The living world is vast and full of mysteries. In this module, we show how to use coding skills to understand the scientifically unexplored corners of the living world. Every day we choose a biological theme and then identify and solve coding problems related to it. The difficulty of the coding problems depends on the coding experience of the class. In generals, the days are filled with plenty of hands-on exercise, where the students log into our cloud-based server to write code and solve problems.
More specifically, you will -
- use your coding skills (R/Python/maybe Java) to play with genome sequences and find important genes.
- learn how to develop computer algorithms to assemble genomes.
- see the big picture of where the new cutting-edge jobs are created for 21st century.
- have a week of fun experience on a challenging and relevant topic
Day 1 - Mushroom Hunters
Mushroom hunters go around the forests of Pacific Northwest to find delicious edible mushrooms. This activity is rewarding, but also has high risks. One must avoid poisonous 'death cap' mushrooms, or else.
Usually mushroom hunters apply visual identification methods to distinguish edible mushrooms from the poisonous ones. Instead you will use DNA sequences to identify mushrooms more accurately and help a group of mushroom hunters.
Details: You will learn to use the search program BLAST, which is like google for DNA sequences. You will also understand various character search algorithms and write code to implement an example.
Day 2 - Is Whale Fish or Mammal?
Scientists always question what they hear and try to confirm using their best evidences. We learned in our biology classes that the whales evolved from land mammals, but the evidence based on physical similarities appeared inconclusive. Can we do better in this age of genes and genome?
Details: You will compare the genes of whale with a number of other organism including fruitfly, zebrafish, cow, mouse and human. This is only possible because a number of researchers recently sequenced the genomes of bowhead and blue whales. Will whale genes closely match fruitfly, zebrafish or one of the mammals? I do not want to reveal the secret and spoil your fun.
Day 3 - Solve a DNA Jigsaw Puzzle
Our chromosomes are very long, and no sequencing instrument can sequence the entire chromosome in one attempt. Instead the sequencing is done by bits and pieces, and the scientists are left with a gigantic jigsaw puzzle with many small pieces. Can you solve one using your coding skills?
Details: You will develop your own algorithm and write code to solve a simple version of the DNA jigsaw puzzle.
Day 4 - A 'Human'gous Bet
How many genes does the human genome have? We will bet on it and find out.
Details: You will use your coding skills to explore genome and genes. Also, you will use the Biopython (Python) or Bioconductor (R) libraries to find information from them in the computer.
Day 5 - Asian Flush Syndrome
Many people of east Asian descent get red face after drinking alcohol. It is known as 'alcohol flush reaction' or 'Asian flush syndrome'. This is caused by a single change in the chromsome. Today you will learn how and why.
Details: You will look into the human genome and genes, and learn about exon/intron. Also, you will explore the mutations causing physical changes.