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Hierarchical Clustering using Euclidean Distance

By the end of this project, you will create a Python program using a jupyter interface that analyzes a group of viruses and plot a dendrogram based on similarities among them. The dendrogram that you will create will depend on the cumulative skew profile, which in turn depends on the nucleotide composition. You will use complete genome sequences for many viruses including, Corona, SARS, HIV, Zika, Dengue, enterovirus, and West Nile viruses.

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Develops skills in coding, data analysis, and visualization, which are vital for diverse career paths

Uses real-world datasets and scenarios to make learning more engaging and applicable

Teaches Python, a widely used and versatile programming language

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Reviews summary

Difficult to understand lectures

This course has received mixed reviews, with the main complaint being that the lecturer is difficult to understand. One reviewer stated, "i cant understand the lecturer."

Activities

Be better prepared before your course. Deepen your understanding during and after it. Supplement your coursework and achieve mastery of the topics covered in Hierarchical Clustering using Euclidean Distance with these activities:

Python Programming Practice

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This course requires a strong foundation in Python programming. Practice writing Python code to improve your skills before taking the course

Browse courses on Python Programming

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Solve Python coding problems on websites like HackerRank or LeetCode
Build small Python projects
Contribute to open source Python projects

Seek guidance from experts in the field

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Connects you with experienced professionals who can provide valuable advice and support, enriching your learning experience.

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Identify experts in the field of virus analysis and dendrogram creation
Reach out to potential mentors and request guidance
Schedule regular meetings or communication channels

Review of Genome Sequencing Techniques

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Before taking this course, you need to have a basic understanding of genome sequencing techniques. This knowledge will be essential for understanding the data that you will be analyzing in the course

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Read articles or books about genome sequencing
Watch videos about genome sequencing
Take an online course on genome sequencing

Ten other activities

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Review Nucleotide composition and their analysis

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Review the concepts of nucleotide composition and their analysis to strengthen your foundational understanding in virology.

Browse courses on Nucleotide Composition

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Revisit the structure and properties of nucleotides.
Explore different methods for analyzing nucleotide composition.
Practice analyzing nucleotide composition using online tools or software.

Review the basics of nucleotide composition

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Refreshes your understanding of nucleotide composition, which is essential for understanding cumulative skew profiles and dendrogram creation.

Browse courses on Nucleotide Composition

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Review the structure and properties of nucleotides
Identify the different types of nucleotide bases
Calculate the nucleotide composition of a given DNA sequence

Engage in peer discussions on virus evolution

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Participate in peer discussions to exchange knowledge and perspectives on the evolution of viruses.

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Join online forums or discussion groups related to virology.
Engage in discussions on topics related to virus evolution.
Share your own knowledge and insights, and learn from others' perspectives.

Jupyter Notebook for Analyzing Virus Dendrograms

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Start a Jupyter notebook project that will test your ability to analyze virus dendrograms. This is a good way to demonstrate your proficiency with the techniques learned during this course

Browse courses on Dendrograms

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Import libraries and load datasets
Write a function to calculate pairwise nucleotide composition distances
Create a distance matrix and calculate the cumulative skew profiles
Use a hierarchical clustering method to create a dendrogram
Visualize the dendrogram

Practice dendrogram construction

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Engage in repetitive exercises to solidify your understanding of dendrogram construction techniques.

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Use online tools or software to construct dendrograms based on given data.
Interpret the results of dendrogram construction and identify patterns.
Compare different dendrogram construction methods and evaluate their strengths and weaknesses.

Practice creating dendrograms from cumulative skew profiles

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Provides hands-on practice with the core concepts of the course, allowing you to solidify your understanding of dendrogram creation and interpretation.

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Create a cumulative skew profile for a given DNA sequence
Use the cumulative skew profile to create a dendrogram
Interpret the dendrogram to identify relationships among viruses

Explore advanced bioinformatics tools

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Seek out and follow tutorials to enhance your proficiency in bioinformatics tools relevant to virology.

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Identify bioinformatics tools that specialize in virology research.
Follow online tutorials or workshops to learn how to use these tools.
Apply the tools to analyze real-world virology datasets.

Develop a Python program to analyze virus data and create a dendrogram

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Challenges you to apply your knowledge by creating a functional program that demonstrates your understanding of virus analysis and dendrogram creation.

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Design the program's architecture and functionality
Implement the program using Python
Test and debug the program
Use the program to analyze virus data and create a dendrogram

Develop a visualization of virus relatedness

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Create a visual representation of the relatedness among different viruses to enhance your understanding of viral diversity.

Browse courses on Data Visualization

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Gather data on the nucleotide sequences of different viruses.
Analyze the data to determine the relatedness among the viruses.
Choose an appropriate visualization technique to represent the relatedness data.
Create the visualization and interpret the results.

Mentor other students in the course

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Provides an opportunity to reinforce your understanding by helping others, while also contributing to the learning community.

