Nucleobase Counting

Motivation

• get our feet wet with parallel programming
• gain experience with the async and finish constructs
• take different approaches to splitting up the work

We will solve the problem sequentially, then split the work up into 2 tasks, then coarsen the work n-ways, and finally split up the work in a divide-and-conquer recursive style.

Background

Bioinformatics

For this assignment, you will be writing sequential and parallel code to count nucleobases in a human X chromosome.

DNA is made up of four nucleobases: cytosine, guanine, adenine, and thymine. A strand of DNA can thus be represented as a string of letters representing these nucleobases, for example: “ACCGCATAAAGTCC.” However, DNA sequencing is typically not 100% accurate, so some of the nucleobases are not read with high certainty. These bases can be represented as an “N.” A sequence then might look something like “NCCGCATNAAGTCC.” Your goal is to write code that counts the number of occurrences a particular nucleobase or uncertain reads.

We will be using actual data pulled from the US National Library of Medicine, a database maintained by the National Institute of Health. We have already provided you the code that you need to access the chromosome from the database and check your work. You must implement a sequential solution and three parallel solutions to count the given bases in these sequences.

For some more optional background on DNA and nucleotide bases, please check out

• https://en.wikipedia.org/wiki/DNA
• https://en.wikipedia.org/wiki/FASTA_format

Parallel Programming

Related Videos

LoopingAndFinal: https://wustl.box.com/s/wix18u57v7x1rdx1d1dgfedf6ibr0n92

SliceArrayDemo: https://wustl.box.com/s/p3ooceekguiaygg4hggw76rbpt28kf6o

AddingParallelism: https://wustl.box.com/s/smckzu78cvg8seocgluuo1afydgd0gmt

Mistakes to Avoid

Warning: Do NOT copy the data. We are simply reading the chromosome data, so there is no reason to copy it.

Code to Implement

class:	NucleobaseCounting.java
methods:	countRange countSequential caclulateMidpoint countParallelLowerUpperSplit countParallelNWaySplit countParallelDivideAndConquerKernel
package:	count.assignment
source folder:	student/src/main/java

You will find the starting point for this assignment is in the count folder. In the count.assignment package you will find [NucleobaseCounting.java].

Utility Methods

method: countRangeSequential (sequential implementation only)

Use a for loop to iterate from min to maxExclusive.

method: calculateMidpoint (sequential implementation only)

In this method, you will need to calculate the midpoint between two numbers. This is as simple as finding the average between the two numbers. There is no need to worry about rounding correctly, just drop everything after the decimal point if the midpoint is not automatically an int.

There are at least two correct ways to implement the midpoint:

Option A: ${\frac {min+max}{2}}$

Option B: $min+{\frac {max-min}{2}}$

It is hard to find 1D references for midpoint. Wolfram MathWorld has a breakdown of Midpoint in 2D and 3D. Pick any dimension you like.

Sequential Solution

method: countSequential (sequential implementation only)

This solution should be achieved with a simple call to one of the utility methods you wrote.

Invoke countRangeSequential from 0 to the chromosome array length.

Parallel Solutions

You need to implement three different parallel solutions to this problem. The first will involve splitting the array into two equal halves, then going through each half of the array in parallel. The second will involve splitting the array into n different pieces, then going through each of those pieces of the array in parallel. The third and final implementation will recursively divide the array until a threshold is reached.

Lower/Upper Split

method: countParallelUpperLowerSplit (parallel implementation required)

In order to start with then two equal halves solution, please modify the countParallelUpperLowerSplit method. When you’re ready to begin, delete the return statement and begin implementing your solution! Again, please refer to your notes from lecture for help, as we tackled a very similar problem in class.

Hint: don’t forget the finish block! The format will be very similar to the examples.

Coarsening N-Way Split

method: countParallelNWaySplit (parallel implementation required)

After you’re finished with that, please modify the countParallelNWaySplit method for the n different pieces solution. As before, when you’re ready to begin, delete the return statement and begin implementing your solution! Again, please refer to your notes from lecture for help, as we tackled a very similar problem in class.

Hint: make an array to store the results of each task. Split the array into n different chunks, each of which contains 1/n elements. Once each task has summed up the results from its chunk, add the results from each chunk to get your final answer.

Divide and Conquer

method: countParallelDivideAndConquerKernel (parallel implementation required)

Testing Your Solution

Correctness

class:	CountTestSuite.java
package:	count.assignment
source folder:	testing/src/test/java

Launch CountTestSuite.java as a JUnit Test to run all of the tests. CountTestSuite.java is located in src/test/java count.assignment package. You can initiate this via right clicking on CountTestSuite.java and selecting "Run As..." -> "JUnit Test". [screenshot]

Performance

class:	NucleobaseCountTiming.java
package:	count.assignment
source folder:	src/main/java

Line Of Red Text On The Mac

In computer science (and life in general) you should not make a habit of ignoring red text.

However, there is a benign bug on the Mac which reports:

"objc[6477]: Class JavaLaunchHelper is implemented in both /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/bin/java and /Library/Java/JavaVirtualMachines/jdk1.8.0_144.jdk/Contents/Home/jre/lib/libinstrument.dylib. One of the two will be used. Which one is undefined."

Reportedly, this has finally been fixed and will be released soon:

https://stackoverflow.com/questions/43003012/class-javalaunchhelper-is-implemented-in-two-places

For now, you should ignore this.

Rubric

As always, please make sure to cite your work appropriately.

Total points: 100

• Correct countRangeSequential (10)
• Correct countSequential (5)
• Correct calculateMidpoint (5)
• Correct and Parallel countParallelLowerUpperSplit (20)
• Correct and Parallel countParallelNWaySplit (25)
• Correct and Parallel countParallelDivideAndConquerKernel (25)
• Clarity and efficiency (10)