À propos de ce cours : This course distills for you expert knowledge and skills mastered by professionals in Health Big Data Science and Bioinformatics. You will learn exciting facts about the human body biology and chemistry, genetics, and medicine that will be intertwined with the science of Big Data and skills to harness the avalanche of data openly available at your fingertips and which we are just starting to make sense of. We’ll investigate the different steps required to master Big Data analytics on real datasets, including Next Generation Sequencing data, in a healthcare and biological context, from preparing data for analysis to completing the analysis, interpreting the results, visualizing them, and sharing the results. Needless to say, when you master these high-demand skills, you will be well positioned to apply for or move to positions in biomedical data analytics and bioinformatics. No matter what your skill levels are in biomedical or technical areas, you will gain highly valuable new or sharpened skills that will make you stand-out as a professional and want to dive even deeper in biomedical Big Data. It is my hope that this course will spark your interest in the vast possibilities offered by publicly available Big Data to better understand, prevent, and treat diseases.
Les destinataires de ce cours : This course is primarily aimed at health care professionals or assistants, and those with a BS/MA/MS in science or technology or equivalent professional experience. Minimum technical skills are a good understanding of using an Excel spreadsheet. Additional prerequisite knowledge in basic statistics would be preferred, however additional resources will be made available to learners to acquire this knowledge. I think that anyone interested in getting insights into how to harness Big Data to better understand, prevent, and treat diseases can take this course because the material can be applied at different levels of expertise.
Créé par : Université d'État de New York
Enseigné par : Isabelle Bichindaritz, Associate Professor
Computer Science
| Niveau | Advanced |
| Engagement | 6 weeks of study, 3-5 hours per week |
| Langue | English |
| Comment réussir | Réussissez tous les devoirs notés pour terminer le cours. |
| Notes des utilisateurs |
Programme de cours
SEMAINE 1
Genes and Data
After this module, you will be able to
1. Locate and download files for data analysis involving genes and medicine.
2. Open files and preprocess data using R language.
3. Write R scripts to replace missing values, normalize data, discretize data, and sample data.
11 vidéos, 2 lectures, 4 quiz pour s'exercer
- Vidéo: Introduction to the Course
- Vidéo: Introduction to Module
- Vidéo: DNA and Genes
- Vidéo: RNA and Proteins
- Cuestionario de práctica: DNA, RNA, Genes, and Proteins
- Vidéo: Transcription Process
- Vidéo: Transcription Animation
- Vidéo: Translation Process
- Vidéo: Translation Animation
- Cuestionario de práctica: Transcription and Translation Processes
- Vidéo: Data, Variables, and Big Datasets
- Cuestionario de práctica: Data, Variables, and Big Datasets
- Vidéo: Working with cBioPortal - Genetic Data Analysis
- Vidéo: Working with cBioPortal - Gene Networks
- Cuestionario de práctica: Working with cBioPortal
- Cuadro de aviso de la discusión: Module 1 Discussion
- Leyendo: Module 1 cBioPortal Data Analytics
- Leyendo: Module 1 Resources
Noté: Module 1 Quiz
Noté: Module 1 cBioPortal Data Analytics
SEMAINE 2
Preparing Datasets for Analysis
After this module, you will be able to:
