VCU Bioinformatics and Bioengineering Summer Institute
Making a model of DNA sequences - Questionnaire

Part I: Basic information

Your name 

A phone number you can be reached at (yours or co-dweller's)? 

Part II: Preliminary
1. How comfortable are you now with what a Markov model is? (perhaps elaborate in box below) 

2. The notes ask you to download a training set of genes. Presumably these are suitable to accomplish the aims of the Scenario. Do you remember what those aims were (after a refresher visit to the Scenario, if necessary)? 

3. What do you suppose would be a good set of genes for our purposes? (answer below)

4. Comments/requests on this section?

Part III: Reading in the training set

5. Were you successful in downloading and getting FastA_module.pm to run within Hamlet.pl? 

6. Were you able to test the reading of the training set sufficiently to convince yourself all was well? 

7. Comments/requests on this section?

Part IV: Add each sequence to the Markov model
8. We haven't really discussed foreach loops as much I'd prefer. How comfortable are you with them?  

9. You were asked a couple of times to search out and destroy certain statements in Hamlet.pl. It's not likely that you understood the meaning of the statements you were looking for. How comfortable are you in doing this? 

10. How good an idea do you have now of what a model of DNA sequences ought to look like (as given by Display_hash.pl)? 

11. How far did you get in this exercise? (answer in box below)

12. Comments/requests on this section?

Part V: Miscellaneous

13. Do you think it would be useful handing in your responses to problem sets?  

14. Your thoughts on the effectiveness of this guided tour changing a Perl program? (in box below)

15. Comments, concerns, questions?

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