Difference between revisions of "Main Page"

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(Initial transcription/revision of course part 2.)
(Initial transcription/revision of course part 3.)
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=== Part 3: Integrating for Research (GRNsight integration) ===
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{| class="schedule-table"
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! #
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! Date
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! Reading
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! Agenda
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! Journal
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|-
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! 11
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| Tuesday<br/>11/7/2017
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|
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| Begin GRNsight integration project
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| rowspan="2" | [[Week 11]]
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 +
(due at 12:01am 11/14)
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|-
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!
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| Thursday<br/>11/9/2017
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|
 +
|
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<!--Dondi out of town-->
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* Status report
 +
* Work session
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 +
 +
{{Course Schedule Divider}}
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|-
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! 12
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| Tuesday<br/>11/14/2017
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|
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| First Set of Journal Club Presentations
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[[Presentation Rubric]]
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[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
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| rowspan="2" | [[Week 12]]
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(due at 12:01am 11/21)
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|-
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!
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| Thursday<br/>11/16/2017
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|
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|
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* Status report
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* Work session
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 +
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{{Course Schedule Divider}}
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|-
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! 13
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| Tuesday<br/>11/21/2017
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|
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| Second Set of Journal Club Presentations
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 +
[[Presentation Rubric]]
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 +
[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
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| '''''No Week 13 assignment'''''
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|-
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! style="background: #ded" |
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| style="background: #efe; border: none" | Thursday<br/>11/23/2017
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| style="background: #efe; border: none" |
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| style="background: #efe; border: none" | Thanksgiving—no class
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| style="background: #efe; border: none" |
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{{Course Schedule Divider}}
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|-
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! 14
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| Tuesday<br/>11/28/2017
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|
 +
|
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* Status report
 +
* Work session
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| rowspan="2" | [[Week 14]]
 +
 +
(due at 12:01am 12/5)
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|-
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!
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| Thursday<br/>11/30/2017
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|
 +
|
 +
* Status report
 +
* Work session
 +
{{Course Schedule Divider}}
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|-
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! 15
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| Tuesday<br/>12/5/2017
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|
 +
|
 +
* Status report
 +
* Work session
 +
| rowspan="2" | [[Week 15]]
 +
 +
(due at 12:01am 12/12)
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|-
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!
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| Thursday<br/>12/7/2017
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|
 +
|
 +
* Status report
 +
* Work session
 +
{{Course Schedule Divider}}
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|-
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! style="background: #edd" | F
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| style="background: #fee; border: none" | Tuesday<br/>12/12/2017
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| style="background: #fee; border: none" |
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| style="background: #fee; border: none" | '''Final project presentations 2:00-4:00 PM'''
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| style="background: #fee; border: none" |
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|-
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!
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| Friday<br/>12/15/2017 4:30 PM
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|
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| '''Project deliverables due 4:30 PM'''
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|
 
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Revision as of 02:24, 23 August 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
  • 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)

Week 2

(due at 12:01am 9/12)

Class Journal Week 2

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)

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

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

Week 5

(due at 12:01am 10/3)

Class Journal Week 5

Thursday
9/28/2017
6 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

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)

Class Journal Week 7

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)

Class Journal Week 8

Thursday
10/19/2017
9 Tuesday
10/24/2017 		Gene regulatory networks (GRNs)
  • Open Source review
  • Group requests due 12:01am Saturday, October 28
 Week 9

(due at 12:01am 10/31)

Class Journal Week 9

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
  • Status report
  • Work session


12 Tuesday
11/14/2017 		First Set of Journal Club Presentations

Presentation Rubric

PowerPoint Guidelines

Week 12

(due at 12:01am 11/21)

Thursday
11/16/2017
  • Status report
  • Work session


13 Tuesday
11/21/2017 		Second Set of Journal Club Presentations

Presentation Rubric

PowerPoint Guidelines

No Week 13 assignment
Thursday
11/23/2017 		Thanksgiving—no class
14 Tuesday
11/28/2017
  • Status report
  • Work session
 Week 14

(due at 12:01am 12/5)

Thursday
11/30/2017
  • Status report
  • Work session
15 Tuesday
12/5/2017
  • Status report
  • Work session
 Week 15

(due at 12:01am 12/12)

Thursday
12/7/2017
  • Status report
  • Work session
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
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