Biology IT Resources


Introduction


A set of resources has been created for essentially every course taught by the biology and microbiology departments. You can see the front end to these resources at: http://bcrc.bio.umass.edu/biol/. Resources can be build for other departments that can provide a person who will act as a coordinator for the resources and as a liason between the BCRC and the faculty of that department. These resources include:
  1. a "simple" way to make basic web pages
  2. a "simple" way to post web pages
  3. a free links page
  4. a Duck practice testing system
  5. a web-based course calendar
  6. a course mailing list
  7. a mailing-list archive
These resources should allow every faculty member to: This document includes a set of directions and a tutorial below that can be used as a guide to accessing these resources from within the BCRC. It is possible to also access all of the resources from any Macintosh or PC within Morrill Science Center and the possibility of making these resources available to other buildings is being explored. Once you are conversant with using the resources from within the BCRC, you should find it much the same from anywhere else as well.

Directions


This section provides information and directions on using the instructional technology resources provided to the biology department. For some actual examples of accomplishing tasks with these resources see the tutorial below.

Making Web Pages with Internet Assistant


You don't need to learn HTML to publish web pages. It helps, but it is not necessary. Internet Assistant is a Micrsoft Word template that will both convert existing MS Word documents to HTML and permit interactive HTML authoring. It does not produce beautiful pages, but it is adequate for basic kinds of pages.

  1. Start Microsoft Word (there is an alias under the **Application folder in the Apple Menu)
  2. Open a Word document (under File menu)
  3. Select Save as
  4. Click the Desktop button
  5. Set File Type to HyperText Markup Language
  6. use a file name that:
  7. Click Save
You now have an HTML document. You may wish to start up Netscape at this point to see what the document looks like. You can find Netscape under the Apple Menu and then select Open File under the File Menu. Click the Desktop button to get to the Desktop. If you don't like the way the file looks, make changes and try saving them. Click the Reload button in Netscape to see what difference the changes have made.

You might consider learning to write basic HTML documents -- its not really that hard. Take a look at my Introduction to HTML to get started.

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Posting Web Pages with Appleshare


Posting a web page, just means saving the file someplace where the Web Server program can find it. The BCRC has created such a place for each course. To use this resource, you will need to have an account on snapper (if you have an account on marlin, you already have an account on snapper).
  1. Select biol, biochm, or micbio from the Web subfolder of the ** Servers folder in the Apple Menu
  2. Log in with your email username and password
  3. Select By Name from the View menu
  4. Double click on the folder for your course -- inside you should see a file called "index.html"
  5. Drag the file you want to post into the folder for your course.
Once you have posted something (dragged it to the folder) all you need to do is figure out what the URL is that points to what you've posted. When we did this the first semester, I hadn't thought about what happens next semester. This time around, I have made things a bit more complex, but the advantage is that the URL for something won't have to change after the course is over. Here's how it works: The first part will always be the same for all courses:
  http://bcrc.bio.umass.edu/courses/

The next part indicates which semester:
  http://bcrc.bio.umass.edu/courses/fall2000/

The next part indicates which department:
  http://bcrc.bio.umass.edu/courses/fall2000/biol/

If your course is Biology 104 then the next part will be "biol104":
  http://bcrc.bio.umass.edu/courses/fall2000/biol/biol104/ (see Note below)

The rest is easy -- if the file you put in the folder is "syllabus.html":
  http://bcrc.bio.umass.edu/courses/spring98/biol/bio104/syllabus.html

Note: If you don't specify a document (or file name), what you're doing is pointing to a folder. It then looks for a file called "index.html". If there is no file called "index.html" it generates an index automatically. Look at http://bcrc.bio.umass.edu/archives/ for an example where this is used.

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Publishing URLs with Free Links


Starting in 1997, the BCRC has offered a Free Links Page that is a place where anyone can add a hyperlink to a docume nt. The form below allows you to enter a title for the hyperlink, the URL that the title will link to, and to select a section where the link will be placed. (Note that the form below is active and will allow you to actually post a link on the BCRC Free Links Page. Feel free to add something useful to our collection).
Title:
URL:
Section to be placed in:

For pilot testing, I created sections of the document for biology courses. One faculty member realized that he could post his own documents (using FTP) and then create links to them using the Free Links page. I saw that if I could provide a way to post documents so that their URLs could be figured out easily, this could be used as a system to integrate instructional technology resources for every course.

For documents posted in your course folder, all you need to enter is the file name. Using cut and paste is still a good idea, to make sure you don't put in any typos.

By default, the document is modifiable only by someone who has set a web-based authentication username and password. Some faculty have found it useful to allow students to add links to the page and build a "peer reviewed" set of resources. Ask your department's representative about making this change.

