Main Page
NOTE: This page is under construction.
Syllabus
The course syllabus can be found at http://myweb.lmu.edu/dondi/fall2010/cmsi367/cmsi367-fall2010-syllabus.pdf.
Announcements
Seminars and Events
Course Assessment
We ask that students in this class participate in the Research on the Integrated Science Curriculum (RISC) Survey which will allow the instructors to evaluate the effectiveness of this course. Please complete the student pre-course survey, using "Dahlquist" as the instructor last name.
Instructors
Students
Final Group Project
- Overall Description of the Gene Database Project, including entire list of deliverables
- Gene Database Project Report Guidelines
| Teams | Guilds |
| Team1 | Project Manager |
| Team2 | GenMAPP User |
| Team3 | Quality Assurance |
| Team4 | Coder |
| Team5 |
Journal Assignments
Final journal submission: As stated on the syllabus, 10% of the course/notebook journal grade will be based on the overall quality of your body of work, evaluated at the end of the semester. You are encouraged to make improvements to previous journal entries as the semester progresses.
| Week 1 | Week 5 | Week 9 | Week 13 |
| Week 2 | Week 6 | Week 10 | Week 14 |
| Week 3 | Week 7 | Week 11 | |
| Week 4 | Week 8 | Week 12 |
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
| # | Date | Reading | Agenda | Journal | |
|---|---|---|---|---|---|
| 1 | Tuesday 8/27/2013 |
Syllabus walkthrough
Pairwise interviews (report back after each sub-bullet)
Discuss the Week 1 assignment (accounts should be ready to wiki at this point)
|
Week 1
(due at midnight 8/30) | ||
| 1 | Thursday 8/29/2013 |
||||
| 2 | Tuesday 9/3/2013 |
Monkey pp. 1-3, 25-45, 451-456
View Secret of Photo 51 (on reserve in Hannon Library or in Keck lab) |
DNA
An overview of computers, networks, files, and databases |
Week 2
(due at midnight 9/6) | |
| 2 | Thursday 9/5/2013 |
||||
| 3 | Tuesday 9/10/2013 |
Monkey pp. 47-82 | Central dogma
Activities
|
Week 3
(due at midnight 9/13) | |
| 3 | Thursday 9/12/2013 |
||||
| 4 | Tuesday 9/17/2013 |
More Text Processing Features |
Genome sequencing and annotation Office hour scheduling Command line lab session
|
Week 4
(due at midnight 9/20) | |
| 4 | Thursday 9/19/2013 |
||||
| 5 | Tuesday 9/24/2013 |
Introduction to NAR Database Issue |
|
Week 5
(due at midnight 9/27) | |
| 5 | Thursday 9/26/2013 |
||||
| 6 | Tuesday 10/1/2013 |
Additional background and details can be found in Chapters 1, 2, and 6 of A First Course in Database Systems (if you have the recommended text). |
|
Week 6
(due at midnight 10/4) | |
| 6 | Thursday 10/3/2013 |
||||
| 7 | Tuesday 10/8/2013 |
Brown_NatGenet_99_microarrays | Week 7
(due at midnight 10/10; Note Different Due Date) | ||
| 7 | Thursday 10/10/2013 |
||||
| 8 | Tuesday 10/15/2013 |
Ashburner_NatGenet_00_GeneOntology |
|
Week 8
(due at midnight 10/18) | |
| 8 | Thursday 10/17/2013 |
||||
| 9 | Tuesday 10/22/2013 |
|
Week 9
(due at midnight 10/25) | ||
| 9 | Thursday 10/24/2013 |
||||
| 10 | Tuesday 10/29/2013 |
|
Week 10
(due at midnight 11/1) | ||
| 10 | Thursday 10/31/2013 |
||||
| 11 | Tuesday 11/5/2013 |
|
Week 11
(due at midnight 11/8) | ||
| 11 | Thursday 11/7/2013 |
||||
| 12 | Tuesday 11/12/2013 |
|
Week 12
(due at midnight 11/15) | ||
| 12 | Thursday 11/14/2013 |
||||
| 13 | Tuesday 11/19/2013 |
|
Week 13
(due at midnight 11/22) | ||
| 13 | Thursday 11/21/2013 |
|
|||
| 14 | Tuesday 11/26/2013 |
|
No Week 14 Assignment | ||
| 14 | Thursday 11/28/2013 |
Thanksgiving—no class | |||
| 15 | Tuesday 12/3/2013 |
|
Week 15
(due at midnight 12/6) | ||
| 15 | Thursday 12/5/2013 |
|
|||
| F | Thursday 12/12/2013 |
Final project presentations 8:00-10:00 AM | |||
| F | Friday 12/13/2013 5:00 PM |
Project deliverables due 4:30 PM |
Course Information
Instructors
- Kam D. Dahlquist, Ph.D.
