Demystifying Biomedical Big Data: A User’s Guide (edX)

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