101.school
CoursesAbout
Search...⌘K
Generate a course with AI...

    Introduction to Python for Biologists.

    Receive aemail containing the next unit.
    • Why Python for Biology?
      • 1.1Introduction: Why Python in Biology?
      • 1.2Python basics: A refresher
      • 1.3Importance of Python for Data Analysis in Biology
    • Biological Data Types and Python
      • 2.1Introduction to Biological Data Types
      • 2.2Processing Biological Data with Python
      • 2.3Case Study: Genomics
    • Sequence Analysis - Part 1
      • 3.1Introduction to Sequence Analysis
      • 3.2Python tools for Sequence Analysis
      • 3.3Case Study: Protein Sequencing
    • Sequence Analysis - Part 2
      • 4.1Advanced Sequence Analysis with Python
      • 4.2Case Study: DNA Sequencing
      • 4.3Possible Challenges & Solutions in Sequence Analysis
    • Image Analysis - Part 1
      • 5.1Introduction to Digital Microscopy/Image Analysis
      • 5.2Python Tools for image processing
      • 5.3Case Study: Cell Imaging
    • Image Analysis - Part 2
      • 6.1Advanced Image Analysis Techniques with Python
      • 6.2Case Study: Tissue Imaging
      • 6.3Troubleshooting Image Analysis Challenges
    • Database Management and Python
      • 7.1Database Management Basics for Biologists
      • 7.2Python tools for Database Management
      • 7.3Case Study: Genomic Database
    • Statistical Analysis in Python
      • 8.1Introduction to Statistical Analysis in Biology
      • 8.2Python tools for Statistical Analysis
      • 8.3Case Study: Phenotypic Variation Analysis
    • Bioinformatics and Python
      • 9.1Introduction to Bioinformatics
      • 9.2Python in Bioinformatics
      • 9.3Case Study: Genomic Data Mining
    • Data Visualization in Python
      • 10.1Introduction to Data Visualization
      • 10.2Python Libraries for Data Visualization
      • 10.3Case Study: Visualizing Genetic Variation
    • Machine Learning for Biology with Python
      • 11.1Introduction to Machine Learning in Biology
      • 11.2Python for Machine Learning
      • 11.3Case Study: Disease Prediction using Machine Learning
    • Project Planning and Design
      • 12.1Transforming Ideas into Projects
      • 12.2Case Study: Genomic Data Processing
      • 12.3Design Your Project
    • Implementing a Biological Project with Python
      • 13.1Project Execution
      • 13.2Case Study: Personalized Medicine
      • 13.3Submit Your Project

    Database Management and Python

    Database Management Basics for Biologists

    organized collection of data in computing

    Organized collection of data in computing.

    In the realm of biological research, databases play a crucial role in storing, organizing, and retrieving vast amounts of data. This unit will provide an introduction to databases, their types, structures, and the basics of SQL, a language used for managing and manipulating databases.

    Introduction to Databases

    A database is a structured set of data. In the context of biology, databases can store a wide range of information, from genomic sequences to patient records, and from ecological data to experimental results. The primary advantage of using databases is that they allow for efficient data retrieval, insertion, update, and deletion.

    Types of Databases

    There are several types of databases, each with its own strengths and weaknesses. The most common types include:

    • Relational Databases: These databases organize data into tables, which can be linked—or related—based on data common to each. This type of database is widely used due to its flexibility and robustness.

    • Hierarchical Databases: In these databases, data is organized into a tree-like structure, with a single root to which all other data is linked. This type is less flexible than the relational model, but it can be more efficient for certain types of data retrieval.

    • Network Databases: These databases allow for complex relationships between data, where each record can have multiple parent and child records.

    • Object-oriented Databases: These databases store data in the form of objects, as used in object-oriented programming.

    Understanding Database Schemas and Structures

    A database schema is the structure described in a formal language supported by the database management system (DBMS). It outlines how data is organized and how the relations among them are associated. It evolves with time; new tables are created, new relations are established, and new fields are added into the existing tables.

    Introduction to SQL

    SQL (Structured Query Language) is a programming language used to communicate with and manipulate databases. Most of the SQL database programs also have their own proprietary extensions in addition to the SQL standard!

    SQL is used in manipulating data stored in Relational Database Management Systems (RDBMS), or for stream processing in a Relational Data Stream Management System (RDSMS).

    SQL involves several types of commands for different operations such as:

    • SELECT: extracts data from a database
    • UPDATE: updates data in a database
    • DELETE: deletes data from a database
    • INSERT INTO: inserts new data into a database
    • CREATE DATABASE: creates a new database
    • ALTER DATABASE: modifies a database
    • CREATE TABLE: creates a new table
    • ALTER TABLE: modifies a table
    • DROP TABLE: deletes a table
    • CREATE INDEX: creates an index (search key)
    • DROP INDEX: deletes an index

    In the next unit, we will explore how Python can be used to interact with databases, including executing SQL commands.

    Test me
    Practical exercise
    Further reading

    Buenos dias, any questions for me?

    Sign in to chat
    Next up: Python tools for Database Management