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== Announcements == | == Announcements == | ||
* [http://lmulibrary.typepad.com/lmu-library-news/2014/10/open-access-advocates-at-lmu.html See this blog post about Open Access Week!] | |||
* | |||
== Schedule == | == Schedule == | ||
Line 27: | Line 23: | ||
|-- | |-- | ||
| '''1''' | | '''1''' | ||
| Aug | | Aug 27 | ||
| | | | ||
| | | | ||
Line 33: | Line 29: | ||
** Slides can be found on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect site] | ** Slides can be found on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect site] | ||
* Introduction to the OpenWetWare Wiki | * Introduction to the OpenWetWare Wiki | ||
* '' | * ''August 29: Last day to add or drop a class without a grade of W'' | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 1 | Week 1 Assignment]] | ||
''Due midnight 9/ | ''Due midnight 9/3'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 1 | Class Journal Week 1]] | ||
|-- | |-- | ||
| '''2''' | | '''2''' | ||
| Sept | | Sept 3 | ||
| Protocols listed on [[BIOL368/ | | Molecular Genetics Explorer Protocols listed on the [[BIOL368/F14:Week 2| Week 2 Assignment page]] | ||
| | | | ||
* | * Molecular Genetics Explorer | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 2 | Week 2 Assignment]] | ||
''Due midnight 9/ | ''Due midnight 9/10'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 2 | Class Journal Week 2]] | ||
|-- | |-- | ||
| '''3''' | | '''3''' | ||
| Sept | | Sept 10 | ||
| [http://0-site.ebrary.com.linus.lmu.edu/lib/loyolamarymount/docDetail.action?docID=10279028 ''Bioinformatics for Dummies''] Introduction, Chapters 1, 2, | | [http://0-site.ebrary.com.linus.lmu.edu/lib/loyolamarymount/docDetail.action?docID=10279028 ''Bioinformatics for Dummies''] Introduction, Chapters 1, 2, | ||
| | | | ||
* Intro to biological databases/literature databases | * Intro to biological databases/literature databases | ||
* Begin | * Guest Lecture by Librarian Glenn Johnson-Grau | ||
| [[BIOL368/ | ** [http://libguides.lmu.edu/BIOL368 LMU LibGuide for BIOL368] | ||
* Begin HIV Evolution Project | |||
| [[BIOL368/F14:Week 3 | Week 3 Assignment]] | |||
''Due midnight 9/ | ''Due midnight 9/17'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 3 | Class Journal Week 3]] | ||
|-- | |-- | ||
| '''4''' | | '''4''' | ||
| Sept | | Sept 17 | ||
| [http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf Markham et al. (1998)] | | [http://bioquest.org/bedrock/problem_spaces/hiv/Markham_1998.pdf Markham et al. (1998)]; [http://www.jci.org/articles/view/34706/pdf Cohen et al. (2008) review]; Exploring HIV Evolution Handout (on [https://mylmuconnect.lmu.edu/ MyLMU Connect]); [http://0-site.ebrary.com.linus.lmu.edu/lib/loyolamarymount/docDetail.action?docID=10279028 ''Bioinformatics for Dummies''] Chapter 3 | ||
| | | | ||
* Journal Club 1 | * Journal Club 1 | ||
** Slides are on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect] | |||
* | * HIV Evolution Project | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 4 | Week 4 Assignment]] | ||
''Due midnight 9/ | ''Due midnight 9/24'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 4 | Class Journal Week 4]] | ||
|-- | |-- | ||
| '''5''' | | '''5''' | ||
| Sept | | Sept 24 | ||
| | | | ||
| | | | ||
* | * HIV Evolution Project | ||
| [[BIOL368/F14:Week 5 | Week 5 Assignment]] | |||
| [[BIOL368/ | |||
''Due midnight 10/ | ''Due midnight 10/1'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 5 | Class Journal Week 5]] | ||
|-- | |-- | ||
| '''6''' | | '''6''' | ||
| Oct | | Oct 1 | ||
| | | | ||
| | | | ||
* [[ | * HIV Evolution Project Presentations | ||
** [[ | ** [[Media:PresentationGuidelines.ppt | Presentation Guidelines]] | ||
* [[BIOL368/ | ** [[BIOL368/F14:Presentation Rubric | Presentation Grading Rubric]] | ||
| [[BIOL368/ | * [[BIOL368/F14:Week 6 | DNA Glycosylase Exercise]] | ||
| [[BIOL368/F14:Week 6 | Week 6 Assignment]] | |||
''Due midnight 10/ | ''Due midnight 10/8'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 6 | Class Journal Week 6]] | ||
|-- | |-- | ||
| '''7''' | | '''7''' | ||
| Oct | | Oct 8 | ||
| | | | ||
* Begin | | | ||
| [[BIOL368/ | * Begin HIV Structure Project | ||
* [http://xkcd.com/1430/ Proteins on XKCD!] | |||
