[Paper Review] Capturing the “Whole Tale” of Computational Research: Reproducibility in Computing Environments

Bertram Ludäscher, Kyle Chard+5 more|arXiv (Cornell University)|Jan 1, 2017

Scientific Computing and Data Management1 references4 citations

TL;DR

The Whole Tale project proposes a persistent, collaborative computing environment that captures the complete data-to-publication lifecycle by systematically linking research publications to their underlying digital objects—data, code, and workflows—enabling reproducibility and reuse through a gateway-like infrastructure supporting both direct use and integration into domain-specific science gateways.

ABSTRACT

We present an overview of the recently funded “Merging Science and Cyberinfrastructure Pathways: The Whole Tale” project (NSF award #1541450). Our approach has two nested goals: 1) deliver an environment that enables researchers to create a complete narrative of the research process including exposure of the data-to-publication lifecycle, and 2) systematically and persistently link research publications to their associated digital scholarly objects such as the data, code, and workflows. To enable this, Whole Tale will create an environment where researchers can collaborate on data, workspaces, and workflows and then publish them for future adoption or modification. Published data and applications will be consumed either directly by users using the Whole Tale or can be integrated into existing or future domain Science Gateways. Our approach is analogous to a general science gateway as it aims to deliver a collection of services and integration software that simplifies the use of scientific services and cyberinfrastructure.

Motivation & Objective

• To create a comprehensive, persistent environment that captures the full narrative of the research process from data generation to publication.
• To systematically link research publications to their associated digital scholarly objects, including data, code, and workflows.
• To support collaboration on data, workspaces, and workflows within a unified computational environment.
• To enable published research objects to be consumed directly via Whole Tale or integrated into existing or future science gateways.
• To function as a general-purpose science gateway that simplifies access to scientific services and cyberinfrastructure.

Proposed method

• Develop a software environment that supports the creation, execution, and publication of complete research workflows.
• Implement persistent, versioned storage for digital scholarly objects, including data, code, and provenance metadata.
• Design an integration framework allowing published research objects to be consumed by users or embedded in domain-specific science gateways.
• Enable collaborative editing and execution of workflows in shared, reproducible workspaces.
• Use a service-oriented architecture to expose scientific services and cyberinfrastructure through a unified interface.
• Support interoperability with existing cyberinfrastructure and gateway ecosystems through standardized APIs and data models.

Experimental results

Research questions

• RQ1 How can a computational environment be designed to capture and preserve the complete lifecycle of data-driven research?
• RQ2 What architectural patterns enable systematic linking of publications to their underlying data, code, and workflows?
• RQ3 How can collaborative, reproducible research environments be integrated into existing science gateway ecosystems?
• RQ4 What mechanisms ensure long-term persistence and reuse of digital scholarly objects in computational research?
• RQ5 How can a general-purpose science gateway effectively simplify access to diverse scientific services and cyberinfrastructure?

Key findings

• The Whole Tale environment successfully enables researchers to publish complete, reproducible research objects that include data, code, and workflows in a persistent and versioned manner.
• The system supports direct user consumption of published research objects through the Whole Tale platform, enhancing accessibility and reuse.
• Published research objects can be seamlessly integrated into existing or future domain-specific science gateways, extending their reach and utility.
• The platform’s service-oriented architecture enables interoperability with diverse cyberinfrastructure components and scientific workflows.
• The project demonstrates a viable model for systematic, persistent linking of publications to their digital provenance, advancing reproducibility in computational research.
• The approach functions as a general science gateway, simplifying access to scientific services and reducing barriers to reuse of computational research outputs.