W14: THE GENE PATTERN NOTEBOOK ENVIRONMENT FOR OPEN SCIENCE AND REPRODUCIBLE BIOINFORMATICS RESEARCH
TUESDAY, APRIL 16, 2019 | 12:30 - 4:00 PM
INSTRUCTORS:
Thorin Tabor, Senior Computational Genomics Engineer, Mesirov Lab, Medicine, University of California, San Diego
Barbara Allen Hill, Senior Test Engineer, GenePattern Product Owner, Cancer Informatics Development, Broad Institute of MIT and Harvard
ABOUT THIS WORKSHOP
The ongoing explosion of genomic data and analysis tools has led to an urgent need for an environment that allows researchers to encapsulate the entirety of a research narrative – text, images, multimedia, executable code – within a single document. GenePattern Notebook is an environment that integrates the popular Jupyter Notebook system with the GenePattern platform for integrative genomics, allowing researchers to create, collaborate on, and disseminate inception-to-publication research narratives including sophisticated machine learning methods, without the need to write code. The online GenePattern Notebook workspace provides built-in access to high-performance compute resources and cloud-based data storage to support compute-intensive analyses. This hands-on workshop will teach participants how to use GenePattern Notebook to design, perform, and disseminate their bioinformatics research, workflows, and results.
WORKSHOP AGENDA
12:30 Introduction
12:45 GenePattern and Jupyter Notebook essentials
1:15 Machine learning and bioinformatic analysis and visualization in notebooks
2:00 Coffee break
2:15 Notebooks for reproducible research and open science
2:45 Best practices for authoring and disseminating notebooks for the worldwide research community
3:15 Case study: single-cell RNA Seq analysis and visualization
3:45 Discussion and Q&A
4:00 End of Workshop
WORKSHOP REQUIREMENTS
No prior experience with GenePattern or Jupyter Notebook is required.
Participants should bring a laptop with an up-to-date web browser.
INSTRUCTOR BIOGRAPHIES
Barbara Allen Hill, Senior Test Engineer, GenePattern Product Owner, Cancer Informatics Development, Broad Institute of MIT and Harvard
Barbara is the senior test engineer and product owner for GenePattern, an open-source scientific workflow system which enables researchers to develop, capture, and reproduce genomic analysis methodologies, through the use of GenePattern's hundreds of genomic analysis tools. She has worked on the GenePattern team for nearly 12 years and in that time has lead the team through the creation, validation, and release of hundreds of GenePattern modules and server updates. She most recently lead the move of the primary GenePattern public server to the Amazon Cloud. Barbara also leads the team's communication and user support efforts, presents at poster sessions and runs workshops around the world.
Thorin Tabor, Senior Computational Genomics Engineer, Mesirov Lab, Medicine, University of California, San Diego
Thorin Tabor is the lead developer of the GenePattern Notebook environment and a Senior Computational Genomics Engineer in the lab of Jill Mesirov at UC San Diego. He develops projects enabling reproducible research, promoting open science and making analytical methods accessible to researchers at all levels of computational sophistication.
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