1. 1. Science with Python
2. 2. SciPy - for Scientific Computing in Python
3. 1. 2.1. Data Science tools in Python
   2. 2.2. Data Analysis resources
4. 3. Python and Biology
5. 1. 3.1. Biopython
   2. 3.2. Biopython background
   3. 3.3. Bio python sequences
   4. 3.4. Download and Read FASTA, GenBank files
   5. 3.5. Search NCBI and Download FASTA and GenBank files
   6. 3.6. Search nucleotids
   7. 3.7. Download nucleotids
   8. 3.8. Exercise: Nucleotid
   9. 3.9. Exercise: Search tool for NCBI
   10. 3.10. Biology background
6. 4. Chemistry
7. 1. 4.1. Chemistry links
   2. 4.2. Python-based Simulations of Chemistry Framework
   3. 4.3. Bond length
   4. 4.4. Covalent radius
   5. 4.5. Python energy landscape explorer
   6. 4.6. Other chemistry links
8. 5. numpy
9. 1. 5.1. What is NumPy
   2. 5.2. Install Numpy
   3. 5.3. Numpy - vector
   4. 5.4. NumPy 2D arrays
   5. 5.5. Numpy - set type
   6. 5.6. NumPy arrays: ones and zeros
   7. 5.7. Numpy: eye
   8. 5.8. NumPy array random
   9. 5.9. NumPy Random integers
   10. 5.10. NumPy array type change by division (int to float)
   11. 5.11. Numpy: Array methods: transpose
   12. 5.12. Numpy: reference, not copy
   13. 5.13. Numpy: copy array
   14. 5.14. Numpy: Elementwise Operations on Arrays
   15. 5.15. Numpy: multiply, matmul, dot for vectors
   16. 5.16. Numpy: multiply, matmul, dot for vector and matrix
   17. 5.17. Numpy: multiply, matmul, dot for matrices
   18. 5.18. Numpy: casting - converting from strings to integer
   19. 5.19. Numpy: indexing 1d array
   20. 5.20. Numpy: slice is a reference
   21. 5.21. Numpy: slice - copy
   22. 5.22. Numpy: abs value on a Numpy array
   23. 5.23. Numpy: Logical not on a Numpy array
   24. 5.24. Numpy: Vectorize a function
   25. 5.25. Numpy: Vectorize len
   26. 5.26. Numpy: Vectorize lambda
   27. 5.27. Numpy: Filtering array (selecting some of the values from an array)
   28. 5.28. Numpy: Filter matrix values
   29. 5.29. Numpy: Filter matrix rows (selecting some rows)
   30. 5.30. Numpy: Some statistics (sum, mean, std, var)
   31. 5.31. Numpy: Serialization (saving an array to a file)
   32. 5.32. Numpy: Load from Matlab file to a Numpy array
   33. 5.33. Numpy: Save a Numpy array as a Matlab file
   34. 5.34. Numpy: Horizontal stack vectors (hstack)
   35. 5.35. Numpy: Append or vertically stack vectors and matrices (vstack)
   36. 5.36. Numpy uint8
   37. 5.37. Numpy int8
   38. 5.38. More Numpy
10. 6. Pandas
11. 1. 6.1. Pandas
    2. 6.2. Datasets
    3. 6.3. Planets data
    4. 6.4. StackOverflow Survey data
    5. 6.5. Planets - Read CSV into Dataframes
    6. 6.6. Planets - DataFrame Statistics
    7. 6.7. Pandas Read CSV various datatypes
    8. 6.8. Pandas Read CSV set dtype
    9. 6.9. Pandas Read CSV convert values
    10. 6.10. Pandas split multivalue column into separate columns
    11. 6.11. Pandas split multivalue column into separate columns - get_dummies
    12. 6.12. Planets - Show first and last rows
    13. 6.13. Planets DataFrame select columns
    14. 6.14. Planets DataFrame select rows
    15. 6.15. Planets DataFrame select rows and columns
    16. 6.16. DataFrame filter rows by size
    17. 6.17. DataFrame filter rows by value
    18. 6.18. DataFrame filter rows by value in list
    19. 6.19. DataFrame filter elementwise boolean and
    20. 6.20. DataFrame sort (sort_values)
    21. 6.21. DataFrame loc vs. iloc
    22. 6.22. Pandas Planets - Add calculated column, remove / delete column (drop)
    23. 6.23. Pandas Planets - calculate
    24. 6.24. Pandas read CSV set index column
    25. 6.25. Count values
    26. 6.26. Select top items
    27. 6.27. Pandas Show histogram
    28. 6.28. Pandas read selected columns
    29. 6.29. Pandas read file in chunks
    30. 6.30. Pandas read selected rows in chunks
    31. 6.31. Combine columns to create a new column
    32. 6.32. Add a new column (conditional)
    33. 6.33. Pandas read Excel
    34. 6.34. Create Excel file for experiment with random data
    35. 6.35. Calculate Genome metrics
    36. 6.36. Exercise: Pandas
    37. 6.37. TODO: Stack Overflow example
12. 7. Other slides
13. 1. 7.1. Pandas Stocks
    2. 7.2. Pandas Stocks
    3. 7.3. Merge Dataframes
    4. 7.4. Analyze Alerts
    5. 7.5. Analyze IFMetrics
    6. 7.6. Calculate Genome metrics - add columns
    7. 7.7. Calculate Genome metrics - vectorized
    8. 7.8. Calculate Genome metrics - vectorized numpy
    9. 7.9. Pandas more
    10. 7.10. Pandas Series
    11. 7.11. Pandas Series with names