Reproducible implementation for article: Reproducibility study of the modular and reusable model of epithelial transport in the proximal convoluted tubule by Leyla Noroozbabaee (14301173)

EthoPy: Reproducible Behavioral Neuroscience Made Simple by Alexandros Evangelou (22235917)

“…To overcome these challenges, we developed EthoPy, an open-source, Python-based behavioral control framework that integrates stimulus presentation, hardware management, and data logging. …”

Representative MSD plots, Fig. 6c,d by Hirotake Udono (21008660)

Performance Benchmark: SBMLNetwork vs. SBMLDiagrams Auto-layout. by Adel Heydarabadipour (22290905)

“…<p>Log–log plot of median wall-clock time for SBMLNetwork’s C++-based auto-layout engine (blue circles, solid fit) and SBMLDiagrams’ implementation of the pure-Python NetworkX spring_layout algorithm (red squares, dashed fit), applied to synthetic SBML models containing 20–2,000 species, with a fixed 4:1 species-to-reaction ratio. …”

Reaction Alignment of the Tricarboxylic Acid (TCA) Cycle Network. by Adel Heydarabadipour (22290905)

(a) System dynamics: schematic representation of all the reactions in the Tree model, which are aging, reproduction, color cycle, and competition. by Fabricio Cravo (21387854)

Simulated dynamics of the Mutual Annihilation protocol [26]. by Fabricio Cravo (21387854)

System Hardware ID Generator Script: A Cross-Platform Hardware Identification Tool by Pavel Izosimov (20096259)

“…</li><li><b>Cross-Platform Compatibility</b>: Designed with cross-platform functionality in mind, the script works seamlessly on Windows, macOS, Linux, Unix, and other operating systems where Python 3.6 or higher is installed.</li><li><b>Modular Design</b>: The script can be used as a standalone tool or imported as a module into other Python projects, enabling developers to easily integrate hardware identification into their applications.…”

A comparison between the static Python-based visualizations of the p65 activity in activated fibroblasts and the dynamic, HTML-based visualizations that use these same reduction me... by Hector Torres (11708207)

“…<p><b>(a)</b> UMAP, t-SNE, PCA, and Diffmap were first generated using the Python libraries Scikit-learn, UMAP, and PyDiffmap within Jupyter to generate static graphs as a starting point. …”

PTPC-UHT bounce by David Parry (22169299)

“…</p><p dir="ltr">Included files:</p><ul><li>Python source code (<code>PTPC_UHT_bounce.py</code>)</li><li>Parameter sets for representative runs (α,β,Tcrit,V(T)\alpha, \beta, T_{\mathrm{crit}}, V(T)α,β,Tcrit​,V(T))</li><li>Output arrays of trajectories across multiple bounces</li><li>Multi-panel plots (PNG/PDF) for a(t)a(t)a(t), H(t)H(t)H(t), T(t)T(t)T(t), S(t)S(t)S(t), R(t)R(t)R(t), and ρT\rho_TρT​</li></ul><p dir="ltr">This dataset ensures full reproducibility of the PTPC simulations and provides a starting point for independent verification, parameter exploration, and future model extensions.…”

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

Data for "A hollow fiber membrane permeance evaluation device demonstrating outside-in and inside-out performance differences" by Timothy Warner (20222838)

“…</li><li>Flux decline data generated by the analysis software.</li><li>Plot data derived from the above data sources.</li><li>Python code to generate figures from the plot data.…”

Segmentation module training details. by Khelina Fedorchuk (19130089)

Workflow of a typical Epydemix run. by Nicolò Gozzi (8837522)

“…<div><p>We present Epydemix, an open-source Python package for the development and calibration of stochastic compartmental epidemic models. …”

Fig 4. - mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data by Guillermo Pérez-Hernández (21156182)

Examples of insights derived from iModulons. by Anand V. Sastry (6619310)

Introduction to the iModulonMiner using public <i>B</i>. <i>subtilis</i> RNA-seq data as a case study. by Anand V. Sastry (6619310)

Overview of the <i>B</i>. <i>subtilis</i> iModulon structure. by Anand V. Sastry (6619310)

Application to Drosophila gastrulation. by Sophie Theis (4126453)

Estimating dopamine effects on humans. by Domenico Guarino (20428000)