| [[BIOL368/F14:Week 7 | Week 7 Assignment]] | |||
''Due midnight 10/ | ''Due midnight 10/15'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 7 | Class Journal Week 7]] | ||
|-- | |-- | ||
| '''8''' | | '''8''' | ||
| Oct | | Oct 15 | ||
| [http://www. | | [http://www.sciencemag.org/content/310/5750/1025.long Huang et al. (2005)], [http://tinyurl.com/Stanfield1999 Stanfield et al. (1999)], [http://www.sciencedirect.com/science/article/pii/S0959440X13000493# Merk & Subramaniam (2013)], [http://0-site.ebrary.com.linus.lmu.edu/lib/loyolamarymount/docDetail.action?docID=10279028 ''Bioinformatics for Dummies''], Ch. 4, 6, 11. Bring book to class. | ||
| | | | ||
* Journal Club 2 | * Journal Club 2 | ||
* | * HIV Structure Project | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 8 | Week 8 Assignment]] | ||
''Due midnight 10/ | ''Due midnight 10/22'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 8 | Class Journal Week 8]] | ||
|-- | |-- | ||
| '''9''' | | '''9''' | ||
| Oct | | Oct 22 | ||
| | | | ||
| | | | ||
* | * HIV Structure Project | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 9 | Week 9 Assignment]] | ||
''Due midnight | ''Due midnight 10/29'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 9 | Class Journal Week 9]] | ||
|-- | |-- | ||
| '''10''' | | '''10''' | ||
| | | Oct 29 | ||
| | | | ||
| | | | ||
* | * HIV Structure Project Presentations | ||
* Introduction to DNA Microarrays | * Introduction to DNA Microarrays | ||
**([https://mylmuconnect.lmu.edu/webapps/login/ slides on MyLMUConnect]) | **([https://mylmuconnect.lmu.edu/webapps/login/ slides on MyLMUConnect]) | ||
* '' | * ''Oct 31: Last day to withdraw or change to credit/no-credit status'' | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 10 | Week 10 Assignment]] | ||
''Due midnight 11/ | ''Due midnight 11/5'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 10 | Class Journal Week 10]] | ||
|-- | |-- | ||
| '''11''' | | '''11''' | ||
| Nov | | Nov 5 | ||
| [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999)] | | [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Brown & Botstein (1999)] | ||
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Campbell & Heyer Chapter 4 (on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect]) | Campbell & Heyer Chapter 4 (on [https://mylmuconnect.lmu.edu/webapps/login/ MyLMUConnect]) | ||
| | | | ||
* Begin | * Begin DNA Microarray Project | ||
**([https://mylmuconnect.lmu.edu/webapps/login/ slides on MyLMUConnect]) | **([https://mylmuconnect.lmu.edu/webapps/login/ slides on MyLMUConnect]) | ||
| [[BIOL368/ | | [[BIOL368/F14:Week 11 | Week 11 Assignment]] | ||
''Due midnight 11/ | ''Due midnight 11/12'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 11 | Class Journal Week 11]] | ||
|-- | |-- | ||
| '''12''' | | '''12''' | ||
| Nov | | Nov 12 | ||
| Individual Journal Club papers on | | Individual Journal Club papers on for DNA Microarray Project | ||
| | | | ||
* | * DNA Microarray Project | ||
|[[BIOL368/F14:Week 12 | Week 12 Assignment]] | |||
|[[BIOL368/ | |||
''Due midnight 11/ | ''Due midnight 11/18'' | ||
'''''Note different due date!''''' | |||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 12 | Class Journal Week 12]] | ||
|-- | |-- | ||
| '''13''' | | '''13''' | ||
| Nov | | Nov 19 | ||
| [http://www.nature.com/ng/journal/v31/n1/full/ng0502-19.html Dahlquist et al. (2002)], [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003)], [http://www.biomedcentral.com/1471-2105/8/217 Salomonis et al. (2007)] | |||
| | |||
* Journal Club 3 | |||
* DNA Microarray Project | |||
| [[BIOL368/F14:Week 13 | Week 13 Assignment]] | |||
''Due midnight 12/3'' | |||
[[BIOL368/F14:Class Journal Week 13 | Class Journal Week 13]] | |||
|-- | |||
| '''14''' | |||
| Nov 26 | |||
| | | | ||
| '''''Thanksgiving Break''''' | | '''''Thanksgiving Break''''' | ||
| '''''No Week | | '''''No Week 14 Assignment''''' | ||
Happy Thanksgiving! | Happy Thanksgiving! | ||
|-- | |-- | ||
| ''' | | '''15''' | ||
| | | Dec 3 | ||
| | | | ||
| DNA Microarray Project | |||
| [[BIOL368/ | | [[BIOL368/F14:Week 15 | Week 15 Assignment]] | ||
''Due midnight 12/ | '' Due midnight 12/10'' | ||
[[BIOL368/ | [[BIOL368/F14:Class Journal Week 15 | Class Journal Week 15]] | ||
