I. Content of 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: Topology of the Genetic Fine Structure (Benzer) Tour: The Discovery of RNA Article: Composition of DNA vs RNA (Belozersky) Tour: Alien Genetic Code
Introduction to BioBIKE	- How to work with a computer language - Concept of iteration	Tour: What is a Gene BioBIKE documentation: Basic Syntax Notes: Introduction to Mapping Notes: Elements of a Loop
Genome Sequencing	- Shotgun sequencing - Sequence assembly	Notes: Overview; Where Genome Sequences Come From Article: A whole-genome assembly of Drosophila
Genome analysis	- Gene identification - Blast (different flavors) - Sequence contrasts       GC-content       Dinucleotide biases       Codon frequencies	Mystery Sequence Analysis Tour: Search for Fragile X genes in Drosophila Notes: Tour of Edwards & Rohwer (2005) Article: Viral metagenomics (Edwards & Rohwer) Notes: Sequence contrasts Article: Detecting anomalous gene clusters… (Karlin)
Evolutionary informatics	Brief overview	Article:  Manuscript evolution Article:  The phage proteomic tree
Statistics	- Chi-square analysis - Comparison of means - Simulations	Tour: Was Mendel Right? Various problems in problem sets
Mentoring	- Molecular biology - Programming - Genome analysis	Tour: What is a Gene Tour: Alien Genetic Code Presentation: Mystery sequence
Metagenome Project	Analysis and annotation of a metagenomic fragment	Article: Viral metagenomics (Edwards & Rohwer) Article: Viral metagenomes from Yellowstone hot springs (Schoenfeld) Notes: Initial analysis of reads Individual meetings Presentation 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?

C. To what degree to you think you have gained a 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 gained a sense of how certain statistics and measures of probability may be applied to bioinformatics problem and what they mean? 

II. The Means of the Course (note that projects are considered separately)

A. In class: Notes / Discussion / Lab
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. Alas -- Didn't always turn out that way.

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

B. 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 enjoyable?
3.  Was feedback helpful?

C. 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 enjoyable? 
3. Was feedback regarding the first exam helpful?  
4. What do you think of the time devoted to exams? 
5. The third exam was somewhat different, with an individual session scheduled in the middle of it. Was this a good idea? 

D. 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? 
3. To what extent did you work with your colleagues outside of class? How valuable was this? Suggestions?

E. Individual sessions

1. Approximately 25% of the class sessions were transformed into weekly interactions between myself and one of you. What did you get out of them?
2. How often did you interact with our TA, Sterling Thomas, outside of class?  Did you get what you came for?

F. 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?

III. Special Projects

A. Mystery Sequence
This project threw you 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. The project also served as an introduction to some tools of sequence analysis.

1. Did you learn much from doing the project? 
2. Did you learn much from hearing your colleagues present their projects? 
3. Do you have any advice or comments on your experience?

B. Mentoring High School Students

1. Did you learn much from the interaction? 
2. Did you think your charges learned much from the interaction? 

C. Metagenome Project
To my mind, this was the center of the course, the place where you actually experienced bioinformatics. But doing real research within the confines of a course is not easy. As with the Mystery Sequence project, you needed to discover for yourself what was of interest in your sequence.

1. Did you learn much from the experience? 
3. Did you gain much by making your presentation? 
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?

IV. 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).

V. 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 bioinformatics?
F. Do you feel more proficient in programming?
G. Do you feel more proficient in molecular biology?
H. 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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