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Loyola Marymount University
BIOL 367-01: Biological Databases
Spring 2024

Announcements

  • Don't forget to sign your class journal entries with your wiki signature! ~~~~

Upcoming Seminars

There are no more seminars for the remainder of the semester.


Instructor

Students

Hailey Ivanson Andrew Sandler
Charlotte Kaplan Natalija Stojanovic
Katherine Miller Dean Symonds
Final Project Links
Overview Deliverables Guilds Project Manager Quality Assurance Data Analysis Coder/Designer
Team Yeast Beasts

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 Thursdays at 12:01am. In cases where subsequent revisions or corrections will be accepted, the instructor will provide feedback and submission deadlines on a per-assignment basis.
  • Reading assignments should be completed before coming to class.
Week
Date
Before Class Reading
During Class Topic After Class Assignment
1 9-Jan
  • Syllabus walkthrough
  • Pairwise interviews and introductions
  • Academic Honesty case studies
  • Wiki account setup
Week 1

(due 12:01am 1/18)


Class Journal Week 1
11-Jan Dahlquist et al. (2017) An Invitation to Modeling
  • What is a model?
  • Model of a cell/model of a computer
2 16-Jan
  • Discuss the Week 1 assignment
    • Wiki syntax overview
    • Lab session to setup User wiki page
Week 2

(due 12:01am 1/25)

Class Journal Week 2
18-Jan DNA structure
3 23-Jan Aipotu work session Week 3

(due 12:01am 2/1)

Class Journal Week 3
25-Jan
4 30-Jan

Introduction to biological databases ( part 1 slides)

  • What is bioinformatics?
  • Open Science Ecosystem
  • DataONE: Data management and the life cycle of data
  • Terminology, types, four "Gold Standard" databases
Week 4

(due 12:01am 2/8)

Class Journal Week 4
1-Feb

Introduction to biological databases ( part 2 slides)

  • A closer look at evaluating biological databases
  • DataONE: Data sharing
5 6-Feb Week 5

(due 12:01am 2/15)

Class Journal Week 5
8-Feb

Database presentations

Part 2: Going Deeper (Gene Expression Data and Relational Databases)
6 13-Feb
  • Moody (2004) Digital Code of Life, Ch. 6 (on Brightspace)
  • Original (2001) Human Genome Project articles in Nature & Science
  • Special issues (2021) "The Human Genome at 20" in Nature & Science
Human Genome Project Week 6

(due 12:01am 2/22)

Class Journal Week 6
15-Feb

Where's my Stuff?

  • Slides are on Brightspace
  • An overview of computers, networks, files, web applications, web services, and databases
  • Names, URLs, identifiers
    • As applied to biology: genes, species
  • “Stuff” on the worldwide web
    • Accessing the web on a browser
7 20-Feb Week 6 work session
  • Please bring ear buds/headphones if possible.
No Week 7 Assignment
22-Feb 'omics analysis
Spring Break 27-Feb No class
29-Feb
8 5-Mar Guest lecture: Dr. Dionisio
  • Relational Databases part 1
Week 8

(due 12:01am 3/14)

Class Journal Week 8
7-Mar Super basic SQL crib sheet Guest lecture: Dr. Dionisio
  • Relational Databases part 2
9 12-Mar Week 8 work session
Week 9

(due 12:01am 3/21)

Class Journal Week 9
14-Mar Transcriptomic analysis (part 1)
  • ANOVA
10 19-Mar "Significant" Transcriptomic analysis (part 2)
  • Multiple testing problem, p value corrections
Week 10

(due 12:01am 4/4, interim deadlines on 3/26 and 4/2)

Class Journal Week 10
21-Mar Transcriptomic analysis (part 3)
  • Clustering and GO term enrichment analysis
11 26-Mar
  • Transcriptomic analysis (part 4)
    • GRN modeling and visualization
Continue with
Week 10 assignment
Easter 28-Mar No class
Part 3: Integrating for Research (GRNsight Gene Expression Database Project)
12 2-Apr Discussion of Week 10 results Week 12

(due 12:01am 4/11)
4-Apr Begin Database Project
  • Overview of project
  • Work session for journal club
13 9-Apr Work session for journal club Week 13

(due 12:01am 4/18)
11-Apr
  • Journal Club Presentations
  • Work session to organize milestones
14 16-Jan
  • Status report
  • Work session
Week 14

