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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.

  • 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)

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前提

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课程大纲

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
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教师

Bassem R. Haddad
Course Director
Georgetown University Medical Center

Sheila Cohen Zimmet
Senior Associate Vice President for Regulatory Affairs, GU Medical Center
Georgetown University

Robert Clarke
Dean for Research and Professor of Oncology
Georgetown University Medical Center

Yuriy Gusev
Course Director
Georgetown University Medical Center

Peter McGarvey
Course Director
Georgetown University Medical Center

John. L. Marshall
Chief, Hematology and Oncology, Lombardi Comprehensive Cancer Center
Georgetown University Medical Center

Krithika Bhuvaneshwar
Research Associate II (Bioinformatics) and Project Manager, Innovation Center for Biomedical Informatics (ICBI)
Georgetown University

Ben Busby
Genomics Outreach Coordinator at the National Center for Biotechnology Information (NCBI)

Ashlea Carver
Deputy Conflicts Officer and Regulatory Affairs Associate
Georgetown University Medical Center

Jerry SH Lee
Deputy Director, Center for Strategic Scientific Initiatives, Office of the Director, National Cancer Institute, National Institutes of Health, Department of Health and Human Services

Subha Madhavan
Director, Innovation Center for Biomedical Informatics (ICBI)
Georgetown University

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Edx

EdX est une plateforme d'apprentissage en ligne (dite FLOT ou MOOC). Elle héberge et met gratuitement à disposition des cours en ligne de niveau universitaire à travers le monde entier. Elle mène également des recherches sur l'apprentissage en ligne et la façon dont les utilisateurs utilisent celle-ci. Elle est à but non lucratif et la plateforme utilise un logiciel open source.

EdX a été fondée par le Massachusetts Institute of Technology et par l'université Harvard en mai 2012. En 2014, environ 50 écoles, associations et organisations internationales offrent ou projettent d'offrir des cours sur EdX. En juillet 2014, elle avait plus de 2,5 millions d'utilisateurs suivant plus de 200 cours en ligne.

Les deux universités américaines qui financent la plateforme ont investi 60 millions USD dans son développement. La plateforme France Université Numérique utilise la technologie openedX, supportée par Google.

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