Dahlquist:Courses: Difference between revisions

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This information can also be found at the Dahlquist Lab [http://myweb.lmu.edu/kdahlqui/Courses.htm Courses] page at Loyola Marymount University.
This information can also be found at the Dahlquist Lab [http://myweb.lmu.edu/kdahlqui/Courses.htm Courses] page at Loyola Marymount University.


== Fall 2009 Courses ==
== Fall 2013 Courses ==
=== Biology 201:  Cell Function ===


=== Biology 201-01: Cell Function ===
Section BIOL 201-03: MWF 11:00-11:50 AM, Doolan 222


Section BIOL 201-01 MWF 10:00-10:50 AM, Pereira 120
Section BIOL 201-04:  MWF 12:00-12:50 PM, Doolan 222


Section BIOL 201-02 MWF 12:00-12:50 PM, Pereira 200
Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.


Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.
Currents Students: For syllabus and course information login to [https://mylmuconnect.blackboard.com/webapps/login/ MyLMU Connect], formerly known as Blackboard (or via [https://my.lmu.edu/portal/page/portal/mylmu/welcome MYLMU])


Currents Students: For syllabus and course information login to [https://mylmuconnect.lmu.edu/webapps/login/ MyLMU Connect], formerly known as Blackboard (or via [https://my.lmu.edu/portal/page/portal/mylmu/welcome MYLMU])
=== Biology/Computer Science 367/Honors 398: Biological Databases ===


=== Biology / Computer Science / Honors 398: Biological Databases ===
TR 9:25-10:40 AM:  Doolan 219


T 4:30-7:00 PM, Doolan 219
[https://xmlpipedb.cs.lmu.edu/biodb/fall2013/index.php/Main_Page Course web site and public wiki]


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 fashion. 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.
== Spring 2013 Courses ==


Currents Students: For syllabus and course information, login to the [https://www.cs.lmu.edu/biodb/fall2009/index.php/Main_Page course wiki].
=== Biology 398-03: Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics ===


== Spring 2009 Courses ==
TR 9:25 - 10:40 AM, Seaver 120


=== Biology 478: Molecular Biology of the Genome ===
[[BIOL398-03/S13 | BIOL398-03/S13 site on this wiki]]


MW 1:00-4:50 PM, Seaver 207 and 215
=== Biology 478: Molecular Biology of the Genome ===


Description: The completion of the Human Genome Project 50 years after Watson and Crick first described the structure of DNA marks a fundamental shift in the way we view ourselves and practice biology. This course will examine the fundamental concepts in molecular biology required to understand the biotechnology that has brought us to the genomics era and beyond. In the laboratory, students will become proficient in the basic techniques of molecular biology and then will get to work with cutting-edge genomics technology. Students will design and carry out a DNA microarray experiment. Students will then use bioinformatics tools to analyze their DNA microarray data and to model biological pathways and networks. By the end of this course, students will be working independently on a research project. Currents Students: For syllabus and course information login to [http://157.242.56.51/webapps/login/ Blackboard] (or via [https://my.lmu.edu/portal/page/portal/mylmu/welcome MYLMU])
== Fall 2011 Courses ==


=== Honors 240-01: On the Nature of Things ===
=== Biology 201: Cell Function ===


MWF 10:00-10:50 AM, Seaver 202
Section BIOL 201-01:  MWF 9:00-9:50 AM, Pereira 140


Descripton: The purpose of this course is to examine the history, philosophy, and nature of scientific discovery, theory, and practice. The completion of the Human Genome Project 50 years after Watson and Crick first described the structure of DNA marks a fundamental shift in the way we view ourselves and in the way biology is practiced. Thus, we will focus on case studies of recent advances in biology, specifically biotechnology and genomics. Ultimately, we will explore the question, “How do I know that I know something?” Furthermore, in the popular media, "the genome is the new soul." We will explore biological (genetic) determinism in relation to what biologists really know about our genes.
Section BIOL 201-03:  MWF 10:00-10:50 PM, Pereira 207
Currents Students: For syllabus and course information login to our [http://sites.google.com/site/lmuonthenatureofthingsspr09/ Google Site].


== Fall 2008 Courses ==
Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.


