Math 5233 lab assignment for Monday January 29

Math 5233 Assignment 1

Do as much of this as you can; don't rush. Don't get frustrated - ask me or your neighbor for help. Answers to part 1 will be discussed in class on Friday.

This is a group assignment. Each group has a protein, given below by its official symbol. The point of this assignment is to give you some familiarity with various online databases. By looking up the protein (and its associated gene) in the following databases, summarize its function, role in human disease (if any), number of exons, genomic neighborhood, and whatever other interesting properties you find.

Suggested databases (you are not limited to these!): KEGG Pathway database, UCSC Genome Browser, OMIM, PubMed, Gene (all available through Entrez) .

Team 1: Lindsey Dietz, Amanda Henke, Sarah Solbrig, Keerthi Jayasundera
Protein: CFTR

Team 2: Shanshan Ding, Matthew Link, Wei Zhang, Gregg Baldeshwiler
Protein: G6PD

Team 3: Annette Katich, Jonathan Bostrom, Elizabeth Souter, Hillary Waterhouse
Protein: GRM8

Team 4: Huimin Liu, Kristin Carlson, Feng Qian, Seth Slettedahl
Protein: FOXP2

Intro to Sage/Python (individual assignment, due W 1/30):
- Log on to one of the sage servers at
  1. ```
  https://131.212.65.98:8000 
```
2. ```
https://131.212.65.100:8000  
```
  3. ```
  https://131.212.66.214:5233  
```
It may be helpful to have a browser tab open to the some sage/python documentation, in particular the tutorial by the creator of Python.
- Create a worksheet called "Assignment 1".
- Enter your first name as a string called my_name by typing
```
 my_name = "Marshall Hampton"
```
  (with your name instead). We can "slice" this string of letters by using the array index notation my_name[start:stop:increment]. For example, try the following:
```
my_name[0:2]
```
```
my_name[0:]
```
```
my_name[1:2]
```
```
my_name[::-1]
```
  As an exercise in "list comprehension", type
```
[letter.upper() for letter in my_name]
```
  You can split a string into a list: try
```
my_name.split()
```
  This is very useful in manipulating data from other files. For example, if you have an Excel file, you can export it to CSV (comma seperated values), read it into python, and split the lines with .split(',').
- For our next Python exercise, you will define a function. Here is an example function that computes the number of As and Ts in a string, after first converting all letters to uppercase:
```
def ATcounter(dna_string):
    '''Computes the number of "A"s and "T"s in a string'''
    temp_string = dna_string.upper() #first convert to uppercase
    A_num = temp_string.count('A')
    T_num = temp_string.count('T')
    return A_num + T_num
```
  The triple-quoted string after the first line is called a docstring; including a docstring is not mandatory but highly recommended. Write a function "namesplitter" that takes your name as a string (i.e. like my_name above) and returns a list consisting of your first name and last name. So if
```
my_name = "Marshall Hampton"
```
  then
```
name_splitter(my_name)
```
  would return
```
['Marshall','Hampton']
```
- Our last exercise is about Python's dictionary data type. In other languages this might be called a hash table, associative array, or lookup table. Dictionaries have keys associated with values. For example, here is a dictionary of endonuclease patterns:
```
 endo_dict = {'EcoRI' : 'gaattc', 'BamHI' : 'ggatcc', 'HindIII' : 'aagctt'}
```
  The keys of endo_dict are the strings EcoRI, BamHI, and HindIII.
  We can access the values through the keys: try
```
endo_dict['BamHI']
```
  You can get all the keys of a dictionary with the .keys(), and all the values with .values().
  
  Write a function name_to_dict that takes a name string as input and returns a dictionary where the key is the first name, and the value is the full name. For example, name_dict('Marshall Hampton') should return {'Marshall':'Marshall Hampton'}.