1. Locate and download files for data analysis involving genes and medicine.
2. Open files and preprocess data using R language.
3. Write R scripts to replace missing values, normalize data, discretize data, and sample data.
13 vidéos, 4 lectures, 6 quiz pour s'exercer
- Vidéo: Introduction to Module
- Vidéo: Datasets and Files
- Vidéo: Data Sources
- Cuestionario de práctica: Datasets and Files
- Vidéo: Importance of Data Preprocessing
- Vidéo: Data Preprocessing Tasks
- Cuestionario de práctica: Data Preprocessing Tasks
- Vidéo: Replacing Missing Values
- Cuestionario de práctica: Replacing Missing Values
- Vidéo: Data Normalization
- Vidéo: Data Discretization
- Cuestionario de práctica: Normalization and Discretization
- Vidéo: Feature Selection
- Vidéo: Data Sampling
- Cuestionario de práctica: Data Reduction
- Vidéo: Principles of R
- Vidéo: R Language
- Cuestionario de práctica: Working with R
- Libreta: Module 2 Notebook
- Vidéo: Jupyter Notebooks 101
- Leyendo: Jupyter Notebooks Essentials
- Leyendo: Notebook Module 2 Tutorial
- Cuadro de aviso de la discusión: Module 2 Discussion
- Leyendo: Module 2 R Data Preprocessing
- Libreta: Module 2 Notebook
- Leyendo: Module 2 Resources
Noté: Module 2 Quiz
Noté: Module 2 R Data Preprocessing
SEMAINE 3
Finding Differentially Expressed Genes
After this module, you will be able to
1. Select features from highly dimensional datasets.
2. Evaluate the performance of feature selection methods.
3. Write R scripts to select features from datasets involving gene expressions.
9 vidéos, 4 lectures, 4 quiz pour s'exercer
- Vidéo: Introduction to Module
- Vidéo: Overview of Feature Selection Methods
- Vidéo: Filter Methods
- Vidéo: Wrapper Methods
- Cuestionario de práctica: Feature Selection Methods
- Vidéo: Evaluation Schemes
- Cuestionario de práctica: Evaluation Schemes
- Vidéo: Selecting Differentially Expressed Genes
- Cuestionario de práctica: Differentially Expressed Genes
- Vidéo: Heatmaps
- Cuestionario de práctica: Heatmaps
- Vidéo: R Scripts for Feature Selection
- Libreta: Module 3 Notebook
- Leyendo: Notebook Module 3 Tutorial
- Leyendo: Jupyter Notebooks Essentials
- Vidéo: Jupyter Notebooks 101
- Cuadro de aviso de la discusión: Module 3 Discussion
- Leyendo: Module 3 R Finding Differentially Expressed Genes
- Libreta: Module 3 Notebook
- Leyendo: Module 3 Resources
Noté: Module 3 Quiz
Noté: Module 3 R Finding Differentially Expressed Genes
SEMAINE 4
Predicting Diseases from Genes
After this module, you will be able to
1. Build classification and prediction models.
2. Evaluate the performance of classification and prediction methods.
3. Write R scripts to classify and predict diseases from gene expressions.
12 vidéos, 4 lectures, 8 quiz pour s'exercer
- Vidéo: Introduction to Module
- Vidéo: Overview of Classification and Prediction Methods
- Cuestionario de práctica: Overview
- Vidéo: Classification Methods Based on Analogy
- Cuestionario de práctica: Classification with Analogy
- Vidéo: Classification Methods Based on Rules
- Cuestionario de práctica: Classification based on Rules
- Vidéo: Classification Methods Based on Neural Networks
- Cuestionario de práctica: Classification with Neural Networks
- Vidéo: Classification Methods Based on Statistics
- Cuestionario de práctica: Classification based on Statistics
- Vidéo: Classification Methods Based on Probabilities
- Cuestionario de práctica: Classification based on Probabilities
- Vidéo: Prediction Methods
- Cuestionario de práctica: Prediction Models
- Vidéo: Evaluation Schemes
- Cuestionario de práctica: Evaluation Schemes
- Vidéo: Prediction Workflow
- Vidéo: R Scripts for Prediction
- Libreta: Module 4 Notebook
- Leyendo: Jupyter Notebooks Essentials
- Vidéo: Jupyter Notebooks 101
- Leyendo: Notebook Module 4 Tutorial
- Cuadro de aviso de la discusión: Module 4 Discussion
- Leyendo: Module 4 R Predicting Diseases from Genes
- Leyendo: Module 4 Resources
Noté: Module 4 Quiz
Noté: Module 4 R Predicting Diseases from Genes
SEMAINE 5
Determining Gene Alterations
After this module, you will be able to
1. List different types of gene alterations.
2. Compare and contrast methods for detecting gene mutations.
3. Compare and contrast methods for detecting methylation.