|-- | |-- | ||
| ''' | | '''Finals''' | ||
| Dec | | Dec 10 | ||
| | | | ||
| | | Wednesday, 2:00-4:00 PM Final Exam period | ||
Final Project Presentations | |||
| | | | ||
<!-- To add another row to the table copy and paste everything from the |-- line to just above this line.--> | <!-- To add another row to the table copy and paste everything from the |-- line to just above this line.--> | ||
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* [[User:Kam D. Dahlquist | Kam D. Dahlquist, Ph.D.]] | * [[User:Kam D. Dahlquist | Kam D. Dahlquist, Ph.D.]] | ||
* Phone: (310) 338-7697 | * Phone: (310) 338-7697 | ||
* [[Special:Emailuser/Kam D. Dahlquist|Email Dr. Dahlquist through OpenWetWare]] | * [[Special:Emailuser/Kam D. Dahlquist|Email Dr. Dahlquist through OpenWetWare]] (Messages sent to me at night or on the weekend will be answered the next school day.) | ||
* Office: Seaver 218 | * Office: Seaver 218 | ||
* Office hours: Tuesdays 2:00-4:00 PM, Thursdays 9:00-11:00 AM '''''and''''' by appointment (send me an e-mail or sign up for a time on the sheet on my office door) | * Office hours: Tuesdays 2:00-4:00 PM, Thursdays 9:00-11:00 AM '''''and''''' by appointment (send me an e-mail or sign up for a time on the sheet on my office door) | ||
==== Teaching Assistant ==== | |||
* Stephen Louie | |||
=== Prerequisites/Recommended Background === | === Prerequisites/Recommended Background === | ||
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Electronic laboratory notebook/journal assignments 140 points | Electronic laboratory notebook/journal assignments 140 points | ||
Journal club presentations 150 points | Journal club presentations 150 points <!--70 points JC2, 80 points JC3--> | ||
Oral lab reports 210 points | Oral lab reports 210 points <!--60 points R1, 70 points R2, 80 points R3--> | ||
Total 500 points | Total 500 points | ||
Grades will be posted on the [https://mylmuconnect.lmu.edu/webapps/login/ MyLMU Connect Grade Center] for this course. | Grades will be posted on the [https://mylmuconnect.lmu.edu/webapps/login/ MyLMU Connect Grade Center] for this course. | ||
<!--For future after oral and info literacy flags approved, point breakdown should be: | |||
Electronic laboratory notebook/journal assignments 140 points | |||
Information Literacy assignments 50 points | |||
Journal club presentations 130 points 60 points JC2, 70 points JC3 | |||
Oral lab reports 200 points 50 points R1, 60 points R2, 70 points R3 | |||
Total 500 points | |||
--> | |||
==== Final course grading scale ==== | ==== Final course grading scale ==== | ||
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≤ 59.9% F | ≤ 59.9% F | ||
==== Electronic Laboratory Notebook ==== | ==== Electronic Laboratory Notebook/Journal ==== | ||
One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. The bioinformatics equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice the documentation skills needed by users of bioinformatics tools by keeping an electronic lab notebook or journal. The technology we will use is a public MediaWiki site hosted by [http://www.openwetware.org OpenWetWare.org], that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the OpenWetWare site to complete the assignments as well. The following guidelines apply: | One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. The bioinformatics equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice the documentation skills needed by users of bioinformatics tools by keeping an electronic lab notebook or journal. The technology we will use is a public MediaWiki site hosted by [http://www.openwetware.org OpenWetWare.org], that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the OpenWetWare site to complete the assignments as well. The following guidelines apply: | ||
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Certain, non-Biology Department seminars may be approved in advance for extra credit at the instructor’s discretion. To receive credit for these non-Biology Department 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. | Certain, non-Biology Department seminars may be approved in advance for extra credit at the instructor’s discretion. To receive credit for these non-Biology Department 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. | ||
