Search Results - dynamic code analysis of python (progress OR 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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Dynamic Generation of Python Bindings for HPC Kernels by Zhu, Steven, AlAwar, Nader, Erez, Mattan, Gligoric, Milos

“… A recent trend among scientists-prototyping applications in dynamic languages such as Python-created a gap between the applications and existing HPKs…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

Python open-source signal processing and modeling/simulation for scientific research in structural dynamics—A review by Slavič, Janko, Zaletelj, Klemen, Gorjup, Domen, Pasca, Dag Pasquale, Aloisio, Angelo, Kvåle, Knut Andreas, Frøseth, Gunnstein Thomas, Weijtjens, Wout, Mujtaba, Ahmed, Česnik, Martin, Zorman, Aleš, Tsialiamanis, George, Tomac, Ivan, Ritto, Thiago G., Ocepek, Domen, Rohe, Dan, Silva, Olavo M., Masmeijer, Thijs C.P., Čufar, Krištof, Bregar, Tomaž, Kodrič, Miha, El Mahmoudi, Ahmed, Pogačar, Miha, Trainotti, Francesco, Göldeli, Mert, Čepon, Gregor, Timbó, Raphael, Cavallini, Aldemir A., Costa, Vinicius T., Santos, Jéssica G.F., Hughes, Aidan J., Vargas, Jacson G., Fernandes, André, Rixen, Daniel J., Worden, Keith, Boltežar, Miha

“… Avoiding duplication of effort leads to faster progress and greater societal benefit. The Python programming language provides readable code and is highly collaborative, leading to a large user community…”
Get full text

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…”
Get full text

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…”
Get more information

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get full text

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…”
Get more information

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…”
Get full text