LMU BioDB 2013 - User contributions [en]

User:Iwang2

2013-08-29T23:13:43Z

Iwang2: deleted berry juices work

== Name ==
:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
# Title of Project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry
:: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
* Watch movies with friends
* Watch medical related shows
* Collect nail polishes

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T23:13:21Z

Iwang2: /* Research experience */

== Name ==
:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
# Title of Project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry
:: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]
# Title of Project: Berry juices and Vegetables and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
* Watch movies with friends
* Watch medical related shows
* Collect nail polishes

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T23:09:26Z

Iwang2: /* Research experience */

== Name ==
:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
# Title of Project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry
:: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]
## Title of Project: Berry juices and Vegetables and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
* Watch movies with friends
* Watch medical related shows
* Collect nail polishes

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T22:39:11Z

Iwang2: added checklist requirements

== Name ==
:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
# Title of Project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry
:: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]
# Title of Project: Berry juices and Vegetables and Their Ability to Inhibit Aggregation of IAPP
:: Mentor: Dr. David A. Moffet, Department of Chemistry and Biochemistry

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
* Watch movies with friends
* Watch medical related shows
* Collect nail polishes

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T22:17:09Z

Iwang2: added name heading

== Name ==
:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
: Title of project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
: Mentor: Dr. David A. Moffet
: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
: When I have a free time, I enjoy watching movies with my friends. I also like to collect nail polishes.

[[ Category: Individual Homework ]]

Main Page

2013-08-29T22:15:27Z

Iwang2: /* Students */

__NOTOC__
<div style="text-align: center; font-size: 175%; margin-bottom: 0.85em">Loyola Marymount University</div>
<div style="text-align: center; font-size: 250%; line-height: 1.25em; margin-bottom: 1em">'''BIOL/CMSI 367-01/HNRS 398-01: Biological Databases'''</div>

<div class="toc-container">__TOC__</div>

== Announcements ==

=== Seminars and Events ===

* '''Biology Department Seminar:''' Thursday, August 29, 12:15 PM, S200, Dr. Victor Carmona, LMU Biology Department, ''Ecology and Global Citizenship: My Fulbright with the only Biology Department in El Salvador''
* '''Bioethics Institute Annual Lecture:''' Tuesday, September 24, 7:00-8:30 PM, UH1000, Dr. Roberto Dell’Oro, Director of the LMU Bioethics Instiute, ''The Ethos of American Bioethics: Between Individual Liberalism and Social Solidarity''


=== Course Assessment ===

We ask that students in this class participate in the [http://www.grinnell.edu/academic/psychology/faculty/dl/risc/ Research on the Integrated Science Curriculum (RISC) Survey] which will allow the instructors to evaluate the effectiveness of this course. Please complete the [https://survey.grinnell.edu/se.ashx?s=2511374543A7A49D student pre-course survey], using "Dahlquist" as the instructor last name.

== Instructors ==
* [[User:Kdahlquist|Kam D. Dahlquist]]
* [[User:Dondi|John David N. Dionisio]]

== Students ==

{| style="width: 50%"
| [[User:Taur.vil|Tauras Vilgalys]]
| [[User:Dwilliams|Dillon Williams]]
| [[User:Lena | Lena Hunt]]
| [[User:vkuehn|Viktoria Kuehn]]
|-
| [[User:Kmeilak|Kevin Meilak]]
| [[User:Mmalefyt|Miles Malefyt]]
| [[User:Slouie | Stephen Louie]]
| [[User:laurmagee|Lauren Magee]]
|-
| [[User:kevinmcgee | Kevin McGee]]
| [[User:HDelgadi| Hilda Delgadillo]]
| [[User:iwang2 | Rachel Wang ]]
| [[User:Student12]]
|-
| [[User:Gleis| Gabriel Leis]]
| [[User:Student14]]
| [[User:Student15]]
| [[User:mpetredi|Mitchell Petredis]]
|}

== 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 Fridays at midnight (Thursday night/Friday 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 Tuesday and Thursday morning office hours can be viewed as unofficial lab sessions: use them for IT help or desktop support

