Difference between revisions of "Main Page"

Revision as of 21:54, 1 April 2013

Syllabus

The course syllabus can be found at http://myweb.lmu.edu/dondi/fall2010/cmsi367/cmsi367-fall2010-syllabus.pdf.

Announcements

Seminars and Events

Course Assessment

We ask that students in this class participate in the Research on the Integrated Science Curriculum (RISC) Survey which will allow the instructors to evaluate the effectiveness of this course. Please complete the student pre-course survey, using "Dahlquist" as the instructor last name.

Instructors

• Kam D. Dahlquist
• John David N. Dionisio

Students

Final Group Project

• Overall Description of the Gene Database Project, including entire list of deliverables
• Gene Database Project Report Guidelines

Journal Assignments

Final journal submission: As stated on the syllabus, 10% of the course/notebook journal grade will be based on the overall quality of your body of work, evaluated at the end of the semester. You are encouraged to make improvements to previous journal entries as the semester progresses.

Course Schedule

The current course schedule is shown below. In addition to the listed in-class agendas, the following guidelines are also notable:

• As mentioned in the syllabus, journals/assignments are due on Sunday night/Monday morning. In cases where subsequent revisions or corrections will be accepted, the instructors will provide feedback and submission deadlines on a per-assignment basis.
• Reading assignments should be completed before coming to that week's class.
• Dr. Dionisio’s Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

Keck Lab Workstation Tips

Here are some tips for using the workstations inside the Keck lab. These tips pertain to the physical machines themselves — you can access this Wiki from anywhere, on any machine that has a modern Web browser and an Internet connection.

Linux Workstations

• Use your Keck lab username and password directly when logging in to a Linux workstation.
• The Linux workstations use the X-Window System as their GUI environment, which will probably feel (understandably) very unfamiliar to some of you; as a quick tip, right-click on the desktop to see the programs that you can run.

Macs and Windows PCs

The Macs and Windows PCs have shared local accounts; login as "Keck Lab User" and enter "keck" as the password. The instructions below apply both to any Macs and Windows PCs in the Keck lab as well as any other Mac or Windows PC with an Internet connection.

• To connect to the Keck lab network from a Mac:
  1. Run the Terminal application
  2. Run this command on the command line that appears, substituting <username> for your Keck lab username (you will then be asked for your Keck lab password):

ssh -X <username>@keck.cs.lmu.edu

• To connect to the Keck lab network from a Windows PC:
  1. Run the PuTTY application (downloadable from http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html — you want putty.exe)
  2. Open an ssh connection to the host keck.cs.lmu.edu
  3. Under the X11 section of the Configuration window, check on "Enable X11 forwarding."
• Once connected, the commands you run in the command window will actually be invoked on the Keck lab network (and the folders/files that are stored there).
• To run GUI programs on the Keck lab network, you should know its command-line equivalent (e.g. firefox, gimp, openoffice). Type that command into the Terminal window; the program's windows should then appear on the Mac mini and you can use them normally.
• To end your connection to the Keck lab network, type this command into the Terminal:

logout

• For in-lab Macs and Windows PCs: Because the "Keck Lab User" accounts are shared, the files that you save on them cannot be guaranteed to remain there between logins. We highly recommend that you bring a flash drive with you so that you can copy your work there whenever your session is done. Alternatively, you can copy your files to your home folder on the Keck lab network. Ask a TA or Dr. Dionisio for help with that.

Academic Honesty Resources

• Honor Code Agreement
• Loyola Marymount University Undergraduate Bulletin 2010-2011
• The Davidson College Department of Biology Statement on Plagiarism
• Guidelines for Literature Citations in a Scientific Paper
• LRC presentation on plagiarism (PowerPoint presentation)
• Notes on plagiarism from an electrical engineering & computer science perspective

Practice your Wiki Skills

Make sure you know how to do the following things:

