BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

Segmentation module training details. by Khelina Fedorchuk (19130089)

PTPC-UHT bounce by David Parry (22169299)

“…<br>It contains the full Python implementation of the PTPC bounce model (<code>PTPC_UHT_bounce.py</code>) and representative outputs used to generate the figures in the paper. …”

ALAAM models for the Deezer networks, with liking “alternative” music as the outcome variable. by Alex Stivala (8356257)

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Apple point cloud generated by python script. by Xiaoyang Liu (1815211)

Models estimated using ALAAMEE for the Deezer networks, with liking jazz as the outcome variable. by Alex Stivala (8356257)

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Overview of the SBML models used in this study. The collection of models was retrieved from Biomodels [43] and a previously reported collection of SBML benchmark models [11]. The n... by Paul van Lent (16876977)

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Jaxkineticmodel allows for hybridizing kinetic models with neural networks. by Paul van Lent (16876977)

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Analysis of convergence properties for a collection of SBML models. by Paul van Lent (16876977)

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EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit by Gonzalo Colmenarejo (650249)

“…In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. …”

Python file of the computational framework. by Benoit Haut (9753029)

2D Orthogonal Planes Split: <b>Python</b> and <b>MATLAB</b> code | <b>Source Images</b> for Figures by Nektarios Valous (20715650)

“…The output files generated by the code include results from both Python and MATLAB implementations; these output images are provided as validation, demonstrating that both implementations produce matching results.…”

Fitting a feast/famine cycle to a glycolysis model. by Paul van Lent (16876977)

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Illustration of the text transformation process before and after synonym replacement: The process begins with a sample initial text segment (Sample text before synonym replacement’... by Enock Niyonkuru (21246879)

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Schematic of the approach: This schematic illustrates the entire workflow of the project. by Enock Niyonkuru (21246879)

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Text Transformation Pipeline: An example of the multi-stage text transformation pipeline applied to a sample abstract (PMID: 30609739). by Enock Niyonkuru (21246879)

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Comparative analysis of WordNet replacement impact on data distribution. by Enock Niyonkuru (21246879)

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Comparison of window size for embedding with Wordnet synonym replacement (WN) and without (PM). While Table 1 compared the effects of different values of using a window size of 10,... by Enock Niyonkuru (21246879)

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