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From LMU BioDB 2017
Loyola Marymount University
BIOL/CMSI 367-01: Biological Databases
Fall 2017
Instructors
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 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 (TR 11:30am–1pm, WR 4:15–6pm, or by appointment) can be viewed as unofficial lab sessions: use them for IT help or desktop support
Part 1: Building Blocks (Genetic Code and Web Services)
| # | Date | Reading | Agenda | Journal |
|---|---|---|---|---|
| 1 | Tuesday 8/29/2017 |
Syllabus walkthrough
Pairwise interviews (report back after each bullet)
|
Week 1
(due at 12:01am 9/5) | |
| Thursday 8/31/2017 |
Discuss the Week 1 assignment (accounts should be ready to wiki at this point)
| |||
| 2 | Tuesday 9/5/2017 |
The life cycle of data
DNA (genes as model)
|
Week 2
(due at 12:01am 9/12) | |
| Thursday 9/7/2017 |
Central model
Genome sequencing and annotation | |||
| 3 | Tuesday 9/12/2017 |
An overview of computers, networks, files, web applications, web services, and databases
|
Week 3
(due at 12:01am 9/19) | |
| Thursday 9/14/2017 |
Command line lab session
| |||
| 4 | Tuesday 9/19/2017 |
Web page construction
|
Week 4
(due at 12:01am 9/26) | |
| Thursday 9/21/2017 |
Command line lab session
| |||
| 5 | Tuesday 9/26/2017 |
Introduction to biological databases
Test your understanding: http://xkcd.com/327/ |
Week 5
(due at 12:01am 10/3) | |
| Thursday 9/28/2017 |
||||
| 6 | Tuesday 10/3/2017 |
Week 6
(due at 12:01am 10/10) | ||
| Thursday 10/5/2017 |
Database presentations | |||
Part 2: Going Deeper (Gene Expression Data and Relational Databases)
| # | Date | Reading | Agenda | Journal |
|---|---|---|---|---|
| 7 | Tuesday 10/10/2017 |
Introduction to DNA microarray data | Week 7
(due at 12:01am 10/17) | |
| Thursday 10/12/2017 |
Merrell et al. (2002) "Vibrio cholerae microarray data" Nature | DNA Microarray Analysis activity part 1
Test your understanding: http://xkcd.com/882/
| ||
| 8 | Tuesday 10/17/2017 |
Week 8
(due at 12:01am 10/24) | ||
| Thursday 10/19/2017 |
||||
| 9 | Tuesday 10/24/2017 |
Gene regulatory networks (GRNs)
|
Week 9
(due at 12:01am 10/31) | |
| Thursday 10/26/2017 |
||||
| 10 | Tuesday 10/31/2017 |
Web services and APIs | Week 10
(due at 12:01am 11/7) | |
| Thursday 11/2/2017 |
||||
Part 3: Integrating for Research (GRNsight integration)
| # | Date | Reading | Agenda | Journal |
|---|---|---|---|---|
| 11 | Tuesday 11/7/2017 |
Begin GRNsight integration project | Week 11
(due at 12:01am 11/14) | |
| Thursday 11/9/2017 |
| |||
| 12 | Tuesday 11/14/2017 |
First Set of Journal Club Presentations | Week 12
(due at 12:01am 11/21) | |
| Thursday 11/16/2017 |
| |||
| 13 | Tuesday 11/21/2017 |
Second Set of Journal Club Presentations | No Week 13 assignment | |
| Thursday 11/23/2017 |
Thanksgiving—no class | |||
| 14 | Tuesday 11/28/2017 |
|
Week 14
(due at 12:01am 12/5) | |
| Thursday 11/30/2017 |
| |||
| 15 | Tuesday 12/5/2017 |
|
Week 15
(due at 12:01am 12/12) | |
| Thursday 12/7/2017 |
| |||
| F | Tuesday 12/12/2017 |
Final project presentations 2:00-4:00 PM | ||
| Friday 12/15/2017 4:30 PM |
Project deliverables due 4:30 PM | |||
