Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Sim2Ls: FAIR simulation workflows and data

Journal Article · · PLoS ONE

Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science and engineering workflows used in research remain poorly documented and often unavailable, involving ad hoc scripts and manual steps, hindering reproducibility and stifling progress. We introduce Sim2Ls (pronounced simtools) and the Sim2L Python library that allow developers to create and share end-to-end computational workflows with well-defined and verified inputs and outputs. The Sim2L library makes Sim2Ls , their requirements, and their services discoverable, verifies inputs and outputs, and automatically stores results in a globally-accessible simulation cache and results database. This simulation ecosystem is available in nanoHUB, an open platform that also provides publication services for Sim2Ls , a computational environment for developers and users, and the hardware to execute runs and store results at no cost. We exemplify the use of Sim2Ls using two applications and discuss best practices towards FAIR simulation workflows and associated data.

Research Organization:
Sandia National Laboratories (SNL-NM), Albuquerque, NM (United States)
Sponsoring Organization:
National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)
Grant/Contract Number:
NA0003525
OSTI ID:
1854296
Alternate ID(s):
OSTI ID: 2469906
Journal Information:
PLoS ONE, Journal Name: PLoS ONE Journal Issue: 3 Vol. 17; ISSN 1932-6203
Publisher:
Public Library of Science (PLoS)Copyright Statement
Country of Publication:
United States
Language:
English

References (22)

Data‐Driven Materials Science: Status, Challenges, and Perspectives journal September 2019
Fast Parallel Algorithms for Short-Range Molecular Dynamics journal March 1995
The potential of atomistic simulations and the knowledgebase of interatomic models journal July 2011
Materials Design and Discovery with High-Throughput Density Functional Theory: The Open Quantum Materials Database (OQMD) journal September 2013
Materials Data Infrastructure: A Case Study of the Citrination Platform to Examine Data Import, Storage, and Access journal June 2016
A high-throughput infrastructure for density functional theory calculations journal June 2011
AFLOW: An automatic framework for high-throughput materials discovery journal June 2012
Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis journal February 2013
AiiDA: automated interactive infrastructure and database for computational science journal January 2016
Machine learning for molecular and materials science journal July 2018
Research Update: The materials genome initiative: Data sharing and the impact of collaborative ab initio databases journal March 2016
The OpenKIM processing pipeline: A cloud-based automatic material property computation engine journal August 2020
Visualization and analysis of atomistic simulation data with OVITO–the Open Visualization Tool journal December 2009
Robust structural identification via polyhedral template matching journal May 2016
Uncertainties in the predictions of thermo-physical properties of thermoplastic polymers via molecular dynamics journal July 2018
Melting line of aluminum from simulations of coexisting phases journal February 1994
ULSI technology development by predictive simulations conference January 1993
Cyber-Enabled Simulations in Nanoscale Science and Engineering journal March 2010
Git journal May 2012
pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage journal January 2020
A data ecosystem to support machine learning in materials science journal October 2019
Towards FAIR principles for research software journal June 2020

Similar Records

Applying the FAIR Principles to computational workflows
Journal Article · Mon Feb 24 00:00:00 UTC 2025 · Scientific Data (Online) · OSTI ID:2530828