume that many other document creation programs are now including html output as an option.  Eventually the disabilities act is going to require teaching materials to all be provided in html so that individuals with visual disability can access them with a web browser driving a voice synthesizer.  Note: that doesn't mean they will have to be posted to a web page; an html file can be handed to someone on a floppy disk, for example.  As far as I know, html is the only format that is attracting the development of software designed for the disabled.  Even Adobe supports its pdf format for the visually disabled by providing a conversion to html.
• Why?
• Html files can be displayed or printed on any computer with a browser without purchasing software.
• Html files can contain hyperlinks to other sources that can greatly increase their information content.
• Html files are easily formatted.
• Html documents can be enlarged by the viewer and the text will word wrap to stay on the screen.
• Html documents can have a title that makes them bookmark gracefully.
• Html documents can contain images, videos, sound files, all kinds of fancy artwork, forms (a method to retrieve information from a user), and scripts and applets (essentially programs embedded in the web page).  Most of this goes beyond the scope of this document, but once one learns to make simple html documents the rest of these features become much more attainable.
• Html has minimal problems caused by incompatibility due to the succession of upgrades to the language definition.  Files in older versions of html always display properly on newer browsers.  Older browsers will display files written with the newest versions of html, although features specific to the newer html standards are ignored.
• What you need:
• If the file is in some proprietary format, then either the program that reads that format has to be able to convert to html, or you have to be able to cut-and-paste a display of the file into a program that does (like Netscape Composer, or Microsoft Word).
• What you need to do:
• After you get an html version of the file produced, you can use Netscape Composer or Microsoft Word to adjust the look of it as desired.
• Then ftp it to your web directory and link it to your home page as above.
• Example:
• Here are the vi instruction converted to html by using Netscape Composer [http://biochem.uthscsa.edu/~hs_lab/frames/vi.html].  This took a few minutes to convert with Netscape Composer, mostly because the indention in the text file was lost when I pasted it into Netscape Composer.  Microsoft Word did less well, choosing to declare each line as a separate paragraph.  Generally I've had better success with Composer than Word for converting text documents.  Both Netscdape Composer and Word allow you to switch between editing in WYSIWYG (what you see is what you get) format and editing at source level.

Adding hyperlinks to an html document.

• What?
• Could be a list of the same sort of links you'd bookmark in your browser.
• Could be links among your own documents.
• Could be references for your documents.
• Often I start to research a topic by accumulating a list of links to web resources.  These can become a bibliography for the document on the topic later.
• Why?
• If you work with multiple computers, bookmarks made in a browser on one computer are not available on the others.  If you instead accumulate them on a web page, then you can access them from any computer.
• If you use links to external resources as references in a document, then the document becomes updated automatically by virtue of the information in the links getting updated.
• For links for which you have a need to refer students or colleagues, you can direct them to look for it in a list of links on your web page and generally expect them to find it.  Otherwise, you're going to end up having to go to the computer yourself to find it for them.  For example students often ask how to search for restriction sites.  All I have to remember is my own web page http: and to tell them to look at the "other sites" page.
• How to do it:
• You can copy a link from a browser to a document being edited by Netscape Composer or Microsoft word with a couple of mouse clicks.
• Links can also be entered manually into documents.  Don't forget to check that they work; typos on manual entry are extremely common.  http: addresses (called URLs) are case sensitive. [adding hyperlinks; details]
• Example:
• The "other sites" page of my web page is at http://biochem.uthscsa.edu/~hs_lab/frames/bkmk.html.
• Note: I'm beginning to notice that the above format for a link where the URL is used as the visible control has some advantages over something more traditional like

"see my bookmarks".  The former retains its information if the document is printed; the later becomes useless.  It's also more obvious if you've used the same link several times in the same document.

Broadcasting a posted web page to a selected group of individuals.

