Search Results - (( (statni OR state:md) python code analysis ) OR ( state python code analysis ))*

PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations by Reis, Pedro B P S, Vila-Viçosa, Diogo, Rocchia, Walter, Machuqueiro, Miguel

“…The protonation of titratable residues has a significant impact on the structure and function of biomolecules, influencing many physicochemical and ADME…”
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PSHRisk-Tool: A Python-Based Computational Tool for Developing Site Seismic Hazard Analysis and Failure Risk Assessment of Infrastructure by Nahar, Tahmina Tasnim, Rahman, Md Motiur, Kim, Dookie

“… vulnerable condition for the infrastructure. This python-code based tool can demonstrate the source identification, probability distribution plot of magnitude and distance…”
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mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data by Pérez-Hernández, Guillermo, Hildebrand, Peter W.

“…) for easy, one-shot analysis and representation of molecular dynamics (MD) simulation data. Building upon the widely used concept of residue-residue contact-frequencies…”
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WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data by Yang, Darian T, Chong, Lillian T

“… Here, we present the WEDAP Python package for simplifying the analysis of data generated from either conventional MD simulations or the weighted ensemble…”
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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations by Michaud-Agrawal, Naveen, Denning, Elizabeth J., Woolf, Thomas B., Beckstein, Oliver

“…MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD…”
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interlab: A Python Module for Analyzing Interlaboratory Comparison Data by Sheen, David A.

“…interlab was developed as a software tool to perform consensus analysis on spectral data from interlaboratory studies…”
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Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module by Pool, René, Heringa, Jaap, Hoefling, Martin, Schulz, Roland, Smith, Jeremy C., Feenstra, K. Anton

“…We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy…”
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Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier by Kim, Eiru, Hart, Traver

“… We previously described the Bayesian Analysis of Gene Essentiality (BAGEL) algorithm for accurate classification of gene essentiality from short hairpin RNA and CRISPR/Cas9 genome-wide genetic screens…”
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iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode by Wang, Jiyao, Youkharibache, Philippe, Marchler-Bauer, Aron, Lanczycki, Christopher, Zhang, Dachuan, Lu, Shennan, Madej, Thomas, Marchler, Gabriele H., Cheng, Tiejun, Chong, Li Chuin, Zhao, Sarah, Yang, Kevin, Lin, Jack, Cheng, Zhiyu, Dunn, Rachel, Malkaram, Sridhar Acharya, Tai, Chin-Hsien, Enoma, David, Busby, Ben, Johnson, Nicholas L., Tabaro, Francesco, Song, Guangfeng, Ge, Yuchen

“… scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node. js scripts…”
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BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Mukhaleva, Elizaveta, Manookian, Babgen, Chen, Hanyu, Sivaraj, Indira R, Ma, Ning, Wei, Wenyuan, Urbaniak, Konstancja, Gogoshin, Grigoriy, Bhattacharya, Supriyo, Vaidehi, Nagarajan, Rodin, Andrei S, Branciamore, Sergio

“… However, the analysis of MD simulation trajectories has not been data-driven but rather dependent on the user's prior knowledge of the systems, thus limiting the scope and utility of the MD simulations…”
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ChatGPT for Univariate Statistics: Validation of AI‐Assisted Data Analysis in Healthcare Research by Ruta, Michael R, Gaidici, Tony, Irwin, Chase, Lifshitz, Jonathan

“… With the recent integration of Python code interpretation into the ChatGPT environment, there has been a significant increase in the potential utility of ChatGPT as a research tool, particularly…”
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UQpy: A general purpose Python package and development environment for uncertainty quantification by Olivier, Audrey, Giovanis, Dimitris G., Aakash, B. S., Chauhan, Mohit, Vandanapu, Lohit, Shields, Michael D.

“…In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ…”
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Development of High Performance Computing Tools for Estimation of High-Resolution Surface Energy Balance Products Using sUAS Information by Nassar, Ayman, Torres, Alfonso, Merwade, Venkatesh, Dey, Sayan, Zhao, Lan, Kim, I Luk, Kustas, William P, Nieto, Hector, Hipps, Lawrence, Gao, Rui, Alfieri, Joseph, Prueger, John, Alsina, Maria Mar, McKee, Lynn, Coopmans, Calvin, Sanchez, Luis, Dokoozlian, Nick, Bambach Ortiz, Nicolas, Mcelrone, Andrew J

“…(small-Unmanned Aircraft System) and advanced surface energy balance models allow detailed assessment and monitoring (at plant scale) of different…”
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An Implementation of the Fundamental Parameters Approach for Analysis of X-ray Powder Diffraction Line Profiles by Mendenhall, Marcus H., Mullen, Katharine, Cline, James P.

“…) models for analysis of X-ray powder diffraction line profiles. The original literature describing these models was examined and code was developed to allow for their use within a Python based least squares refinement algorithm…”
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GenEvaPa: A generic evaporation package for modeling evaporation in molecular dynamics simulations by Harris, Bradley, Liu, Gang-yu, Faller, Roland

“…This work presents a novel general tool for modeling the process of evaporation without the need for modifying existing software using Python…”
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Analysis methods and code for very high-precision mass measurements of unstable isotopes by Karthein, J., Atanasov, D., Blaum, K., Lunney, D., Manea, V., Mougeot, M.

“…We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase…”
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Preliminary Experience and Learning Outcomes by Infusing Interactive and Active Learning to Teach an Introductory Programming Course in Python by Rahman, Md Mahmudur, Paudel, Roshan

“…A core challenge in introductory programming courses during the freshmen year is getting students to understand how a static textual representation (source code…”
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Handwritten Code Recognition for Pen-and-Paper CS Education by Md Sazzad Islam, Moussa Koulako Bala Doumbouya, Manning, Christopher D, Piech, Chris

“… Optical character recognition (OCR) of handwritten code is challenging…”
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PFΔScreen — an open-source tool for automated PFAS feature prioritization in non-target HRMS data by Zweigle, Jonathan, Bugsel, Boris, Fabregat-Palau, Joel, Zwiener, Christian

“…Per- and polyfluoroalkyl substances (PFAS) are a huge group of anthropogenic chemicals with unique properties that are used in countless products and…”
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Fitting Splines to Axonal Arbors Quantifies Relationship Between Branch Order and Geometry by Athey, Thomas L., Teneggi, Jacopo, Vogelstein, Joshua T., Tward, Daniel J., Mueller, Ulrich, Miller, Michael I.

“… It is also implicated in neurological disease. However, standard morphological analysis focuses on macroscopic features such as branching frequency and connectivity between regions, and often neglects the internal geometry of neurons…”
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