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Using the Web-based Calendar System WebEvent


The course calendar system (and, by default, the course links system) requires that you set a username and password to be used over the web in order to assure that not just anyone can change the events in your calendar.
  1. Start Netscape
  2. Click Courses
  3. Click Course Calendar
  4. Click next month or jump to month to get to the month you want to modify
  5. Click on the number of the day you want to add an event to
  6. Enter a title and write a description.
  7. There is a radio button for whether or not your description is in plain text or HTML.
  8. Click the Create button
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Managing Course Mailing Lists with Majordomo


Using mailing lists for courses is becoming increasingly popular -- it is a powerful way to help students participate in discussions around course topics and to give students a voice in the class. Below you'll find directions for interacting with Majordomo. Majordomo is fairly straightforward -- you send commands to Majordomo in the body of your email, and it does what you ask and sends you email telling you what it did. Using a course mailing list to greatest effect is more challenging. As a first step, check out the results of the Mailing List Survey we conducted last semester. Beyond that, take a look at eForums an internet resource for electronic forums.

Majordomo is just a program that manages lists of email addresses. If you send email to majordomo@bio.umass.edu, this program receives your email and interprets any commands that are in the body of the message. Here is a summary of the commands you can send to Majordomo:

In the description below items contained in [ ]'s are optional. When
providing the item, do not include the [ ]'s around it.  Items in angle
brackets, such as <address>, are meta-symbols that should be replaced
by appropriate text without the angle brackets.

Majordomo understands the following commands:

    subscribe <list> [<<address>]
	Subscribe yourself (or <address> if specified) to the named <list>.
	
    unsubscribe <list> [<address>]
	Unsubscribe yourself (or <address> if specified) from the named <list>.
	"unsubscribe *" will remove you (or <address>) from all lists.  This
	_may not_ work if you have subscribed using multiple addresses.

    get <list> <filename>
        Get a file related to <list>.

    index <list>
        Return an index of files you can "get" for <list>.

    which [<address>]
	Find out which lists you (or <address> if specified) are on.

    who <list>
	Find out who is on the named <list>.

    info <list>
	Retrieve the general introductory information for the named <list>.

    intro <list>
	Retrieve the introductory message sent to new users.  Non-subscribers
	may not be able to retrieve this.

    lists
	Show the lists served by this Majordomo server.

    help
	Retrieve this message.

    end
	Stop processing commands (useful if your mailer adds a signature).

Commands should be sent in the body of an email message to
Majordomo@bio.umass.edu. Multiple commands can be processed provided each occurs on a separate line.

Commands in the "Subject:" line are NOT processed.

If you have any questions or problems, please contact
Majordomo-Owner@bio.umass.edu.
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Mailing List Archive Services with Hypermail


There aren't really any "directions" for Hypermail because you don't need any -- it should just work without requiring any interference. To get the most out of Hypermail, however, it is useful to understand a bit about how it works.

Hypermail is a program that takes a file of mail messages in UNIX mailbox format and generates a set of cross-referenced HTML documents. Each file that is created represents a separate message in the mail archive and contains links to other articles, so that the entire archive can be browsed in a number of ways by following links. Archives generated by Hypermail can be incrementally updated, and Hypermail is set by default to only update archives when changes are detected.

Each HTML file that is generated for a message contains (where applicable):

In addition, Hypermail will convert references in each message to email addresses and URLs to hyperlinks so they can be selected. Email addresses can be converted to mailto: URLs or links to a CGI mail program. Note that not all World-Wide Web browsers support the mailto: URL yet.

To complement each set of HTML messages, four index files are created which sort the articles by date received, thread, subject, and author. Each entry in these index files are links to the individual articles and provide a bird's-eye view of every archived message.

Hypermail was originally developed and designed by Tom Gruber for Enterprise Integration Technologies (EIT) in Common Lisp. It was later rewritten in C by Kevin Hughes at EIT.

Including HTML in messages: One can include formatted HTML in message bodies by enclosing the HTML with the <HTML> tag (in either uppercase or lowercase). This tag must be on a line by itself:

   This text will not be parsed...
   <html>
   this text will be parsed as HTML.
   </html>
   This text will not be parsed...

There is no limit to how often the <HTML> tag can be used in an article.

Filenames: In the specified directory, articles will be read out in the order that they were read in from a mailbox or standard input. Filenames start at zero and increase in this fashion: 0000.html, 0001.html, 0002.html, etc. In the same directory:

Sorting: In the date and thread index files, note that these lists are sorted by the date the articles were received by the system's mail daemon, not by the date they were written on. The order of articles in the date index may not necessarily match the order in which the article files are written and linked together. Because of this, it is a good idea to make sure the mailbox is sorted by date with the most recent messages towards the bottom.

