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Loyola Marymount University
BIOL/CMSI 367-01: Biological Databases
Fall 2015

Announcements

Please note that this version is similar, but not identical, to the process shown in class (Dondi misremembered the function to use; it was supposed to be match, as shown in the wiki page, and not lookup). Furthermore, instructions for exporting from PostgreSQL (you might recall that the numbers did not match there either) are included. —Dondi (talk) 18:49, 29 October 2015 (PDT)
  • TriBeta Halloween Party and Costume Contest: Friday, October 30, 6:00 PM, LSB Terrace, $3 (to cover food). RSVP to ralkhaya at lion dot lmu dot edu. Come see if you can beat me in the costume contest! — Kdahlquist (talk) 09:46, 28 October 2015 (PDT)
  • An initial round of feedback to the Week 6 assignment has been posted to your respective user talk pages. The database part is not finished, but I figured some feedback and basics on the best practice stuff will be useful as you prepare your Week 8 work (as in, get used to making the best practices routine so you can avoid nagging deductions week after week). —Dondi (talk) 21:30, 25 October 2015 (PDT)
  • To report issues with the configuration of the computers in Seaver 120, please record it on this wiki page. The complete list of software that should be installed for this course is found here. Note that this configuration is Windows-specific. Some software may not be available for a Mac or may look differently.

Upcoming Seminars

  • Chemistry & Biochemistry Department Seminar: Thursday, October 29, 11:50 AM, Seaver 200, Presentation by first candidate for the Biochemistry Faculty Search.
  • Biology Department Seminar: Friday, October 30, 2:00 PM, LSB Auditorium, Dr. Ashley Robart, LMU Biology, MALE QUALITY INFLUENCES PARENTAL CARE, BUT NOT FEMALE COMPETITION, IN A MONOGAMOUS, BIPARENTAL FISH.
  • Noyce Poster Session: Friday, October 30, 4:00 – 6:00 PM, Hannon Courtyard of the LSB (area just outside the west entrance). The NOYCE Summer Interns will be presenting the posters they made highlighting the research they have done. The Poster Session will be a fantastic opportunity to talk to the presenters and ask them all about their research! To receive the extra credit, fill out one of the "seminar" sheets available according to the instructions and turn it in to a professor before you leave the poster session.
  • Chemistry & Biochemistry Department Seminar: Thursday, November 5, 11:50 AM, Seaver 200, Presentation by second candidate for the Biochemistry Faculty Search.
  • Biology Department Seminar: Friday, November 6, 2:00 PM, LSB Auditorium, Dr. Wes Dowd, LMU Biology.
  • Chemistry & Biochemistry Department Seminar: Tuesday, November 10, 11:50 AM, Seaver 200, Presentation by third candidate for the Biochemistry Faculty Search.
  • Chemistry & Biochemistry Department Seminar: Thursday, November 12, 11:50 AM, Seaver 200, Presentation by fourth candidate for the Biochemistry Faculty Search.
  • Biology Department Seminar: Friday, December 4, 2:00 PM, LSB Auditorium, Dr. Deepa Dabir, LMU Biology.


Instructors

Students

Mary Alverson Ron Legaspi Trixie Roque Jake Woodlee
Nicole Anguiano Brandon Litvak Mahrad Saeedi Kevin Wyllie
Brandon Klein Elena Olufson Emily Simso Erich Yanoschik
Josh Kuroda Veronica Pacheco Anindita Varshneya Kristin Zebrowski

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 Tuesdays at midnight (Monday night/Tuesday 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 office hours (T 11am–12:30pm, W 3–6pm, R 1–2:30pm, or by appointment (except on weekends)) can be viewed as unofficial lab sessions: use them for IT help or desktop support

Part 1: Building Blocks (Genetic Code and Manipulating Text)

# Date Reading Agenda Journal
1 Tuesday
9/1/2015 		Syllabus walkthrough
  • my.cs.lmu.edu account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
  • Class wiki account: Set up a username and password for this wiki site

Pairwise interviews (report back after each bullet)

  • Basic acquaintance information
  • Like a cell/not like a cell; like a computer/not like a computer
 Week 1

(due at midnight 9/8)

Class Journal Week 1

Thursday
9/3/2015

Voices of Computing and Computing is a Natural Science by Peter Denning (these links should be accessed from within LMU to get the full article)

Chapter 1 of On Becoming a Biologist by John Janovy, Jr. (on MyLMUConnect)

Discuss the Week 1 assignment (accounts should be ready to wiki at this point)
  • Quick wiki overview
  • User wiki page setup


2 Tuesday
9/8/2015 		Ch. 1.1 Genomes 2

Watson & Crick (1953)

Franklin & Gosling (1953)

DNA Week 2

(due at midnight 9/15)

Class Journal Week 2

Thursday
9/10/2015 		On MyLMUConnect:

Nirenberg (2004) Deciphering the Genetic Code

Kaji & Kaji (2004) Setting the Record Straight

Moody (2004) Digital Code of Life, Ch. 1

Hayes (2004) Ode to the Code

Brown, T.A. (2002) Genomes 2, Ch. 3, especially section 3.3.2

Central dogma


3 Tuesday
9/15/2015 		Ford (2015) What is Code?
  • Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further

Where's my Stuff?

