AnVIL in the Classroom: Cloud-scale educational resources for modern genomics
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The shift of biomedical data and computational tools to the cloud is opening new opportunities for research-grade resources to be accessible by a wide range of audiences, including students, regardless of their institute’s computational infrastructure. Educators can now leverage these exciting cloud data and tools to make basic genomics concepts and applications more tangible to students.
While the growth of cloud-based resources is an exciting development for experienced researchers, using such resources to create educational materials requires dedicated effort. Educators need to know how the cloud products and platforms work together, and how to make use of these resources for their teaching objectives. The aim of this webinar is to support educators by demonstrating how they can find and use cloud-based tools and data to build exercises for their students, and helping them fit these resources into a curricular structure.
This webinar explores how educators can apply the NHGRI Analysis Visualization and Informatics Lab-space (AnVIL) to their genomics curriculum. It will showcase different cloud platforms and tools for bioinformatic analysis like Terra, Dockstore, Jupyter Notebooks, and Galaxy. Participants will learn how to find open-source example datasets in the cloud that match teaching needs and how to make those datasets accessible to students so that they can explore different genomic concepts like sequencing formats, whole-genome analysis, and gene expression analysis.
Participants will walk away with teaching examples they can use as templates for their own course. The skills participants will learn in this webinar will extend to other scientific use cases, datasets, and tools beyond the examples shown.
Overview of Presentation
- Select open-source example data and make it accessible to students through AnVIL
- Identify educational resources they can use as building blocks for a course
- Design hands-on exercises using AnVIL features to teach basic genomics
Geraldine Van der Auwera
Director of Outreach and Communications
The Broad Institute of MIT and Harvard
Dr. Geraldine Van der Auwera directs outreach and communication efforts for the Data Sciences Platform at the Broad Institute. As part of that role, she serves as an educator and advocate for researchers who use DSP software and services including GATK, the Broad's industry-leading toolkit for variant discovery analysis; the Cromwell/WDL workflow management system; and Terra.bio, a cloud-based analysis platform that integrates computational resources, methods repository and data management in a user-friendly environment. She is the co-author of Genomics in the Cloud, a book published by O'Reilly Media and available at https://oreil.ly/genomics-cloud.
Dr. Van der Auwera received her Ph.D. in Biological Engineering from the Université catholique de Louvain (UCL) in Louvain-la-Neuve, Belgium in 2007, and trained as a postdoctoral fellow in the Kolter lab at Harvard Medical School, Department of Microbiology.
Ninad Oak, PhD (Moderator)
Bioinformatics Research Scientist
Division of Cancer Predisposition, Oncology, St. Jude Children’s Research Hospital
Dr. Ninad Oak is a bioinformatics research scientist within the Division of Cancer Predisposition, Department of Oncology at St. Jude Children’s Research Hospital. During his 9+ years of research experience in the field of human genetics and bioinformatics, Ninad has focused on understanding the genetic predisposition to adult and pediatric cancers through development of novel bioinformatic approaches. Dr. Oak has a PhD in molecular and human genetics from Baylor College of Medicine which focused on identification of microRNA sequence variants from large-scale control and adult cancer datasets. Dr. Oak continues to contribute to several professional organizations, notably chairing Alumni Student and Ambassador Board at Baylor College of Medicine and as a member of a working group (OPPE) in American Society of Human Genetics. At St. Jude, Ninad feels high sense of commitment to the noble mission of St. Jude with the ultimate goal of making patients’ lives better.