Python for Biologists

Focused View

Ahmed Karam, M.Sc.

9:44:43

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1. Requirements and tips for talking with a computer

1. Introduction.mp4

02:52

2. Defining the programming language and installing python on Windows and Mac.mp4

05:20

3. Ways to write and run python codes Interactive interpreter.mp4

03:01

4. Ways to write and run python codes Python script.mp4

02:09

5. Ways to write and run python codes IDE.mp4

04:39

6. Summary.mp4

00:15

7.1 C4.zip

7. Full course scripts.html

8. Create a variable.mp4

04:03

9. Create a variable.html

10. Tips for writing the variable name or identifier.mp4

02:48

11. Correct the code.html

12. Summary.mp4

00:23

13. Reduce the risk of using reserved words with the case sensitivity feature.mp4

02:09

14. Correct the code.html

15. Summary.mp4

00:27

16. The difference between comments and codes.mp4

02:46

17. Correct the code.html

18. Summary.mp4

00:14

19. Receiving and processing user data and producing output..mp4

03:57

20. Correct the code.html

21. Summary.mp4

00:28

22. Optional tips for organizing variables.mp4

01:56

23. Summary.mp4

00:16

2. Data containers in python (types and conversions)

1. Refresh.mp4

00:53

2. Number data type.mp4

02:07

3. Create a variable that stores a number.html

4. String data type.mp4

01:44

5. Create a variable that stores a string.html

6. List and tuple data types.mp4

01:24

7. Create a variable that stores a list or tuple.html

8. Dictionary data type.mp4

01:27

9. Create a variable that stores a dictionary.html

10. Summary.mp4

00:33

11. The problem of receiving data, whether from the command interface or a file.mp4

01:05

12. Convert from an integer to a float or vice versa.mp4

02:52

13. Complete the code Convert from integer to float and vice versa.html

14. Work with the complex.mp4

01:58

15. Convert from a number to a string and vice versa.mp4

03:16

16. Complete the code Convert from a number to a string and vice versa.html

17. Complete the code Convert from a number to a string.html

18. Summary.mp4

00:22

19. Convert from a string to a list or tuple.mp4

03:07

20. Complete the code Convert from a string to a list or tuple.html

21. Convert from a list or tuple to a dictionary.mp4

02:58

22. Summary.mp4

00:23

3. Access the items in the data containers

1. Introduction.mp4

01:17

2. The forward index.mp4

05:10

3. The reverse index.mp4

02:54

4. Create a data type from items of another data type using the index.mp4

01:40

5. The dictionary key.mp4

04:02

6. Summary.mp4

00:22

4. Congratulations, this is your first program using the Python language

1. Prepare and save external data in a data type in python Create small database.mp4

04:06

2. The first code Unraveling the mystery of the IUPAC ambiguity codes.mp4

02:03

3. The second code The inverse of the first code.mp4

06:11

5. Perform operations and set conditions or questions

1. Introduction Arithmetic operators Addition and subtraction.mp4

03:13

2. Arithmetic operators Multiplcation, division, floor division, and exponent.mp4

02:02

3. Arithmetic operators Modulus.mp4

01:46

4. Summary.mp4

00:31

5. Arithmetic operators Handling string and list.mp4

02:59

6. Summary.mp4

00:22

7. Arithmetic operators Operator precedence.mp4

01:39

8. Summary.mp4

00:31

9. Create a code that calculates extra nucleotides in DNA before translation.mp4

06:17

10. Create a code that calculates extra nucleotides in DNA before translation.mp4

03:23

11. Summary.mp4

00:22

12. Assignment operators.mp4

04:27

13. Summary.mp4

00:10

14. Comparison operators Equality.mp4

04:32

15. Comparison operators Greater than and less than.mp4

03:00

16. Summary.mp4

00:23

17. Create a code that compares two sequences in terms of both length and content.mp4

03:51

18. Summary.mp4

00:41

19. Membership operators.mp4

02:24

20. Summary.mp4

00:14

21. Create a code that searches for a restriction recognition site in DNA.mp4

02:14

22. Logical operators.mp4

04:07

23. Summary.mp4

01:00

24. Create a code that searches for MULTIPLE restriction recognition sites in DNA.mp4

04:01

25. Summary.mp4

00:25

26. Identity operators.mp4

04:39

27. Summary.mp4

00:07

28. Bitwise operators Convert from an integer to a binary and vice versa.mp4