==== Work Load Expectations ==== | |||
In line with LMU’s Credit Hour Policy (http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf), the work load expectation for this course is that for every unit of course credit, you will complete a minimum of two hours of out-of-class student work each week. This is a 1-unit course. Thus, the expectation is that you will complete 2 hours of studying outside of class per week. | |||
=== University Policy on Academic Honesty === | === University Policy on Academic Honesty === | ||
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==== Academic Honesty Resources ==== | ==== Academic Honesty Resources ==== | ||
* [[Media: | * [[Media:BIOL368_Fall2014_HonorCodeAgreement.pdf|Honor Code Agreement]] | ||
* [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2014-2015 University Bulletin]. | * [http://bulletin.lmu.edu/lmu-honor-code-and-process.htm LMU Honor Code and Process, 2014-2015 University Bulletin]. | ||
* [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism] | * [http://www.bio.davidson.edu/dept/plagiarism.html The Davidson College Department of Biology Statement on Plagiarism] | ||
* [[BIOL368_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] | * [[Media:BIOL368_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] | ||
* [http://www.lmu.edu/Asset388.aspx LRC presentation on plagiarism] (PowerPoint presentation) | * [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] | * [http://myweb.lmu.edu/dondi/share/misc/plagiarism.pdf Notes on plagiarism from an electrical engineering & computer science perspective] | ||
=== Special Accommodations === | === Special Accommodations === | ||
Students with special needs who | 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 for additional information. In addition, please schedule an appointment with the instructor early in the semester to discuss any accommodations for this course for which you have been approved. | ||
=== Revision Notice === | === 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 course web site at http://www.openwetware.org/wiki/BIOL368/ | 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 course web site at http://www.openwetware.org/wiki/BIOL368/F14. | ||
Latest revision as of 12:31, 8 January 2015
Announcements
Schedule
Updates to the schedule will be posted here. Readings need to be completed in preparation for class. Readings or slides that cannot be posted here due to copyright restrictions will be posted on MyLMUConnect.
Week | Date | Reading | Topic | Assignment |
1 | Aug 27 |
|
Week 1 Assignment
Due midnight 9/3 | |
2 | Sept 3 | Molecular Genetics Explorer Protocols listed on the Week 2 Assignment page |
|
Week 2 Assignment
Due midnight 9/10 |
3 | Sept 10 | Bioinformatics for Dummies Introduction, Chapters 1, 2, |
|
Week 3 Assignment
Due midnight 9/17 |
4 | Sept 17 | Markham et al. (1998); Cohen et al. (2008) review; Exploring HIV Evolution Handout (on MyLMU Connect); Bioinformatics for Dummies Chapter 3 |
|
Week 4 Assignment
Due midnight 9/24 |
5 | Sept 24 |
|
Week 5 Assignment
Due midnight 10/1 | |
6 | Oct 1 |
|
Week 6 Assignment
Due midnight 10/8 | |
7 | Oct 8 |
|
Week 7 Assignment
Due midnight 10/15 | |
8 | Oct 15 | Huang et al. (2005), Stanfield et al. (1999), Merk & Subramaniam (2013), Bioinformatics for Dummies, Ch. 4, 6, 11. Bring book to class. |
|
Week 8 Assignment
Due midnight 10/22 |
9 | Oct 22 |
|
Week 9 Assignment
Due midnight 10/29 | |
10 | Oct 29 |
|
Week 10 Assignment
Due midnight 11/5 | |
11 | Nov 5 | Brown & Botstein (1999)
Campbell & Heyer Chapter 4 (on MyLMUConnect) |
|
Week 11 Assignment
Due midnight 11/12 |
12 | Nov 12 | Individual Journal Club papers on for DNA Microarray Project |
|
Week 12 Assignment
Due midnight 11/18 Note different due date! |
13 | Nov 19 | Dahlquist et al. (2002), Doniger et al. (2003), Salomonis et al. (2007) |
|
Week 13 Assignment
Due midnight 12/3 |
14 | Nov 26 | Thanksgiving Break | No Week 14 Assignment
Happy Thanksgiving! | |
15 | Dec 3 | DNA Microarray Project | Week 15 Assignment
Due midnight 12/10 | |
Finals | Dec 10 | Wednesday, 2:00-4:00 PM Final Exam period
Final Project Presentations |
Course Information
Instructor
- Kam D. Dahlquist, Ph.D.
