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Psi4 1.4: Open-source software for high-throughput quantum chemistry.

ABSTRACT: PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

SUBMITTER: Smith DGA

PROVIDER: S-EPMC7228781 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Smith Daniel G A DGA Burns Lori A LA Simmonett Andrew C AC Parrish Robert M RM Schieber Matthew C MC Galvelis Raimondas R Kraus Peter P Kruse Holger H Di Remigio Roberto R Alenaizan Asem A James Andrew M AM Lehtola Susi S Misiewicz Jonathon P JP Scheurer Maximilian M Shaw Robert A RA Schriber Jeffrey B JB Xie Yi Y Glick Zachary L ZL Sirianni Dominic A DA O'Brien Joseph Senan JS Waldrop Jonathan M JM Kumar Ashutosh A Hohenstein Edward G EG Pritchard Benjamin P BP Brooks Bernard R BR Schaefer Henry F HF Sokolov Alexander Yu AY Patkowski Konrad K DePrince A Eugene AE Bozkaya Uğur U King Rollin A RA Evangelista Francesco A FA Turney Justin M JM Crawford T Daniel TD Sherrill C David CD

The Journal of chemical physics 20200501 18

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Pyth ...[more]

PMID: 32414239

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Project description:PurposeThe primary aim of this study was to develop an open-source Python-based software for the automated analysis of dynamic cell behaviors in microphysiological models using non-confocal microscopy. This research seeks to address the existing gap in accessible tools for high-throughput analysis of endothelial tube formation and cell invasion in vitro, facilitating the rapid assessment of drug sensitivity.MethodsOur approach involved annotating over 1000 2 mm Z-stacks of cancer and endothelial cell co-culture model and training machine learning models to automatically calculate cell coverage, cancer invasion depth, and microvessel dynamics. Specifically, cell coverage area was computed using focus stacking and Gaussian mixture models to generate thresholded Z-projections. Cancer invasion depth was determined using a ResNet-50 binary classification model, identifying which Z-planes contained invaded cells and measuring the total invasion depth. Lastly, microvessel dynamics were assessed through a U-Net Xception-style segmentation model for vessel prediction, the DisPerSE algorithm to extract an embedded graph, then graph analysis to quantify microvessel length and connectivity. To further validate our software, we reanalyzed an image set from a high-throughput drug screen involving a chemotherapy agent on a 3D cervical and endothelial co-culture model. Lastly, we applied this software to two naive image datasets from coculture lumen and microvascular fragment models.ResultsThe software accurately measured cell coverage, cancer invasion, and microvessel length, yielding drug sensitivity IC50 values with a 95% confidence level compared to manual calculations. This approach significantly reduced the image processing time from weeks down to h. Furthermore, the software was able to calculate cell coverage, microvessel length, and invasion depth from two additional microphysiological models that were imaged with confocal microscopy, highlighting the versatility of the software.ConclusionsOur free and open source software offers an automated solution for quantifying 3D cell behavior in microphysiological models assessed using non-confocal microscopy, providing the broader Cellular and Molecular Bioengineering community with an alternative to standard confocal microscopy paired with proprietary software.This software can be found in our GitHub repository: https://github.com/fogg-lab/tissue-model-analysis-tools.Supplementary informationThe online version contains supplementary material available at 10.1007/s12195-024-00821-2.

Dataset Information

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Publications

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

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