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Introduction

Questions:

  • What is Whole Tale?
  • What is a tale?
  • What is a recorded run?
  • What are Docker and repo2docker and why are they used in Whole Tale?

Objectives:

  • Learn about the Whole Tale project and platform
  • Learn what a "tale" is and how it relates to similar research objects
  • Learn what Docker and repo2docker are and how they relate to Whole Tale
  • Learn about the key features of Whole Tale

What is Whole Tale?

Whole Tale is an open-source platform for creating and publishing transparent and reproducible computational research artifacts.

Researchers create tales that can be published to research data repositories.

What is a "tale"?

A tale is a standards-based research object that combines:

  • Data
  • Code
  • Workflow
  • Documentation
  • Results
  • Information about the computational environment

Tales are intended to be transparent, executable, and verifiable.

Tales are published to external research repositories to obtain a digital object identifier (DOI).

What is a digital object identifier or DOI?

A persistent link and globally unique identifier commonly used by research repositories to provide access to published materials (e.g., papers, data, code, etc). They require a commitment from an institution or provider to maintain access to the URL. DOIs are commonly issued by publishers and research repositories.

Whole Tale enables researchers to publish (or deposit) tales to DOI-issuing research repositories.

What is a research (data) repository?

Institutional and data repositories provide a way to preserve and provide access to research materials and artifacts. It is common today for peer-reviewed journals to require authors to deposit data and other computational artifacts in a suitable repository.

Whole Tale integrates with repository platforms including Zenodo, Dataverse, DataONE, and Globus.

Reproducible computational research

Communities use different terms to describe conventions and practices for sharing reproducible computational research artifacts. Below are two historical definitions.

The concept of a replication data set (King, 1995) is widely adopted in the social sciences:

Replication data sets include all information necessary to replicate empirical results. For quantitative researchers, these might include original data, specialized computer programs, sets of computer program recodes, extracts of existing publically available data (or very clear directions for how to obtain exactly the same ones you used), and an explanatory note (usually in the form of a "read-me" file) that describes what is included and explains how to reproduce the numerical results in the article.

The concept of a research compendium (Gentleman and Lang, 2004) originated in the statistics community and has been adopted by others:

"...as both a container for the different elements that make up the document and its computations (i.e. text, code, data, ...), and as a means for distributing, managing and updating the collection" for reproducible research.

Reproducible computational research artifacts are increasingly being deposited or published in research repositories.

Activity 1: Exploring a "research compendium"

Research compendium package for d'Alpoim Guedes and Bocinsky 2018

Consider the following:

What is Docker?

Docker is a popular virtualization ("container") platform that has been widely adopted for the packaging, distribution, and deployment of software -- including scientific software.

From https://www.docker.com/resources/what-container:

A container is a standard unit of software that packages up code and all its dependencies so the application runs quickly and reliably from one computing environment to another. A Docker container image is a lightweight, standalone, executable package of software that includes everything needed to run an application: code, runtime, system tools, system libraries and settings... Containers isolate software from its environment and ensure that it works uniformly despite differences for instance between development and staging.

A Dockerfile is a simple text file that contains instructions used to build a Docker image.

A Docker registry is a library of pre-built images. Users can push or pull images from the registry. For example, https://hub.docker.com.

Activity 2: Exploring Dockerfiles

Because Whole Tale relies on Docker, we will consider a very brief example.

The following Dockerfile can be used to build an image:

FROM ubuntu:20.04
RUN apt-get update -y && \
    apt-get install -y python-minimal=3.8.2-0ubuntu2

Questions:

  • What does this Dockerfile do?
  • What is ubuntu and what does 20.04 mean?
  • Why do you think Whole Tale uses Docker images?

Note:

  • The FROM instruction specifies the base image, in this case ubuntu:20.04
  • This is a Long Term Support (LTS) version of the Ubuntu (Linux) operating system
  • The RUN instruction uses the apt package manager to install a specific version of Python
  • An image built from these instructions can be run on a variety of operating systems.
  • Using Docker, research results can be packaged and archived along with the exact versions of software used in their creation

What is repo2docker ?

repo2docker is part of the Binder platform developed by the Jupyter community. As suggested by the name, repo2docker provides a way to convert a repository (e.g., Github) into a Docker image. If your repository (or local directory) contains some well-defined and commonly used configuration files, repo2docker can be used to build and run a Docker container with the specified software packages installed.

Takeaway: Users do not need to know how to write Dockerfiles.

Activity 3: Exploring repo2docker

Look at the list of supported configuration files

Question:

  • Do you recognize or use any of the configuration files?
  • What is the base operating system used on repo2docker generated images?
  • What configuration file would you use to create the previous example?

Note:

  • repo2docker images are based on Ubuntu LTS. Windows is not currently supported by Whole Tale.
  • The apt.txt file can be used to specify OS-level packages.

Activity 4: Exploring a replication package

Replication Data for: Parliamentary Constraints and Long-term Development: Evidence from the Duchy of Württemberg

Consider the following:

  • This "replication package" has been published in conformance with journal policy (see also AJPS Verification Policy)
  • It contains code, data, and instructions required to reproduce results
  • It has been independently verified
  • It uses STATA, a commercial software package

Note:

  • Whole Tale extends repo2docker to add support for commercial packages including STATA and MATLAB

Activity 5: Exploring a tale

Here is an example tale based on the above replication package: https://sandbox.zenodo.org/record/1059962

Consider the following:

  • It contains the same code, data, and instructions as Activity 4
  • It has a "recorded run" with associated outputs (figures)
  • It can be imported and re-executed in Whole Tale

What is a "recorded run"?

How do you know that the provided code, data, workflow, and environment were used to obtain a particular result?

A "recorded run" executes a tale workflow in an isolated container, capturing:

  • An immutable version of the tale including all output files as well as standard out/error.
  • Usage information (memory, CPU, I/O)

Key points

  • Whole Tale is an open-source platform for transparent and reproducible computational research
  • Tales are a way to package and publish your research artifacts
  • Whole Tale uses Docker to build and distribute container images
  • Whole Tale uses repo2docker to simplify the process of creating Docker images
  • Whole Tale includes support for commercial software including STATA and MATLAB
  • Recorded runs can be used to demonstrate that specific code/data/workflow were used to obtain results

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