- Phone: (310) 338-7697
- E-mail: kdahlquist at lmu dot edu
- Office: Seaver 218
- Office hours: TBA and by appointment
- John David N. Dionisio, Ph.D.
- Phone: (310) 338-5782
- E-mail: dondi at lmu dot edu
- Office: Doolan 106
- Office hours: TBA 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 LMU’s Community Standards for the Student Conduct Code or to 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 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.
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:
Weekly electronic lab notebook/journal assignments (10 points each) 140 points Oral presentations 90 points Information literacy 45 points Final Project Deliverables (including written report) 175 points Total 450 points
Electronic Laboratory Notebook
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
Journal Club Presentation
Your final project will begin with a “Journal Club” where students will present and lead discussion of research articles from the primary literature. Because that day’s class content is dependent upon each student being ready to present and lead discussion, late journal club presentations will not be accepted.
Research Presentation
The final step in the scientific method is communication of the results to the scientific community. This 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 a research presentation (oral lab report) for your final project. Because that day’s class content is dependent upon each student being ready to give his or her presentation, late research presentations will not be accepted.
Final Project Written Report
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 here. The Final Written Report cannot be accepted any later than Friday, May 10 at 5:00 PM.
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.” 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
- Loyola Marymount University Undergraduate Bulletin 2010-2011
- 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
Keck Lab Workstation Tips
Here are some tips for using the workstations inside the Keck lab. These tips pertain to the physical machines themselves — you can access this Wiki from anywhere, on any machine that has a modern Web browser and an Internet connection.
Linux Workstations
- Use your Keck lab username and password directly when logging in to a Linux workstation.
- The Linux workstations use the X-Window System as their GUI environment, which will probably feel (understandably) very unfamiliar to some of you; as a quick tip, right-click on the desktop to see the programs that you can run.
Macs and Windows PCs
The Macs and Windows PCs have shared local accounts; login as "Keck Lab User" and enter "keck" as the password. The instructions below apply both to any Macs and Windows PCs in the Keck lab as well as any other Mac or Windows PC with an Internet connection.
- To connect to the Keck lab network from a Mac:
- Run the Terminal application
- Run this command on the command line that appears, substituting <username> for your Keck lab username (you will then be asked for your Keck lab password):
ssh -X <username>@keck.cs.lmu.edu
- To connect to the Keck lab network from a Windows PC:
- Run the PuTTY application (downloadable from http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html — you want putty.exe)
- Open an ssh connection to the host
keck.cs.lmu.edu - Under the X11 section of the Configuration window, check on "Enable X11 forwarding."
- Once connected, the commands you run in the command window will actually be invoked on the Keck lab network (and the folders/files that are stored there).
- To run GUI programs on the Keck lab network, you should know its command-line equivalent (e.g. firefox, gimp, openoffice). Type that command into the Terminal window; the program's windows should then appear on the Mac mini and you can use them normally.
- To end your connection to the Keck lab network, type this command into the Terminal:
logout
- For in-lab Macs and Windows PCs: Because the "Keck Lab User" accounts are shared, the files that you save on them cannot be guaranteed to remain there between logins. We highly recommend that you bring a flash drive with you so that you can copy your work there whenever your session is done. Alternatively, you can copy your files to your home folder on the Keck lab network. Ask a TA or Dr. Dionisio for help with that.
Practice your Wiki Skills
Make sure you know how to do the following things:
- Every time you edit a page (whether it is a content page or discussion page), enter a meaningful description of your change in the Summary field at the bottom of the editor. This allows other users to easily see (say via the Special:RecentChanges or history pages) what has happened to the page since they last visited it.