- Phone: (310) 338-7697
- Email Dr. Dahlquist through OpenWetWare (Messages sent to me at night or on the weekend will be answered the next school day.)
- Office: Seaver 218
- Office hours: Tuesdays 2:00-4:00 PM, Thursdays 9:00-11:00 AM and by appointment (send me an e-mail or sign up for a time on the sheet on my office door)
Teaching Assistant
- Stephen Louie
Prerequisites/Recommended Background
Biology 112 (General Biology Laboratory II), Biology 202 (Genetics), Chemistry 220 (Organic Chemistry I)
Class Meetings & Attendance
Wednesdays 1:00 PM – 4:50 PM, Seaver 120
This is a hands-on laboratory course, thus attendance at all class meetings is required. This class meets continuously between 1:00 PM and 4:50 PM and will rarely, if ever, "get out early". An unexcused absence from class will result in a 5% deduction from the overall course grade. The instructor should be notified as soon as possible, electronically or by phone, of the reasons for all absences.
Mutual Responsibilities
This course is designed to foster your development as a 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 instructor is to provide the expert coaching to support and assist you on your journey. All of the laboratory exercises, readings, assignments, and policies detailed below have been designed with this purpose in mind.
Classroom and Laboratory Environment
We are all responsible for maintaining a classroom and laboratory environment that is safe and conducive to learning. As such, we will observe the following:
- 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.
- You are responsible for your own learning and for being a good class citizen.
- Class will start promptly on time.
- You are expected to come to class having done the assigned reading and preparatory work so that you are ready to participate in discussions and to perform the laboratory exercises.
- 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 away out of sight. Your own laptops and/or tablet may be used to conduct the class exercises; however, if they are being used for other purposes and become distracting to you or others, you will be asked to put them away.
- All students are governed by LMU Community Standards Publication.
Course Web Site
This is the course web site. You will need to register with OpenWetWare.org to be able to edit the wiki and complete coursework. I will post updates to the course schedule and electronic copies of all handouts, assignments, and readings on that 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 BIOL 368 on MyLMUConnect (formerly known as Blackboard). The MyLMUConnect site may be used for materials that cannot be made public on the OpenWetWare.org wiki.
Required Texts
- Claverie, Jean-Michel & Notredame, Cedric (2006) Bioinformatics for Dummies, Wiley, ISBN-10: 0470089857.
- You do not need to purchase this text. A class set of books will be made available to students in the class.
- The LMU library also has this book available electronically. There is only one license so only one person may access it at at time.
- Specific readings are given on the schedule and may be revised. Check back on this page for the latest reading assignments.
- Readings will also be assigned from other sources and will be posted on the course web site or on MyLMU Connect.
