Search Results - standalone python code~

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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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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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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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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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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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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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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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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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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GymProxy: A lightweight Python wrapper for seamless integration of standalone simulators into Gymnasium environments by Park, Sae Hyong, Shin, Seungjae, Ko, Namseok, Kim, Taeyeon, Lee, Dongman

“… Integrating agents into existing standalone simulators typically requires code modifications and careful implementation of the synchronization mechanisms that ensure the agent and simulator execute…”
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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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A Data-Driven Approach to Compare the Syntactic Difficulty of Programming Languages by Lokkila, Erno, Christopoulos, Athanasios, Laakso, Mikko-Jussi

“… difficulty of two modern, but fundamentally different, programming languages: Java and Python. To achieve this objective, we introduce…”
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SBML2HYB: a Python interface for SBML compatible hybrid modeling by Pinto, José, Costa, Rafael S, Alexandre, Leonardo, Ramos, João, Oliveira, Rui

“…Abstract Summary Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML…”
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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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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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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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PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences by Muhammod, Rafsanjani, Ahmed, Sajid, Md Farid, Dewan, Shatabda, Swakkhar, Sharma, Alok, Dehzangi, Abdollah

“… Here we present PyFeat as a practical and easy to use toolkit implemented in Python for extracting various features from proteins, DNAs and RNAs…”
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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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PiNN: A Python Library for Building Atomic Neural Networks of Molecules and Materials by Shao, Yunqi, Hellström, Matti, Mitev, Pavlin D, Knijff, Lisanne, Zhang, Chao

“… This calls for reliable, general-purpose, and open-source codes. Here, we present a python library named PiNN as a solution toward this goal…”
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