Complex Systems, Spring 1998
Bio 367: Computational Models of Biological Organization
CS 246: Programming Paradigms


Paul Grobstein, Bryn Mawr College Department of Biology
Clare Congdon, Bryn Mawr College Computer Science Program
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Keeping Web Journals

Journal entries are due each Thursday by the start of class; they should be approximately one page in length and discuss both the reading for that week and the lab work you've done that week. (Feel free to write more.)

Each week's journal entries will be displayed on the web at the end of each week. To display these files on the web, and link them into the class web page, we have to have them all in Unix, and you have to follow (strictly!) some conventions so that we can automate the process of displaying them on the web. (The part that you have to follow strictly is the name you give to your weekly entry, the Unix directory you place it in, and the permissions that it has. More on these below.)

Note that your journal entries must be in HTML. See the local guide to HTML for more info, and week0.html for a template file that you can use as a starter.

Using the Macs to write your journal entries

Use SimpleText as an editor (in the Applications folder). When you're done with your entry, move it to your Unix account on Mainline. See the guide to Using Mainline as a File Server for the Macs for details about storing your Mac files on Mainline.

  1. Save your file as "week1.html" (or whatever the appropriate week is).
  2. You can look at your file in Netscape to check formatting, etc. as follows:
    1. Start up Netscape
    2. Go to the File menu and select Open File
    3. Navigate your way with the dialog box to specify the location of the file.
  3. When you're happy with your file, use the Chooser to login to your account on mainline. You should now have a new icon on the desktop, and you're done with the Chooser.
  4. Click on the mainline icon to see the files there. You should have a folder named public_html, and within that, a folder named Journals. (If not, we need to create one.)
  5. Drag the icon for "week1.html" to your Journals folder on mainline.
Note that even though this file is stored on Mainline (a Unix machine), if you open up Mainline with the Chooser, you can still edit it with SimpleTeext.

Using Unix to write your journal entries

Those of you who know Unix already may prefer to write your files on Unix and skip the SimpleText/Mac business:

Your journals should go in a directory called "Journals" within your "public_html" directory, and the permissions should be set so that "the world" can read these directories. (You probably don't have to futz with the permissions, but if things aren't working, that's one thing to check.)

Use emacs, vi, or textedit on mainline to create the file "week1.html" (or whatever the current week is) in your Journals directory. Make sure that this file is permitted so that "the world" can read it. (E.g., chmod 755 week1.html). You can use week0.html as a template for the html; you can get a copy of it via the "Save As" function in Netscape (described above), or you can just copy it from the class directory into your own Journals directory:

cp /www/Courses/cs246/spring98/week0.html ~/public_html/Journals

What we'll do with your files

We'll be using "server-side includes" on mainline so that your HTML files will automatically be linked in to a central page available from the class home page. If you don't name your file correctly, it won't show up, so please follow our conventions.

The pages will be set up so that we can view the journal entries two different ways. We'll be able to look at everyones' entries for any given week, and we'll be able to look at each student's entries for the whole semester.

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[Biology home page] Biology [CS home page] Computer Science [Bowdoin home page] Bryn Mawr College

Maintained by:

Clare Bates Congdon (ccongdon@brynmawr.edu)
Paul Grobstein (pgrobste@brynmawr.edu)
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