(due 12:01am 4/25)
18-Apr
  • Status report
  • Work session
15 23-Apr
  • Status report
  • Work session
Week 15

(due 12:00 noon 5/3)
25-Apr
  • Status report
  • Work session
Finals 2-May Final Presentations 11:00am
3-May Project Deliverables Due 12:00 noon

Course Information

Instructor

Kam D. Dahlquist, Ph.D.

http://kdahlquist.github.io/DahlquistLab/index.htm
Phone: (310) 338-7697
E-mail: kdahlquist at lmu dot edu
Office: Life Sciences Building 289
Office Hours (Spring 2024): Mondays 2:00-3:30 PM, Tuesdays 3:15-4:45, and by appointment; check Brightspace for a Calendly link to make an appointment for a Zoom or in-person meeting.

Prerequisites/Recommended Background

BIOL 201 and MATH 123 or MATH 132 or MATH 204 or MATH 205.

Class Meetings and Attendance

TR 1:45-3:00pm, 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 12 point (2.5%) 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 instructor 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 January 12. The withdrawal or credit/no-credit status deadline is April 5.

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 instructor 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 and other ancillary 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, provided that you have confirmed with the instructor that you have the correct versions of software installed for the exercise. If, however, the laptops/tablets 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 the Student Conduct 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.

Course Website

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/spring2024/. You will need to have a user account on this wiki 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 the course page on Brightspace. The site will be used for materials that cannot be made public on this wiki, including grades.

Email Communication

At times I will communicate with the entire class using campus email systems, so it is essential that you regularly check your lion.lmu.edu email address or forward your lion account email to your preferred email address. Messages sent to the instructor at night or on the weekend will be answered the next school day.

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 Brightspace site. Specific reading assignments are given on the course schedule and should be completed before coming to class.

  • 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 or folder with all course handouts
  • Pen, pencil, extra paper
  • USB flash drive to back-up data
  • Account for this wiki

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 your discipline and different disciplines

University Core Curriculum

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

  • Integrations: Interdisciplinary Connections

Course Work and Grading

Your work in this course will be assessed in the following areas:

Weekly electronic lab notebook/journal assignments, individual (usually 12 points each) 168 points
Weekly electronic lab notebook/journal assignments, shared (usually 3 points each) 42 points
Oral presentations (3 @ 35, 45, 60 points) 140 points
Final Project Deliverables (including written report) 100 points
Total 450 points

Final course grading scale:

94.0-100.0%		A
90.0- 93.9%		A-
86.0- 89.9%		B+
82.0- 85.9%		B
78.0- 81.9%		B-
74.0- 77.9%		C+
70.0- 73.9%		C
67.0- 69.9%		C-
60.0- 66.9%		D
   ≤  59.9%		F

Current grades will be made available at Brightspace.

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. The wiki software is the same one that runs Wikipedia and many other wiki sites, so proficiency gained here is easily transferable to other applications.

You will create an individual user page and make weekly entries that the instructor 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 12:01am on Thursday Pacific time; consult the schedule for specific due dates for each assignment.
  • Each weekly assignment has an individual component and a shared component. You will earn 12 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 instructor 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.
  • For most weeks in the semester, you will be assigned a "homework partner". You will be expected to consult with your partner 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).
  • Generally, your journal entries will consist of:
    • Your electronic laboratory notebook (workflow and other documentation) for hands-on exercises and projects
    • Answers to any specific questions posed in the exercise
    • Acknowledgments section (see Week 1 assignment for details)
    • References section (see Week 1 assignment for details)
    • Shared reflection on your learning, assigned readings, or ethics case studies.

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

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 will be posted later in the semester. The Final Written Report cannot be accepted any later than Friday, May 3 at 12:00pm. The Final Written Report must be completed to receive a passing grade in the course.

Life happens, what do I do then? Use your tokens!

To succeed in this course it is important to come to each class session and keep up with the work. However, I understand that circumstances may arise from time-to-time that could interfere with this. To responsibly manage these circumstances, the following token system is in place.

