Agenda

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) History and Motivation for Reproducible Research video - Luis

• History of scientific societies and publications
  • Leeuwenhoek was The Man!
  • The Invisible College
  • Nullius in Verba

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) History and Motivation for Reproducible Research video - Luis

• Image gathering, storage, and sharing (10 min)
  • Figshare (www.figshare.com)
  • Hands on: Upload the images
• 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) History and Motivation for Reproducible Research video - 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) History and Motivation for Reproducible Research video - 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) History and Motivation for Reproducible Research video - Steve

• Software versioning, collaboration, and citation
  • Keeping track of changes
  • Unique hashes
  • DOI
• Hands on:
  • Create a branch
  • Make a commit
  • Push the branch
  • Create a citable version

10:00 am Break (15 min)

10:15 am Third Session

Regression Testing

Regression Testing (30 min) History and Motivation for Reproducible Research video - 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) History and Motivation for Reproducible Research video - 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) History and Motivation for Reproducible Research video - 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