Search Results - dynamic code analysis of python process~

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics by Haiman, Zachary B., Zielinski, Daniel C., Koike, Yuko, Yurkovich, James T., Palsson, Bernhard O.

“… MASSpy adds dynamic modeling tools to the COnstraint-Based Reconstruction and Analysis Python (COBRApy…”
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pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods by Behdenna, Abdelkader, Colange, Maximilien, Haziza, Julien, Gema, Aryo, Appé, Guillaume, Azencott, Chloé-Agathe, Nordor, Akpéli

“…Background Variability in datasets is not only the product of biological processes…”
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Efficient Space–Time Reduced Order Model for Linear Dynamical Systems in Python Using Less than 120 Lines of Code by Kim, Youngkyu, Wang, Karen, Choi, Youngsoo

“…A classical reduced order model (ROM) for dynamical problems typically involves only the spatial reduction of a given problem…”
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Deeptime: a Python library for machine learning dynamical models from time series data by Hoffmann, Moritz, Scherer, Martin, Hempel, Tim, Mardt, Andreas, de Silva, Brian, Husic, Brooke E, Klus, Stefan, Wu, Hao, Kutz, Nathan, Brunton, Steven L, Noé, Frank

“… Deeptime is a general purpose Python library offering various tools to estimate dynamical models based on time-series data including conventional linear learning methods, such as Markov state models (MSMs…”
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PyGEE-SWToolbox: A Python Jupyter Notebook Toolbox for Interactive Surface Water Mapping and Analysis Using Google Earth Engine by Owusu, Collins, Snigdha, Nusrat J., Martin, Mackenzie T., Kalyanapu, Alfred J.

“… challenges. PyGEE-SWToolbox is a freely available Google Earth Engine-enabled open-source toolbox developed with Python to be run in Jupyter Notebooks that provides an easy-to-use graphical user interface (GUI…”
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3DDA: A Novel Python Toolkit to Analyze 3D‐Dynamic Contact Angles from Molecular Dynamics Simulations by Maslov, Andrea, Tiwari, Manish K., Seveno, David

“… Herein, 3DDA, a Python‐based code that uses the 3D droplet geometry to determine contact angles and analyze dynamic changes during spreading processes at the nanoscale, is presented…”
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CRYSTALpytools: A Python infrastructure for the Crystal code by Camino, Bruno, Zhou, Huanyu, Ascrizzi, Eleonora, Boccuni, Alberto, Bodo, Filippo, Cossard, Alessandro, Mitoli, Davide, Ferrari, Anna Maria, Erba, Alessandro, Harrison, Nicholas M.

“…CRYSTALpytools is an open source Python project available on GitHub that implements a user-friendly interface to the Crystal code for quantum-mechanical condensed matter simulations…”
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Tensorpac: An open-source Python toolbox for tensor-based phase-amplitude coupling measurement in electrophysiological brain signals by Combrisson, Etienne, Nest, Timothy, Brovelli, Andrea, Ince, Robin A. A., Soto, Juan L. P., Guillot, Aymeric, Jerbi, Karim

“… In particular, there is accumulating evidence that phase-amplitude coupling (PAC), a specific form of cross-frequency interaction, plays a key role in numerous cognitive processes…”
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PyCDFT: A Python package for constrained density functional theory by Ma, He, Wang, Wennie, Kim, Siyoung, Cheng, Man‐Hin, Govoni, Marco, Galli, Giulia

“…‐principles molecular dynamics code, Qbox, and we benchmark its accuracy by computing the electronic coupling between diabatic states for a set of organic molecules…”
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A Python-based stochastic library for assessing geothermal power potential using the volumetric method in a liquid-dominated reservoir by Pocasangre, Carlos, Fujimitsu, Yasuhiro

“…•A Python-based stochastic library is presented for assessing geothermal potential…”
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Discovering Stochastic Dynamical Equations from Ecological Time Series Data by Nabeel, Arshed, Karichannavar, Ashwin, Palathingal, Shuaib, Jhawar, Jitesh, Brückner, David B, Raj M, Danny, Guttal, Vishwesha

“…AbstractTheoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways…”
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Glycosylator: a Python framework for the rapid modeling of glycans by Lemmin, Thomas, Soto, Cinque

“… The covalent linkage of a carbohydrate to the nitrogen atom of an asparagine, a process referred to as N- linked glycosylation, plays an important role in the physiology of many living organisms…”
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PyCHAM (v2.1.1): a Python box model for simulating aerosol chambers by O'Meara, Simon Patrick, Xu, Shuxuan, Topping, David, Alfarra, M. Rami, Capes, Gerard, Lowe, Douglas, Shao, Yunqi, McFiggans, Gordon

“…In this paper the CHemistry with Aerosol Microphysics in Python (PyCHAM) box model software for aerosol chambers is described and assessed against benchmark simulations for accuracy…”
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Verification of a Python-based TRANsport Simulation Environment for density-driven fluid flow and coupled transport of heat and chemical species by Kempka, Thomas

“…Numerical simulation has become an inevitable tool for improving the understanding on coupled processes in the geological subsurface and its utilisation…”
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SuperflexPy 1.3.0: an open-source Python framework for building, testing, and improving conceptual hydrological models by Dal Molin, Marco, Kavetski, Dmitri, Fenicia, Fabrizio

“…Catchment-scale hydrological models are widely used to represent and improve our understanding of hydrological processes and to support operational water resource management…”
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Constructing and analysing dynamic models with modelbase v1.2.3: a software update by van Aalst, Marvin, Ebenhöh, Oliver, Matuszyńska, Anna

“…Background Computational mathematical models of biological and biomedical systems have been successfully applied to advance our understanding of various regulatory processes, metabolic fluxes, effects…”
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AmPyfier: Test amplification in Python by Schoofs, Ebert, Abdi, Mehrdad, Demeyer, Serge

“… These test amplification tools heavily rely on analysis techniques that benefit a lot from type declarations present in the source code of projects written in statically typed languages…”
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Automating HotSpot health physics code for enhanced radiological risk assessment using python by Maglas, Najeeb N.M., Najar, Merouane, Qiang, Zhao

“… However, its manual data input and analysis processes limit its efficiency in complex scenarios requiring extensive parameter variations…”
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Bayesian modelling of time series data (BayModTS)—a FAIR workflow to process sparse and highly variable data by Höpfl, Sebastian, Albadry, Mohamed, Dahmen, Uta, Herrmann, Karl-Heinz, Kindler, Eva Marie, König, Matthias, Reichenbach, Jürgen Rainer, Tautenhahn, Hans-Michael, Wei, Weiwei, Zhao, Wan-Ting, Radde, Nicole Erika

“… A pervasive challenge in quantitative dynamical modelling is the integration of time series measurements, which often have high variability and low sampling resolution…”
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GraphPyRec: A novel graph-based approach for fine-grained Python code recommendation by Zong, Xing, Zheng, Shang, Zou, Haitao, Yu, Hualong, Gao, Shang

“… Significant progress has been made in code recommendation for static languages in recent years, but it remains challenging for dynamic languages like Python as accurately determining data flows…”
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