Search Results - dynamic code analysis of python (programs OR progress)

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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Introduction to Python Dynamic Diffraction Toolkit ( PyDDT ): structural refinement of single crystals via X-ray phase measurements by Penacchio, Rafaela F. S., Estradiote, Maurício B., Remédios, Cláudio M. R., Calligaris, Guilherme A., Torikachvili, Milton S., Kycia, Stefan W., Morelhão, Sérgio L.

“…PyDDT is a free Python package of computer codes for exploiting X-ray dynamic multiple diffraction in single crystals…”
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SciPy 1.0: fundamental algorithms for scientific computing in Python by Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul

“… Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages…”
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Generative Type Inference for Python by Peng, Yun, Wang, Chaozheng, Wang, Wenxuan, Gao, Cuiyun, Lyu, Michael R.

“… However, its dynamic type system can lead to potential type errors, leading researchers to explore automatic type inference approaches for Python programs…”
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i-PI: A Python interface for ab initio path integral molecular dynamics simulations by Ceriotti, Michele, More, Joshua, Manolopoulos, David E.

“… Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program…”
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SIMA: Python software for analysis of dynamic fluorescence imaging data by Kaifosh, Patrick, Zaremba, Jeffrey D., Danielson, Nathan B., Losonczy, Attila

“… However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools…”
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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…”
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Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors by Peng, Yun, Gao, Shuzheng, Gao, Cuiyun, Huo, Yintong, Lyu, Michael R.

“… Although the dynamic type system of Python facilitates the developers in writing Python programs, it also brings type errors at runtime which are prevalent yet not easy to fix…”
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DefAP: A Python code for the analysis of point defects in crystalline solids by Neilson, William D., Murphy, Samuel T.

“… into a material’s defect chemistry, it is essential to link the energies calculated to thermodynamic variables that fully describe its operating conditions…”
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ACPYPE - AnteChamber PYthon Parser interfacE by Sousa da Silva, Alan W, Vranken, Wim F

“… topologies and parameters for a variety of molecular dynamics programmes like GROMACS, CHARMM and CNS…”
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TESTING THE DYNAMIC EXECUTION OF PYTHON PROGRAM CODE DURING THE CERTIFICATION TESTING (DEVELOPMENT) STAGE IN THE CERTIFICATION SYSTEM OF THE MINISTRY OF DEFENSE OF RUSSIA by V.V. Samarov

“… When checking applications developed in the Python language for compliance of their code with the requirements of the governing document "Protection against unauthorized access to information. Part 1…”
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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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pyIAST: Ideal adsorbed solution theory (IAST) Python package by Simon, Cory M., Smit, Berend, Haranczyk, Maciej

“…Ideal adsorbed solution theory (IAST) is a widely-used thermodynamic framework to readily predict mixed-gas adsorption isotherms from a set of pure-component adsorption isotherms…”
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Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS by Vieira, Ivo Henrique Provensi, Botelho, Eduardo Buganemi, de Souza Gomes, Thales Junior, Kist, Roger, Caceres, Rafael Andrade, Zanchi, Fernando Berton

“…Background The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures…”
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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

“… Current research in the field is not only hampered by the absence of a gold standard for PAC analysis, but also by the computational costs of running exhaustive computations on large and high…”
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Detecting Memory Errors in Python Native Code by Tracking Object Lifecycle with Reference Count by Ma, Xutong, Yan, Jiwei, Zhang, Hao, Yan, Jun, Zhang, Jian

“…Third-party Python modules are usually implemented as binary extensions by using native code (C/C++…”
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PyISOLVER-A Fast Python OOP Implementation of LRDFIT Model by Yang, Fanghao, Menard, Jonathan E.

“… on the commercial software license. In this article, the original procedural program was ported from its commercial platform to an open-source Python platform and refactored into the object…”
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PyAnalyzer: An Effective and Practical Approach for Dependency Extraction from Python Code by Jin, Wuxia, Xu, Shuo, Chen, Dawei, He, Jiajun, Zhong, Dinghong, Fan, Ming, Chen, Hongxu, Zhang, Huijia, Liu, Ting

“… However, dynamic language features in Python make code behaviors obscure and nondeter-ministic…”
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PyCG: Practical Call Graph Generation in Python by Salis, Vitalis, Sotiropoulos, Thodoris, Louridas, Panos, Spinellis, Diomidis, Mitropoulos, Dimitris

“… We propose a pragmatic, static approach for call graph generation in Python. We compute all assignment relations between program identifiers of functions, variables, classes, and modules through an inter-procedural analysis…”
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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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