{| style="width: 100%; margin: 1em 0" cellpadding="5ex"
! style="width: 1em; background: #ddd" | #
! style="width: 2em; background: #ddd" | Date
! style="width: 5em; background: #ddd" | Reading
! style="background: #ddd" | Agenda
! style="background: #ddd" | Journal
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right" | Tuesday 8/27/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Syllabus walkthrough
* ''my.cs.lmu.edu'' account: Visit https://secure.cs.lmu.edu to get a computer science account if you don’t already have one
* 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

| style="vertical-align: top; text-align: center" | [[Week 1]]

(due at midnight 8/30)

[[Class_Journal_Week_1 | Class Journal Week 1]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 1
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 8/29/2013
| style="vertical-align: top; background: #eee" |
[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/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D Chapter 1 of ''On Becoming a Biologist''] by John Janovy, Jr. (on MyLMUConnect)
| style="vertical-align: top; background: #eee" | Discuss the [[Week 1]] assignment (accounts should be ready to wiki at this point)
* Quick wiki overview
* User wiki page setup
* Technical skills—what do you consider to be the most advanced task that you can perform on a computer?
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right" | Tuesday 9/3/2013
| style="vertical-align: top" | [http://www.ncbi.nlm.nih.gov/books/NBK21134/#A5234 Ch. 1.1 ''Genomes 2'']

[http://www.nature.com/nature/dna50/watsoncrick.pdf Watson & Crick (1953)]

[http://www.nature.com/nature/dna50/franklingosling.pdf Franklin & Gosling (1953)]

| style="vertical-align: top" | DNA
* Discussion/lecture about DNA structure

| style="vertical-align: top; text-align: center" | [[Week 2]]

(due at midnight 9/6)

[[Class Journal Week 2]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 2
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/5/2013
| style="vertical-align: top; background: #eee" | On [https://mylmuconnect.blackboard.com/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_35506_1%26url%3D MyLMUConnect]:

Nirenberg (2004) ''Deciphering the Genetic Code''

Moody (2004) ''Digital Code of Life'', Ch. 1

Hayes (2004) ''Ode to the Code''

[http://www.ncbi.nlm.nih.gov/books/NBK21121/ Ch. 3 ''Genomes 2''], Chapters 8-12, as needed for the final project
| style="vertical-align: top; background: #eee" | Central dogma

* [http://www.youtube.com/watch?v=u9dhO0iCLww Berkeley translation video]
* This [http://www.dnai.org/a/index.html web site] has links to animations of the replication, transcription, and translation processes.

* [[Media:20100914_CentralDogma.pdf | Slides shown in class]]
* [[Central Dogma Pencil Exercise]]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right" | Tuesday 9/10/2013
| style="vertical-align: top" | [http://myweb.lmu.edu/dondi/share/intro/wheres-my-stuff.pdf Where's my Stuff?]

[[Introduction to the Command Line]]
| style="vertical-align: top" | An overview of computers, networks, files, and databases
* Manipulating DNA sequences on the command line
* [[Using the XMLPipeDB Match Utility]] 
| style="vertical-align: top; text-align: center" | [[Week 3]]

(due at midnight 9/13)

[[Class Journal Week 3]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 3
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/12/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Hands-on practice
* Discuss [[Week 3]] assignment tasks
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right" | Tuesday 9/17/2013
| style="vertical-align: top" | [[More Text Processing Features]]

[[How to Read XML Files]]

[[Media:Moody_DigitalCodeofLife_Ch6_04.pdf | Showing the Data]]

[http://www.nature.com/news/2010/100623/pdf/4651000a.pdf Science After the Sequence]

[http://www.nature.com/news/2010/100623/full/4651000a.html Nature Special: Human Genome at 10]
| style="vertical-align: top" | Genome sequencing and annotation
* [[Media:20100921_HGP.pdf | Slides shown in class]]

| style="vertical-align: top; text-align: center" | [[Week 4]]

(due at midnight 9/20)

[[Class Journal Week 4]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 4
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/19/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Command line lab session
* Review assignment issues
* Discuss [[Week 4]] computer portion

| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right" | Tuesday 9/24/2013
| style="vertical-align: top" |
[http://nar.oxfordjournals.org/content/41/D1/D1.full Introduction to ''NAR'' Database Issue]
| style="vertical-align: top" | [[Media:20100928_BiologicalDatabases.pdf | Introduction to biological databases]]
| style="vertical-align: top; text-align: center" | [[Week 5]]

