[Paper Review] Crystal Toolkit: A Web App Framework to Improve Usability and Accessibility of Materials Science Research Algorithms

Matthew Horton, Jimmy‐Xuan Shen+22 more|arXiv (Cornell University)|Feb 13, 2023

Scientific Computing and Data Management8 citations

TL;DR

Crystal Toolkit is an open-source web app framework for visualizing and transforming crystal structures and related materials data, accelerating web app development and making materials algorithms accessible to non-programmers; it powers the Materials Project frontend.

ABSTRACT

Crystal Toolkit is an open source tool for viewing, analyzing and transforming crystal structures, molecules and other common forms of materials science data in an interactive way. It is intended to help beginners rapidly develop web-based apps to explore their own data or to help developers make their research algorithms accessible to a broader audience of scientists who might not have any training in computer programming and who would benefit from graphical interfaces. Crystal Toolkit comes with a library of ready-made components that can be assembled to make complex web apps: simulation of powder and single crystalline diffraction patterns, convex hull phase diagrams, Pourbaix diagrams, electronic band structures, analysis of local chemical environments and symmetry, and more. Crystal Toolkit is now powering the Materials Project website frontend, providing user-friendly access to its database of computed materials properties. In the future, it is hoped that new visualizations might be prototyped using Crystal Toolkit to help explore new forms of data being generated by the materials science community, and that this in turn can help new materials scientists develop intuition for how their data behaves and the insights that might be found within. Crystal Toolkit will remain a work-in-progress and is open to contributions from the community.

Motivation & Objective

• Promote a human-centered approach to scientific visualization and tool design.
• Provide faithfully represented, composable visualizations tied to common software objects in materials science.
• Lower the barrier to entry so researchers with limited programming skills can build web apps using Python.
• Enable rapid prototyping of data exploration tools and foster community contributions.

Proposed method

• Offer a library of ready-to-use components mapped to pymatgen data types ( Structures, Molecules, Band Structures, Pourbaix Diagrams, etc.).
• Build on Dash (Python) and React to allow interactive web apps with single-file Python development and hot-module reloading.
• Ensure visualizations faithfully reflect underlying software objects and scientific abstractions, with composability across objects.
• Adopt an open-source BSD license with GitHub-driven development to encourage broad community participation and sustainability.
• Integrate with Materials Project to demonstrate scalability and real-world usage, including apps like Catalysis Explorer and MOF Explorer.

Figure 1: A timeline of molecular and crystallographic visualizations with several key advances highlighted. Throughout the history of chemistry and materials science, effective visualization has proven an invaluable tool to help develop intuition and unlock key new insights that have advanced the f

Experimental results

Research questions

• RQ1 How can Crystal Toolkit improve usability and accessibility of complex materials science data visualization for researchers with varying programming experience?
• RQ2 Can a library of composable, faithful visualizations mapped to common data objects reduce errors and improve intuition across publications, notebooks, and web apps?
• RQ3 To what extent can the framework scale to large datasets and high-traffic web apps while remaining extensible to new data types?
• RQ4 How effectively can Crystal Toolkit empower community contributions and lead to faster development of new visualization tools in materials science?
• RQ5 What is the impact of integrating with existing libraries (e.g., pymatgen) on the fidelity and usefulness of visualizations?

Key findings

• Crystal Toolkit provides ready-to-use components that map to common materials science data types and can be linked to deliver coherent visualizations.
• The framework is used to power the Materials Project frontend, enabling user-friendly access to a large database of computed materials properties.
• It supports diverse visualizations (e.g., crystal structures, band structures, Pourbaix diagrams, X-ray spectra, phase diagrams, symmetry, diffraction patterns) and interactive capabilities.
• The project demonstrates open-source development with community contributions and ongoing evolution of components.
• Crystal Toolkit enabled rapid development of new apps within Materials Project, such as Catalysis Explorer and MOF Explorer, leveraging MPContribs data.
• Images for all 146,000 crystal structures in Materials Project were generated using Crystal Toolkit as a demonstration.

Figure 2: A design goal of Crystal Toolkit is to provide human-centered representations of software objects, and specifically to ensure that the default representations are as faithful to the underlying software object as possible so as to help the user gain intuition about the use of these objects.