Difference between revisions of "Main Page"

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(Start writing out initial course page.)
(Initial transcription/revision of course part 1.)
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* Reading assignments should be completed ''before'' coming to class.
 
* Reading assignments should be completed ''before'' coming to class.
 
* Dr. Dionisio’s office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support
 
* Dr. Dionisio’s office hours ({{ Dondi Office Hours }}) can be viewed as unofficial lab sessions: use them for IT help or desktop support
 +
 +
=== Part 1: Building Blocks (Genetic Code and Web Services) ===
 +
 +
{| class="schedule-table"
 +
! #
 +
! Date
 +
! Reading
 +
! Agenda
 +
! Journal
 +
|-
 +
! 1
 +
| Tuesday<br/>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
 +
<!--** Disk/flash drive; soup can; hard-boiled egg; Etch-a-Sketch; battery; toy flute/recorder; clock-->
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| rowspan="2" | [[Week 1]]
 +
 +
(due at 12:01am 9/5)
 +
 +
[[Class_Journal_Week_1 | Class Journal Week 1]]
 +
|-
 +
!
 +
| Thursday<br/>8/31/2017
 +
| <!--
 +
[http://dl.acm.org/ft_gateway.cfm?id=1378711 ''Voices of Computing''] and [http://dl.acm.org/ft_gateway.cfm?id=1272529 ''Computing is a Natural Science''] by Peter Denning (these links should be accessed from within LMU to get the full article)
 +
 +
[https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
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-->
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| Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
 +
* Quick wiki overview
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* User wiki page setup
 +
 +
 +
{{Course Schedule Divider}}
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|-
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! 2
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| Tuesday<br/>9/5/2017
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| <!--
 +
[http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']
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 +
[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]
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[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]
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-->
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| The life cycle of data
 +
 +
DNA (genes as model)
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* DNA structure and Genetic Code
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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 shown in class on MyLMU Connect]
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| rowspan="2" | [[Week 2]]
 +
 +
(due at 12:01am 9/12)
 +
 +
[[Class Journal Week 2]]
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|-
 +
!
 +
| Thursday<br/>9/7/2017
 +
| <!--
 +
On [https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset MyLMUConnect]:
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 +
Nirenberg (2004) ''Deciphering the Genetic Code''
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Kaji & Kaji (2004) ''Setting the Record Straight''
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Moody (2004) ''Digital Code of Life'', Ch. 1
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 +
Hayes (2004) ''Ode to the Code''
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[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Brown, T.A. (2002) ''Genomes 2'', Ch. 3, especially section 3.3.2]
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-->
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| Central model
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* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
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* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.
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* Slides shown in class
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* [[Media:BIOL367_Fall2015_GeneticCode-GeneExpression.pdf | Genetic Code-Gene Expression Pencil Exercise]]
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 +
Genome sequencing and annotation
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{{Course Schedule Divider}}
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|-
 +
! 3
 +
| Tuesday<br/>9/12/2017
 +
| <!--
 +
[http://www.bloomberg.com/graphics/2015-paul-ford-what-is-code/ Ford (2015) ''What is Code?'']
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* Emphasis on first two sections (“The Man in the Taupe Blazer” and “Let’s Begin”), but feel free to read further
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[http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]
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[[Introduction to the Command Line]]
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-->
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| An overview of computers, networks, files, web applications, web services, and databases
 +
* Useful help resource: http://explainshell.com
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* Accessing the web on the command line
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| rowspan="2" | [[Week 3]]
 +
 +
(due at 12:01am 9/19)
 +
 +
[[Class Journal Week 3]]
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|-
 +
!
 +