(due at midnight 9/27)

[[Class Journal Week 5]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 5
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 9/26/2013
| style="vertical-align: top; background: #eee" |
[http://myweb.lmu.edu/dondi/share/db/relational1.pdf The Relational Data Model: Structure]

[http://myweb.lmu.edu/dondi/share/db/sql.pdf An Overview of SQL]

[http://myweb.lmu.edu/dondi/share/db/pgsql-quickstart.pdf PostgreSQL Quick Start]

[[PostgreSQL Tutorial]]
| style="vertical-align: top; background: #eee" | Introduction to relational databases
* [[PostgreSQL Tutorial]]
* Relating XML structure to relational structure
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right" | Tuesday 10/1/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Database presentations
* [[Some Topics to Consider When Critiquing Talks]]
| style="vertical-align: top; text-align: center" | [[Week 6]]

(due at midnight 10/4)

[[Class Journal Week 6]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 6
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/3/2013
| style="vertical-align: top; background: #eee" | 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).
| style="vertical-align: top; background: #eee" | SQL and working with relational databases continued
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right" | Tuesday 10/8/2013
| style="vertical-align: top" | [[Media:Brown_NatGenet_99_microarrays.pdf | Brown_NatGenet_99_microarrays]]

[[Media:Campbell_Heyer_Ch4.pdf | Campbell & Heyer Chapter 4]]

[[Media:Campbell_Heyer_Ch4_figures.pdf | Chapter 4 Color Figures]]
| style="vertical-align: top" | [[Media:20101012_Microarrays.pdf | Introduction to DNA microarray data, Gene Ontology, and GenMAPP/MAPPFinder]]
| style="vertical-align: top; text-align: center" | [[Week 7]]

(due at midnight 10/10; ''Note Different Due Date'')

[[Class Journal Week 7]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 7
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/10/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | [http://www.opensource.org/ Open Source]
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right" | Tuesday 10/15/2013
| style="vertical-align: top" | [[Media:Ashburner_NatGenet_00_GeneOntology.pdf | Ashburner_NatGenet_00_GeneOntology]]

[[Media:Doniger_GenomeBiology_03_MAPPFinder.pdf | Doniger_GenomeBiology_03_MAPPFinder]]

[[Media:Merrell_Nature_02_vibriomicroarray.pdf | Merrell_Nature_02_vibriomicroarray]]
| style="vertical-align: top" | Journal Club Presentations
| style="vertical-align: top; text-align: center" | [[Week 8]]

(due at midnight 10/18)

[[Class Journal Week 8]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 8
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/17/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | [http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae DNA Microarray Analysis] activity part 1
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right" | Tuesday 10/22/2013
| style="vertical-align: top" |


| style="vertical-align: top" | [http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols DNA Microarray Analysis] activity part 2
| style="vertical-align: top; text-align: center" | [[Week 9]]

(due at midnight 10/25)

[[Class Journal Week 9]]
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 9
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/24/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | 
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right" | Tuesday 10/29/2013
| style="vertical-align: top" |

| style="vertical-align: top" |
* Introduction to XMLPipeDB: export a database

** [[Running GenMAPP Builder]]
* [http://www.opensource.org/ Open Source] review
* Assign groups and species

| style="vertical-align: top; text-align: center" | [[Week 10]]

(due at midnight 11/1)


|-
| style="vertical-align: top; text-align: center; background: #ddd" | 10
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 10/31/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right" | Tuesday 11/5/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Integrity analysis of Vibrio Gene Database
* [[How Do I Count Thee? Let Me Count The Ways]]
* [[Gene Database Testing Report Sample | Complete your Gene Database Testing Report for ''Vibrio cholerae'']]
| style="vertical-align: top; text-align: center" | [[Week 11]]

(due at midnight 11/8)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 11
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/7/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Begin [[Gene_Database_Project | group projects]]
* Select genome paper for journal club
* Select microarray paper in consultation with Dr. Dahlquist
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right" | Tuesday 11/12/2013
| style="vertical-align: top" |
| style="vertical-align: top" | Journal Club Presentations: introduction to my species
| style="vertical-align: top; text-align: center" | [[Week 12]]

