CCMI - Presentation

UCSD – Integrative Genomic Analysis with GenePattern

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Instructor: Michael Reich, Asst. Director of Bioinformatics, UC San Diego
Organized by the Cancer Cell Map Initiative (CCMI)

GenePattern, www.genepattern.org, enables researchers at all levels of computational expertise to use hundreds of tools for the analysis of gene expression, sequence variation, proteomics, and more, through an intuitive interface that requires no coding. 

GenePattern makes reproducible research easy: analyses can be rerun at any time with the same inputs; every version of each tool is tracked, so that a result can be reproduced even if the code that produced it changes in the future; and researchers can chain analyses together to encapsulate and share their research as reproducible workflows. 

A new GenePattern Notebook environment, www.genepattern-notebook.org, based on the popular Jupyter Notebook system, further allows users to interleave text, graphics, and analyses in unified "research narratives" that can be shared and published. 

Agenda 

  • 1:00 PM Introduction
  • 1:45 PM GenePattern and Jupyter Notebook essentials 
  • 2:15 PM Machine learning and bioinformatic analysis and visualization in notebooks 
  • 3:00 PM Coffee break 
  • 3:15 PM Notebooks for reproducible research and open science 
  • 3:45 PM Best practices for authoring and disseminating notebooks for the worldwide research community 
  • 4:15 PM Case study: single-cell RNA Seq analysis and visualization 
  • 4:45 PM Discussion and Q&A 

Coffee and light refreshments provided


No Show Policy
While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation. 

Directions 
A map of the Skaggs Pharmaceutical Sciences Building (PSB) can be viewed HERE. The closest parking lots include the Osler Parking Structure, P602, P603 and the Gilman Parking structure. Hourly rates are posted at meters; cards are accepted. Additionally, Valet Parking is available in lot P610 on Osler Lane. If using the UC San Diego Shuttle, exit at Gilman Drive and Meyers Lane, then walk south towards School of Medicine.  

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