1. Every time you edit a page (whether it is a content page or discussion page), enter a meaningful description of your change in the Summary field at the bottom of the editor. This allows other users to easily see (say via the Special:RecentChanges or history pages) what has happened to the page since they last visited it.
2. Create a new Wiki page: [[new page title]] — When you include a non-existent link in a page (say, your user page), the software can tell that this page doesn't exist and colors it red instead of blue/purple. When you click on the red link, you are then given the option to edit (and thus create) the page.
   • We suggest you practice this by creating your Week 2 journal entry page. The name for the page should be in the format "username Week 2" (i.e., that is the text you put between the square brackets when you link to this page).
3. Link to a page within our Wiki: [[page title|optional visible label]]
   • Go to the Main Page and link your name to your own user page.
4. Link to an external Web page: http://address or [http://address visible label]
   • The second form of the link is preferred because it looks neater on the page.
5. Use headings: === title === (number of equals signs indicates heading level)
   • By convention, start your largest heading with two equals signs. The single equals sign is for the title of the page and is automatically created when you create the page.
6. Create a bulleted list: *
   • Note that you can create sub-bullets underneath by using multiple asterisks, e.g., **, ***, etc.
7. Create a numbered list: #
   1. Note that you can create numbered sub-lists by using multiple number signs, e.g., ##, ###, etc.
   2. You can also mix bullets and numbers, e.g., *#, #*, or even #*#, etc.
   3. Do not skip lines between your bulleted or numbered lists, or the wiki will not interpret your syntax correctly.
8. "Comment out" your Wiki code: <!-- commented-out Wiki text --> When you "comment out" your wiki code, the code will be visible on the Edit page, but will not be visible on the wiki page itself. "Commenting" is a common practice in coding that is used to explain the meaning of the code for someone else reading it. In this situation, commenting can be used to keep a rough draft of a wiki page invisible until you are ready for it to be seen.
9. Upload an image file: Click Upload file then follow the instructions.
   • Use the image on your page: [[Image:exact-name-of-image-file]]
   • REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest you include an image of yourself that would be suitable for a professional resume.
10. Upload another type of file (such as .pdf): Click Upload file then follow the instructions.
    • Link to the file you uploaded on your Wiki page: [[Media:exact-name-of-uploaded-file|visible label]]
    • REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest that you include something professional, such as the Word or PDF version of your paper resume, a scientific paper you have written, etc.
11. Assign one or more categories to your page: [[Category:category name]] This creates an automatic "table of contents" for the wiki. When you click on a category link at the bottom of a page, a new page opens giving you a list of all wiki pages that have been assigned that category.
    • Throughout the course, you will use the category [[Category:Journal Entry]] for all of the journal entry pages and [[Category:Shared]] for all of the shared journal pages.
12. Use the discussion page to make a comment. Wiki etiquette requires that you sign your comments with your "signature": ~~~~ (4 tildes in a row). These tildes get converted automatically, for example, into: Kdahlquist 15:47, 28 August 2008 (UTC)
    • You can fulfill this by posting your comment on (Drs. Dahlquist and Dionisio user talk pages).
13. Create a template for yourself and use it on your user page. A template is a block of wiki text that you want to use over and over again on various pages. Instead of having to either re-type that content or even copy-and-paste it multiple times, you can simply put the content on a special Template page. You then use code to invoke the template on any other page in which you want that text to appear. There are two steps to creating a Template.
    • Create your template page like you would create any other new wiki page, but using the prefix Template: as part of the page name. For example, your template should be called [[Template:username]].
    • Click on the link and put content on this page that you will want to use over and over again. At the minimum, you should use it to create a set of navigation links that you will use in each week's journal entry. Each week as part of your journal assignment, you will be asked to create a link to your user page, the assignment page, your journal entry page, and the shared journal page, as well as add the category "Journal Entry" to your page. If you put these links on your template and then invoke the template on your journal page, this will automatically be taken care of for you. You may also wish to include any other links that you would find useful.
    • Once you have added and saved the content to your Template page, you need to use your template on your user page. To do so, invoke the template by using the following syntax: Template:Username in the place you wish the content of the template page to appear. For example, this set of wiki instructions is controlled by the Template:Wiki Checklist, and you can include it in any page by saying: {{Wiki Checklist}}. This will "expand" the template to its full contents on the actual page.