<b>Dataset for manuscript: </b><b>Phylogenetic and genomic insights into the evolution of terpenoid biosynthesis genes in diverse plant lineages</b> by Puguang Zhao (19023065)

“…</p><p dir="ltr"> 'boxplot.py': This script is executed in Visual Studio Code, using Python 3.10.4 as the runtime environment.…”

Genomic Surveillance of Pemivibart (VYD2311) Escape-Associated Mutations in SARS-CoV-2: December 2025 BioSamples (n=2) by Tahir Bhatti (20961974)

“…Full source code and version details are available upon request.…”

End-to-end example-based sim-to-real RL policy transfer based on neural stylisation with application to robotic cutting by Jamie Hathaway (10285367)

“…</p><h3>policy/</h3><p dir="ltr">This folder contains pickled trajectories, in the form of a Python list.</p><p dir="ltr">The list's elements are TrajWithRew dataclass objects from the Imitation Python library (https://imitation.readthedocs.io/en/latest/)</p><p dir="ltr">TrajWithRew contains 4 main fields</p><ul><li> obs - the (unnormalised) observations, in the form of a [WINDOW_LENGTH * NUM_CHANNELS] array</li><li> acts - the actions in the form of a [WINDOW_LENGTH - 1 * NUM_ACTS] array</li><li> infos - the info values at each timestep, as a [WINDOW_LENGTH - 1] array of dicts</li><li> terminals - boolean indicating if that trajectory segment is a terminal segment</li><li> rews - the rewards as a [WINDOW_LENGTH - 1] array</li></ul><p dir="ltr">Each TrajWithRew represents not a full episodic trajectory, as is usually the case with Imitiation - rather they represent segments of a full episodic trajectory, of length WINDOW_LENGTH. …”

Attention and Cognitive Workload by Rui Varandas (11900993)

“…</p><p dir="ltr">The data for subject 2 do not include the 2nd part of the acquisition (python task) because the equipment stopped acquiring; subject 3 has the 1st (N-Back task and mental subtraction) and the 2nd part (python tutorial) together in the <code>First part</code> folder (file <code>D1_S3_PB_description.json</code> indicates the start and end of each task); subject 4 only has the mental subtraction task in the 1st part acquisition and in subject 8, the subtraction task data is included in the 2nd part acquisition, along with python task.…”

Bacterial persistence modulates the speed, magnitude and onset of antibiotic resistance evolution by Giorgio Boccarella (22810952)

“…</p><p dir="ltr">Repository structure</p><p dir="ltr">Fig_1/</p><ul><li>Probability of emergence analysis</li><li>Fig_1.py: contour plot generation</li></ul><p dir="ltr">Fig_2/</p><ul><li>MIC evolution simulations</li><li>Fig_2_a/: R-based simulation analysis</li><li>Fig_2_b/: Python visualization</li><li>Fig_2_c/: speed of resistance evolution analysis</li><li>Fig_2_d/: time to resistance analysis</li></ul><p dir="ltr">Fig_3/</p><ul><li>Distribution analysis</li><li>Fig_3_a-b.R: density plots and bar charts (empirical and simulated)</li></ul><p dir="ltr">Fig_4/</p><ul><li>Mutation analysis</li><li>Fig_4_a-b/: mutation counting analysis</li><li><ul><li>Fig_4_a/: simulation data (sim)</li><li>Fig_4_b/: empirical data (emp)</li></ul></li><li>Fig_4_c/: gene ontology and functional analysis</li></ul><p dir="ltr">Fig_5/</p><ul><li>Large-scale evolutionary simulations</li><li>Fig_5_a-b/: heatmap visualizations</li><li>Fig_5_c/: MIC and extinction analysis (empirical)</li></ul><p dir="ltr">Fig_6/</p><ul><li>Population size effects</li><li>Fig_6.py: population size analysis simulations</li></ul><p dir="ltr">S1_figure/</p><ul><li>Supplementary experimental data</li></ul><p dir="ltr">S2_figure/</p><ul><li>Supplementary frequency analysis</li></ul><p dir="ltr">S3_figure/</p><ul><li>Supplementary probability analysis</li></ul><p dir="ltr">scripts_simulations_cluster/</p><ul><li>Large-scale, cluster-optimized simulations</li></ul><p dir="ltr">complete_data/</p><ul><li>Reference to the full data sheet (full data set deposited elsewhere)</li></ul><p dir="ltr">Script types and languages</p><p dir="ltr">Python scripts (.py)</p><ul><li>Mathematical modeling: survival functions, probability calculations</li><li>Stochastic simulations: tau-leaping population dynamics</li><li>Data processing: mutation analysis, frequency calculations</li><li>Visualization: plotting with matplotlib and seaborn</li><li>Typical dependencies: numpy, pandas, matplotlib, seaborn, scipy</li></ul><p dir="ltr">R scripts (.R)</p><ul><li>Statistical analysis: distribution fitting, density plots</li><li>Advanced visualization: publication-quality figures (ggplot2)</li><li>Data manipulation: dplyr / tidyr workflows</li><li>Typical dependencies: dplyr, tidyr, ggplot2, readxl, cowplot</li></ul><p dir="ltr">Data requirements</p><p dir="ltr">The scripts are designed to run using the complete_data.xlsx file and, where relevant, the raw simulation outputs and empirical data sets as described above. …”