- Create a new Wiki page: [[new page title]] — When you include a non-existent link in a page (say, your user page), the software can tell that this page doesn't exist and colors it red instead of blue/purple. When you click on the red link, you are then given the option to edit (and thus create) the page.
- We suggest you practice this by creating your Week 2 journal entry page. The name for the page should be in the format "username Week 2" (i.e., that is the text you put between the square brackets when you link to this page).
- Link to a page within our Wiki: [[page title|optional visible label]]
- Go to the Main Page and link your name to your own user page.
- Link to an external Web page: http://address or [http://address visible label]
- The second form of the link is preferred because it looks neater on the page.
- Use headings: === title === (number of equals signs indicates heading level)
- By convention, start your largest heading with two equals signs. The single equals sign is for the title of the page and is automatically created when you create the page.
- Create a bulleted list: *
- Note that you can create sub-bullets underneath by using multiple asterisks, e.g., **, ***, etc.
- Create a numbered list: #
- Note that you can create numbered sub-lists by using multiple number signs, e.g., ##, ###, etc.
- You can also mix bullets and numbers, e.g., *#, #*, or even #*#, etc.
- Do not skip lines between your bulleted or numbered lists, or the wiki will not interpret your syntax correctly.
- "Comment out" your Wiki code: <!-- commented-out Wiki text --> When you "comment out" your wiki code, the code will be visible on the Edit page, but will not be visible on the wiki page itself. "Commenting" is a common practice in coding that is used to explain the meaning of the code for someone else reading it. In this situation, commenting can be used to keep a rough draft of a wiki page invisible until you are ready for it to be seen.
- Upload an image file: Click Upload file then follow the instructions.
- Use the image on your page: [[Image:exact-name-of-image-file]]
- REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest you include an image of yourself that would be suitable for a professional resume.
- Upload another type of file (such as .pdf): Click Upload file then follow the instructions.
- Link to the file you uploaded on your Wiki page: [[Media:exact-name-of-uploaded-file|visible label]]
- REMEMBER: DO NOT SUBMIT COPYRIGHTED WORK WITHOUT PERMISSION! We suggest that you include something professional, such as the Word or PDF version of your paper resume, a scientific paper you have written, etc.
- Assign one or more categories to your page: [[Category:category name]] This creates an automatic "table of contents" for the wiki. When you click on a category link at the bottom of a page, a new page opens giving you a list of all wiki pages that have been assigned that category.
- Throughout the course, you will use the category [[Category:Journal Entry]] for all of the journal entry pages and [[Category:Shared]] for all of the shared journal pages.
- Use the discussion page to make a comment. Wiki etiquette requires that you sign your comments with your "signature": ~~~~ (4 tildes in a row). These tildes get converted automatically, for example, into: Kdahlquist 15:47, 28 August 2008 (UTC)
- Create a template for yourself and use it on your user page. A template is a block of wiki text that you want to use over and over again on various pages. Instead of having to either re-type that content or even copy-and-paste it multiple times, you can simply put the content on a special Template page. You then use code to invoke the template on any other page in which you want that text to appear. There are two steps to creating a Template.
- Create your template page like you would create any other new wiki page, but using the prefix Template: as part of the page name. For example, your template should be called [[Template:username]].
- Click on the link and put content on this page that you will want to use over and over again. At the minimum, you should use it to create a set of navigation links that you will use in each week's journal entry. Each week as part of your journal assignment, you will be asked to create a link to your user page, the assignment page, your journal entry page, and the shared journal page, as well as add the category "Journal Entry" to your page. If you put these links on your template and then invoke the template on your journal page, this will automatically be taken care of for you. You may also wish to include any other links that you would find useful.
- Once you have added and saved the content to your Template page, you need to use your template on your user page. To do so, invoke the template by using the following syntax: Template:Username in the place you wish the content of the template page to appear. For example, this set of wiki instructions is controlled by the Template:Wiki Checklist, and you can include it in any page by saying:
{{Wiki Checklist}}. This will "expand" the template to its full contents on the actual page.
