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Rajvir Dua
and
Neelesh Tiruviluamala
In this capstone project course, we'll compare genome sequences of COVID-19 mutations to identify potential areas a drug therapy can look to target. The first step in drug discovery involves identifying target subsequences of theirs genome to target. We'll start by comparing the genomes of virus mutations to look for similarities. Then, we'll perform PCA to cut down our number of dimensions and identify the most common features. Next, we'll use K-means clustering in Python to find the optimal number of groups and trace the lineage of the virus. Finally, we'll predict similarity between the sequences and use this to pick a target subsequence. Throughout the course, each section will consist of a programming assignment coupled with a guide video and helpful hints. By the end, you'll be well on your way to discovering ways to combat disease with genome sequencing.
Register for this course and see more details by visiting:
OpenCourser.com/course/75ilcs/capstone
What's inside
Syllabus
Comparing Genome Sequences
In this module, we'll start to get familiar with our dataset by performing some basic EDA and comparing genome sequences. By analyzing the mutations of the COVID-19 virus, we'll be able to identify some common properties of the genome that our drug should look to target.
Read more
Syllabus
Comparing Genome Sequences
In this module, we'll start to get familiar with our dataset by performing some basic EDA and comparing genome sequences. By analyzing the mutations of the COVID-19 virus, we'll be able to identify some common properties of the genome that our drug should look to target.
Read more
Principal Component Analysis on Genome Sequences
In this module, we'll continue to work with out genome sequence data - using PCA to identify groups and delicate the most important features. After reducing the number of dimensions in the dataset, we'll be able to use K-means to form clusters and visualize the different areas in 2-D space.
Feature Analysis using K-Means Clustering
In this module, we'll cluster the genome sequences using the K-means algorithm. We'll optimize the number of clusters by comparing silhouette scores across a wide variety of inputs to identify the greatest drop-off. Finally, we'll set ourselves up to using prediction pipelines to predict bit scores and drug therapies in the last module.
Predicting Bit Score to Find Sequence Matches
In this module, we'll test a variety of regressors to see which one performs best in predicting bit scores for each genome sequence. Then, we'll use our chosen model to find the genome equines that are most closely related and trace out a possible subsequence to target with a combative drug.
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Develops programming, bioinformatics, and data analysis skills, all of which are essential in the medical field and the biotechnology industry
Uses Python and R to perform complex analyses, which are commonly used technologies in data science
Taught by Neelesh Tiruviluamala who has a Ph.D. in bioengineering from the University of California, San Diego and Rajvir Dua who had a PhD in Microbiology and Immunology from McGill University
Examines topics fundamental to drug discovery, such as genome sequencing and molecular biology, which are important foundational skills and knowledge for those in the life sciences
Suitable for those with prior experience in programming and a basic understanding of biology, making it an appropriate choice for those already invested in this field
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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 Capstone Project: Advanced AI for Drug Discovery with these
activities:
Review Molecular Biology Concepts
Show steps
Refresh your understanding of key molecular biology concepts to strengthen your foundation for the course.
Browse courses on
Molecular Biology
Show steps
-
Read your lecture notes or textbook.
-
Take a practice quiz or exam.
Read 'Understanding Bioinformatics'
Show steps
Review foundational concepts in molecular biology, sequence analysis, and bioinformatics analysis techniques.
Show steps
-
Read the introductory chapters.
-
Complete the practice exercises in each chapter.
-
Summarize the key concepts in your own words.
Explore Python Libraries for Bioinformatics
Show steps
Expand your knowledge of Python libraries and their applications in bioinformatics.
Browse courses on
Python
Show steps
-
Install the necessary Python libraries.
-
Follow tutorials on using these libraries.
-
Experiment with the libraries on your own.
Five other activities
Expand to see all activities and additional details
Show all eight activities
Practice Sequence Alignment Algorithms
Show steps
Sharpen your understanding of sequence alignment techniques and improve your ability to perform them.
Browse courses on
Sequence Alignment
Show steps
-
Use an online sequence alignment tool.
-
Implement a simple sequence alignment algorithm in a programming language.
-
Analyze the results of different alignment algorithms.
Learn Genome Analysis Tools
Show steps
Enhance your skills in using genome analysis tools to extract meaningful insights from genomic data.
