This project was prepared as part of a BioQUEST faculty development workshop entitled Chautauqua Short Course -- Bioinformatics Education Dissemination: Reaching Out, Connecting, and Knitting-together at Grand Valley State University in August 2006. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:

Upcoming events               BEDROCK Problem Spaces

 
RNA-Folding Programming Project for High-Performance Computing
 
 
Authors          Audiences          Overview           Materials          Resources           Future Directions
 

 


Authors


Susan Haynes
Eastern Michigan University


Joel Adams
Calvin College

 
   
 


Possible Audiences:

Undergraduate computer science/engineering students in a high performance computing or parallel programming course.  

 
 


Brief Overview:

This project is to develop an interesting set of programming assignments, lecture materials, and readings, with easily explained problems and algorithmic solutions. Students will write programs that will solve the problems (e.g., compute the folds of different RNA sequences).

Criteria:

  • Students will experience changing speedups based on different algorithms, parallel architectures, and partitionings. Preferably, at least one algorithm will not be communication intensive;
  • Students will be able to visualize the fold computed by their program.
 

 
   
 


Project Materials:

To be determined.  

 
 


Resources and References:

 

 
   
 


Future Directions:

Questions:

  • Is there a freeware visualization tool available that can be used to visualize RNA folds?
  • Is there a standard format for representing RNA folds?
  • What parallel algorithms have been developed for this problem?
  • Is there more than one solution that's equally valid?
  • Are there web resources to which we can point students for the biological concepts (RNA nucleotides, base pairs, folding, etc.)
 

 
 


Attachments


- projectSequence.txt