• What?
• Any document you want to call to the attention of a known collection of individuals.  Could be abstracts for a seminar or journal club, administrative documents like seminar or class schedules, teaching materials, background information for a committee meeting, or data being shared with a collaborator.
• How?
• Post the document and e-mail the URL.  If you format the e-mail in html, then an active hyperlink can be inserted.
• Post the document and communicate the URL by any means.  For example, it could be given to students in a class by writing it on the blackboard.
• Why?
• Assuming that you link it to your home page, it's now filed for later easy reference by both you or any of the recipients.
• If a recipient needs to direct someone else's attention to it, they can just say to look for it on your web page.
• If the recipients expect frequent updates of this document, you don't have to keep redistributing it.  They will always get the latest version when they access the document with their browser.
• If you put the link to the document in a parent document with other information, you can then broadcast the URL of the parent document rather than the specific document.  This can be used to make a recipient see the additional information on the way to finding specific information that you know they want to see.  This opens a subtle avenue for introducing people to things that they might not otherwise look into.
• Note: Nothing stops you from both posting and also sending a document as an attachment, or posting and also putting a printed copy in people's mailboxes.
• Example:
• Here's a page I posted to transmit supplementary information to the freshman biochemistry dental students that they had requested from TA's and lecturers. [http://biochem.uthscsa.edu/~hs_lab/dent.html].  Note a couple of points in this example.
• We put the URL in the initial handout with the class schedule and other basic information.  The students knew to look there on a continuing basis, so we didn't have to redistribute anything to them with each new posting of information.
• One of the links goes off to a page on Andy Hinck's computer.  That means he can post things whenever he wants and it shows up through this page without me having to do anything.
• The page has some links to other materials I'm trying to interest the students in looking into.
• The TA's were able to post stuff without me having to do anything.

Updating files after posting.

• What?
• Any posted file can be downloaded with a browser and editing resumed with just a mouse click.
• Why?
• When working from multiple computers, it can be more convenient to make the posted web version the working draft than shipping the working draft around from site to site in some other way.
• You can choose to make the developing draft invisible to others, or visible to selected individuals (see password protection, below).  So collaborators helping to write the document can see it and comment on it while you are working on it.
• This format is ideal for documents that are updated frequently.  You don't have to keep track of which file has the most recent version.  The version retrieved by the browser is always the most recent version. [However, you have to remember to click reload or refresh to not get caught looking at an old version from the browser cache].  [You should always save each new version to a hard disk somewhere in your system.   It's always a possibility that some hacker would manage to trash biochem. Never assume that someone else is responsible for keeping backups for you]
• How?
• With Netscape just access the file on the web and click <file><edit page> and start editing.  When done, use scp to send it back to biochem the same way the original was sent there.  Don't change the name; you want it to overwrite and replace the original on biochem.
• With Microsoft Internet explorer, access the file and click <file><edit with word>.  Alternatively save to disk and edit it with word (or other editor). Use scp to send the edited file back to biochem.  Don't change the name, you want it to overwrite and replace the original on biochem  [retrieving and editing with Composer] [retrieving and editing with Explorer and Word]
• Examples:
• Every document mentioned here including this one was done this way.  My bookmark list mentioned above is in a continuous state of being updated with new links.
• Here's a document containing my personal notes on how to do an hsqc NMR experiment.

[ http://instinct.v24.uthscsa.edu/~nmrref/hsqc1214.shtml]. [Backup at http://biochem.uthscsa.edu/~hs_lab/hsqc1214.htm].  I went through many drafts of this trying to get a comprehensive grasp of how to do this experiment.  Each time I'd try to do this experiment, I'd discover lots of errors to fix in my understanding of it, and have lots of additions to make.  The web document could be accessed from the NMR console itself, from the data processing computer, or from my home or office.  From any of those sites I could know I was looking at the most recent version, and make patches to it an put it back.  Since Andy Hinck was interested in using it as part of the documentation for his NMR web page, he looked at it on several occasions and pointed out lots of stuff that I'd probably have taken months to figure out on my own.  The document continues to evolve.  If I'd have tried to just write the instructions into my notebook the way procedures are usually recorded: 1) all the revising would have made a mess of it, and 2) I'd have been unlikely to have the same quality of information exchange with Dr. Hinck.  Meanwhile, the document in each of its revisions has been available to others trying to learn these experiments.

Limiting access with passwords

• What?
• Any document you don't want just anyone looking at.
• Note: passwords can be guessed or stolen, so do not rely on them to protect truly sensitive information.  I wouldn't post an exam under construction.  Patient information would be a definite no-no.
• Why?
• You might want to limit research results, drafts of papers, etc. to just access by collaborators and lab members.
• How?
• When a text file with the right name and contents  is placed in a web directory, it directs the web server to impose password restrictions on files in that directory.
• You would group files into sub directories of public_html according to desired access.
• The username and password could be sent along with the URL to the intended recipients of the information.  In this way of doing it, the username wouldn't really have anything to do with the user.  It would just be the first part of a two part password.

[password; details]