Python Programming for Biological Problems

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Jones Granatyr,IA Expert Academy,Guilherme Matos Passarini, phD

6:57:47

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1. Introduction

1. Course content - Jones.mp4

04:31

2.1 python_for_biology_intro.PDF

2. Course content - Guilherme.mp4

05:21

3. Introduction to Python.mp4

04:09

4. Installation.mp4

07:34

5. Python IDEs.mp4

12:42

2. Variables, data types, and inputs

1. Variables and constants.mp4

14:08

2. Mathematical operations.mp4

05:59

3. Exercises.mp4

02:13

4. Exercise 1 Ki calculation.mp4

03:36

5. Exercise 2 Recombination of genotypes.mp4

03:34

3. Logical and relational operators

1. Logical and relational operators.mp4

08:27

2. Exercise.mp4

01:28

3. Exercise 1 Comparing weights of proteins.mp4

02:12

4. Strings

1. Strings.mp4

11:06

2. Exercises.mp4

01:48

3. Sequences to be used in exercise 2.html

4. Solution abbreviating scientific names.mp4

04:17

5. Solution Extracting an exon from a gene.mp4

02:32

5. Conditional operators

1. Conditional operators.mp4

10:25

2. Exercises.mp4

01:52

3. Solution Taxonomic families.mp4

02:29

4. Solution Codons in a RNA sequence.mp4

03:28

6. Loops

1. For loop.mp4

11:16

2. While loop.mp4

10:25

3. Exercises.mp4

01:32

4. Solution transcription of DNA.mp4

02:27

5. Solution Bacterial growth.mp4

02:47

7. Collections

1. Tuples and lists.mp4

08:51

2. Dictionaries and sets.mp4

09:56

3. Matrices.mp4

07:02

4. Exercises.mp4

01:38

5. Dicitionary with the symbols of their aas and the mass.html

6. Solution mass of aminoacid sequeces.mp4

05:00

7. Solution transcription of DNA.mp4

02:54

8. Project 1 Simulating a biology test.mp4

01:32

9. Questions for the test.html

10. Solution part 1.mp4

01:51

11. Solution part 2.mp4

03:04

12. Solution part 3.mp4

02:40

8. Functions

1. Functions.mp4

10:07

2. Exercises.mp4

01:47

3. Solution function of recombination.mp4

02:04

4. Solution Ki calculation.mp4

03:36

5. Solution transcription function.mp4

03:28

6. Project 2 calculating gene frequencies.mp4

04:27

7.1 CHI SQUARE TABLE.pdf

7. Chi-square distribution table.html

8. Project 2 part 1.mp4

05:28

9. Project 2 part 2.mp4

04:57

9. Modules

1. Math and datetime.mp4

09:43

2. Random and time.mp4

11:10

3. Exercises.mp4

01:46

4. Solution generation of random DNA sequence.mp4

02:14

5. Solution function of population growth.mp4

02:39

10. Custom modules

1. Creating packages.mp4

07:04

2. Exercises.mp4

02:30

3. Solution DNA module.mp4

04:47

4. Solution module for ecology functions.mp4

05:14

11. Errors and exceptions

1. Errors and exceptions.mp4

14:22

2. Exercise.mp4

01:32

3. Solution validation of numerical inputs.mp4

03:44

4. Project 3 - Identification key.mp4

06:59

5.1 Identification key.pdf

5. Image of the key.html

6. Solution part 1.mp4

02:07

7. Solution part 2.mp4

07:53

12. Text files

1. Reading and writing text files.mp4

05:52

2. Genetic databases.mp4

03:06

3. Protein database PDB.mp4

04:03

4. Exercises.mp4

01:21

5. Solution reading a DNA sequence.mp4

03:04

6. Solution reading a .pdb sequence.mp4

03:57

7. Project 4 - Reading and processing gene sequences.mp4

03:48

8. Solution part 1.mp4

08:31

9. Solution part 2.mp4

05:32

10. Solution part 3.mp4

06:13

13. Regular expressions

1. Introduction.mp4

13:06

2. Search, match and find all.mp4

12:42

3. Regular expressions - main metacharacters and quantifiers.html

4. Exercise.mp4

01:50

5. Solution Identifying species names in a text.mp4

02:35

6. Sample sequence for exercise 2.html

7. Solution Analyzing a genetic sequence.mp4

02:21

14. Object oriented

1. Introduction.mp4

06:40

2. Practical.mp4

13:47

3. Exercise.mp4

01:38

4. Solution Class Plant.mp4

04:53

5. Solution Class DNA.mp4

03:52

15. Final remarks

1. Final remarks.mp4

02:32

Description

Solve more than 30 exercises and 4 Biology projects using Python programming language! Step by step implementations!

What You'll Learn?

Learn the basic syntax of Python language quickly and easily
Implement the main Python language operators: mathematical, logical, relational and conditional
Create loop structures using for and while commands
Implement functions for modularization of programs
Implement the main Python language collections: tuples, lists, dictionaries, sets and arrays
Manipulate text files
Perform error and exception handling
Learn the basic intuition and practice about regular expressions
Learn the basic intuition and practice of Object Orientation
Estimate the rate of recombination between genes
Analyze genetic sequences
Model bacterial growth
Write a code that simulates a biology test, where at the end the grade is calculated
Analyze gene sequence files directly from databases in .fasta format
Analyze protein structure files in .pdb format
Build a basic identification key for plant species

Who is this for?

Biology students or similar areas, such as biomedicine, pharmacy, forestry engineering, etc.

