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Revision as of 17:48, 11 June 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

Course Information

Instructors

• Kam D. Dahlquist, Ph.D.
  • Phone: (310) 338-7697
  • E-mail: kdahlquist at lmu dot edu
  • Office: Seaver 218
  • Office hours: TBA and by appointment
• John David N. Dionisio, Ph.D.
  • Phone: (310) 338-5782
  • E-mail: dondi at lmu dot edu
  • Office: Doolan 106
  • Office hours: TBA and by appointment

Prerequisites/Recommended Background

To take this course, you must have upper division standing in either the College of Science and Engineering or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

Class Meetings and Attendance

TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

Mutual Responsibilities

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

Classroom Conduct

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to LMU’s Community Standards for the Student Conduct Code or to the Lion’s Code. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:

1. You are responsible for your own learning and for being a good class citizen.
2. We will act with honesty and integrity at all times.
3. We will always treat individuals with respect.
4. Class will start promptly on time.
5. You are expected to come to class having done the assigned reading and preparatory work.
6. You are expected to bring the required materials to each class session.
7. Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

Course Web Site

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

Required Materials

Texts

• David P. Clark and Lonnie Dee Russell, Molecular Biology Made Simple and Fun (a.k.a. “the monkey book”). Cache River Press, 1997.
• Recommended but not required: Jeffrey Ullman and Jennifer Widom, A First Course in Database Systems, Third Edition. Prentice Hall, 2008.
• Assorted handouts, articles, and sample code to be distributed throughout the semester.
• Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

Materials (must be brought to each class meeting)

• 3-ring binder with all course handouts
• Pen, pencil, extra paper
• USB flash drive to store data
• Keck lab account

Course Description

Course Objectives and Learning Outcomes

This course is built upon L. Dee Fink’s taxonomy of significant learning, as applied to biological databases. Long after the course concludes, our hope is that:

• You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
• You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
• You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
• You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
• You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
• You learn how to communicate and work effectively with colleagues from different disciplines

Course Work and Grading

Graded coursework consists of quizzes (10%), presentations (10%), an ongoing, online course notebook/journal (40%), and 1 biological database project (40%). Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

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.