(due at midnight 11/15)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 12
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/14/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | Guild meetings and work session
* Export of Gene Database for your group's species
* Document ID types for your species
* Begin DNA microarray analysis
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right" | Tuesday 11/19/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 13]]

(due at midnight 11/22)

|-
| style="vertical-align: top; text-align: center; background: #ddd" | 13
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 11/21/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 14
| style="vertical-align: top; text-align: right" | Tuesday 11/26/2013
| style="vertical-align: top" |
| style="vertical-align: top" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | '''''No Week 14 assignment'''''

|-
| style="vertical-align: top; text-align: center; background: #ded" | 14
| style="vertical-align: top; text-align: right; background: #efe" | Thursday 11/28/2013
| style="vertical-align: top; background: #efe" |
| style="vertical-align: top; background: #efe" | Thanksgiving—no class
| style="vertical-align: top; text-align: center; background: #efe" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right" | Tuesday 12/3/2013
| style="vertical-align: top" |
| style="vertical-align: top; background: #fff" |
* Status report
* Work session
| style="vertical-align: top; text-align: center" | [[Week 15]]

(due at midnight 12/6)
|-
| style="vertical-align: top; text-align: center; background: #ddd" | 15
| style="vertical-align: top; text-align: right; background: #eee" | Thursday 12/5/2013
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" |
* Status report
* Work session
| style="vertical-align: top; text-align: center; background: #eee" |
{{Course Schedule Divider}}
|-
| style="vertical-align: top; text-align: center; background: #edd" | F
| style="vertical-align: top; text-align: right; background: #fee" | Thursday 12/12/2013
| style="vertical-align: top; background: #fee" |
| style="vertical-align: top; background: #fee" | '''Final project presentations 8:00-10:00 AM'''
| style="vertical-align: top; text-align; background: #fee" |
|-
| style="vertical-align: top; text-align: center; background: #ddd" | F
| style="vertical-align: top; text-align: right; background: #eee" | Friday 12/13/2013 4:30 PM
| style="vertical-align: top; background: #eee" |
| style="vertical-align: top; background: #eee" | '''Project deliverables due 4:30 PM'''
| style="vertical-align: top; text-align: center; background: #eee" |
|
|}

== Course Information ==

=== Instructors ===

* [[User:Kdahlquist | Kam D. Dahlquist, Ph.D.]]
** http://myweb.lmu.edu/kdahlqui
** Phone: (310) 338-7697
** E-mail: kdahlquist at lmu dot edu
** Office: Seaver 218
** Office hours: Mondays, Tuesdays, and Thursdays 1:30-3:00 PM and by appointment
* [[User:Dondi|John David N. Dionisio, Ph.D.]]
** http://myweb.lmu.edu/dondi
** Phone: (310) 338-5782
** E-mail: dondi at lmu dot edu
** Office: Doolan 106
** Office hours: Tuesdays and Thursdays 11 AM–12 noon, Tuesdays 3–5 PM, and by appointment

=== Prerequisites/Recommended Background ===

To take this course, you must have upper division standing in either the College of Science and Engineering
or the Honors Program. Otherwise, there are no strict prerequisites. Backgrounds in biology and computer science, as well as prior experience with database or information management applications, may be helpful but not necessary.

=== Class Meetings and Attendance ===
TR 9:25 – 10:40 AM, Doolan 219

This is a hands-on, participatory course, thus attendance at all class meetings is required. An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructors should be notified as soon as possible, electronically or by phone, of the reasons for all absences.

Note that the last day to add or drop a class without a grade of W is August 30. The withdrawal or credit/no-credit status deadline is November 1.

=== Mutual Responsibilities ===

This course is designed to foster your development as a biologist and computer scientist and to give you an authentic research experience. We will be engaged together in discovering, examining, and practicing the personal qualities, technical skills, and community standards of the scientific community. While you are ultimately responsible for your own learning, you are not alone. Our class constitutes a team where we will be learning from each other. The role of the instructors is to provide the expert coaching to support and assist you on your journey. All of the exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.

