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MOSAIC: A Data Model and File Formats for Molecular Simulations

https://doi.org/10.1021/ci400599y
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/(sici)1096-987x(20000130)21:2<79::aid-jcc1>3.0.co;2-bopenalex-snapshot
The molecular modeling toolkit: A new approach to molecular simulations
inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot
Scalable molecular dynamics with NAMD
inferredcites →https://doi.org/10.1002/jcc.20290openalex-snapshot
The Amber biomolecular simulation programs
inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
inferredcites →https://doi.org/10.1002/prot.20449openalex-snapshot
The CCPN data model for NMR spectroscopy: Development of a software pipeline
inferredcites →https://doi.org/10.1007/s00894-010-0948-5openalex-snapshot
Trajectory NG: portable, compressed, general molecular dynamics trajectories
inferredcites →https://doi.org/10.1016/j.cpc.2014.01.018openalex-snapshot
H5MD: A structured, efficient, and portable file format for molecular data
inferredcites →https://doi.org/10.1021/ci400197wopenalex-snapshot
Modeling, Informatics, and the Quest for Reproducibility
inferredcites →https://doi.org/10.1038/467775aopenalex-snapshot
Computational science: ...Error
inferredcites →https://doi.org/10.1038/nsb1203-980openalex-snapshot
Announcing the worldwide Protein Data Bank
inferredcites →https://doi.org/10.1063/1.4821598openalex-snapshot
A comparison of reduced coordinate sets for describing protein structure
inferredcites →https://doi.org/10.1063/1.4823996openalex-snapshot
Model-free simulation approach to molecular diffusion tensors
inferredcites →https://doi.org/10.1093/bioinformatics/btt055openalex-snapshot
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
inferredcites →https://doi.org/10.1109/mcse.2012.108openalex-snapshot
Caring for Your Data
inferredcites →https://doi.org/10.1126/science.1213847openalex-snapshot
Reproducible Research in Computational Science
inferredcites →https://doi.org/10.1126/science.1231535openalex-snapshot
Troubling Trends in Scientific Software Use
inferredcites →https://doi.org/10.1186/1758-2946-3-44openalex-snapshot
CML: Evolution and design
inferredcites →https://doi.org/10.1371/journal.pone.0072467openalex-snapshot
Two Failures to Replicate High-Performance-Goal Priming Effects
inferredcites →https://doi.org/10.59350/mzxbj-vzd18openalex-snapshot
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← backgroundhttps://doi.org/10.5281/zenodo.10735zenodo-depositor-declared
pyMosaic 0.3.0
inferred← backgroundhttps://doi.org/10.5281/zenodo.11648zenodo-depositor-declared
pyMosaic 0.3.1
inferred← backgroundhttps://doi.org/10.5281/zenodo.56545zenodo-depositor-declared
pyMosaic 0.4.0
inferred← backgroundhttps://doi.org/10.5281/zenodo.7648zenodo-depositor-declared
pyMosaic 0.2.0
inferred← citeshttps://doi.org/10.1002/jcc.24405openalex-snapshot
Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier
inferred← citeshttps://doi.org/10.1016/j.cpc.2014.01.018openalex-snapshot
H5MD: A structured, efficient, and portable file format for molecular data
inferred← citeshttps://doi.org/10.1021/ci500359eopenalex-snapshot
HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.001.0001openalex-snapshot
Computer Simulation of Liquids
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0003openalex-snapshot
Copyright Page
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0004openalex-snapshot
Dedication
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0005openalex-snapshot
Preface
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0006openalex-snapshot
From the Preface to the First Edition
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0009openalex-snapshot
List of Acronyms
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0010openalex-snapshot
List of Greek Symbols
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0011openalex-snapshot
List of Roman Symbols
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0012openalex-snapshot
List of Examples
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.002.0013openalex-snapshot
List of Codes
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0001openalex-snapshot
Introduction
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0002openalex-snapshot
Statistical mechanics
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0003openalex-snapshot
Molecular dynamics
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0004openalex-snapshot
Monte Carlo methods
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0005openalex-snapshot
Some tricks of the trade
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0006openalex-snapshot
Long-range forces
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0007openalex-snapshot
Parallel simulation
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0008openalex-snapshot
How to analyse the results
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0009openalex-snapshot
Advanced Monte Carlo methods
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0010openalex-snapshot
Rare event simulation
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0011openalex-snapshot
Nonequilibrium molecular dynamics
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0012openalex-snapshot
Mesoscale methods
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0013openalex-snapshot
Quantum simulations
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.003.0014openalex-snapshot
Inhomogeneous fluids
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0001openalex-snapshot
Computers and computer simulation
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0002openalex-snapshot
Reduced units
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0003openalex-snapshot
Calculation of forces and torques
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0004openalex-snapshot
Fourier transforms and series
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0005openalex-snapshot
Random numbers
inferred← citeshttps://doi.org/10.1093/oso/9780198803195.005.0006openalex-snapshot
Configurational temperature
inferred← citeshttps://doi.org/10.1107/s1399004715007191openalex-snapshot
Protein secondary-structure description with a coarse-grained model
inferred← citeshttps://doi.org/10.12688/f1000research.5773.1openalex-snapshot
Platforms for publishing and archiving computer-aided research
inferred← citeshttps://doi.org/10.12688/f1000research.5773.2openalex-snapshot
ActivePapers: a platform for publishing and archiving computer-aided research
inferred← citeshttps://doi.org/10.12688/f1000research.5773.3openalex-snapshot
ActivePapers: a platform for publishing and archiving computer-aided research
inferred← citeshttps://doi.org/10.26053/0h-kgzc-vb00openalex-snapshot
Biomolecular Simulation Data Management in Heterogeneous Environments
inferred← citeshttps://doi.org/10.48550/arxiv.1605.02960openalex-snapshot
Scientific notations for the digital era
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