Search Results - standalone python code*

ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures by Thormann, Kolja A., Tozzi, Viola, Starke, Paula, Bickeböller, Heike, Baum, Marcus, Rosenberger, Albert

“… Conclusions The source code (Python version 3.9.4), a standalone executive file, and example data for ImputAccur are freely available at https://gitlab.gwdg.de/kolja.thormann1/imputationquality.git …”
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LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer by Babalyan, K., Sultanov, R., Generozov, E., Sharova, E., Kostryukova, E., Larin, A., Kanygina, A., Govorun, V., Arapidi, G.

“…Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their…”
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COYOTE: Sequence-derived structural descriptors-based computational identification of glycoproteins by Abbasi, Wajid Arshad, Anjam, Asma, Khalil, Sadia, Andleeb, Saiqa, Bibi, Maryum, Abbas, Syed Ali

“…Glycoproteins play an important and ubiquitous role in many biological processes such as protein folding, cell-to-cell signaling, invading microorganism…”
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BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models by Tharayil, Joseph James, Blanco Alonso, Jorge, Farcito, Silvia, Lloyd, Bryn, Romani, Armando, Boci, Elvis, Cassara, Antonino, Schürmann, Felix, Neufeld, Esra, Kuster, Niels, Reimann, Michael

“…As the size and complexity of network simulations accessible to computational neuroscience grows, new avenues open for research into extracellularly recorded…”
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Sensitivity analysis of thermal contact conductance modeling to inform MiniFuel irradiation capsule designs by Meehan, Nicholas A., Gorton, Jacob P., Capps, Nathan A., Brown, Nicholas R.

“…•Sensitivity analysis to identify high-impact parameters that contribute to fuel temperature variance.•Parameters identified include the initial subcapsule gas…”
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CABS-dock standalone: a toolbox for flexible protein–peptide docking by Kurcinski, Mateusz, Pawel Ciemny, Maciej, Oleniecki, Tymoteusz, Kuriata, Aleksander, Badaczewska-Dawid, Aleksandra E, Kolinski, Andrzej, Kmiecik, Sebastian

“…Abstract Summary CABS-dock standalone is a multiplatform Python package for protein…”
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Aggrescan3D standalone package for structure-based prediction of protein aggregation properties by Kuriata, Aleksander, Iglesias, Valentin, Kurcinski, Mateusz, Ventura, Salvador, Kmiecik, Sebastian

“…Abstract Summary Aggrescan3D (A3D) standalone is a multiplatform Python package for structure-based prediction of protein aggregation properties and rational design of protein solubility…”
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NATYA-AI: A Cultural AI Framework for Multimodal Interpretation of Bharatanatyam by Veena, G., Thushara, M. G., Nambiar, Geethika K. P. K., Kumar, Nandana M.

“…Bharatanatyam is a classical Indian dance form that conveys structured narratives through a combination of symbolic hand gestures (mudras), facial expressions…”
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Prompt Alchemy: Automatic Prompt Refinement for Enhancing Code Generation by Ye, Sixiang, Sun, Zeyu, Wang, Guoqing, Guo, Liwei, Liang, Qingyuan, Li, Zheng, Liu, Yong

“…Code generation has gained increasing attention as a task to automate software development by transforming high-level descriptions into executable code…”
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Omics Pipe: a community-based framework for reproducible multi-omics data analysis by Fisch, Kathleen M., Meißner, Tobias, Gioia, Louis, Ducom, Jean-Christophe, Carland, Tristan M., Loguercio, Salvatore, Su, Andrew I.

“…Motivation: Omics Pipe ( http://sulab.scripps.edu/omicspipe ) is a computational framework that automates multi-omics data analysis pipelines on high…”
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OutPyR: Bayesian inference for RNA-Seq outlier detection by Salkovic, Edin, Abbas, Mostafa M., Belhaouari, Samir Brahim, Errafii, Khaoula, Bensmail, Halima

“…High-throughput RNA sequencing technologies (RNA-Seq) have recently started being used as a tool for helping diagnose rare genetic disorders, as they can…”
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Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits by Poretsky, Elly, Cagirici, Halise Busra, Andorf, Carson M, Sen, Taner Z

“…Abstract The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic…”
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ChatDBG: Augmenting Debugging with Large Language Models by Levin, Kyla H., van Kempen, Nicolas, Berger, Emery D., Freund, Stephen N.

“…Debugging is a critical but challenging task for programmers. This paper proposes ChatDBG, an AI-powered debugging assistant. ChatDBG integrates large language…”
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PhyloMatcher: a tool for resolving conflicts in taxonomic nomenclature by Rader, Jonathan A, Pivovarnik, Madelyn A, Vantilburg, Matias E, Whitehouse, Logan S

“…Abstract Summary Large-scale comparative studies rely on the application of both phylogenetic trees and phenotypic data, both of which come from a variety of…”
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ONIX: An open-source depletion code by de Troullioud de Lanversin, J., Kütt, M., Glaser, A.

“…•New open-source depletion software for nuclear reactor physics simulations.•Provides coupling with open-source transport code OpenMC as well as standalone capability…”
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Umbrella sampling: a powerful method to sample tails of distributions by Matthews, Charles, Weare, Jonathan, Kravtsov, Andrey, Jennings, Elise

“…Here, we present the umbrella sampling (US) technique and show that it can be used to sample extremely low probability areas of the posterior distribution that…”
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Nirjas: An open source framework for extracting metadata from the source code by Bhardwaj, Ayush, Sahil, Kaushlendra Pratap, Mishra, Gaurav

“…Metadata and comments are critical elements of any software development process. In this paper, we explain how metadata and comments in source code can play an essential role in comprehending software…”
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ChatDBG: An AI-Powered Debugging Assistant by Levin, Kyla, Nicolas van Kempen, Berger, Emery D, Freund, Stephen N

“…Debugging is a critical but challenging task for programmers. This paper proposes ChatDBG, an AI-powered debugging assistant. ChatDBG integrates large language…”
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Cloud-based applications for accessing satellite Earth observations to support malaria early warning by Wimberly, Michael C., Nekorchuk, Dawn M., Kankanala, Ramcharan R.

“… REACH can be implemented using the GEE code editor and JavaScript API, as a standalone web app, or as package…”
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PDFgetX3: a rapid and highly automatable program for processing powder diffraction data into total scattering pair distribution functions by Juhás, P., Davis, T., Farrow, C. L., Billinge, S. J. L.

“…PDFgetX3 is a new software application for converting X‐ray powder diffraction data to an atomic pair distribution function (PDF). PDFgetX3 has been designed…”
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