Browse courses on
Genome Analysis
Show steps
-
Find tutorials on using genome analysis tools.
-
Follow the tutorials and practice using the tools.
-
Apply the tools to analyze your own data.
Join a Study Group
Show steps
Enhance your understanding of the course material through discussions and collaboration with peers.
Show steps
-
Meet with your study group regularly.
-
Discuss the lecture material.
-
Work on assignments together.
Create a Genome Visualization
Show steps
Develop your skills in visualizing and interpreting genomic data.
Show steps
-
Choose a genome to visualize.
-
Select a visualization tool.
-
Create a visualization that highlights interesting features of the genome.
-
Present your visualization to the class.
Contribute to Open-Source Bioinformatics Projects
Show steps
Gain practical experience and contribute to the bioinformatics community through open-source projects.
Browse courses on
Open Source
Show steps
-
Find an open-source bioinformatics project.
-
Identify areas where you can contribute.
-
Submit a pull request.
Review Molecular Biology Concepts
Show steps
Refresh your understanding of key molecular biology concepts to strengthen your foundation for the course.
Browse courses on
Molecular Biology
Show steps
Show steps
Show steps
- Read your lecture notes or textbook.
- Take a practice quiz or exam.
Read 'Understanding Bioinformatics'
Show steps
Review foundational concepts in molecular biology, sequence analysis, and bioinformatics analysis techniques.
Show steps
Show steps
Show steps
- Read the introductory chapters.
- Complete the practice exercises in each chapter.
- Summarize the key concepts in your own words.
Explore Python Libraries for Bioinformatics
Show steps
Expand your knowledge of Python libraries and their applications in bioinformatics.
Browse courses on
Python
Show steps
Show steps
Show steps
- Install the necessary Python libraries.
- Follow tutorials on using these libraries.
- Experiment with the libraries on your own.
Five other activities
Expand to see all activities and additional details
Show all eight activities
Practice Sequence Alignment Algorithms
Show steps
Sharpen your understanding of sequence alignment techniques and improve your ability to perform them.
Browse courses on
Sequence Alignment
Show steps
Show steps
Show steps
- Use an online sequence alignment tool.
- Implement a simple sequence alignment algorithm in a programming language.
- Analyze the results of different alignment algorithms.
Learn Genome Analysis Tools
Show steps
Enhance your skills in using genome analysis tools to extract meaningful insights from genomic data.
Browse courses on
Genome Analysis
Show steps
Show steps
Show steps
- Find tutorials on using genome analysis tools.
- Follow the tutorials and practice using the tools.
- Apply the tools to analyze your own data.
Join a Study Group
Show steps
Enhance your understanding of the course material through discussions and collaboration with peers.
Show steps
Show steps
Show steps
- Meet with your study group regularly.
- Discuss the lecture material.
- Work on assignments together.
Create a Genome Visualization
Show steps
Develop your skills in visualizing and interpreting genomic data.
Show steps
Show steps
Show steps
- Choose a genome to visualize.
- Select a visualization tool.
- Create a visualization that highlights interesting features of the genome.
- Present your visualization to the class.
Contribute to Open-Source Bioinformatics Projects
Show steps
Gain practical experience and contribute to the bioinformatics community through open-source projects.
Browse courses on
Open Source
Show steps
Show steps
Show steps
- Find an open-source bioinformatics project.
- Identify areas where you can contribute.
- Submit a pull request.
Career center
Learners who complete Capstone Project: Advanced AI for Drug Discovery will develop knowledge and skills
that may be useful to these careers:
Microbiologist
Microbiologist
As a Microbiologist, you study microorganisms, such as bacteria, viruses, and fungi, and their role in health and disease. You'll use a variety of techniques, including microscopy, culturing, and molecular biology, to identify and characterize microorganisms, and you'll work to develop new drugs and treatments for infectious diseases. If you want to be a Microbiologist, this Capstone Project will be an excellent fit for you. The focus on comparing genome sequences of COVID-19 mutations aligns well with the work Microbiologists do on a daily basis.
Medical Scientist
Medical Scientist
As a Medical Scientist, you use your knowledge of medicine, biology, and other sciences to research and develop new drugs and treatments for diseases. You'll work in a laboratory setting to conduct experiments and analyze data, and you'll often collaborate with other scientists and clinicians to bring new therapies to market. The Capstone Project simulates the process of developing new drugs and therapies. You'll be using many of the same techniques that Medical Scientists use in their day-to-day work, making this course an excellent choice if you are interested in this career path.