| Thursday<br/>9/14/2017
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|
 +
| Command line lab session
 +
* Hands-on practice
 +
* Discuss [[Week 3]] assignment tasks
 +
 +
 +
{{Course Schedule Divider}}
 +
|-
 +
! 4
 +
| Tuesday<br/>9/19/2017
 +
| <!--
 +
[https://mylmuconnect.blackboard.com/webapps/blackboard/content/listContentEditable.jsp?content_id=_1103141_1&course_id=_62090_1&mode=reset Moody (2004) Chapter 6 (on MyLMU Connect)]
 +
 +
[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]
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[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]
 +
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* [http://www.sciencemag.org/content/vol291/issue5507/index.dtl Human Genome Project articles in ''Science'']
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* [http://www.nature.com/nature/journal/v409/n6822/index.html Human Genome Project articles in ''Nature'']
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-->
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| Web page construction
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* HTML
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* Bootstrap
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* Web browser development tools
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| rowspan="2" | [[Week 4]]
 +
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(due at 12:01am 9/26)
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 +
[[Class Journal Week 4]]
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|-
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!
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| Thursday<br/>9/21/2017
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|
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<!-- [[More Text Processing Features]]
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 +
[[How to Read XML Files]] -->
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| Command line lab session
 +
* Review assignment issues
 +
* Discuss [[Week 4]] computer portion
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<!-- * Public wiki
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* Introduction to software/licensing/open source
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* Open source/open access publishing -->
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 +
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{{Course Schedule Divider}}
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|-
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! 5
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| Tuesday<br/>9/26/2017
 +
| <!--
 +
[http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]
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 +
[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]
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[http://myweb.lmu.edu/dondi/share/db/pgsql-quickstart.pdf PostgreSQL Quick Start]
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-->
 +
 +
[https://academic.oup.com/nar/article/45/D1/D1/2770636/The-24th-annual-Nucleic-Acids-Research-database The 24th annual Nucleic Acids Research database issue]
 +
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[http://www.oxfordjournals.org/nar/database/a/ The NAR Molecular Biology Database Collection]
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| Introduction to biological databases
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* [https://mylmuconnect.blackboard.com/bbcswebdav/pid-1146580-dt-content-rid-1944592_1/courses/M_46692.201530/20150922_HGP_IntroBiolDB.pdf Slides shown in class (MyLMU Connect)]
 +
* [http://www.dataone.org/sites/all/documents/L01_DataManagement.pptx DataONE: Why Data Management]
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* [http://www.dataone.org/sites/all/documents/L02_DataSharing.pptx DataONE: Data Sharing]
 +
 +
* Case study from one of the NAR databases: http://www.rhesusbase.org <!-- Injection query sequence: INSR' and genefullname = 'insulin receptor
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then try: INSR'; select * from gene where to reveal error then finally include alias like '%PP for successful injection -->
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* Relating XML structure to relational structure
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 +
Test your understanding: http://xkcd.com/327/
 +
| rowspan="2" | [[Week 5]]
 +
 +
(due at 12:01am 10/3)
 +
 +
[[Class Journal Week 5]]
 +
|-
 +
!
 +
| Thursday<br/>9/28/2017
 +
| <!--
 +
Additional background and details can be found in Chapters 1, 2, and 6 of ''A First Course in Database Systems'' (on reserve at the library).
 +
-->
 +
| <!--
 +
SQL and working with relational databases continued
 +
* [[PostgreSQL Tutorial]]
 +
-->
 +
 +
{{Course Schedule Divider}}
 +
|-
 +
! 5
 +
| Tuesday<br/>10/3/2017
 +
|
 +
|
 +
| rowspan="2" | [[Week 6]]
 +
 +
(due at 12:01am 10/10)
 +
 +
[[Class Journal Week 6]]
 +
|-
 +
!
 +
| Thursday<br/>10/5/2017
 +
|
 +
| Database presentations
 +
 +
[[Presentation Rubric]]
 +
 +
[[Media:PresentationGuidelines.ppt | PowerPoint Guidelines]]
 +
<!--Introduction to the [http://www.opensource.org/ open source] culture-->
 +
|}

Revision as of 19:58, 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
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

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