03:56

29. Bitwise operators And, or, xor.mp4

03:47

30. Bitwise operators 2s complement, and left and right shift.mp4

04:19

31. Summary.mp4

00:30

6. Decision making support

1. If statement, if-else statement, and if-elif-else statement.mp4

06:33

2. Summary.mp4

00:12

3. Create a code that determines whether the sequence is DNA or RNA.mp4

02:22

4. Zero, non-zero, null, and non-null values.mp4

04:38

5. Nested if.mp4

04:23

7. Repeat commands in loops

1. The while loop.mp4

08:24

2. Summary.mp4

00:45

3. Calculating the GC content using the while loop.mp4

12:00

4. The for loop.mp4

04:22

5. Calculating the GC content using the for loop.mp4

03:36

6. Control loops with break, continue, and pass.mp4

05:34

7. Summary.mp4

00:28

8. Functions and methods for handling string data type

1. Review.mp4

02:52

2. Summary.mp4

00:14

3. Non-printable characters.mp4

08:27

4. Summary.mp4

00:11

5. String formatting part 1.mp4

04:41

6. Summary.mp4

00:14

7. String formatting part 2.mp4

01:36

8. Summary.mp4

00:13

9. Capitalize the first letter of a string.mp4

00:45

10. Center a string to total width columns.mp4

00:51

11. Left and right adjustment of a string for the total width of the columns.mp4

00:53

12. Count how many times a string or substring occurs in a string.mp4

01:08

13. Test if a string or substring of the string ends with a certain suffix.mp4

01:34

14. Test if a string or substring of the string starts with a certain prefix.mp4

00:43

15. Expand tabs in string to multiple spaces.mp4

01:18

16. Find starting index of a string or substring that occurs in a string.mp4

01:54

17. Find starting index of a string or substring that occurs backwards in a string.mp4

01:03

18. Search starting index of a string or substring that occurs in a string.mp4

00:40

19. Search starting index of a string or substring that occurs backwards in a string.mp4

00:36

20. Test if a string contains alphanumeric character(s).mp4

00:46

21. Test if a string contains alphabetic character(s).mp4

01:21

22. Test if a string contains digits only.mp4

00:58

23. Test if a string contains upper- or lower-case and convert from one to another.mp4

02:31

24. The difference between numbers test.mp4

02:23

25. Test if a string contains white space(s).mp4

00:28

26. Test if a string is a title and create title.mp4

01:00

27. Concatenate list or tuple items into a string.mp4

01:51

28. Obtain a string length.mp4

00:41

29. Remove leading or tailing character(s) or from both sites of a string part 1.mp4

01:53

30. Remove leading or tailing character(s) or from both sites of a string part 2.mp4

00:38

31. Replace a string or substring of a string part 1.mp4

00:50

32. Replace a string or substring of a string part 2.mp4

00:35

33. Create a translation table and translate a string.mp4

02:37

34. Obtain the minimum and maximum character from a string.mp4

01:53

35. Split a string based on delimiter string or substring to a list of substrings.mp4

04:23

36. Swap string characters from upper- to lowercase and vice versa.mp4

00:35

37. Fill a string using zero(s).mp4

00:38

9. Functions and methods for handling list data type

1. Review.mp4

02:28

2. Obtain a list length, and minimum and maximum items of a list.mp4

02:06

3. Add an item to the end or certain location of a list.mp4

01:36

4. Extend a list by another list.mp4

00:53

5. Count how many times an item occurs in a list.mp4

00:36

6. Search starting index of an item that occurs in a string.mp4

01:02

7. Remove an item using its index or content.mp4

01:27

8. Sort list items.mp4

00:59

9. Reverse the order of a list.mp4

00:56

10. Remove a duplicate items of a list.mp4

01:36

10. Functions for handling tuple data type

1. Obtain a tuple length, and minimum and maximum items of a tuple.mp4

03:44

11. Functions and methods for handling dictionary data type

1. Review.mp4

02:00

2. Obtain a dictionary length.mp4

00:30

3. Remove dictionary items.mp4

01:40

4. Copy a dictionary.mp4

02:09

5. Convert a tuple items into a dictionary keys.mp4

01:37

6. Control errors while accessing the dictionary keys.mp4

04:21

7. Convert a dictionary to a list of tuples and extract keys and values separately.mp4

01:24

8. Update a dictionary.mp4

00:48

