Course Themes
CS313 is an interdisciplinary course bridging computer science and molecular biology. Some of the themes running throughout the course include:
- Many bioinformatics methods are hypothesis-generating. When viewed through the lens of the scientific method, these approaches often emphasize that part of the scientific method relating to generating hypotheses, in contrast to more experimentally oriented approaches that often emphasize that part of the scientific method relating to testing hypotheses. Computational and experimental approaches generally are not competing approaches for addressing the same problem but rather are complimentary approaches in the application of the scientific method.
- When computational approaches generate hypotheses, it is often useful if the probabilities that the generated hypotheses are correct can be estimated. For many problems, randomly generated data can be used to estimate the significance of an observation, i.e., how likely the observation is to have occurred merely by chance.
- Statistical inference is a means for drawing conclusions from data that have significant uncertainty.
- Some problems cannot be solved computationally. Some problems can be solved computationally, but not efficiently. Some provlems can be solved efficiently computationally. It is not always obvious which of the abovementioned classes a problem may fall into. Identiyfing various properties of a problem can be the difference between finding a solution to the problem or not, and identifying such properties often requires algorithmic insights.
- Some problems are solved exactly or optimally. Other problems are addressed using a heuristic approach. Heuristic methods for solving a problem may not solve a problem exactly or optimally, but they can generate good possibly suboptimal solutions, and often they can do so much more efficiently.
- Heuristic approach often offer a trade-off between sensitivity and specificity.
- Many computational approaches are improved by incorporating additional biological insights into their underlying method or model.
- Recent advances have enabled scientists to gather large amounts of, often heterogeneous, data. One of the roles of many bioinformatics methods is efficient analysis of large data sets with the aim of extracting new biological insights from the wealth of data.
Instructor
| Instructor | Office | Phone | Office Hours | |
|---|---|---|---|---|
| Brian Tjaden | SCI-E106 | x3354 | btjaden@wellesley.edu |
Mondays 9:30am - 11:00am Wednesdays 10:00am - 12:00pm |
Class Meetings
There are two 70-minute meetings each week, which will introduce the main content of the course. Approximately two-thirds of the meetings will follow a lecture format and approximately one-third of the meetings will be lab work on computers.
Prerequisites
The prerequisite for CS313 is CS230: Data Structures. Students with comparable experience (including knowledge of Java) who have not taken CS230 may take the course with permission of the instructor.
Grading
Your final grade will be based on a weighted average of the following components:
| Lab Exercises | 30% |
| Projects | 70% |
At the end of the semester, we will compute a weighted average for each student and assign letter grades. In general, the mapping from numerical score to letter grades looks like this: >= 93.33 is an A, >= 90.00 is an A-, >= 86.67 is a B+, >= 83.33 is a B, >= 80.00 is a B-. >= 76.67 is a C+, >= 73.33 is a C, >= 70.00 is a C-, >= 60.00 is a D and < 60.00 is an F.
Depending on the overall performance of the class, we may adjust this mapping.
Exercises
Periodically, there will be online problem-solving exercises in the computer laboratory. The exercises provide hands-on practice with new material and with problems similar to the projects. For the lab exercises, students work at their own pace and can get help from the instructor. Normally, lab exercises will be completed in teams of two students each.
Projects
Projects will help you develop a working knowledge of the concepts presented in class. Projects are due at the start of class on their due date. By that time, you should submit both (1) a hardcopy of your project and (2) a softcopy (i.e., electronic copy) of all your code. More detailed instructions for submitting projects are included in each project.
Instructions for turning in each project will be included with the project. We ask you to keep track of the time you spend on each aspect of the project to help us design projects for future semesters. Each project will come with a header sheet on which you can report the times you spent on the various problems.
Many of the projects will be challenging. Keep in mind that programming often consumes more time than you expect. Start your projects early! This will give you time to think about the problems and ask questions if you hit an impasse.
In order for us to grade and return projects promptly, we cannot accept late projects. In extenuating circumstances (e.g., sickness, personal crisis, family problems, religious holidays), you may request an extension. We will often require that an extension request be made on your behalf by your dean.
