BIO/CSC 295 2011F Bioinformatics : Handouts

Types of Class Work


Because of the nature of bioinformatics, there will necessary be a variety of kinds of work for this course. For example, you will be expected to read and respond to material from the primary literature and you will be expected to collaboratively develop some programs that solve interesting problems in bioinformatics. (As Sam's statement on teaching and learning suggests, such a variety is good for all courses. It is particularly important for bioinformatics.) Because some forms of work are likely to be new to students, this document provides some detail about the different kinds of work.

Response Papers

In addition to having you read our textbook, we will also ask you to read some pieces from the primary literature. For some of these readings, we will ask you to prepare a one-page response in advance of the class discussion of the reading.

Because of the nature of response papers, we will not accept late responses.

Reading papers are generally individual work. However, you should feel free to discuss readings with your colleagues, provided you then cite them in the work you turn in.

More details can be found in Writing Response Papers.


In studying how students use and benefit from their class work, reseachers have found that students too rarely reflect retrospectively on their work in a course, or consider how their work and thought processes change throughout a course (or an academic career). Portfolios have proven to be a successful mechanism for helping students to reflect on past work and to consider growth.

A typical portfolio consists of a few pieces of student work, selected by the student. The student writes a short narrative for each piece, explaining what the piece demonstrates (or fails to demonstrate). The student also writes an introductory essay that summarizes the content and ideas of the portfolio.

Toward the end of the semester, we will ask you to prepare a portfolio of work from this course. At that point, we will provide further details about how much work to include and how much and what kind of narrative writing is required.

To prepare yourself for creating your Bioinformatics portfolio, you should make sure to keep a copy of all of your work for the course. You may also find it beneficial to keep both ungraded and graded copies of each assignment.

While portfolios are primarily individual work, students should feel free to consult with their colleagues as they prepare the portfolio.

See the guidelines for portfolios for more information.

Web Explorations

In each chapter, our textbook includes a series of Web Exploration Questions that ask you to use standard bioinformatics resources to find out more about an issue or problem. At times, we will devote class time to these Web explorations. At others, we will ask you to do them on your own time. In a few cases (including both in-class and out-of-class explorations), we will ask you to turn in a write-up of the Web explorations.

Web explorations are group work. When you explore the Web, you should do it with your (assigned) peers and discuss each question. When you turn in answers to Web exploration questions, you need turn in only one assignment for the whole group.

In addition to discussing the Web explorations with your colleagues in the group, you may also discuss them with members of other groups. In such cases, you should make sure to include a citation when you turn in your assignment.

Programming Projects

There are basically two kinds of programming projects that you will do in this class: guided projects and open-ended projects. There will also be a significant programming component to the final project.

Guided projects, usually taken through the book, guide you through a series of exercises to help you develop a working solution to a standard program in bioinformatics, such as protein matching or gene sequencing. We will typically allocate a full class period for a guided project, but you may also need time beyond the class period to complete the guided project. We will rarely ask you to turn in your work on a guided project.

On-Your-Own projects provide followup work to the guided projects. TYpically, the ask you to extend your programs from the guided projects in novel and interesting ways. At times, we will also ask you to use these programs to explore new domains and to explain the results of our explorations.

Final Project

Toward the end of the semester, we will ask each group to pick an interesting problem in bioinformatics, to write a program that helps gather information that can be useful in exploring that problem, and to analyze the results that the program produces. Ideally, the project will require significant contributions from both biology experts and computer science experts.

A sample project is that of finding olfactory receptor genes. In order to write a program to find such receptors, one would first determine typical patterns of DNA that make it likely that the code for a receptor is nearby (biologic expertise). One would then write a program that detects such patterns, handling possible variations and approximation (computer science expertise). Next, one would run the program to ensure that it identifies known olfactory receptor genes and to see if it also identifies new areas of the geneome that may code for olfactory receptors (mixed expertise).

Throughout the semester, we will try to suggest possible projects based on the current topic.

The final project is, necessarily, group work. Students should certainly work closely with other members of their group. They may also discuss their project with colleagues outside the group.

Further details about the project will follow after fall break.

Peer Review

We will regularly ask you to review the work of your colleagues. Details on what we expect for each peer review will be distributed with that peer review assignment.

Disclaimer: I usually create these pages on the fly, which means that I rarely proofread them and they may contain bad grammar and incorrect details. It also means that I tend to update them regularly (see the history for more details). Feel free to contact me with any suggestions for changes.

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