12. Handling files and operating systems

1. Review.mp4

05:30

2. Summary.mp4

00:50

3. The modes for opening a file..mp4

05:55

4. Open a file for read-only purpose.mp4

05:37

5. Summary.mp4

00:42

6. Open a file for overwrite-only purpose.mp4

02:47

7. Convert fasta multi-lines to fasta two-lines Method1.mp4

19:35

8. Convert fasta multi-lines to fasta two-lines Method2.mp4

13:51

9. Open a file for append-only purpose.mp4

04:20

10. Summary.mp4

00:21

11. Open a file for read and write purposes.mp4

03:19

12. Summary.mp4

00:32

13. Open a file for write and read purposes.mp4

03:53

14. Summary.mp4

00:27

15. Open a file for append and read purposes.mp4

01:47

16. Summary.mp4

00:26

17. Dealing with the content of the open file for the purpose of reading.mp4

02:50

18. Dealing with read lines one by one.mp4

04:32

19. Output a list in a file.mp4

03:20

20. Read files with for loop Preserving memory from complexity.mp4

05:15

21. The second and preferred way to open files Don't be afraid to close files.mp4

03:45

22. Handle paths The current path and how to go and get the contents.mp4

04:01

23. Creating a folder or folders.mp4

03:11

24. Delete a folder.mp4

05:50

25. Delete folders.mp4

01:43

26. Rename a folder or folders.mp4

02:16

13. Handling time and date

1. Dealing with time and date.mp4

07:11

2. Which is faster Calculating the time taken for two GC content calculator codes.mp4

06:02

3. Dealing with a specific format of time and date in terms of output or reading.mp4

06:31

4. Wait in Python.mp4

02:23

14. Creating python function Arranging and organizing codes in an effective format

1. Modify some codes to use as examples.mp4

13:24

2. Modify some codes to use as examples.mp4

00:47

3. Create and call functions and the difference between print and return.mp4

14:30

4. Summary.mp4

00:27

5. The arguments and their function are pass-throughs of data across the function.mp4

05:28

6. Summary.mp4

00:47

7. Global (outside) variables and local (inside) variables.mp4

05:34

8. Summary.mp4

00:46

9. The required and default arguments and the argument keyword.mp4

05:55

10. Summary.mp4

00:24

11. Argument for unlimited items.mp4

03:09

12. Summary.mp4

00:49

13. The lambda as an alternative function in case of small code.mp4

01:46

14. Summary.mp4

00:33

15. Modules and scripts as a small product for your code

1. Import modules, see python paths, and import methods.mp4

09:16

2. Summary.mp4

00:47

3. Combine module and script using if name == main.mp4

09:04

4. Summary.mp4

00:24

5. Further clarification of the importance of if name == main.mp4

00:59

6. Summary.mp4

00:12

7. Further clarification of ways to import modules or functions within modules.mp4

05:22

8. Summary.mp4

00:10

9. Get global and local variables contained in functions.mp4

04:03

10. Summary.mp4

00:33

16. Create a python package from scratch Producing a python application for users

1. Obtain RNA-seq data from ENA Browser - European Nucleotide Archive.html

2. Create the first module to estimate the quality of nucleotides in the FASTQ file.mp4

14:04

3. Completing the creation of the first module.mp4

08:26

4. Summary.mp4

01:33

5. Improve the first module to deal with several files.mp4

03:39

6. Create the second module to convert a FASTQ file to a FASTA.mp4

08:50

7. Modifications to the second module.mp4

01:43

8. Create the third module to extract specific IDs from the FASTQ.mp4

09:40

9. Create the package First module test.mp4

09:02

10. Improving the first module to receive quality and its percentage from the user.mp4

03:52

11. Correction of errors discovered in the first module.mp4

06:43

12. The end A short story for the last tip.mp4

00:48

Description

Bioinformatics, computational biology, biotechnology, genetics, molecular biology, microbiology, etc. need Python

What You'll Learn?

The Python syntax
The data types and conversions
Performing operations and setting different conditions or questions
Making decisions and using loops
The functions and methods that deal with data types
Opening, creating, reading and writing files
Working with the operating system
Handling time and date
Creating your own functions
Creating your own modules and scripts
Creating your own packages

Who is this for?