Introduction to the Command Line

An overview of computers, networks, files, and databases Week 3

(due at midnight 9/22)

Class Journal Week 3

Thursday
9/17/2015 		Command line lab session
  • Hands-on practice
  • Discuss Week 3 assignment tasks


4 Tuesday
9/22/2015 		Moody (2004) Chapter 6 (on MyLMU Connect)

Science After the Sequence

Nature Special: Human Genome at 10

Introduction to NAR Database Issue

Commentary on NAR Database Issue

Genome sequencing and annotation

Introduction to biological databases

Week 4

(due at midnight 9/29)

Class Journal Week 4

Thursday
9/24/2015 		More Text Processing Features

How to Read XML Files

Command line lab session
  • Review assignment issues
  • Discuss Week 4 computer portion


5 Tuesday
9/29/2015 		The Relational Data Model: Structure

An Overview of SQL

Introduction to relational databases

Test your understanding: http://xkcd.com/327/

Week 5

(due at midnight 10/6)

Class Journal Week 5

Thursday
10/1/2015 		Additional background and details can be found in Chapters 1, 2, and 6 of A First Course in Database Systems (on reserve at the library). SQL and working with relational databases continued


6 Tuesday
10/6/2015 		President Synder’s Inauguration Day Week 6

(due at midnight 10/13)

Class Journal Week 6

Thursday
10/8/2015 		Database presentations
  1. Nicole, Erich, Kristen, Josh
  2. Mary, Emily, Brandon L., Kevin
  3. Lena, Jake, Anu, Veronica
  4. Ron, Mahrad, Brandon K., Trixie

Presentation Rubric

PowerPoint Guidelines

Part 2: Going Deeper (Gene Expression Data and Relational Databases)

# Date Reading Agenda Journal
7 Tuesday
10/13/2015 		Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays

Brown & Botstein (1999) "Microarrays" Nature Genetics

Campbell & Heyer Chapter 4 (on MyLMU Connect)

DeRisi et al. (1997) Science 278: 680-686.

Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder Week 7

(due at midnight 10/20)

Class Journal Week 7

Thursday
10/15/2015 		Merrell et al. (2002) "Vibrio cholerae microarray data" Nature DNA Microarray Analysis activity part 1

Test your understanding: http://xkcd.com/882/


8 Tuesday
10/20/2015 		Ashburner et al. (2000) "Gene Ontology" Nature Genetics

Doniger et al. (2003) "MAPPFinder" Genome Biology

DNA Microarray Analysis activity part 2 Week 8

(due at midnight 10/27)

Class Journal Week 8

Thursday
10/22/2015 		Work session to complete DNA Microarray Analysis part 1 and part 2


9 Tuesday
10/27/2015 		Week 9

(due at midnight 11/3)

Class Journal Week 9

Thursday
10/29/2015 		Dimmer et al. (2012) "UniProt-GOA Database" Nucleic Acids Research

Heidelberg et al. (2000) "Vibrio cholerae Genome Sequence" Nature

Integrity analysis of Vibrio Gene Database

Part 3: Integrating for Research (Gene Database Project)

# Date Reading Agenda Journal
10 Tuesday
11/3/2015
  • Annotated bibliography of genomics papers for your species
  • Course LibGuide: http://libguides.lmu.edu/BIOL367
    • Select genome paper for journal club
    • Select microarray paper
 Week 10

(due at midnight 11/10)

Thursday
11/5/2015 		Begin group projects


11 Tuesday
11/10/2015 		Guild meetings and work session
  • Export of Gene Database for your group's species
  • Document ID types for your species
  • Begin DNA microarray analysis
 Week 11

(due at midnight 11/17)

Thursday
11/12/2015
  • Status report
  • Work session


12 Tuesday
11/17/2015 		First Set of Journal Club Presentations
  1. TBD
  2. TBD
  3. TBD
  4. TBD

Presentation Rubric

PowerPoint Guidelines

Week 12

(due at midnight 11/24)

Thursday
11/19/2015
  • Status report
  • Work session


13 Tuesday
11/24/2015 		Second Set of Journal Club Presentations
  1. TBD
  2. TBD
  3. TBD
  4. TBD

Presentation Rubric

PowerPoint Guidelines

No Week 13 assignment
Thursday
11/26/2015 		Thanksgiving—no class
14 Tuesday
12/1/2015
  • Status report
  • Work session
 Week 14

