pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Ardita Shkurti; Ramon Goni; Pau Andrio; Elena Breitmoser; Iain Bethune; Modesto Orozco; Charles Laughton

doi:10.1016/j.softx.2016.04.002

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Ardita Shkurti, Ramon Goni, Pau Andrio, Elena Breitmoser, Iain Bethune, Modesto Orozco, Charles Laughton

School of Physics and Astronomy

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

Original language	English
Journal	SoftwareX
Early online date	19 Apr 2016
DOIs	https://doi.org/10.1016/j.softx.2016.04.002
Publication status	Published - 2016

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10.1016/j.softx.2016.04.002Licence: Creative Commons: Attribution (CC-BY)

1-s2.0-S2352711016300036-mainAccepted author manuscript, 833 KB

S12-CHE: ExSTASY Extensible Tools for Advanced Sampling and analYsis
Bethune, I.
EPSRC
1/07/13 → 30/09/16
Project: Research

Cite this

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title = "pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data",

abstract = "The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.",

author = "Ardita Shkurti and Ramon Goni and Pau Andrio and Elena Breitmoser and Iain Bethune and Modesto Orozco and Charles Laughton",

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doi = "10.1016/j.softx.2016.04.002",

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T1 - pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

AU - Shkurti, Ardita

AU - Goni, Ramon

AU - Andrio, Pau

AU - Breitmoser, Elena

AU - Bethune, Iain

AU - Orozco, Modesto

AU - Laughton, Charles

PY - 2016

Y1 - 2016

N2 - The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

AB - The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

U2 - 10.1016/j.softx.2016.04.002

DO - 10.1016/j.softx.2016.04.002

M3 - Article

SN - 2352-7110

JO - SoftwareX

JF - SoftwareX

ER -

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

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S12-CHE: ExSTASY Extensible Tools for Advanced Sampling and analYsis

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