Assignment
a. What does a VCF file contain and how is the data formatted? How is it generated? Be sure to include any relavant fields that are standard to the format?
b. What are local optima in the text of phylogeny? What are some approaches to avoid them?
c. In Linux, what does the apt command do? When would you use it?
d. You have a spreadsheet with the five columns: ID, condition, and 100 columns of protein mass spec measurement values. Would you use PCA or LDA to analyze this data and why? How many dimensions of data are there? How many axes?
e. What is ANN( Artificial Neural NNetworks), Feed-Forward neural Network, Convolutional Neural Networks(CNN), and Generative Adversarial netwroks (GAN). What is the different between them?
f. Describe how Kmers can be used to assemble a genome from shotgun sequence data
g. What is the difference between the input, hidden, and output layers in an ANN?
h. Which Linux command would you use to create a new directory? Give an example
i. Describe how a hash function works, using both descriptive text and diagram with examples.
Format your assignment according to the give formatting requirements:
a. The answer must be double spaced, typed, using Times New Roman font (size 12), with one-inch margins on all sides.
b. The response also includes a cover page containing the title of the assignment, the course title, the student's name, and the date. The cover page is not included in the required page length.
c. Also include a reference page. The references and Citations should follow APA format. The reference page is not included in the required page length.