If you have not completed an project, you should still turn in your work for partial credit. If there is something that you cannot get to work, do the best you can and comment out code that does not compile. Including a description of your strategy and what is going wrong in the comments can result in some partial credit.
Collaboration Policy
We believe that collaboration fosters a healthy and enjoyable educational environment. For this reason, we encourage you to talk with other students about the course material and to form study groups.
For projects, students are allowed to discuss the problems with other students and exchange ideas about how to solve them. However, there is a thin line between collaboration and plagiarizing the work of others. Therefore, we require that each student must compose her own solution to each project. You may discuss strategies for approaching the programming problems with your classmates and may receive general debugging advice from them, but you are required to write and debug all of your own code. Furthermore, you should never look at another student's code. For example, it is OK to borrow code from a textbook, from materials discussed in class, and from other sources as long as you give proper credit. However it is unacceptable and constitutes a violation of the Honor Code (1) to write a program together (with someone else) and turn in two copies of the same program, (2) to copy code written by your classmates, (3) to read another student's code or (4) to view projects and solutions from previous terms of CS313.
In keeping with the standards of the scientific community, you must give credit where credit is due. If you make use of an idea that was developed by (or jointly with) others, please reference them appropriately in your work. It is unacceptable for students to work together but not to acknowledge each other in their write-ups.
For lab exercises, you will be allowed to form a two-person "team" with a partner. The two team members must work closely together on the exercises and turn in a single hard- and soft-copy of the exercises for the team. The grade received on such a submission will be given to both team members.
Team efforts on lab exercises are subject to the following ground rules:
The work must be a true collaboration in which each member of the team
will carry her own weight. It is not acceptable for two team members
to split the problems in the exercises between them and work on them
independently. Instead, the two team members must actively work together on all
parts of the exercises. In particular, almost all programming on the exercises
should be done with the two team members working at the same computer. It is
strongly recommended that both team members share the responsibility of "driving"
(i.e., typing at the keyboard), swapping every so often.
Computers
All programming in CS313 will be done using the Java programming
language. You are free to use any platform to develop your code. Each
CS313 student will have a password-protected account on the CS
fileserver, puma. The Linux workstations in the minifocus
will be available for you to use. You can also access these workstations
remotely through MACs and PCc. You will have a limited amount of space on
puma to store your course-related files.
Course Directory
The CS313 course directory is located at
/home/cs313 on puma. This directory
contains material relevant to the class, including course
software, and online versions of projects and programs.
All of the course Java software will be placed in the download
folder inside the /home/cs313 directory.
Course Site on Sakai
There is a CS313 site on Sakai named CS-313-01 FA 11.
This site has several purposes. We will use it to make
class announcements, such as corrections to projects and
clarifications of material discussed in class. We encourage you
to post questions or comments that are of interest to students
in the course. Please do not post significant amounts of Java
code (i.e. more than one or two lines of code) in your messages
on the Sakai site! The instructor will read messages
posted in the site on a regular basis and post
answers to questions found there. If you know the answer to a
classmate's question, feel free to post a reply yourself. The
course site is also a good place to find people to join
a study group. You should plan on reading site messages
on a regular basis.
Finding Help
If you have any questions at all about the class (whether big or small, whether on projects, lectures, reading, or whatever) please the instructor. Simple questions can often be answered via the Sakai site or e-mail. Questions of general interest (e.g. clarifying ambiguities in a project, wondering why posted programs do not work as expected) should be posted to the CS313 Sakai site. Other questions can be emailed to your instructor.
If you have a complex question or need help in understanding the material, you are encouraged to see the instructor. The best time to see the instructor is during office hours. If these times are not convenient, we can schedule an appointment for another time. You can schedule an appointment in person or by e-mail.
Finally, when looking for help, do not overlook other students. Get to know your classmates early in the term so that you can help each other out!
Students with Disabilities
Students with disabilities who are taking this class and who need disability-related accomodations are encouraged to work with the Pforzheimer Learning and Teaching Center (for learning or attention disabilities), or Jim Wice, Director of Disability Services (for physical disabilities), to arrange accomodations. Their offices are in Clapp Library.
Mathematical Modeling Distribution
CS313 counts for one Mathematical Modeling (MM) distribution credit.