Biology or related professionals who wish to learn a programming language

Developers or IT professionals who are interested in applying programming knowledge in the field of biology

Undergraduate students taking programming courses

People interested in programming languages

What You Need to Know?

Programming logic

Basic biological knowledge

More details

Description
Biologists, biology students, and professionals in related fields generally have little or no contact with computer programming. However, the growing of data in genomic, protein and organism databases can be used to model the solution for some problems, such as the discovery of medicines and insecticides. It leads biologists to benefit from computer programming knowledge, so that they can develop useful applications in molecular biology, ecology, research on diseases, among others.
This course was developed with the purpose of introducing biologists, students of biology, biomedicine, ecology, pharmacy and professionals in related areas to programming using Python, which is nowadays one of the most used programming languages. It has a clear syntax and is easy to learn especially if you are a professional who are not familiar with technology. Many tools used in the field of biology were written in Python, which makes it a great option for establishing your first contact with computer programming. You will learn the following topics:
Python installation and main tools (IDEs)
Variables, constants and strings
Math operations
Logical, relational and conditional operators
Loops (for and while)
Functions
Lists, dictionaries, tuples, sets and arrays
Manipulation of text files
Error and exception handling
Regular expressions
Object oriented
After learning the basic concepts of Python, you will be able to apply the concepts in exercises, challenges and practical projects related to â€‹â€‹Biology. Below are some of the case studies that we will implement step by step:

Prediction of the mass of a peptide sequence according to its amino acid composition
Schedule a biology test that calculates the grade and whether the user got each question right or wrong
Creating classes related to objects in the biological world
.fasta gene sequence analysis
Analysis of gene frequencies according to the Hardy-Weinberg Theorem
Creating functions for population ecology calculations
Discover patterns in RNA sequences
Estimation of gene distances
Basic species identification
Troubleshooting gene frequencies
Creating scripts for parsing .pdb-type protein sequence files
Transcription of DNA sequences into RNA
There are more than 80 classes, concepts, code demonstration, and exercises with solutions! More than 30 proposed challenges and 4 small projects applying the concepts learned in each section in a biological context, with step-by-step resolution.
Who this course is for:
Biology students or similar areas, such as biomedicine, pharmacy, forestry engineering, etc.
Biology or related professionals who wish to learn a programming language
Developers or IT professionals who are interested in applying programming knowledge in the field of biology
Undergraduate students taking programming courses
People interested in programming languages

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Olá! Meu nome é Jones Granatyr e já trabalho em torno de 10 anos com Inteligência Artificial (IA), inclusive fiz o meu mestrado e doutorado nessa área. Atualmente sou professor, pesquisador e fundador do portal IA Expert, um site com conteúdo específico sobre Inteligência Artificial. Desde que iniciei na Udemy criei vários cursos sobre diversos assuntos de IA, como por exemplo: Deep Learning, Machine Learning, Data Science, Redes Neurais Artificiais, Algoritmos Genéticos, Detecção e Reconhecimento Facial, Algoritmos de Busca, Mineração de Textos, Buscas em Textos, Mineração de Regras de Associação, Sistemas Especialistas e Sistemas de Recomendação. Os cursos são abordados em diversas linguagens de programação (Python, R e Java) e com várias ferramentas/tecnologias (tensorflow, keras, pandas, sklearn, opencv, dlib, weka, nltk, por exemplo). Meu principal objetivo é desmistificar a área de IA e ajudar profissionais de TI a entenderem como essa tecnologia pode ser utilizada na prática e que possam visualizar novas oportunidades de negócios.

IA Expert Academy

Instructor's Courses

A plataforma IA Expert tem o objetivo de trazer cursos teóricos e práticos de fácil entendimento sobre sobre Inteligência Artificial e Ciência de Dados, para que profissionais de todas as áreas consigam entender e aplicar os benefícios que a IA pode trazer para seus negócios, bem como apresentar todas as oportunidades que essa área pode trazer para profissionais de tecnologia da informação. Também trazemos notícias atualizadas semanais sobre a área em nosso portal.

Guilherme Matos Passarini, phD

Instructor's Courses

English:Hi, my name is Guilherme, I have a bachelor's degree in Biological Sciences, a master's degree in Experimental Biology, and a Ph.D. also in Experimental Biology, both from the Federal University of Rondônia (Brazil). My main research area is the search for compounds that are active against the parasites of malaria and leishmaniasis. I also have been programming for a while, especially in the programming languages Python and R. My main interests are biology, biotechnology, programming, medicinal chemistry, and artificial intelligence. My main goal here in Udemy is therefore spreading the knowledge related to these areas to people around the world.Português:Bacharel e licenciado em Ciências Biológicas pela Universidade Federal de Rondônia, mestre em Biologia Experimental pela Universidade Federal de Rondônia e doutor também em Biologia Experimental pela Universidade Federal de Rondônia. Desenvolveu seus trabalhos de iniciação científica e mestrado na busca de moléculas de plantas bioativas contra os parasitas da malária e leishmaniose, tendo trabalhado com fitoquímica e ensaios antiparasitários in vitro. No final do mestrado, começou a se interessar por bioinformática, química medicinal e programação, aplicando alguns programas de bioinformática e quimioinformática para auxiliar na descoberta de drogas antimaláricas. Possui experiência com as linguagens Python e R, e iniciou a programar em Javascript. Seu projeto de doutorado se constitui em avaliar um composto antimalárico já testado durante o mestrado de forma mais aprofundada contra o parasita da malária, realizando análises virtuais, como verificação de características físico-químicas e farmacocinéticas, docking molecular (interação virtual entre ligante e proteína-alvo do parasita) e ensaios em placas de cultura.

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