=== Classroom Conduct ===

As an LMU Lion, by the Lion’s Code, you are pledged to join the discourse of the academy with honesty of voice and integrity of scholarship and to show respect for staff, professors, and other students. Refer to [http://studentaffairs.lmu.edu/media/lmustudentaffairs/administration/judicialaffairs/Community%20Standards%20Booklet.pdf LMU’s Community Standards] for the Student Conduct Code or to [http://www.lmu.edu/AssetFactory.aspx?vid=30313 the Lion’s Code]. Disruptive behavior which is persistent or significantly interferes with classroom activities may be subject to disciplinary action. A student may be referred to the Office of Student Judicial Affairs if his or her behavior constitutes a violation of the conduct code. Specifically for this course, the following rules apply:
# You are responsible for your own learning and for being a good class citizen.
# We will act with honesty and integrity at all times.
# We will always treat individuals with respect.
# Class will start promptly on time.
# You are expected to come to class having done the assigned reading and preparatory work.
# You are expected to bring the required materials to each class session.
# Cell phones, pagers, and other communication or music devices must be turned off and put out of sight during class sessions.

=== Course Web Site ===

This is the course web site and wiki, hosted by http://xmlpipedb.cs.lmu.edu/biodb/fall2013/. You will need to register  to be able to edit the wiki and complete coursework. Updates to the course schedule and electronic copies of all handouts, assignments, and readings will be posted to this site. You will also use the site to keep an electronic lab notebook/journal for the course. In addition, students have been automatically enrolled in [<add link> BIOL 367-01 on MyLMUConnect]. The MyLMUConnect site may be used for materials that cannot be made public on this wiki, including grades.

=== Required Materials ===

==== Texts ====

There is no required text to purchase for the course; materials will be put on reserve at Hannon Library or will be available online on the this wiki or MyLMUConnect site. Specific reading assignments are given on the course schedule and should be completed before coming to class.
* This text has been placed on reserve at the library: Jeffrey Ullman and Jennifer Widom, ''A First Course in Database Systems'', Third Edition. Prentice Hall, 2008.
* Assorted handouts, articles, and sample code will be distributed throughout the semester.
* Additional information is also available on the web; do not hesitate to look for further sources of information regarding the concepts, techniques, tools, and paradigms that we will discuss.

==== Materials (must be brought to each class meeting) ====

* 3-ring binder with all course handouts
* Pen, pencil, extra paper
* USB flash drive to store data
* Keck lab account

=== Course Description ===

The disciplines of biology and computer science come together in bioinformatics, where computational tools are needed to manage and analyze the flood of data coming from new genomics technologies. Biological databases form a significant part of this young and exciting field. This course introduces students to both the biology and computer science expertise needed to understand, use, and develop biological databases. Biology topics include the fundamentals of genetics, molecular biology, and biochemistry needed to understand the data stored in biological databases, as well as the biotechnologies used to gather these data in a high-throughput manner. Computer science topics include what biological databases are, why they are important (and needed), and the challenges that arise in compiling them effectively. Biology and computer science lectures on topics that are relevant to biological databases are coupled with hands-on experience with a variety of software packages ranging from bioinformatics utilities to general-purpose database and software development tools. After learning how to use a biological database, students will be asked to build one of their own.

==== Course Objectives and Learning Outcomes ====

This course is built upon L. Dee Fink’s ''taxonomy of significant learning'', as applied to biological databases. Long after the course concludes, our hope is that:
* You understand how biological information is encoded in the genome and can apply this knowledge to a variety of biological tasks and problems
* You understand the core concepts, structure, and functions of a database, ranging from individual files to a full relational database management system, and can perform useful tasks with such data
* You show discipline and proficiency in day-today science and engineering best practices, such as maintaining journals and notebooks, managing your files and code, and critically evaluating scientific and technical information
* You recognize and care about how the biological and technological issues presented in this course relate to and affect society, our daily lives, and ourselves
* You have some skills and tools for “leaving your comfort zone,” flourishing outside of it, and learning more about biology and computer science on your own
* You learn how to communicate and work effectively with colleagues from different disciplines

=== Course Work and Grading ===

Letter grades are determined as follows: ≥ 90% gets an A– or better; ≥ 80% gets a B– or better; ≥ 70% gets a C– or better. The instructors may curve grades upward based on qualitative considerations such as degree of difficulty, effort, class participation, time constraints, and overall attitude throughout the course. Grades are never curved downward. Current grades will be made available at MyLMU Connect (the system formerly known as Blackboard).