=== Biology 201-01: Cell Function ===
Currents Students: For syllabus and course information login to [https://mylmuconnect.lmu.edu/webapps/login/ MyLMU Connect], formerly known as Blackboard (or via [https://my.lmu.edu/portal/page/portal/mylmu/welcome MYLMU])


MWF 10:00-10:50 AM, Pereira 120
=== Biology 368: Bioinformatics Laboratory ===


Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.
Section BIOL 368-01: W 1:00-4:50 PM, Seaver 120
Currents Students: For syllabus and course information login to [http://157.242.56.51/webapps/login/ Blackboard] (or via [https://my.lmu.edu/portal/page/portal/mylmu/welcome MYLMU])


=== Biology / Computer Science / Honors 398-01: Biological Databases ===
[[BIOL368/F11 | BIOL368/F11 site on this wiki]]


TR 9:25-10:50, Doolan 219
== Previous Courses ==


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 fashion. 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.
* '''Spring 2011 Courses'''
Currents Students: For syllabus and course information, see the course [http://myweb.lmu.edu/dondi/fall2008/cmsi398/ web site] or login to the [https://www.cs.lmu.edu/biodb/wiki/index.php/Biological_Databases_Fall_2008 wiki].
** Biology 398-01:  Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics
*** [[BIOL398-01/S11 | BIOL398-01/S11 site on this wiki]]
* '''Fall 2010 Courses'''
** Biology 201-01, -02: Cell Function
*** Protein Structure Exploration exercises are hosted [[BIOL201/F10 | here on this wiki]].  NOTE:  these are currently under construction.
** Biology / Computer Science 367-01/ Honors 398-05: Biological Databases
*** [https://www.cs.lmu.edu/biodb/fall2010 Course wiki on the CS network]
*** [[BIOL367/F10 | BIOL367/F10 site on this wiki]]
* '''Spring 2010 Courses'''
** Biology 398-01: Bioinformatics Laboratory
*** See [[BIOL398-01/S10 | BIOL398-01/S10 site on this wiki]].
** Biology 478: Molecular Biology of the Genome
* '''Fall 2009 Courses'''
** Biology 201-01, -02: Cell Function
** Biology / Computer Science / Honors 398-01: Biological Databases
*** [https://www.cs.lmu.edu/biodb/fall2009/index.php/Main_Page Course wiki] (for students in the course only).
* '''Spring 2009 Courses'''
** Biology 478: Molecular Biology of the Genome
** Honors 240-01: On the Nature of Things
***[http://sites.google.com/site/lmuonthenatureofthingsspr09/ Course Google Site] (for students in the course only).
* '''Fall 2008 Courses'''
** Biology 201-01: Cell Function
** Biology / Computer Science / Honors 398-01: Biological Databases
*** [http://myweb.lmu.edu/dondi/fall2008/cmsi398/ Course web site]
** Biology 398-01: Bioinformatics Laboratory
*** [http://sites.google.com/site/lmubioinformaticslabfall2008/Home Course Google Site] (for students in the course only).


==== Problem Space: Analysis of Prostate Cancer DNA Microarray Data ====
== Problem Space: Analysis of Prostate Cancer DNA Microarray Data ==


* [[Media:BIOL398-01_GenMAPP_ExpressionDatasetManager_20081023.pdf | GenMAPP Prostate Cancer Exercise Part 1]]
* [[Media:BIOL398-01_MAPPFinder_20081021.pdf | GenMAPP Prostate Cancer Exercise Part 2 (MAPPFinder)]]
* GenMAPP and MAPPFinder are available from [http://www.genmapp.org http://www.genmapp.org]
* GenMAPP and MAPPFinder are available from [http://www.genmapp.org http://www.genmapp.org]
* Data for this exercise was published in this paper: <biblio>#Paper1 pmid=12154061</biblio>
* Data for this exercise was published in this paper: <biblio>#Paper1 pmid=12154061</biblio>
* Review article on prostate cancer: <biblio>#Paper2 pmid=12878745</biblio>
* Review article on prostate cancer: <biblio>#Paper2 pmid=12878745</biblio>
 
* [[Media:BIOL398-01_GenMAPP_ExpressionDatasetManager_20081023.pdf | GenMAPP Prostate Cancer Exercise Part 1]]
=== Biology 398-01: Bioinformatics Laboratory ===
** This is the link to the data file, [[Media:Hs_ED_ProstateCancer_edited.txt | <Hs_ED_ProstateCancer_edited.txt>]], mentioned in step 3 of the protocol.
 