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Identify students who need support
Offer assistance and guidance on course-related topics
Provide feedback and encouragement

Career center

Learners who complete Hierarchical Clustering using Euclidean Distance will develop knowledge and skills that may be useful to these careers:

Data Scientist

Data scientists use data analysis and modeling techniques to solve business problems. They work on projects such as improving customer service, optimizing marketing campaigns, and predicting future trends. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in data science. By taking this course, you may be able to gain the skills and knowledge necessary to analyze data and solve business problems.

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Machine Learning Engineer

Machine learning engineers build and deploy machine learning models to solve business problems. They work on projects such as developing self-driving cars, improving medical diagnosis, and predicting customer behavior. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in machine learning. By taking this course, you may be able to gain the skills and knowledge necessary to analyze data and build machine learning models.

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Bioinformatics Scientist

Bioinformatics scientists use computational tools and techniques to analyze and interpret biological data. They work on projects such as developing new drugs and treatments, understanding the genetic basis of disease, and improving crop yields. This course, which covers topics such as hierarchical clustering and Euclidean distance, could help you gain the necessary skills to analyze biological data. This could be a valuable asset in the field of bioinformatics.

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Quantitative Analyst

Quantitative analysts use data analysis and modeling techniques to make investment decisions. They work on projects such as developing trading strategies, analyzing risk, and forecasting financial markets. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in quantitative finance. By taking this course, you may be able to learn the skills and knowledge necessary to analyze data and make investment decisions.

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Actuary

Actuaries use data analysis and modeling techniques to assess and manage risk. They work on projects such as pricing insurance policies, developing pension plans, and evaluating financial risks. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in actuarial science. By taking this course, you may be able to learn the skills and knowledge necessary to analyze data and assess risk.

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Statistician

Statisticians collect, analyze, and interpret data to provide insights and make predictions. They work in a variety of fields, including finance, healthcare, and marketing. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in statistics. By taking this course, you may be able to learn the skills and knowledge necessary to analyze data and make informed decisions.

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Data Engineer

Data engineers design, build, and maintain data pipelines to support data analysis and machine learning. They work on projects such as developing data warehouses, streaming data pipelines, and data lakes. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in data engineering. By taking this course, you may be able to learn the skills and knowledge necessary to analyze data and build data pipelines.

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Computational Biologist

Computational biologists use computer science, mathematics, and statistics to analyze and interpret biological data. They study the complex interactions of biological systems, such as DNA and proteins, using computational tools and techniques. The skills you gain in this course, such as analyzing and interpreting data using hierarchical clustering and Euclidean distance, would be valuable in computational biology. It could help you build a foundation for understanding the complex interactions of biological systems.

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Epidemiologist

Epidemiologists investigate the patterns and causes of disease and injury in human populations. They use data analysis and modeling techniques to track and predict the spread of disease and identify risk factors. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in epidemiology. By taking this course, you may be able to learn the skills and knowledge necessary to analyze epidemiological data.

See salaries and explore the career path for Epidemiologist

Medical Scientist

Medical scientists conduct research to understand the causes and treatments of disease. They use a variety of techniques, including data analysis, to study the human body and develop new treatments. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in medical research. By taking this course, you may be able to gain the skills and knowledge necessary to analyze medical data.

See salaries and explore the career path for Medical Scientist

Public Health Analyst

Public health analysts use data analysis and modeling techniques to identify and address public health problems. They work on projects such as preventing the spread of disease, improving nutrition, and reducing environmental hazards. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in public health. By taking this course, you may be able to learn valuable skills to apply to public health work.

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Software Engineer

Software engineers design, develop, and maintain software systems. They work on a variety of projects, from developing mobile apps to building enterprise software. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in software engineering. By taking this course, you may be able to learn the skills and knowledge necessary to analyze data and develop software systems.

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Research Scientist

Research scientists conduct research to understand the world around us. They use a variety of techniques, including data analysis, to study everything from the human body to the stars. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to data analysis in research. By taking this course, you may be able to learn valuable skills to apply to research work.

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Biostatistician

Biostatisticians apply statistical methods to address scientific questions in biology and medicine. Through the use of data analysis, they can enhance the interpretation of biological and medical data. This course covers topics such as hierarchical clustering and Euclidean distance, which are relevant to statistical analysis. By taking this course, you may be able to gain a solid understanding of these concepts, which could be an asset in the field of biostatistics.

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Data Analyst

Data analysts take complex data and turn it into easy-to-understand formats, using statistical analysis and modeling techniques. The ability to read and analyze data is an important skill for data analysts and, by taking this course, you may be able to learn valuable skills to apply to data science work. The program uses Python, a commonly used programming language for data analysis.

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Reading list

We've selected 12 books that we think will supplement your learning. Use these to develop background knowledge, enrich your coursework, and gain a deeper understanding of the topics covered in Hierarchical Clustering using Euclidean Distance.

Molecular Evolution and Phylogenetics

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An advanced textbook that provides a thorough overview of molecular evolution and phylogenetics. Discusses advanced methods for phylogenetic analysis, including hierarchical clustering and Bayesian inference.

Hierarchical Clustering using Euclidean Distance

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Reviews summary

Difficult to understand lectures

Activities

Career center

Reading list

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