Required Materials (must be brought to each class meeting)
- 3-ring binder with all course handouts
- Pen, pencil, extra paper
- USB flash drive to store bioinformatics data (the more memory the better)
Course Description
Bioinformatics is the application of information technology (informatics) to biological data. Informatics is the representation, organization, manipulation, distribution, maintenance, and use of digital information. When applied to biological data, informatics provides databases and analytical tools for answering biological questions. Bioinformatics is inherently interdisciplinary, involving aspects of biology, computer science, mathematics, physics, and chemistry. While computers have been used to analyze biological data since their invention, the need for computational methods has recently exploded due to the huge amounts of data produced by genome sequencing projects and other high-throughput technologies. Bioinformatics techniques are being used to move the field of biology from a “one gene at a time” approach, to the analysis of whole systems. In this course, students will learn current bioinformatics techniques to address systems-level biological questions. Topics include sequence alignment and phylogeny, protein structural biology, and the analysis of DNA microarray data.
Course Objectives and Learning Outcomes
- To gain foundational knowledge about molecular evolution, protein structure, and gene expression.
- To gain computer, data, and information literacy skills.
- To ask your own biological questions and answer them with the appropriate bioinformatics tools and techniques.
- To read and critically evaluate the primary scientific literature.
- To give effective scientific presentations.
- To be confident in "leaving your comfort zone", flourishing outside of it, and learning more about bioinformatics on your own.
Course Work & Grading
Your work in this course will be assessed in three areas:
Electronic laboratory notebook/journal assignments 140 points Journal club presentations 150 points Oral lab reports 210 points Total 500 points
Grades will be posted on the MyLMU Connect Grade Center for this course.
Final course grading scale
94.0-100% A 90.0-93.9% A- 86.0-89.9% B+ 82.0-85.9% B 78.0-81.9% B- 74.0-77.9% C+ 70.0-73.9% C 67.0-69.9% C- 60.0-66.9% D ≤ 59.9% F
Electronic Laboratory Notebook/Journal
One of the most important skills you can develop as a scientist is keeping an excellent laboratory notebook. The bioinformatics equivalent of the biology paper-based lab notebook is documentation of your “workflow”. For this course you will practice the documentation skills needed by users of bioinformatics tools by keeping an electronic lab notebook or journal. The technology we will use is a public MediaWiki site hosted by OpenWetWare.org, that we will create and edit during the semester. You will create an individual user page and make weekly entries that the instructor will read and grade. You will use the OpenWetWare site to complete the assignments as well. The following guidelines apply:
- Your weekly journal entry is due every midnight on Wednesday PDT (Tuesday night/Wednesday morning). Note that the OpenWetWare server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00 on the server.
- 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 instructor will read and comment on how to improve your journal entries on your User Talk page.
- 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
Journal Club Presentations
Each bioinformatics project will begin with a "Journal Club" where students will present and lead discussion of research articles from the primary literature. In addition, we may also discuss ethical case studies relating to the topics in the course. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations and ethics case studies will not be accepted.
Oral Lab Reports
The final step in the scientific method is communication of the results to the scientific community. In bioinformatics, the communication takes place in the form of peer-reviewed papers, presentations and posters at conferences, and through web sites. To build your scientific communication skills, you will give an oral lab report for each of the bioinformatics projects assigned in the course. Because that day’s class content is dependent upon each student being ready to give his or her presentation, late oral lab reports will not be accepted.
Extra Credit
Students may accumulate up to 2.5% of their final grade in extra credit by attending Biology Department seminars and completing the seminar sheets. Each seminar attended is worth 0.5% with up to 5 seminars (2.5%) total. Students arriving late to the seminar will not be granted credit—so don’t be late!
Certain, non-Biology Department seminars may be approved in advance for extra credit at the instructor’s discretion. To receive credit for these non-Biology Department 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.
Work Load Expectations
In line with LMU’s Credit Hour Policy (http://www.lmu.edu/Assets/LMU+Credit+Hour+Policy_Final.pdf), the work load expectation for this course is that for every unit of course credit, you will complete a minimum of two hours of out-of-class student work each week. This is a 1-unit course. Thus, the expectation is that you will complete 2 hours of studying outside of class per week.
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.” 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
- Honor Code Agreement
- LMU Honor Code and Process, 2014-2015 University Bulletin.
- The Davidson College Department of Biology Statement on Plagiarism
- Guidelines for Literature Citations in a Scientific Paper
- LRC presentation on plagiarism (PowerPoint presentation)
- Notes on plagiarism from an electrical engineering & computer science perspective
Special Accommodations
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 for additional information. In addition, please schedule an appointment with the instructor 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 course web site at http://www.openwetware.org/wiki/BIOL368/F14.