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Announcements

Seminars and Events

• Bellarmine Forum: Monday, October 28, 6:00-8:30 PM, UH1000, Dr. Eric Strauss, LMU Biology and Dr. Scott Wood, Director, CURes Restorative Justice Project, Restoring Healthy Communities
• Biology Department Seminar: Tuesday, October 29, 12:15 PM, SEA 200, Tatiana Kuzmenko, LMU Biology, Emotions Are Essential for Long-term Memory Formation, Demonstrated by Ants
• Special Projects Poster Session: Thursday, October 31, 12:15-1:30, Seaver First Floor Foyer. To receive extra credit for attending, you must speak with at least five poster presenters and turn in a one page reflection on what you learned by the following Thursday. In your reflection, give the names of the presenters you spoke with and the titles of their posters.
• Biology Department Seminar: Thursday, November 7, 12:15 PM, SEA 200, Diane Lynch, LMU Biology alumna, Environmental Advisor for ExxonMobil Refining & Supply, Careers in Environmental Compliance
• Bioethics Institute Lecture Series: Wednesday, November 13, 7:00-8:30 PM, UH1000, Dr. Kevin Fitzgerald, S.J., Georgetown University, Regenerative Medicine and the Illusion of Immortality: Promising Future, Perilous Path?
• Biology Department Seminar: Tuesday, November 19, 12:15 PM, SEA 200, Dr. Michele Romolini, CURes/US Forest Service postdoc, Green Infrastructure for Resilient Cities: Urban Tree Canopy & Environmental Stewardship

Class Locations

• October 24: lab
• October 29: lab
• October 31: lab
• November 5: lab
• November 7: classroom

Group Projects

• Gene Database Project
• Gene Database Project Report Guidelines

Teams

Guilds

Instructors

• Kam D. Dahlquist
• John David N. Dionisio

Students

Course Schedule

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

• Unless otherwise stated on the schedule, your weekly journals/assignments are due on Fridays at midnight (Thursday night/Friday 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 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.
  • http://myweb.lmu.edu/kdahlqui
  • Phone: (310) 338-7697
  • E-mail: kdahlquist at lmu dot edu
  • Office: Seaver 218
  • Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
• John David N. Dionisio, Ph.D.
  • http://myweb.lmu.edu/dondi
  • Phone: (310) 338-5782
  • E-mail: dondi at lmu dot edu
  • Office: Doolan 106
  • Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, 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

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.

• This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, A First Course in Database Systems, Third Edition. Prentice Hall, 2008.
• Assorted handouts, articles, and sample code will 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

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

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

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).

Your work in this course will be assessed in four areas:

Electronic Laboratory Notebook/Journal

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:

• Your weekly journal entry is typically due every midnight on Friday PST (Thursday night/Friday morning); consult the schedule for specific due dates for each assignment.
• You will earn 10 points per weekly submission. Late journal entries will be accepted up to one week later for up to half credit.
• The instructors will read and comment on how to improve your journal entries.
• Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
• Generally, your journal entries will consist of:
  • Workflow and other documentation for hands-on exercises and projects
  • Answers to any specific questions posed in the exercise
  • Reflection on your learning

Oral Presentations

You will give four oral presentations in this course. The first three will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The fourth will be a research presentation on your final project. Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.

Final Group Project

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

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted here. The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.

Work Load Expectations

In line with LMU’s Credit Hour Policy, the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

Extra Credit

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar within one week of the date of the seminar or they will not count as extra credit.

University Policy on Academic Honesty

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” Click here for an online version of the LMU Honor Code and Process.

You are required to sign the Honor Code Agreement for this course.

Academic Honesty Resources

• Honor Code Agreement
• LMU Honor Code and Process, 2013-2014 University Bulletin.
• 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

Special Accomodations

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

Revision Notice

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

Keck Lab Workstation Guidelines

Please visit this page for guidelines and instructions on using the Keck computer science lab.