TimelineTimeline

Assignment 1 – DNA ModelingLevel: 0 (no experience required)

Objective: The student will create structurally accurate models of DNA out of pipe cleaners.

Materials: pipe cleaners, scissors

Tested on: C&I 47330 Curriculum and Instruction in Reading and Writing (Fall 2006)see timeline pictures

Assignment 2 – Evolution Models ILevel: 1 (basic knowledge of graph theory)

Objective: The student will create diagrams of binary evolution trees.

Program: graphics package (optional)

Tested on: CS10051 Introduction to Computer Science (Spring 2006)

Assignment 3 – Evolution Models IILevel: 1 (basic knowledge of graph theory)

Objective: The student will build on assignment 2 to create diagrams of the incremental k-leaf root evolution model.

Program: graphics package (optional)

Tested on: CS10051 Introduction to Computer Science (Spring 2006)

Assignment 4 – DNA Pattern StatisticsLevel: 2 (Python programming)

Objective: The student will write a program to perform pattern matching statistics on DNA.

Program: Python programming language

Tested on: CS10061 Introduction to Programming (Spring 2007)

Assignment 5 – DNA VisualizationLevel: 2 (Python programming)

Objective: The student will implement and test the chaos-game representation of DNA.

Program: Python programming language (with Tkinter graphics library)

Tested on: CS10061 Introduction to Programming (Spring 2007)

Assignment 6 – Longest Common SubsequenceLevel: 2 (C++ programming)

Objective: The student will implement and test the longest common subsequence dynamic programming algorithm.

Program: C++ programming language

Tested on: CS33001 Data Structures (Spring 2007)

Further Activities• Create model of an actual DNA sequence. • Longer strands: strands of length 100 can be

completed in about two hours, once the procedure is learned and practiced.

• In groups, use an “assembly line” approach to create a very long DNA strand.

• Fundraisers (“DNA for a Buck!”)• Class contests

–create the longest DNA strand–create the strongest DNA strand

Step 3: …and do the TwistIn “ladder” form, the DNA strand may look inconsistent in size. When twisted into a double-helix form, the inconsistencies tend to work themselves out.

NIFTY BIOINFORMATICS ASSIGNMENTSDean ZellerDepartment of Computer Science

Contact: Dean Zeller, dzeller@cs.kent.edu

Assignment 1 – DNA ModelingAssignment 1 – DNA ModelingSpecific Goals

• Create “teachable” and “enjoyable” lessons on bioinformatics suitable for a biology, computer science, or mathematics class.

• Test these lessons to evaluate effectiveness on college level students.

Long Term Goals

• Instruct K12 teachers in the areas of bioinformatics education.

• Educate the next generation of bioinformaticists.

GoalsGoals

Assignment SummariesAssignment Summaries

QuotesQuotes

“Most of the fundamental ideas of science are essentially simple, and may, as a rule, be expressed in a language comprehensible to everyone.”

Albert Einstein (1879-1955)German/U.S. physicist

“Science can be introduced to children well or poorly. If poorly, children can be turned away from science; they can develop a lifelong antipathy; they will be in a far worse condition than if they had never been introduced to science at all.”

Isaac Asimov (1920-1992)US science fiction novelist and scholar

Basic Idea

• The Special Interest Group of Computer Science Education (SIG-CSE) holds a “Nifty Assignment” series at the annual convention.

• Presenters demonstrate assignments in computer science that have been tested in an actual classroom environment.

• These assignments follow SIG-CSE’s concept of nifty assignments for all levels of bioinformatics.

Step 0: SetupA. Select colors for DNA stalks

and nucleotides (A, T, C, G).B. Cut the nucleotide pipe

cleaners in fourths.C. Put in AT/CG pairs.

Step 1B

Step 1D Step 1D

Step 1E

Step 2

Step 2B Step 2C

Step 2C

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Step 1: Create nucleotidesUse these steps to create nucleotide pairs.A. Select two pipe cleaner pieces of the

appropriate colors to form a nucleotide pair (AT or CG).

B. Put in a V-shape with a small overlap (1/4”). Choose a long end and corresponding short end.

C. Coil a long end three or four revolutions around the other short end, covering it completely. There should be some extra left over to attach to a stalk.

D. Bend the remaining long and short ends 90° to form a T-shape.

E. Repeat step 1C with the remaining long and short ends.

Step 2: Connect Nucleotides to Stalks

Attach nucleotides to stalks to form a “ladder”

A. Attach one side of nucleotide to stalk by wrapping extra length around stalk twice (once on the left, and once on the right). Wrap any remaining length around itself.

B. Repeat for other nucleotides, spreading evenly across the stalk.

C. Attach opposite stalk in similar way. Leave enough room at ends to connect to other DNA strands.

Setup

Step 3

Step 1C

Step 2A

Step 1E