This is the last of five programming assignments in a semester-long CS-1-like course named DNA to introduce students to programming within the context of genomics: the analysis of DNA within a single cell of an organism. Originally, the course targeted students in the life sciences but it now attracts students across the academy. The goal of these assignments is to prepare students to obtain enough confidence with scripting and associated scientific write-ups to conduct a small computational experiment in a final project.

This programming assignment requests a Python program to generate a report that serves as a preliminary study to compare and contrast certain features of sequences between multiple organisms. Comparative genomics is the analysis and comparison of genomes from different species. This assignment focuses on “genomic signature” to help infer if a region of DNA is “like” other regions of DNA. The genomic signature refers to the “characteristic frequency of oligonucleotides (e.g., motifs of length 4 bp are referred to as tetramers) in a genome or sequence. It has been observed that the genomic signature of phylogenetically related genomes is similar.

This is the fourth of five programming assignments in a semester-long CS-1-like course named DNA to introduce students to programming within the context of genomics: the analysis of DNA within a single cell of an organism. Originally, the course targeted students in the life sciences but it now attracts students across the academy. The goal of these assignments is to prepare students to obtain enough confidence with scripting and associated scientific write-ups to conduct a small computational experiment in a final project.

This programming assignment assumes that you have already located a specific gene (perhaps using some of the software written in the previous assignment) but now you want to investigate the regulatory DNA sequences “upstream” (just prior to or to the left of) that gene. Regulatory (or promoter) sequences in intergenic regions (between the genes) are vitally important in the process of protein production. Promoter motifs (DNA "words") often are repetitive and/or "fuzzy" (variable) DNA sequences upstream of genes. This assignment applies regular expressions to locate certain categories of repetitions (direct and mirror repeats).

This is the third of five programming assignments in a semester-long CS-1-like course named DNA to introduce students to programming within the context of genomics: the analysis of DNA within a single cell of an organism. Originally, the course targeted students in the life sciences but it now attracts students across the academy. The goal of these assignments is to prepare students to obtain enough confidence with scripting and associated scientific write-ups to conduct a small computational experiment in a final project.

This programming assignment requests a Python program to work the steps in a simplified view of the Central Dogma of molecular biology that relates DNA, RNA, and proteins. Briefly put, the DNA sequence (gene) provides instructions for the protein's production. The program produces all three reading frames of an mRNA and outputs the results of four elementary tests to help a human reader pick the “valid” protein.

This is the first of five programming assignments in a semester-long CS-1-like course named DNA to introduce students to programming within the context of genomics. This assignment requests a Python program to perform an introductory analysis of a "snip" of DNA that includes some upstream (intergenic) sequence and the beginning (but not all) of a gene (genic sequence). A "Starter Kit" includes a template of a Python source file that shows, by example, good introductory and inline documentation, the use of good (camelCase) variable names, and a healthy dose of print statements that produce meaningful and neat output. 

This is the second of five programming assignments in a semester-long CS-1-like course named DNA to introduce students to programming within the context of genomics. This programming assignment requests a Python program to open and read a FASTA-formatted file filled with DNA and print a neat summary of Chargaff’s numbers, defined as: the number/proportion/percentage of A, C, G, T nucleotides in the file of DNA. Students are required to research and download the genome of an entire microbe of their choice. In addition to submitting source code, students must practice their scientific writing in a report of their program as applied to an entire microbial genome of their choice. The report must include the sections of Introduction, Methods, Results, and Discussion.

In this assignment, students implement some simple filters on sound objects, including reversing a sound, mixing arbitrary-length lists of sounds, and changing volumes of sounds. These functions can each be written in ten or fifteen lines of code, using objects that represent sounds and samples from our media module. Then, calling on these functions, students write a "song generator": a function that takes a string of note data (a notestring) and produces its representative sound object that can be played or saved as a wav file.

In this 2012 Nifty assignment, students use fundamental CS topics to explore digital sound processing. Using variables, functions, conditionals, and assignment operators in conjunction with the Pygraphics library, students perform various manipulations on sound files. Vocals are removed from the wav files by using the vocal-removing algorithm to subtract channels and isolate the single vocal track along a particular frequency range. Additional manipulations on the sound files, such as fading in and out and panning, are covered so that students can examine the various capabilities of using Python to manipulate digital sound. This assignment is ideal for students with an understanding of implementing libraries and an interest in digital sound processing.

In this lab, students demonstrate their understanding of while loops and computation by simulating populations of rabbits and foxes in an ecosystem. Students are provided with formulas to compute populations from one year to the next, using previous populations of rabbits and foxes for each. This activity is a good simulation for students beginning to learn about while loops.

In this assignment, students will be creating mosaics in Python. Students will work to generate tessellations, such as Ring and Hex. Functions must be composed to generate the various images.

In this assignment students use dictionaries, lists, tuples, and functions and then create a tag cloud of transcripts from one of the 2012 U.S. Obama-Romney Presidential debates. The program must parse the information and create a tag cloud in an HTML document.