Your work in this course will be assessed in four areas:
{| style="border: 1px dashed rgb(47, 111, 171); background: rgb(249, 249, 249); margin: 1em 0; padding: 1em" cellpadding="5ex"
| Weekly electronic lab notebook/journal assignments (10 points each)
| style="text-align: right" | 140
| points
|-
| Oral presentations
| style="text-align: right" | 90
| points 
|-
| Information literacy
| style="text-align: right" | 45
| points
|-
| Final Project Deliverables (including written report)
| style="text-align: right" | 175
| points
|-
| '''Total'''
| style="text-align: right" | '''450'''
| '''points'''
|}


==== Electronic Laboratory Notebook/Journal ====

One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. For computational research, the equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice documentation skills by keeping an electronic lab notebook or journal. The technology we will use is this wiki, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructors will read and grade. You will use the wiki to complete the assignments as well. The following guidelines apply:
* Your weekly journal entry is typically due every midnight on Friday PST (''Thursday night/Friday morning''); consult the schedule for specific due dates for each assignment.
* You will earn 10 points per weekly submission. '''''Late journal entries will be accepted up to one week later for up to half credit.'''''
* The instructors will read and comment on how to improve your journal entries.
* Depending on the type of assignment for that week, you may be given the opportunity to make improvements to previous journal entries as the semester progresses.
* Generally, your journal entries will consist of:
** Workflow and other documentation for hands-on exercises and projects
** Answers to any specific questions posed in the exercise
** Reflection on your learning

==== Oral Presentations ====

You will give four oral presentations in this course. The first three will be in the format of a “Journal Club” presentation where students will present and lead discussion of research articles from the primary literature. The fourth will be a research presentation on your final project. '''''Because that day’s class content is dependent upon each student being ready to present, late oral presentations will not be accepted.'''''

==== Final Group Project ====

* Overall Description of the [[Gene Database Project]], including entire list of deliverables
* [[Gene Database Project Report Guidelines]]

{| style="width: 50%"
| '''Teams'''
| '''Guilds'''
|-
| [[Team1]]
| [[Project Manager]]
|-
| [[Team2]]
| [[GenMAPP User]]
|-
| [[Team3]]
| [[Quality Assurance]]
|-
| [[Team4]]
| [[Coder]]
|}

In addition to the research presentation, the culmination of your final project will be the preparation of a written laboratory report in the style of a manuscript that could be submitted to a peer-reviewed journal. Specific instructions are posted [[Gene Database Project Report Guidelines | here]]. '''''The Final Written Report cannot be accepted any later than Friday, December 13 at 4:30 PM.'''''

==== Work Load Expectations ====
In line with [http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf LMU’s Credit Hour Policy], the work load expectation for this course is that for every one hour (50 minutes) of classroom instruction, you will complete a minimum of two hours of out-of-class student work each week. This is a 3-unit course with 3 hours (150 minutes) of instruction per week. Thus the expectation is that you will complete 6 hours of work outside of class per week.

==== Extra Credit ====

Students may accumulate up to 2.5% of their final grade in extra credit by attending Department seminars in Biology or Electrical Engineering & Computer Science and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. You must attend the entire seminar from start to finish and personally turn in your seminar sheet to a faculty member at the end of the seminar.

Certain, non-Biology/Computer Science Department seminars may be approved in advance for extra credit at the instructors’ discretion. To receive credit for these seminars, you must turn in a one-page summary of the seminar '''''within one week''''' of the date of the seminar or they will not count as extra credit.

=== University Policy on Academic Honesty ===

Loyola Marymount University expects high standards of honesty and integrity from all members of its community. All students are expected to follow the LMU honor code. As stated in the LMU Undergraduate Bulletin, “Examples of academic dishonesty include, but are not limited to, the following: all acts of cheating on assignments or examinations, or facilitating other students’ cheating; plagiarism; fabrication of data, including the use of false citations; improper use of non-print media; unauthorized access to computer accounts or files or other privileged information and improper use of Internet sites and resources.” [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm Click here for an online version of the LMU Honor Code and Process].

You are required to sign the Honor Code Agreement for this course.