Biologists working with biotechnology data in any discipline.

Beginners in programming.

Beginners in Python.

What You Need to Know?

The latest version of Python is required to be installed. (Explained inside the course)

Visual studio code is required to be installed. (Explained inside the course)

The Microsoft Python extension for visual studio code is required to be installed. (Explained inside the course)

More details

Description
Course description

This course is designed for beginners in programming with a biological background who want to deal with biotechnology data such as DNA, RNA, and protein, or who want to enter the field of bioinformatics.

This course requires you to install Python (this was explained in detail in the first section), and we will also need to install the Integrated Development Environment in order to write codes in it (this was also explained in the first section).

All the Python files in which the codes were written, which you will see in the videos from the beginning to the end of the course, we have provided in a folder that you will download from the first section of the course.

I want you to read this well because it will explain many things to you that will help you to continue learning the Python language by clarifying the fruit of each section of the course.

In the first section, you will install Python, then you will know the modes through which you can write the codes, then you will learn the basics of the Python language, such as variables and what is related to them, comments, printing data to the user, and receiving data from the user.
From this part, you will be able to learn how to receive data from the user, how to store the data inside the code, and how to output data to the user.

In the second section, you will learn about data types in Python. The meaning of data types in Python is the form in which Python understands user data. And you will learn about converting from one data type to another.
One of the fruits of the first section is storing data in variables. Here you will learn more about the format in which the data will be stored in these variables, and this varies according to the nature of the data that the user will enter. It may be a number, DNA sequence, table, file, and so on.

In the third section, you will learn how to access just one element of data.
After storing the data in a type of Python data, you will be able to delve into the data through Python, so you can access a very small part of the data and thus be able to deal with it however you want.

In the fourth section, you will work with me on simple code. We will rely mostly on the information that we learned in the first three sections, where we will store data in Python, then receive data from the user, then search for it in the stored data, and output information to the user related to the information entered.

In the fifth section, which is extremely important, we will learn operations that can be performed on the entered data and how the data can be updated. We will also put questions or conditions about the data that will give us one of two answers, either true or false.
This section will give you the power to make decisions about the data.

In the sixth section, you will learn how to write your decisions in code and help write procedures based on the decisions made.
This part is very related to the fifth part, so they must be linked together.

In the seventh section, you will learn how to use loops.
These are precisely the ones that a person is unable to perform because they are characterized by repeating a set of commands at the speed of a computer, and therefore they can do complex things that a person cannot do in a short time, and therefore you must understand them well.

In the eighth, ninth, tenth, and eleventh sections, we will learn many functions in Python that manipulate data.
Knowing many functions enables the programmer to manipulate data, which is reflected in the effectiveness of the extracted information.

In the twelfth section, one of the most important sections in the language in general and in the field of bioinformatics in particular, in which you will learn a new method of input and output, where input and output were functions, but now they are files, which are the biological data storage unit.
You will also handle operating system paths within Python.

In the thirteenth section, you will learn how to deal with time and date, and this section may be useful in calculating the time and printing it in the output.
You will find, for example, in some programs that contain more than one process, that the time and date are printed for each process.

In the fourteenth section, you will learn how to separate code and put it into structures that only work by calling, which is building your own functions.
This is the first way to build the code for the user in a usable form.

In the fifteenth section, you will learn to build scripts and modules that are considered the official output from the codes. That is, once you reach this stage, you can create your codes in modules that can be imported into Python easily.

In the sixteenth section, you will learn to build the package, which is a collection of modules.
There will be a project consisting of three modules that will be implemented step by step in front of you, and there will be improvements and error corrections, and therefore you will get good information and experience from this section.

In the end, you will find that the course will teach you information and experiences about how to receive data from the user, how to deal with it, and finally how to output the information that the user wants.
This is what you will need to build your code, whether it will be complete applications or some code that deals with data slightly, or contribute to the use of existing Python packages.
Who this course is for:
Biologists working with biotechnology data in any discipline.
Beginners in programming.
Beginners in Python.

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I hold a master's degree in genetics and a bachelor's degree in biotechnology, and I am interested in the field of bioinformatics. I have participated in research projects related to the field of molecular genetics. I have published posters at international and local conferences and research papers in the field of bioinformatics.

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