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Agenda

[TOC]

8:00 am First Session

Getting Started

  • Get acquainted and verify preparations (5 min) - Matt
    • Say Hi! to the instructors
    • Introduce yourself to the person sitting next to you, they will be your partner
    • Recall successfully completing the preparation tasks
    • Interact with other participants throughout the tutorial on the MoPad

Introduction

History and Motivation for Reproducible Research (10 min) - Luis

Data Acquisition

Image Acquisition (25 min) - Matt

  • Replication of the early microscope experiments by Antonie Leeuwenhoek
    • Cell camera phone microscope
    • With drop of interesting water
    • Hands on: each pair acquires images

Data Sharing

Data Sharing - (20 min) - Luis

  • Image gathering, storage, and sharing (10 min)
  • Download data via RESTful API (10 min)
    • REST download via Python standard library
    • Checksum verification
    • Hands on: Download the data via HTTP

9:00 am Second Session

Reproducible Computational Environment

Computational Environment (20 min) - Aashish

  • Reproducible computational environment
    • Docker
    • Package versioning
    • Virtual Machines
    • Cloud services
  • Hands on:
    • Create a Docker image and container
    • Run our tutorial package verification script
    • Upload your Docker image to DockerHub

Developing Reproducible Scripts and Modules

IPython Notebook, Scripts, and SimpleITK (20 min) - Matt

  • Reproducible code development
    • IPython Notebook to combine notes, code, and results
    • Avoid duplication with re-usable modules
  • Hands on:
    • Run analysis on new data
    • Generate histogram for the data

Revision Control

Revision Control with Git and GitHub (20 min) - Steve

  • Software versioning, collaboration, and citation
    • Keeping track of changes
    • Unique hashes
    • DOI
  • Hands on:

10:00 am Break (15 min)

10:15 am Third Session

Regression Testing

Regression Testing (30 min) - Jc

  • Quality code development with regression tests
    • Testing code hypothesis: the scientific method applied to development
    • Unit testing
    • Integration testing
    • Continuous integration dashboards
  • Hands on:
    • Run the test suite
    • Add coverage for another method to the unit tests

Literate Programming

Literate Programming with Dexy (30 min) - Ana

  • Article generation
  • RST to HTML, etc
  • GitHub replication and sharing
  • Hands on: run dexy to generate a PDF document

11:15 am Fourth Session

Open Science Publication

Submitting an article to a Reproducible Journal (20 min) - Luis

  • Open Science Publication
    • Open Access
    • Publishes article, data, and code
  • Hands on:
    • Submit Article to the Insight Journal
    • Point to GitHub fork for source code

Replicate or Perish !

Attempt to replicate your peers' articles (40 min)

  • Replicate the publications of groups next to you
  • Share your observations