Example ALAAMEE goodness-of-fit output. by Alex Stivala (8356257)

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ZILLNB_Model by Qinhuan Luo (21288548)

“…<p dir="ltr">Acquire latent variables using deep-learning based model implemented in python</p>…”

Bursty model and Refractory model simulation results. (A) Bursty model simulation results ( samples). The production of nascent mRNA occurs in bursts and degrade after delay time <... by Ziyan Jin (21021976)

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Flowchart representation of lion optimization algorithm for hyperparameter tuning in the HCAP model. by Mohanad Faeq Ali (21354273)

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DeepB3Pred - code by Saleh Musleh (22263718)

Code by Baoqiang Chen (21099509)

“…We divided the dataset into training and test sets, using 70% of the genes for training and 30% for testing. We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”

RNA Velocity model simulation results. (A) Simulation results for RNA Velocity model without delay ( samples). The simulation is composed of an up-regulation phase (both production... by Ziyan Jin (21021976)

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Modeling lung cancer AST network and its perturbation with a SOX2 degrader. (A) Lung Cancer AST Network and the corresponding stochastic equations. Parameters are , , , , , , , , w... by Ziyan Jin (21021976)

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DeepB3Pred_source_code by Muhammad Arif (17012472)

DataSheet1_Prostruc: an open-source tool for 3D structure prediction using homology modeling.PDF by Shivani V. Pawar (20355171)

“…</p>Methods<p>Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. …”

DataSheet1_Prostruc: an open-source tool for 3D structure prediction using homology modeling.PDF by Shivani V. Pawar (20355171)

“…</p>Methods<p>Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. …”

Scripts, data and figures underpinning 'Towards the Creation of Legible Octilinear Power Grid Diagrams Using Mixed Integer Linear Programming' by Paul Cuffe (2937081)

“…<p dir="ltr">These Python notebooks implement the techniques described in the paper "Towards the Creation of Legible Octilinear Power Grid Diagrams Using Mixed Integer Linear Programming".…”

Code and data for reproducing the results in the original paper of DML-Geo by Pengfei CHEN (8059976)

“…<p dir="ltr">This asset provides all the code and data for reproducing the results (figures and statistics) in the original paper of DML-Geo</p><h2>Main Files:</h2><p dir="ltr"><b>main.ipynb</b>: the main notebook to generate all the figures and data presented in the paper</p><p dir="ltr"><b>data_generator.py</b>: used for generating synthetic datasets to validate the performance of different models</p><p dir="ltr"><b>dml_models.py</b>: Contains implementations of different Double Machine Learning variants used in this study.…”

High-Throughput Mass Spectral Library Searching of Small Molecules in R with NIST MSPepSearch by Andrey Samokhin (20282728)

“…Despite the availability of numerous library search algorithms, those developed by NIST and implemented in MS Search remain predominant, partly because commercial databases (e.g., NIST, Wiley) are distributed in proprietary formats inaccessible to custom code. …”

Efficient, Hierarchical, and Object-Oriented Electronic Structure Interfaces for Direct Nonadiabatic Dynamics Simulations by Sascha Mausenberger (22225772)

“…We present a novel, flexible framework for electronic structure interfaces designed for nonadiabatic dynamics simulations, implemented in Python 3 using concepts of object-oriented programming. …”

SEPARATE Code Repository by Gyuri Kim (21424973)

Reproducible Code and Data for figures by Bonyad Ahmadi (20750327)

“…</i></p><p dir="ltr">It contains:</p><p dir="ltr">✅ <b>Python Code</b> – Scripts used for data preprocessing, and visualization.…”

Tracking module training details. by Khelina Fedorchuk (19130089)

Simulation Code and Raw Data by Melih Özkurt (22278520)

“…<p dir="ltr">Reproducible code (Python) implementing a symmetrized split-step Fourier method (SSFM), with configuration files for all scans. …”

software code of NeoDesign by Wenqian Yu (19730101)

“…<h2>Implementation and Dependencies</h2><p dir="ltr">neoDesign was developed with python (recommend>3.9) and shell (bash) language. …”