==== Academic Honesty Resources ====
* [[Media:BIOL-CMSI367-HNRS398_HonorCodeAgreement_Fall2013.pdf|Honor Code Agreement]]
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2013-2014 University Bulletin].
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism]
* [[Guidelines for Literature Citations in a Scientific Paper]]
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation)
* [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective]

=== Special Accomodations ===

Students with special needs who require reasonable modifications, special assistance, or accommodations in this course should promptly direct their request to the Disability Support Services (DSS) Office. Any student who currently has a documented disability (ADHD, Autism Spectrum Disorder, Learning, Physical, or Psychiatric) needing academic accommodations should contact the DSS Office (Daum Hall 2nd floor, 310-338-4216) as early in the semester as possible. All discussions will remain confidential. Please visit [http://www.lmu.edu/dss www.lmu.edu/dss] for additional information. In addition, please schedule an appointment with the instructors early in the semester to discuss any accommodations for this course for which you have been approved.

=== Revision Notice ===

If necessary, this syllabus and its contents are subject to revision; students are responsible for any changes or modifications announced in class. The most current version of this information resides on this page, the course web site at http://xmlpipedb.cs.lmu.edu/biodb/fall2013/.

== Keck Lab Workstation Guidelines ==

Please visit [[Keck Lab Workstation Guidelines|this page]] for guidelines and instructions on using the Keck computer science lab.

User:Iwang2

2013-08-29T22:14:38Z

Iwang2: added personal hobbies

:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
: Title of project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
: Mentor: Dr. David A. Moffet
: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Hobbies ==
: When I have a free time, I enjoy watching movies with my friends. I also like to collect nail polishes.

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T22:13:17Z

Iwang2: added research file and work experience

:Rachel In Wang

== Contact Information ==
: Email: iwang2@lion.lmu.edu
: Loyola Marymount University
: 1 LMU Drive, MS B-7904
: Los Angeles, CA 90045

== Education ==
: Biology Major
: Graduation year: May 2015
: Upper division courses: Currently enrolled in Biochemistry
===Research experience===
: Title of project: Non-Steroidal Anti-Inflammatory Drugs and Their Ability to Inhibit Aggregation of IAPP
: Mentor: Dr. David A. Moffet
: [[File:NSAIDS_Research_Symposium_ppt.pdf|200px|thumb|left]]

== Work Experience ==
: Position: BIOL 111 TA
: Employer: Dr. Dowd, Dr. Urbinati
: Date: August 2013- December 2013
: Responsibility: I am responsible for interacting and teaching students in order to help them improve their laboratory skills, such as using a microscope.

== Personal Interests ==
:

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T22:08:54Z

Iwang2: linking file

User:Iwang2

2013-08-29T22:07:38Z

Iwang2:

File:NSAIDS Research Symposium ppt.pdf

2013-08-29T22:05:59Z

Iwang2: Loyola Marymount University Research Symposium powerpoint slides.

Loyola Marymount University Research Symposium powerpoint slides.

User:Iwang2

2013-08-29T21:58:58Z

Iwang2: added education and research experience

User:Iwang2

2013-08-29T21:47:47Z

Iwang2: added email address

== Rachel In Wang ==

== Contact Information ==

: iwang2@lion.lmu.edu

Loyola Marymount Univeristy, Los Angeles

: Bachelor of Science, Biology

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T17:17:00Z

Iwang2: Edit category

== Education ==

=== September 2011 to May 2015 ===

Loyola Marymount Univeristy, Los Angeles

: Bachelor of Science, Biology

[[ Category: Individual Homework ]]

User:Iwang2

2013-08-29T17:15:53Z

Iwang2: Add education and category

== Education ==

=== September 2011 to May 2015 ===

Loyola Marymount Univeristy, Los Angeles

: Bachelor of Science, Biology

(( Category: Individual Homework))

User:Iwang2

2013-08-29T17:00:04Z

Iwang2:

== Education ==

=== September 2011 to May 2015 ===

Loyola Marymount Univeristy, Los Angeles

: Bachelor of Science, Biology

User:Iwang2

2013-08-29T16:42:23Z

Iwang2: Blanked the page

User:Iwang2

2013-08-29T16:40:08Z

Iwang2: First time doing Wiki

Hello biological databases