I. Goals of the course

There are no questions in this section... I feel compelled to start off restating what I feel were the primary goals of the course:

• Progress towards independence - Framing your own questions
  The ability to make your own sense of a poorly defined problem and find a path towards its solution. When you find the way blocked, analyzing what you need and expressing the need and the reason for it to others to gain useful aid.
   
• Progress towards independence - Digesting information yourself
  The ability to find useful information within research articles, without predigestion by someone else.
   
• Progress towards independence - Finding your own motivation
  Making educational choices for what you may learn from them rather than for an imposed reward dangled in front of you.
   
• Progress towards independence - Learning that you can use the computer in ways that are not bound by inflexible software
  You don't have to be a computer nerd to program the computer
   
• Learning something about bioinformatics

II. Content of the course

As a reminder, here are the semester's topics at a glance:
 

Topic	Substance	Tools
Introduction to Molecular Biology	From gene to protein to function	Notes: Strategies of Life; Protein; Flow of Information Tour: What is a Gene Article/Tour: Differential expression... (Belasco et al.) Tour/Simulation: Alien Genetic Code Problem Sets: 1 - 3
Introduction to BioBIKE	- How to work with a computer language - Concept of iteration - Concept of functions - Concept of tables	Tour: What is a Gene BioBIKE documentation: Basic Syntax Notes: Introduction to Mapping Notes: Elements of a Loop Problem Sets: 2, 4, 6
Genome Sequencing	- Shotgun sequencing - Sequence assembly	Notes: Overview of Genome Sequencing Notes: Where Genome Sequences Come From Article/Tour: A whole-genome assembly of Drosophila (Myers et al.) Problem Set: 3
Genome analysis	- Gene identification - Blast (different flavors) - Dotplots - Sequence contrasts       GC-content       Dinucleotide biases       Codon frequencies	Tour: Search for Fragile X genes in Drosophila Notes: Sequence contrasts Article/Tour: Comparative Genomics... (Hatfull et al.) Article/Tour: Detecting anomalous gene clusters...(Karlin) Problem Set: 5 - 7
Evolutionary informatics	Brief overview	Article/Tour: The Phage Proteomic Tree (Rohwer & Edwards) Article: Manuscript Evolution (Howe et al) Article: Phylogeny for the faint hearted (Baldauf) Problem Set: 8
Statistics	- Chi-square analysis - Comparison of means - Simulations	Tour/Simulation: Was Mendel Right? Problem Set: 6
Phage Genome Project	Analysis and annotation of mycobacteriophage genomes	Article/Tour: Comparative Genomics... (Hatfull et al.) Article/Tour: In silico analysis...Che12... (Gomathi et al.) Experiment summary from research article Group meetings Symposium Final Report

A. How useful was the Introduction to Molecular Biology? 

Apart from the basic review, the main purpose was to help you get beyond the usual abstractions and to grapple with the question of what really is a gene.

B. How useful was the Introduction to BioBIKE?

This was not and could not be a course in computer programming. Nonetheless, did you get enough to see how computer programming might be useful to you? Enough to use it to explore molecular biology and bioinformatics? Enough to make headway in your project?

C. To what degree to you think you have increased your sense of what bioinformatics is about? 

Rather than survey bioinformatics and its tools, the course attempted to provide you with an opportunity for you to taste bioinformatics in action.
Your thoughts on this choice and its effectiveness?

D. To what degree to you think you have increased your sense of how quantitative thinking, certain statistics, and measures of probability may be applied to bioinformatics problem and what they mean? 

III. The Means of the Course (note that the project is considered separately)

A. In class: Notes / Class discussion / Questionnaires
The goal was to have the notes on well in advance of class so that you could read them at your leisure, try things out, and determine which areas would be good to discuss in class.

1. Did this scheme work for you?
2. Time in class well spent?

B. In class: Lab
The goal for the lab was to provide an environment where you could perform computational experiments with guidance (so you might gain the habit of performing such experiments on your own. At first the experiments were provided. By the end they were whatever you said you needed for your project.