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Duck


Duck is a system for making practice questions available to students. If you want to know why I wrote Duck and why it's designed the way it is, you can read a lengthy diatribe here. The short answer is that Duck doesn't try to keep track of 'right and wrong' answers: each answer can have unique feedback from the instructor associated with it and students can interact with a question until they're ready to go on to the next question.

Duck requires students to log in, but it doens't actually keep anyone out -- any username and password will work. We often ask students to use something like this for a username: lastname.f.m and the last four digits of their student number as a password. Then you can pretty easily check and see who's using the system.

You administer the resources by going to the duck 'pond'. Go to the student log in page for your course (there is a link on your course's home page) and type the word 'pond' after the URL. You should be prompted for a username and password (if you have not yet authenticated) and then you should see a page with three links. The first link allows you to author questions. When you click the link, it will take you to a page where you can enter the name of a 'content area' for a group of questions, or just go to the 'new' aread to start authoring.

You author questions on-line, but many faculty 'cut and paste' questions from word or wherever. Be a little careful of special symbols in Word (like their stupid 'smart' quote marks). These will not be translated propertly. (The questions are actually in html, so you can write html formatting or character codes, if you like).

Content areas whose names begin with an asterisk (*) are invisible. The content areas 'hidden' and 'new' are also invisible. The idea is to use 'hidden' as a storehouse of the questions you're writing. Select and move the questions you want to put into a new content into 'new'. Then you can rename this content area to have the name you want.

Questions in a content area are numbered alphabetically by looking at the first 15 characters. This means that if you put a number at the beginning of a questions, it will be used to number the questions.

Questions can be multiple choice, short-answer, or 'extended response'. Each question type uses the information you enter a little differently. Multiple Choice questions don't use the 'default' feedback. Whatever you enter in the 'response' fields, will be shown to the student as a clickable link. Whatever you put in the 'feedback' fields, will be shown to students if they select the associated response.

Short answer questions provide a field for students to type an answer, which must match more-or-less exactly in order to elicit the feedback. (I think ignores trailing 's' and '.') For numeric answers, you can also specify a range. For example, if the answer is '5', you could set the first response to be 5 (for if they get it right), then the second answer could be set to '5 5' (5 plus or minus 5) and the third could be '50 50' (50 plus or minus 50) each with appropriate feedback. The 'default' feedback is provided if nothing matches. The default feedback is also provided in the event that no feedback was written for an item in a multiple-choice question.

Extended response questions can send answers as email with an indication of what username the person logged in as. Note: because we don't check authentication tokens, you should take these usernames with a grain of salt. Extended response questions always return the 'default feedback' to students.

There are some basic tools for seeing whether students are using the system and for evaluating which responses students look at. I hope to develop these further.

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A Tutorial


Jane Faculty, who is teaching BIOL241 would like to use the instructional technology resources. First she decides to write a syllabus using Microsoft word. After finishing it, she saves it on a disk, and brings the disk down to the BCRC. After selecting Microsoft Word from the Application folder in the Apple Menu, she selects Open from the file menu, pops in her disk, finds her syllabus, and then selects Save As from the file menu. She changes the file type to "Hypertext Markup Language (HTML)". She clicks the Desktop button and saves her file with the name syllabus.html (all lower case with no spaces). After she quits Microsoft Word, she selects Web from the Servers Folder in the Apple Menu. She selects By Name from the View Menu, she finds the biol241 folder and then drags syllabus.html from the desktop to the course folder. She then informs Steve Brewer that she has posted her syllabus and that he can make her link active.

Jane decides she would like to provide some notes regarding a reading she is asking the students to do. She creates the html document called notes.html and posts it as above and then goes to the biol241 free links page. She makes up a title and enters it, and then enters the file name for the file she moved into her course directory. She selects "Official" from the pop-up menu to put the link into the Official section of the page, and then clicks "Add". She is challenged to enter a username and password and then her link is automatically added to the correct section of the document.

Jane would like to let students know about the new resources she has posted. She has already distributed a note to the students that explains how they can subscribe to the mailing list for their course. She writes a piece of email and sends it to <biol241@bio.umass.edu>. The students receive the email and it is also archived at http://bcrc.bio.umass.edu/digests/biol241-digest/. When it is archived, the URL, which she had included in the email, is converted into an active link.

Jane notices that in a month Nova will run a special presentation about something relevant to her course. She would like to let students know when it is going to be on. She posts to the email list, but would like to have something that would continue to remind them about the upcoming event. She goes to her course calendar page and clicks on the number of the day of the event. She enters a title and a description of the event and clicks "Add". She is challenged to enter a username and password and then her event is added to the calendar.

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Revised 10/19/2000 Brewer