  • Each student begins the semester with 4 tokens that can be used as follows:
    • 1 token = turning in a individual journal entry up to one week later without penalty or dropping a missed shared journal entry from the final grade without penalty.
    • 3 tokens = dropping a missed individual journal club entry from the final grade without penalty.
    • 4 tokens = excusing an absence without penalty beyond the two automatically excused.
  • To use tokens, the instructor must be emailed about your intention to use the token(s) at the day/time of usage (due date or absence). Requests to use tokens after one week from the due date or absence has passed will not be honored. Unused tokens have no point value.
  • Up to two additional tokens may be earned by attending extra credit seminars (see below).

Extra Credit

Students may accumulate up to 12.5 points toward their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 2.5 points with up to 5 seminars (12.5 points) total.

Alternately, you may elect to earn a token for attending the seminar instead of the extra credit points. Only two tokens may be earned this way, and the instructor must be notified of your intention to earn a token instead of extra credit at the time of the seminar by writing it on the seminar sheet on the day of the seminar.

Certain non-Biology Department seminars may be approved in advance for extra credit at the instructor's 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.

Biology Department Seminar Attendance Policy
  • To receive course credit for attending a Biology Department Seminar, students must do the following:
    • Arrive early at the seminar venue (usually FEA auditorium) and obtain a paper seminar sheet from a faculty member.
      • Seminar sheets will only be available until 3:05 PM, at which time no further sheets will be distributed.
      • You must pick up the seminar sheet yourself. You may not obtain seminar sheets for others.
    • Completely fill out the seminar sheet during the seminar, including:
      • Your name as it appears on PROWL
      • All course numbers, section numbers, professor and TA names for the courses for which you would like to receive credit
      • Day and time of seminar, speaker name, and title
      • Answer the other questions on the seminar sheet.
    • Stay quietly in your seat for the entire seminar, including the question and answer period.
    • At the end of the seminar, take a picture of the seminar sheet and upload it to the survey link accessed via a posted QR code.
    • Turn in the paper seminar sheet to a faculty member before exiting the room.
      • You must turn in your own seminar sheet; you may not turn it in for someone else.
  • Note that students arriving after 3:05 PM will not receive a seminar sheet and must enter through the back entrance on the second floor of the FEA auditorium so as not to disturb the seminar in progress.

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 is a community dedicated to academic excellence. Academic honesty in scholarship and creative work stands at the center of LMU's academic life, and is essential for true learning and creation of knowledge to take place. As a university in the Jesuit and Marymount traditions, this community expects its members to act in accordance with the highest standards of honesty and ethics at all times. Violations of academic honesty undermine the fundamental educational mission of the University and cannot be tolerated.

Academic dishonesty will be treated as an extremely serious matter with severe consequences. The minimum penalty for an instance of academic dishonesty in this course, even on a 1-point assignment or extra credit assignment, is a one-letter grade penalty in the course and a zero on the assignment. It is never permissible to turn in any work that has not been authored by the student, such as work that has been copied from another student or copied from a source (including the Internet) without properly acknowledging the source. Note that students may not submit assignment or paper prompts to CourseHero, Chegg, online artificial intelligence tools, or any other such website; answers or papers derived from such sites are considered to be a direct violation of the Academic Honesty policy. It is the student's responsibility to make sure that your work meets the standard set forth in the “Academic Honesty Policy” (see http://academics.lmu.edu/honesty.) You are responsible for contacting the instructor before assignments are due to proactively resolve any questions you may have.

You are required to sign the Academic Honesty 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 http://www.lmu.edu/dss for additional information. In addition, please schedule an appointment with the instructor early in the semester to discuss any accommodations for this course for which you have been approved.

Health and Wellness

There are many resources for student wellness on campus. A central website for students is: http://lionwellness.lmu.edu.

COVID-19

All University mandated COVID-19 safety guidelines are to be followed. The LMU Together and Need to Know A-Z Index websites contain updated information. If you have COVID-19 symptoms and/or test positive, please contact the COVID Support Team (COVIDSupportTeam@lmu.edu or 310-568-6868) for instructions.

Emergency Preparedness

To report an emergency or suspicious activity, contact the LMU Department of Public Safety by phone (x222 or 310-338-2894) or at the nearest emergency call box. In the event of an evacuation, follow the evacuation signage throughout the building to the designated safe refuge area where you will receive further instruction from Public Safety or a Building Captain. For more safety information and preparedness tips, visit http://www.lmu.edu/emergency.

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/spring2024/.