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Loyola Marymount University

BIOL/CMSI 367-01: Biological Databases

Fall 2017

Instructors

• Kam D. Dahlquist
• John David N. Dionisio

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 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 12:01am 9/5) Class Journal Week 1
	Thursday 8/31/2017		Discuss the Week 1 assignment (accounts should be ready to wiki at this point) Quick wiki overview User wiki page setup
2	Tuesday 9/5/2017		The life cycle of data DNA (genes as model) DNA structure and Genetic Code Slides shown in class on MyLMU Connect	Week 2 (due at 12:01am 9/12) Class Journal Week 2
	Thursday 9/7/2017		Central model Berkeley translation video This web site has links to animations of the replication, transcription, and translation processes. Slides shown in class Genetic Code-Gene Expression Pencil Exercise Genome sequencing and annotation
3	Tuesday 9/12/2017		An overview of computers, networks, files, web applications, web services, and databases Useful help resource: http://explainshell.com Accessing the web on the command line	Week 3 (due at 12:01am 9/19) Class Journal Week 3
	Thursday 9/14/2017		Command line lab session Hands-on practice Discuss Week 3 assignment tasks
4	Tuesday 9/19/2017		Web page construction HTML Bootstrap Web browser development tools	Week 4 (due at 12:01am 9/26) Class Journal Week 4
	Thursday 9/21/2017		Command line lab session Review assignment issues Discuss Week 4 computer portion
5	Tuesday 9/26/2017	The 24th annual Nucleic Acids Research database issue The NAR Molecular Biology Database Collection	Introduction to biological databases Slides shown in class (MyLMU Connect) DataONE: Why Data Management DataONE: Data Sharing Case study from one of the NAR databases: http://www.rhesusbase.org Relating XML structure to relational structure Test your understanding: http://xkcd.com/327/	Week 5 (due at 12:01am 10/3) Class Journal Week 5
	Thursday 9/28/2017
5	Tuesday 10/3/2017			Week 6 (due at 12:01am 10/10) Class Journal Week 6
	Thursday 10/5/2017		Database presentations Presentation Rubric PowerPoint Guidelines