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Johns Hopkins University

Computing for Cancer Informatics

Johns Hopkins University via Coursera

Overview

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One of the key cancer informatics challenges is dealing with and managing the explosion of large data from multiple sources that are often too large to work with on typical personal computers. This course is designed to help researchers and investigators to understand the basics of computing and to familiarize them with various computing options to ultimately help guide their decisions on the topic. This course aims to provide research leaders with awareness and guidance about: Basic computing terminology Concepts about how computers and computing systems work Differences between shared computing resources Appropriate etiquette for shared computing resources Computing resources designed for cancer research Considerations for computing resource decisions Target audience: This course is intended for researchers (including postdocs and students) with limited to intermediate experience with informatics research. The conceptual material will also be useful for those in management roles who are collecting data and using informatics pipelines. Curriculum: We will provide you with familiarity with fundamental computing terms. We will also discuss relevant concepts about how computers and shared computing resources work. We will explore the differences between various computing resource options, as well as provide guidance on how to make important computing discussions. This course is part of a series of courses for the Informatics Technology for Cancer Research (ITCR) called the Informatics Technology for Cancer Research Education Resource. This material was created by the ITCR Training Network (ITN) which is a collaborative effort of researchers around the United States to support cancer informatics and data science training through resources, technology, and events. This initiative is funded by the following grant: National Cancer Institute (NCI) UE5 CA254170. Our courses feature tools developed by ITCR Investigators and make it easier for principal investigators, scientists, and analysts to integrate cancer informatics into their workflows. Please see our website at www.itcrtraining.org for more information.

Syllabus

  • Welcome
    • In this module we will introduce you to how the material will be presented and the goals for the course.
  • Basic Building Block of Computers
    • In this module we will start by describing some basics about how computers work. We feel that familiarity with this information will be helpful for you when you need to make computing decisions for your work.
  • Binary data to computations
    • In this module we will talk about how computers store and process data. This will be helpful for understanding computing and storage requirements for your work.
  • Computing Resources
    • In this module we will describe some basics about file sizes and computing capacity. We will specifically focus on common types of files used in cancer research. We will also introduce some general concepts for shared computing resource, which can be a great option if you wish to do work that might be too intensive for your personal computer.
  • Shared Computing Etiquette
    • In this module we will describe some common good practices for using traditional shared computing resources like clusters. These guidelines will help ensure that you don't use shared resources in a way that might bother others, so that you can continue to have access to such shared resources.
  • Research Platforms
    • In this module we will take you through a tour of some computing resource platforms designed for researchers, including some that may be especially useful to cancer researchers.
  • Data Management Decisions
    • In this final module we will provide guidance about how to decide what computing resources would be most beneficial for your work.

Taught by

Carrie Wright, PhD

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