Whether you are a student, basic scientist, researcher, clinician, or librarian, this course is designed to help you understand, analyze, and interpret biomedical big data.
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With the continuous generation of massive amounts of biomedical data on a daily basis, whether from research laboratories or clinical labs, we need to improve our ability to understand and analyze the data in order to take full advantage of its power in scientific discoveries and patient care. For non-bioinformaticians, “handling” big data remains a daunting task. This course was designed to facilitate the understanding, analysis, and interpretation of biomedical big data to those in the biomedical field with limited or no significant experience in bioinformatics. The goal of this course is to “demystify” the process of analyzing biomedical big data through a series of lectures and online hands-on training sessions and demos. You will learn how to use publicly available online resources and tools for genomic, transcriptomic, and proteomic data analysis, as well as other analytic tools and online resources. This course is funded by a research grant from the US National Institutes of Health (NIH)-Big Data to Knowledge (BD2K) Initiative.
What you'll learn
- Understand how biomedical data are being generated and processed
- Learn about various biomedical big data resources (e.g. TCGA, G-DOC, UNIPROT, etc.)
- Explore and analyze genomic, transcriptomic, and proteomic data using various online analysis tools
- Make sense of big data using systems biology resources and tools
- Appreciate the value of big data in biomedical research and clinical practice (e.g. enabling precision medicine)
Course Syllabus
Week 1: Introduction and Overview of Bioinformatics Platforms and Resources
-Introduction to the Course -Interview with Bioinformatics at Georgetown University Medical Center. Dr. Robert Clarke, Dean for Research, at Georgetown University Medical Center
-Biomedical Informatics: Enabling Research and Health Care. Interview with Dr. Subha Madhavan, Director of the Innovation Center for Biomedical Informatics (ICBI) at Georgetown University
-Biomedical Big Data: Enabling Personalized Medicine. Interview with Dr. John Marshall, Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center internationally recognized medical oncologist
Week 2: Translational Research and Big Data
Translational Research
Translational Research Lecture, Part 1 Part I
Translational Research Lecture, Part 2 Part II
The Cancer Genome Atlas
The Cancer Genome Atlas Lecture
The Cancer Genome Atlas Demo
The Cancer Genome Atlas Exercise
Introduction to G-DOC
G-DOC Lecture
G-DOC Demo
G-DOC Exercise
Week 3: DNA and Big Data
DNA Copy Number
DNA Copy Number Lecture
DNA Copy Number Demo
DNA Copy Number Exercise
Genome Sequencing
Genome Sequencing Lecture, Part 1
Genome Sequencing Lecture, Part 2
Genome Sequencing Demo
Genome Sequencing Exercise
Week 4: RNA and Big Data
Gene Expression
Gene Expression Lecture
Gene Expression Demo
Gene Expression Exercise
MicroRNA
MicroRNA Lecture
MicroRNA Demo
MicroRNA Exercise
Week 5: Proteins and Big Data Part I
Proteomics
Protein Sequences Lecture
Protein Interactions Lecture
Mass Spec Proteomics, Lecture
Proteomics Exercise
Week 6: Proteins and Big Data Part II
Proteomics (Continued)
Data Sharing, Metadata, Data Formats
Ontologies
Proteomics Demo, Part 1
Proteomics Demo, Part 2
Proteomics Demo, Part 3
Proteomics Exercise
Week 7: Systems Biology and Big Data
Systems Biology
Systems Biology Lecture, Part 1
Systems Biology Lecture, Part 2
Systems Biology and Data Analysis Demo
Systems Biology Exercise
Week 8: Perspectives from the Field and Course Conclusion
Perspectives from the Field
-Regulatory issues Issues related Related to biomedical Biomedical big Big dataData. Sheila Zimmet, JD, Senior Associate Vice President for Regulatory Affairs, and Ashley Carver, JD, Deputy Conflicts Officer and Regulatory Affairs Associate, Georgetown University Medical Center.
-Enabling Everyone to Share and Use Public Datasets. Interview with Dr. Ben Busby, genomics Genomics outreach Outreach coordinator Coordinator at the National Center for Biotechnology Information (NCBI)
-Interview withCancer Moonshot. Dr. Jerry Lee, Deputy Director, Center for Strategic Scientific Initiatives, Office of the Director, National Cancer Institute, National Institutes of Health