1. Did this scheme work for you?
2. Time in lab well spent?

C. Problem Sets
Intended to be nontrivial opportunities to help you integrate what you've learned within a realistic context.

1. Did they work for you? 
2. Were they interesting?
3.  Was feedback helpful?

D. Exams
Intended to be an intense problem set that makes new connections between the material and the world. The idea was that spreading the exam over the better part of a week would enable people to contact me to overcome obstacles as they arose. This hardly ever happened. In the great majority of cases, people waited until the last 24 hours before beginning the exam, by which time consultation was no longer an option, and the exam became a virtually impossible task. Given human nature, do you think this kind of exam can work?

1. Did they work for you? 
2. Were they interesting? 
3. Was feedback helpful?  
4. What do you think of the time devoted to exams? 

E. Time outside of class

1. How much time per week did you spend outside of class (excluding projects and exams)? 
2. What do you think of that amount? 

F. Group sessions and interaction with others

1. During the first half of the semester the class sometimes broke up into groups to consider problems. Was this valuable to you?
2. 5 weeks out of a 14-week semester we met in small group sessions instead of class. What did you get out of them?
3. To what extent did you work with your colleagues outside of class and group sessions? How valuable was this? Suggestions?

G. Web site

1. Did the course web site provide what you needed to get a feel for the course? 
2. Did the Calendar help inform you what was going on (and what went on)? 
3. Suggestions for things that should be added/subtracted/modified?

H. Help

1. Did you feel you had adequate opportunity to get help you needed? 
2. How often did you interact with our TA, Harry Caufield, outside of class and lab? Did you get what you came for?

 

IV. Genome project

A. Summary of experiment
Sifting through dozens, maybe hundreds of articles of no use to you in search of one that illuminated your topic, and then dissecting one experiment from that article... that was intended to introduce you to your research project and how others have done similar things to what you were attempting. Many flailed around in this exercise. It's difficult to avoid.
      Focusing on one experiment may help you make a connection that few undergraduates make, one between generalities and actual knowledge -- observations unadorned by theory or preconceptions. Making that connection is a necessary major leap to gain independence from predigested views of the world.

1. Did you learn much from finding the article and writing the summary? 
2. Do you have any advice or comments on your experience?
 

B. Group/Individual slice of the genome project
To my mind, this was the center of the course. You were thrown into a situation that is rare in the classroom but all too common in the real world: a problem to be solved without clear definition. You had to find for yourself what was of interest and how to pursue it.

1. Did you learn much from the experience? 
3. Did you gain much by making your presentation at the symposium? 
4. Did you gain much by listening to others' presentations? 
5. Did you gain much by writing your report? 
6. About how much time did you spend outside of individual sessions on the project? 
7. Your thoughts and comments on your experience?

 

V. BioBIKE
You are amongst the only people on earth to have used BioBIKE, a language designed to facilitate the transition to computational functionality by biologists with little or no prior computer experience. I and the other developers of the language would love to hear your insights regarding your experience.

1. Did you find the language relatively easy to learn (sufficiently to do the tasks at hand)? 
2. Did you find the language sufficiently powerful to do the tasks at hand? 
3. Vent your spleen! What features of BioBIKE irritated you to distraction?
    What advice could you give as to features that should be added/changed?
    Compare this experience with your first exposure to programming (if there was one).

 

 

VI . Grading and Miscellany

A. Feedback and grading
Please give your views of feedback and grading (or lack of), from the perspective of the goals of the course and your own goals. 

B. Feedback web page
Please go to the course web site, Course at a Glance, Feedback, (username/password). It is behind a password because some have indicated that they found the content offensive. What on this page do you find offensive? 

VII. Bottom line

A. Three things you'd advise that this class never to do again?

B. Three things you'd advise that this class keep doing at all costs?

C. Three ideas that would make the course better for those that come after you? (I know... make shorter questionnaires)

 

D. Did you get what you wanted out of the course?
E. Do you feel more proficient in some way? If so, how?
F. What if anything do you think will still be with you from the course in five years?

A LONG questionnaire... Thanks!

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