4. Compare and contrast methods for detecting copy number variations.
5. Quantify genomic alterations.
6. Connect genomic alterations to differential expression of genes.
7. Write programs in R for determining gene alterations and their relationship with gene expression.
9 vidéos, 4 lectures, 6 quiz pour s'exercer
- Vidéo: Introduction to Module
- Vidéo: Overview of Gene Alterations
- Cuestionario de práctica: Gene Alterations
- Vidéo: Genetic Mutations
- Vidéo: Finding Genetic Mutations
- Cuestionario de práctica: Gene Mutations
- Vidéo: Methylation
- Cuestionario de práctica: Methylation
- Vidéo: Copy Number Alterations
- Cuestionario de práctica: Copy Number Alterations
- Vidéo: Genomic Alterations and Gene Expressions
- Cuestionario de práctica: Genomic Alterations and Gene Expressions
- Vidéo: R Scripts for Gene Alterations
- Libreta: Module 5 Notebook
- Vidéo: Jupyter Notebooks 101
- Leyendo: Notebook Module 5 Tutorial
- Leyendo: Jupyter Notebooks Essentials
- Cuadro de aviso de la discusión: Module 5 Discussion
- Cuestionario de práctica: Module 5 Quiz (Temporary)
- Leyendo: Module 5 R Gene Alterations
- Leyendo: Module 5 Resources
Noté: Module 5 Quiz
Noté: Module 5 R Gene Alterations
SEMAINE 6
Clustering and Pathway Analysis
After this module, you will be able to 1. Find clusters in biomedical data involving genes.2. Analyze and visualize biological pathways. 3. Write R scripts for clustering and for pathway analysis.
12 vidéos, 5 lectures, 3 quiz pour s'exercer
- Vidéo: Introduction to Module
- Vidéo: Overview of Clustering Methods
- Vidéo: Similarity Assessment
- Cuestionario de práctica: Clustering
- Vidéo: Clustering with KMeans
- Vidéo: Density Based Clustering
- Vidéo: Hierarchical Clustering
- Cuestionario de práctica: Clustering Methods
- Vidéo: Pathway Analysis
- Vidéo: Pathway Discovery
- Vidéo: Pathway Visualization
- Cuestionario de práctica: Pathways
- Vidéo: R Scripts for Clustering and Pathway Analysis
- Libreta: Module 6 Notebook
- Vidéo: Jupyter Notebooks 101
- Leyendo: Jupyter Notebooks Essentials
- Leyendo: Notebook Module 6 Tutorial
- Cuadro de aviso de la discusión: Module 6 Discussion
- Leyendo: Module 6 R Clustering and Pathways
- Leyendo: Module 6 Resources
- Vidéo: Concluding Remarks
- Leyendo: Acknowledgements
Noté: Module 6 Quiz
Noté: Module 6 R Clustering and Pathways
FAQ
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Créateurs
Université d'État de New York
The State University of New York, with 64 unique institutions, is the largest comprehensive system of higher education in the United States. Educating nearly 468,000 students in more than 7,500 degree and certificate programs both on campus and online, SUNY has nearly 3 million alumni around the globe.
Tarification
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Notation et examens
prof.Bichindaritz is very kind, the course useful for beginners interested in bioinformatics. And many useful resources are provided. Hope for more weeks introducing life science data analysis!
I am very grateful with Dr. Isabelle Bichindaritz and her team that made it possible this course. This course was excellent for me and now I want to learn more about Bioinformatics.
Excellent course for an introduction to Big data and bioscience.
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I do like how in depth this was so that you can get a real taste of how some of this analysis is performed as well as the fundamentals behind it. Balancing all of the biology, informatics, statistics to an audience where you don't know everyone's backgrounds is very challenging but I think this course does a fairly good job of it. I do wish some of the answers were updated, as when you go through some of the analysis using the public tools they may have changed because certain answers I got were very slightly off (1-3) and I had thought it was my fault at first until I checked the forums, so that was annoying at worst. I liked all of the cbio portal lessons and the quizzes where we had to go into the code and change some numbers. The work in the jupyter notebooks felt overwhelming sometimes so I wish I all the codes were slightly more thoroughly explained, but otherwise a satisfying course.