(due at midnight 12/8)

Thursday
12/3/2015
  • Status report
  • Work session
15 Tuesday
12/8/2015
  • Status report
  • Work session
 Week 15

(due at midnight 12/15)

Thursday
12/10/2015
  • Status report
  • Work session
F Tuesday
12/15/2015 		Final project presentations 2:00-4:00 PM
Friday
12/18/2015 4:30 PM 		Project deliverables due 4:30 PM

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: Life Sciences Building 289
Office Hours: Tuesdays 9:00-11:00 AM, Wednesdays 1:30-3:30 PM and by appointment. I keep a sign-up sheet on my office door to facilitate appointment-making.

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: T 11am–12:30pm, W 3–6pm, R 1–2:30pm, or by appointment (except on weekends)

Prerequisites/Recommended Background

To take this course, you must have upper division standing in the Seaver College of Science and Engineering. 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 2:40–3:55pm, Seaver 120

This is a hands-on, participatory course, thus attendance at all class meetings is required. Each student is allowed two “sick” days (automatically excused absences) during the semester. Further unexcused absences from class will result in a 5% deduction from the overall course grade for each absence. Every effort should be made to attend class on oral presentation days as the content of that day's class is dependent on student participation. Unexcused absences from an oral presentation will result in a grade of zero for the presentation. 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 September 4. The withdrawal or credit/no-credit status deadline is November 6.

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

We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:

  1. 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.
  2. You are responsible for your own learning and for being a good class citizen.
  3. Class will start promptly on time.
  4. You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
  5. You are expected to bring the required materials to each class session.
  6. Cell phones, pagers, and other communication or music devices must be turned off and put away out of sight. Your own laptop and/or tablet may be used to conduct the class exercises; however, if they are being used for other purposes and become distracting to you or others, you will be asked to put them away.
  7. All students are governed by LMU Community Standards Publication. 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.

Course Website

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2015/. 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 BIOL/CMSI 367-01 on MyLMUConnect. The two cross-listed sections are using the same site, which is listed as "Biological Databases Fall 2015" with no department or course number. The MyLMUConnect site will be used for materials that cannot be made public on this wiki, including grades.

E-mail Communication

At times we will communicate with the entire class using campus e-mail systems, so it is essential that you regularly check your lion.lmu.edu e-mail address or forward your lion account e-mail to your preferred e-mail address. Messages sent to the instructors at night or on the weekend will be answered the next school day. Please CC both instructors on all e-mail messages related to this class.

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 this wiki or the 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)

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-to-day 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

University Core Curriculum

This course fulfills the following requirements in the University Core Curriculum:

  • Integrations: Interdisciplinary Connections
  • Upper Division Information Literacy Flag
  • Upper Division Oral Communication Flag

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 five areas:

Weekly electronic lab notebook/journal assignments, individual (10 points each) 140 points
Weekly electronic lab notebook/journal assignments, shared (3 points each) 42 points
Oral presentations 105 points
Information literacy (additional points added to two journal assignments) 24 points
Final Project Deliverables (including written report) 175 points
Total 486 points

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 Tuesday PST (Monday night/Tuesday morning); consult the schedule for specific due dates for each assignment.
  • Each weekly assignment has an individual component and a shared component. You will earn 10 points per weekly submission for the individual journal entry and 3 points per submission for the shared journal entry. 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 on your user talk pages.
  • 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:
    • Your electronic laboratory notebook and other documentation for hands-on exercises and projects
    • Answers to any specific questions posed in the exercise
    • Reflection on your learning
  • For most weeks in the semester, you will be assigned a "homework partner" from the complementary biology or computer science discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed).

Oral Presentations

You will give three oral presentations in this course. The first two 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 third will be a research presentation on your final project. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted. An unexcused absence from a journal club presentation will result in a grade of zero for the presentation.

Final Group Project

Teams Guilds
Team1 Project Manager
Team2 GenMAPP User
Team3 Quality Assurance
Team4 Coder

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 18 at 4:30 PM. The Final Written Report must be completed to receive a passing grade in the course.

Extra Credit

Students may accumulate up to 12.5 points toward 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 2.5 points with up to 5 seminars (12.5 points) 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 hard copy of your summary of the seminar in class, within one week of the date of the seminar or they will not count as extra credit.

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.

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.” Attempting to gain extra credit for a seminar that you did not attend or assisting another student to do this are examples of academic dishonesty and will be considered a violation of the Honor Code. 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

Americans with Disabilities Act—Special Accommodations

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/fall2015/.


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