Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must be able to access computing resources. One way to provide such resources is through High-Performance Computing (HPC) centers. Many academic research institutions offer their own HPC Centers but struggle to make the computing resources easily accessible and user-friendly. Here we present SHABU, a RESTful Web API framework that enables S & E communities to access resources from Boston University's Shared Computing Center (SCC). The SHABU requirements are derived from the use cases described in this work.
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http://dx.doi.org/10.4236/jsea.2022.156011 | DOI Listing |
J Chem Phys
January 2025
Department of Chemistry and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.
Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph neural networks (GNNs) are used as universal geometric featurizers. By pretraining equivariant GNNs on a large dataset of molecular conformations with a self-supervised denoising objective, we obtain transferable structural representations that are useful for learning conformational dynamics without further fine-tuning.
View Article and Find Full Text PDFGlob Chang Biol
January 2025
Department of Civil, Environmental, and Geo-Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
Stomata control plant water loss and photosynthetic carbon gain. Developing more generalized and accurate stomatal models is essential for earth system models and predicting responses under novel environmental conditions associated with global change. Plant optimality theories offer one promising approach, but most such theories assume that stomatal conductance maximizes photosynthetic net carbon assimilation subject to some cost or constraint of water.
View Article and Find Full Text PDFJ Dent Sci
January 2025
Department of Dentistry, School of Dentistry, College of Medicine, National Taiwan University, Taipei, Taiwan.
Background/purpose: Studies have demonstrated a relation between hypercholesterolemia and development of apical periodontitis (AP), but the underlying mechanism is uncertain. 27-hydroxycholesterol (27HC), produced by cytochrome P450 27A1 (CYP27A1)-catalyzed hydroxylation of cholesterol, is known to possess pro-inflammatory activity. Felodipine is an anti-hypertensive agent able to inhibit CYP27A1.
View Article and Find Full Text PDFJ Transl Med
January 2025
Department of General Surgery & Laboratory of Gastric Cancer, State Key Laboratory of Biotherapy / Collaborative Innovation Center of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
Background: Artificial intelligence has made significant contributions to oncology through the availability of high-dimensional datasets and advances in computing and deep learning. Cancer precision medicine aims to optimize therapeutic outcomes and reduce side effects for individual cancer patients. However, a comprehensive review describing the impact of artificial intelligence on cancer precision medicine is lacking.
View Article and Find Full Text PDFBMC Genomics
January 2025
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, 30332, Georgia, USA.
The interaction relationship between miRNAs and genes is important as miRNAs play a crucial role in regulating gene expression. In the literature, several databases have been constructed to curate known miRNA target genes, which are valuable resources but likely only represent a small fraction of all miRNA-gene interactions. In this study, we constructed machine learning models to predict miRNA target genes that have not been previously reported.
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