* [[Media:BIOL398-01_MAPPFinder_20081021.pdf | GenMAPP Prostate Cancer Exercise Part 2 (MAPPFinder)]]
TR 3:00-5:00 PM, Seaver 120
** This part of the exercise can be completed independently of Part 1 by downloading the GenMAPP Expression Dataset <Hs_ED_ProstateCancer_20060130.gex> from GenMAPP.org using the Data Acquisition Tool from within the GenMAPP program.
 
*# Launch GenMAPP.
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 biological databases, sequence alignment and phylogeny, comparative genomics, protein structure prediction, modeling pathways and networks, and the analysis of high-throughput genomic and proteomic data.
*# Select the menu item, Data > Download Data from GenMAPP.org
Currents Students: For syllabus and course information login to our [http://sites.google.com/site/lmubioinformaticslabfall2008/Home Google Site].  
*# Expand the "Expression Datasets" folder, and click on "Homo sapiens" to see the file.
 
*# Check the box next to the filename.
 
*# Click the Start button to download.


[[Category:Lab]]
[[Category:Lab]]

Revision as of 10:40, 12 September 2013

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This information can also be found at the Dahlquist Lab Courses page at Loyola Marymount University.

Fall 2013 Courses

Biology 201: Cell Function

Section BIOL 201-03: MWF 11:00-11:50 AM, Doolan 222

Section BIOL 201-04: MWF 12:00-12:50 PM, Doolan 222

Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.

Currents Students: For syllabus and course information login to MyLMU Connect, formerly known as Blackboard (or via MYLMU)

Biology/Computer Science 367/Honors 398: Biological Databases

TR 9:25-10:40 AM: Doolan 219

Course web site and public wiki

Spring 2013 Courses

Biology 398-03: Biomathematical Modeling/Mathematics 388-01: Survey of Biomathematics

TR 9:25 - 10:40 AM, Seaver 120

BIOL398-03/S13 site on this wiki

Biology 478: Molecular Biology of the Genome

Fall 2011 Courses

Biology 201: Cell Function

Section BIOL 201-01: MWF 9:00-9:50 AM, Pereira 140

Section BIOL 201-03: MWF 10:00-10:50 PM, Pereira 207

Description: The purpose of this course is to introduce students to the core concepts of cellular biology that needed to succeed in upper-division biology courses. The overall theme for this course is how structure implies function for macromolecules and cells. Course topics include: cellular and sub-cellular structures and functions, DNA and RNA structure and function, protein synthesis and structure, enzyme function, metabolic pathways, and membrane function.

Currents Students: For syllabus and course information login to MyLMU Connect, formerly known as Blackboard (or via MYLMU)

Biology 368: Bioinformatics Laboratory

Section BIOL 368-01: W 1:00-4:50 PM, Seaver 120

BIOL368/F11 site on this wiki

Previous Courses

  • Spring 2011 Courses
  • Fall 2010 Courses
  • Spring 2010 Courses
  • Fall 2009 Courses
    • Biology 201-01, -02: Cell Function
    • Biology / Computer Science / Honors 398-01: Biological Databases
  • Spring 2009 Courses
    • Biology 478: Molecular Biology of the Genome
    • Honors 240-01: On the Nature of Things
  • Fall 2008 Courses
    • Biology 201-01: Cell Function
    • Biology / Computer Science / Honors 398-01: Biological Databases
    • Biology 398-01: Bioinformatics Laboratory

Problem Space: Analysis of Prostate Cancer DNA Microarray Data

  • GenMAPP Prostate Cancer Exercise Part 1
  • GenMAPP Prostate Cancer Exercise Part 2 (MAPPFinder)
    • This part of the exercise can be completed independently of Part 1 by downloading the GenMAPP Expression Dataset <Hs_ED_ProstateCancer_20060130.gex> from GenMAPP.org using the Data Acquisition Tool from within the GenMAPP program.
    1. Launch GenMAPP.
    2. Select the menu item, Data > Download Data from GenMAPP.org
    3. Expand the "Expression Datasets" folder, and click on "Homo sapiens" to see the file.
    4. Check the box next to the filename.
    5. Click the Start button to download.
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