Introduction to Bioinformatics (Fall 2003)
Questionnaire on notes: Implementing a Simulation
(please press SUBMIT button when finished)

I. Basic Information and Miscellaneous

A. Your name 
II. Code to produce the model
A. How comfortable are you with the overall strategy of the simulation to predict how likely it is to find an NtcA-binding site? 

B. How comfortable are you in changing the foreach loop in Roll_dice so that it is appropriate for its new task? 

C. How comfortable are you with making a new subroutine, Random_nucleotide (in its simplest form)? 

D. How comfortable are you with in changing, Random_nucleotide to return a random nucleotide? 

E. How far did you get in changing DiceRoll.pl so that it created a random sequence and testing it to make sure it worked? 

F. Please identify study questions that you would most like discussed in class:

SQ1 SQ2 SQ3 SQ4
 
Comments for Section II:
III. Code to look for identical matches in the simulated sequence
A. How comfortable are you in writing a pattern that represents a putative NtcA-binding site? 

B. How far did you get in changing AnyMatches so that it successfully finds exact matches of putative NtcA-binding sites? 

C. Please identify whether you'd like to discuss the following question in class:

SQ5
 
Comments for Section III:
IV. Program to look for specific sequences in a real genome
A. How comfortable are you with FindMatches.pl, i.e. overall what it does and how to change it to suit your purposes? 

B. How far did you get in changing FindMatches.pl so that it does what you want? 

C. Please identify study questions that you would most like discussed in class:

SQ6 SQ7 SQ8 SQ9
 
Comments for Section IV:
V. Finishing up the simulation program
B. How far did you get in changing making the ultimate changes to your new program? 

C. Please identify study questions that you would most like discussed in class:

SQ10  SQ11  SQ12
 
Comments for Section IV:
VI. Miscellaneous
A. Are you fully back to normal?  Put here any other miscellaneous comments, questions, suggestions, concerns you may have.

Thanks!

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