CSC483 - Applied Biological Data Science - Week 2,3 & 4

Georgia Doing (doingg@union.edu)

1/13/26

1/26/26

A first notebook in data exploration.

• Uses the PANDAS library.

• Data is metadata of all RNA sequences experiments done on the bacterium Escherichia coli that are publicly available in the USA or EU.

• Make a copy of the data for your google drive: https://drive.google.com/file/d/1BB7M3eWo8zPuxmlwSKMzE_RBeYrjv1n0/view?usp=sharing

• Another data file: https://drive.google.com/file/d/18_PkR_sOLsQshSM4O1n2hVOcZoxgn8E0/view?usp=sharing

• Yet another: https://drive.google.com/file/d/1_cJGV1gwHXzgUe7DMwHVI28nhJcma2tt/view?usp=sharing

Setup

Load library and mount you google drive folders

# pandas is installed on Colab runtime environments
#import pandas as pd

# https://pandas.pydata.org/docs/user_guide/options.html
#pd.set_option('display.max_columns', None)
#pd.set_option('display.max_rows', None)

# similar to first HW
#from google.colab import drive
#drive.mount('/content/drive/')

First Look at the “Meta” data

note: “meta” data here means information about the experiments that were done rather than the “biological data” that was collected during the experiments themselves

# load the data into a Pandas DataFrame
#df = pd.read_csv('drive/MyDrive/Teaching/CSC483-W26/data/SraRunTable_Ec_07_25_25_working_v4.csv')
# take a lok at the first 5 rows
#df.head()

• what are the rows and columns?
• is this all the rows? columns?
• do you recognize any words?

2+3