GeoGraphNetworks: Shapefile-Derived Datasets for Accurate and Scalable Graphical Representations by Harish Sharma (18881935)

“…The rail line infrastructure of the USA is represented as a single network that covers the entire country and includes connectivity to Canada. …”

Physiotherapist-Assisted Wrist Movement Protocol for EEG-Based Corticokinematic Coherence Assessment by Fanni Kovács (21733838)

“…</li></ol><h4><b>Movement File Structure</b></h4><p dir="ltr">Each entry contains:</p><ul><li><code><strong>time</strong></code>: a 32-bit unsigned integer indicating the timestamp in milliseconds,</li><li><code><strong>x</strong></code>, <code><strong>y</strong></code>, <code><strong>z</strong></code>: 16-bit signed integers representing acceleration along the respective axes,</li><li><code><strong>trigger</strong></code>: an 8-bit unsigned integer used to mark event-related triggers for synchronization with the EEG data (e.g., movement onset).…”

Cognitive Fatigue by Rui Varandas (11900993)

“…<br></p><p dir="ltr"><b>HCI features</b> encompass keyboard, mouse, and screenshot data. Below is a Python code snippet for extracting screenshot files from the screenshots CSV file.…”

Multisession fNIRS-EEG data of Post-Stroke Motor Recovery: Recordings During Intact and Paretic Hand Movements by Aleksandra Medvedeva (21221383)

“…The fNIRS .snirf files are accompanied by event files as .txt tables, containing arrays of event timestamps and corresponding event codes. The code for signal reading, preprocessing, and epoching is provided with the dataset in the “Preprocessing” file. …”

Digital Twin for Chemical Sciences by Jin Qian (19339035)

“…The procedure for generating data in Figure 3 can be found in the demo notebook in Supplementary Code. The procedure for generating data of Figure 4 has been uploaded in fig4_figshare.zip file. …”

Sonification of Warming Stripes by Christopher Harrison (9448751)

“…The sonification was produced using the STRAUSS sonification Python package.</p><p dir="ltr">Here we release:<br>1. …”

Sonification of Growing Black Hole by Rose Shepherd (20328444)

“…We used the open source Python package STRAUSS to produce the sonification (Trayford and Harrison 2023). …”

2024 HUD Point in Time Count Data by State and CoC with Serious Mental Illness and Chronic Substance Use Counts by Benjamin Gorman (21648794)

“…</p><p dir="ltr">HUD PIT Count reports for states, Washington, DC, and the 384 CoCs were systematically downloaded from the HUD Exchange website using a Python script developed using Cursor software. Cursor uses large language models, especially Claude Sonnet 4 (Anthropic), to generate code. …”

Minami_etal_2025 by Keiichi Mochida (4670800)

“…<h2>Code files related to Minami et al (2025)</h2><p dir="ltr">accession_plot.py:Python script used to generate Fig4a.…”

Genomic Epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 by Pablo Tsukayama (22614461)

“…</p><p dir="ltr"><b>Contents:</b></p><p><b>1. Analysis Code</b></p><p>Core Python scripts used to curate metadata, process genomic data, perform lineage assignments, compute summary statistics, and prepare inputs for downstream phylogenetic and phylogeographic analyses. …”

Image 1_An explainable analysis of depression status and influencing factors among nursing students.png by Yingying Li (50341)

“…Data cleaning was performed in Excel, and statistical analyses were conducted using SPSS Statistics version 27.0 and Python 3.9.</p>Results<p>The incidence of depression among nursing students is 28.60%. …”

<b>IEEE 14 bus test systems row data </b> by meysam shahriyari (22599314)

“…Each row in the dataset represents one simulated case, and each column corresponds to an input feature used in the deep learning model.…”

Building footprtints from 1970s Hexagon spy satellite images for four global urban growth hotspots by Franz Schug (10165159)

“…The data represent the final results, that means, after merging models with different chip sizes and post-processing (see manuscript). …”

Indirect Reciprocity and the Evolution of Prejudicial Groups by Gualtiero Colombo (19078925)

“…This is conducted through an agent based model over a population of agents that interact through a `donation game' in which resources are donated to third parties at a cost without receiving a direct benefit. …”

Summary of Tourism Dataset. by Jing Zhang (23775)

“…The proposed TourVaRNN integrates variational autoencoders to capture latent variables representing visitor preferences and spending habits, while recurrent neural networks model complex temporal dependencies in tourism data. …”