Difference between revisions of "Main Page"

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(Initial transcription/revision of course part 1.)
(Initial transcription/revision of course part 2.)
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{{Course Schedule Divider}}
 
{{Course Schedule Divider}}
 
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! 5
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! 6
 
| Tuesday<br/>10/3/2017
 
| Tuesday<br/>10/3/2017
 
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[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
 
[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
 
<!--Introduction to the [http://www.opensource.org/ open source] culture-->
 
<!--Introduction to the [http://www.opensource.org/ open source] culture-->
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|}
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=== Part 2: Going Deeper (Gene Expression Data and Relational Databases) ===
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{| class="schedule-table"
 +
! #
 +
! Date
 +
! Reading
 +
! Agenda
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! Journal
 +
|-
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! 7
 +
| Tuesday<br/>10/10/2017
 +
| <!--
 +
[http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]
 +
 +
[http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999) "Microarrays" ''Nature Genetics'']
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 +
Campbell & Heyer Chapter 4 (on [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1 MyLMU Connect])
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 +
DeRisi et al. (1997)  [http://www.sciencemag.org/content/278/5338/680.full ''Science'' 278: 680-686.]
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-->
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| Introduction to DNA microarray data
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<!-- * [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&content_id=_1103141_1 Slides on MyLMU Connect] -->
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* [http://www.dataone.org/sites/all/documents/L04_DataEntryManipulation.pptx DataONE: Data Entry and Manipulation]
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* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
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| rowspan="2" | [[Week 7]]
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 +
(due at 12:01am 10/17)
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 +
[[Class Journal Week 7]]
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|-
 +
!
 +
| Thursday<br/>10/12/2017
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| [http://www.nature.com/nature/journal/v417/n6889/full/nature00778.html Merrell et al. (2002) "''Vibrio cholerae'' microarray data" ''Nature'']
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| [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis activity part 1]
 +
 +
Test your understanding: [http://xkcd.com/882/ http://xkcd.com/882/]
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 +
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{{Course Schedule Divider}}
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|-
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! 8
 +
| Tuesday<br/>10/17/2017
 +
| <!--
 +
[http://www.nature.com/ng/journal/v25/n1/full/ng0500_25.html Ashburner et al. (2000) "Gene Ontology" ''Nature Genetics'']
 +
 +
[http://www.genomebiology.com/content/4/1/R7 Doniger et al. (2003) "MAPPFinder" ''Genome Biology'']
 +
-->
 +
|
 +
| rowspan="2" | [[Week 8]]
 +
 +
(due at 12:01am 10/24)
 +
 +
[[Class Journal Week 8]]
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|-
 +
!
 +
| Thursday<br/>10/19/2017
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|
 +
|
 +
{{Course Schedule Divider}}
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|-
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! 9
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| Tuesday<br/>10/24/2017
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|
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| Gene regulatory networks (GRNs)
 +
* [http://www.opensource.org/ Open Source] review
 +
* Group requests due 12:01am Saturday, October 28
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| rowspan="2" | [[Week 9]]
 +
 +
(due at 12:01am 10/31)
 +
 +
[[Class Journal Week 9]]
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|-
 +
!
 +
| Thursday<br/>10/26/2017
 +
| <!--
 +
[http://nar.oxfordjournals.org/content/40/D1/D565.full Dimmer et al. (2012) "UniProt-GOA Database" ''Nucleic Acids Research'']
 +
 +
[http://www.nature.com/nature/journal/v406/n6795/full/406477A0.html Heidelberg et al. (2000) "''Vibrio cholerae'' Genome Sequence" ''Nature'']
 +
-->
 +
|
 +
{{Course Schedule Divider}}
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|-
 +
! 10
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| Tuesday<br/>10/31/2017
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|
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| Web services and APIs
 +
<!--
 +
* Annotated bibliography of genomics papers for your species
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* ''Course LibGuide:'' http://libguides.lmu.edu/BIOL367
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** Select genome paper for journal club
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** Select microarray paper
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--->
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| rowspan="2" | [[Week 10]]
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 +
(due at 12:01am 11/7)
 +
 +
<!--[[Class Journal Week 10]]-->
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|-
 +
!
 +
| Thursday<br/>11/2/2017
 +
|
 +
|
 +
|
 
|}
 
|}

Revision as of 21:09, 22 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
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