Pharmaceutical Scientist
Pharmaceutical Scientist
As a Pharmaceutical Scientist, you research, develop, and manufacture drugs and other pharmaceutical products. You'll work in a laboratory setting to conduct experiments and analyze data, and you'll often collaborate with other scientists and clinicians to bring new therapies to market. This Capstone Project can be an excellent foundation for a Pharmaceutical Scientist. You'll be using many of the same techniques that Pharmaceutical Scientists use in their day-to-day work, gaining valuable experience in the research and development of new drugs.
Computational Biologist
Computational Biologist
A Computational Biologist uses computer science, applied mathematics, and statistics to solve biological problems. You'll analyze and interpret biological data like DNA and protein sequences to understand the structure and function of proteins, predict protein-protein interactions, and simulate biological systems. This Capstone Project will help you build a solid foundation for your career as a Computational Biologist as you'll be using computational science to work through a biological problem. Specifically, you'll use genome sequence comparisons and other techniques to identify potential targets for drug therapy.
Research Scientist
Research Scientist
As a Research Scientist, you conduct scientific research to develop new knowledge and technologies. You'll work in a laboratory setting to conduct experiments and analyze data, and you'll often collaborate with other scientists to publish your findings in scientific journals. This Capstone Project can help if you wish to be a Research Scientist. You'll learn how to use advanced methods to develop new drugs and therapies, which can provide you with valuable skills for your research career in drug discovery.
Molecular Biologist
Molecular Biologist
As a Molecular Biologist, you study the structure and function of biological molecules, such as DNA, RNA, and proteins. You'll use a variety of techniques, such as molecular cloning, gene expression analysis, and protein purification, to investigate how these molecules work and how they are regulated. You'll also use your knowledge to develop new drugs and treatments for diseases. For individuals interested in Molecular Biology, this Capstone Project aligns well with the advanced techniques and skills used by professionals in this field.
Research Associate
Research Associate
A Research Associate conducts scientific research under the supervision of a senior scientist. You'll work in a laboratory setting to conduct experiments and analyze data, and you'll often collaborate with other scientists to publish your findings in scientific journals. If you want to become a Research Associate, this Capstone Project can provide you with a solid foundation. You'll learn how to use advanced techniques to develop new drugs and therapies, which can help you succeed in your research career.
Geneticist
Geneticist
A Geneticist studies genes and their role in health and disease. You'll use a variety of techniques, including genetic sequencing and analysis, to identify and characterize genes that are associated with disease, develop diagnostic tests, and design new therapies. This Capstone Project can be helpful in building your foundation as a Geneticist and expand your knowledge of how to use advanced techniques to develop new drugs and therapies.
Statistician
Statistician
As a Statistician, you collect, analyze, and interpret data to help businesses and organizations make informed decisions. You'll use your skills in statistics and data analysis to solve problems and improve outcomes. This Capstone Project can provide a foundation if you are interested in becoming a Statistician in the field of drug discovery. You'll learn about many of the advanced techniques and methods used in this industry, which you can apply to your work as a Statistician.
Epidemiologist
Epidemiologist
As an Epidemiologist, you investigate the causes and patterns of disease and other health problems in human populations. You'll use your knowledge of epidemiology, biostatistics, and public health to design and conduct studies, analyze data, and make recommendations to prevent and control disease. This Capstone Project will be helpful in building your understanding of disease and how to use advanced methods to help inform future drug development, and how to approach similar problems in the future.
Science Writer
Science Writer
As a Science Writer, you communicate complex scientific information to a non-scientific audience. You'll write articles, blog posts, and other content that explains the latest scientific discoveries and their implications for society. If you're interested in becoming a Science Writer with a specialization in drug discovery and the pharmaceutical industry, you may find this Capstone Project helpful. You'll learn how to use advanced methods to develop new drugs and therapies, which will enable you to communicate about these topics effectively with your audience.
Physician
Physician
As a Physician, you diagnose and treat patients with a variety of medical conditions. You'll use your knowledge of medicine, science, and the human body to provide comprehensive care to your patients. If you're interested in becoming a Physician, you may find this Capstone Project useful. You'll learn how to use advanced methods to develop new drugs and therapies, which can help you provide the best possible care to your patients.
Data Scientist
Data Scientist
As a Data Scientist, you work with large and complex data to uncover hidden patterns and insights, identify trends, and make predictions using statistical modeling, machine learning algorithms, and data visualization tools. You'll use your skills to solve a variety of problems in a variety of industries, such as healthcare, finance, and manufacturing. If you are interested in Data Science and working with biological data to help solve complex problems, you may find this Capstone Project helpful in building a foundation as you'll be learning how to use data science techniques to analyze genome sequences and identify potential drug targets.
Bioinformatics Scientist
Bioinformatics Scientist
A Bioinformatics Scientist researches, develops, and applies computational tools and approaches to analyze big biological data, such as genomics, to identify drug targets for disease diagnostics and therapeutics. You'll use your knowledge of computational biology, statistics, and machine learning to develop new algorithms, software, and databases to help understand and predict biological processes, study the evolution of viruses, and design new drugs. With the Capstone Project's focus on comparing genome sequences of COVID-19 mutations to identify potential areas a drug can target, this course may be useful in helping you build a foundation as a Bioinformatics Scientist.
Professor
Professor
As a Professor, you teach and conduct research at a college or university. You'll specialize in a particular field of study, such as biology, chemistry, or physics, and you'll work with students to help them learn and grow. The Capstone Project can be an excellent way to build the specialized and advanced knowledge required as a Professor. You'll be learning about many of the latest techniques and methods used in the field today and will be able to apply this knowledge directly to your teaching and research.
For more career information including salaries, visit:
OpenCourser.com/course/75ilcs/capstone
Reading list
We've selected 11 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
Capstone Project: Advanced AI for Drug Discovery.
Provides a comprehensive overview of the field of genomics for drug discovery, covering topics such as target identification, biomarker development, and personalized medicine.
Provides a comprehensive overview of statistical methods used in bioinformatics. It covers a wide range of topics, including probability theory, hypothesis testing, and data analysis.
Provides an introduction to deep learning methods for drug discovery, covering topics such as convolutional neural networks, recurrent neural networks, and graph neural networks.
Provides a practical overview of bioinformatics methods. It covers a wide range of topics, including data management, analysis, and interpretation.
Provides a practical guide to using R for computational genomics. It covers a wide range of topics, including data import, analysis, and visualization.
Provides an introduction to the field of pharmaceutical biotechnology, covering topics such as recombinant DNA technology, protein expression, and drug delivery.
Provides a comprehensive overview of the principles of drug action, covering topics such as drug absorption, distribution, metabolism, and excretion.
Provides a comprehensive overview of the principles of medicinal chemistry, covering topics such as drug design, drug synthesis, and drug evaluation.
Provides a comprehensive overview of the field of pharmacology and therapeutics, covering topics such as drug mechanisms of action, drug interactions, and drug side effects.
Provides an introduction to the field of medicinal chemistry, covering topics such as drug discovery, drug design, and drug synthesis.
Provides an introduction to the field of pharmaceutical chemistry, covering topics such as drug discovery, drug design, and drug synthesis.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/75ilcs/capstone
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Effort
3 weeks of study, 3-5 hours/week
Level
Intermediate
Via
Coursera
Institution
LearnQuest
Instructors
Rajvir Dua
Neelesh Tiruviluamala
Language
English
Transcripts
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中文
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This course belongs to a
collection
called
AI for Scientific Research. It's comprised of four courses:
- Capstone Project: Advanced AI for Drug Discovery (viewing)
- Introduction to Data Science and scikit-learn in Python
- Neural Networks and Random Forests
- Machine Learning Models in Science
Good to know
Develops programming, bioinformatics, and data analysis skills, all of which are essential in the medical field and the biotechnology industry
Uses Python and R to perform complex analyses, which are commonly used technologies in data science
Taught by Neelesh Tiruviluamala who has a Ph.D. in bioengineering from the University of California, San Diego and Rajvir Dua who had a PhD in Microbiology and Immunology from McGill University
Examines topics fundamental to drug discovery, such as genome sequencing and molecular biology, which are important foundational skills and knowledge for those in the life sciences
Suitable for those with prior experience in programming and a basic understanding of biology, making it an appropriate choice for those already invested in this field
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