Supplementary file 1_ParaDeep: sequence-based deep learning for residue-level paratope prediction using chain-aware BiLSTM-CNN models.docx حسب Piyachat Udomwong (22563212)

"…The implementation is freely available at https://github.com/PiyachatU/ParaDeep, with Python (PyTorch) code and a Google Colab interface for ease of use.…"

Discovery of a Latent Entropy-Based Physiologic State Variable Governing Multisystem Instability in Critical Illness حسب Jordan Rabbani (22800074)

Tipping points of marine phytoplankton to multiple environmental stressors حسب Zhan Ban (11627098)

Data for: An effective methodology to quantify cooling demand in the UK housing stock حسب Lloyd Corcoran (19094369)

Global Aridity Index and Potential Evapotranspiration (ET0) Database: Version 3.1 حسب Robert Zomer (12796235)

A model of neural population dynamics for flexible sensorimotor control حسب Hari Kalidindi (17123467)

Methodological Approach Based on Structural Parameters, Vibrational Frequencies, and MMFF94 Bond Charge Increments for Platinum-Based Compounds حسب Gloria Castañeda-Valencia (20758502)

"…The developed bci optimization tool, based on MMFF94, was implemented using a Python code made available at https://github.com/molmodcs/bci_solver. …"

Void-Center Galaxies and the Gravity of Probability Framework: Pre-DESI Consistency with VGS 12 and NGC 6789 حسب Jordan Waters (21620558)

"…<br><br><br><b>ORCID ID: https://orcid.org/0009-0009-0793-8089</b><br></p><p dir="ltr"><b>Code Availability:</b></p><p dir="ltr"><b>All Python tools used for GoP simulations and predictions are available at:</b></p><p dir="ltr"><b>https://github.com/Jwaters290/GoP-Probabilistic-Curvature</b><br><br>The Gravity of Probability framework is implemented in this public Python codebase that reproduces all published GoP predictions from preexisting DESI data, using a single fixed set of global parameters. …"

The data of the paper "Remote spectral detection of canopy functional strategies varying within and across forest types". حسب Fengqi Wu (20149158)

"…Canopy_2024_PLSR_ST_canopy_run_refit.py</p><p dir="ltr">This is the python code used for PLSR modeling.</p><p dir="ltr"><br></p><p dir="ltr">3. python_code_get_model_details.zip</p><p dir="ltr">This is the python code to get model performance, coefficients, VIPs, and so on.…"

Albumin Degradome Foundation Atlas حسب Axel Petzold (7076261)

"…</p><h2><b>Data Format and Access</b></h2><ul><li><b>Primary file:</b> <code>Albumin_Degradome_Foundation_Atlas_v1.tar.xz</code><br>(contains all peptide tables in standard CSV format)</li><li><b>File Type:</b> ASCII comma-separated values (CSV)</li><li><b>Compression:</b> <code>xz -9 -T0</code> for maximal CPU-parallelised compression</li><li><b>Compatibility:</b></li><li><ul><li>R, Python, MATLAB, SAS</li><li>Excel, LibreOffice</li><li>Any proteomics workflow (e.g., Skyline, MaxQuant preprocessing, MS/MS spectral libraries)</li></ul></li></ul><h2><b>FAIR Principles</b></h2><p dir="ltr">This dataset is fully aligned with FAIR data standards:</p><ul><li><b>Findable:</b> Rich metadata, stable DOI, search-optimised description</li><li><b>Accessible:</b> Open-access Figshare repository</li><li><b>Interoperable:</b> Standard numeric and CSV formats</li><li><b>Reusable:</b> Transparent, reproducible Python source code included</li></ul><h2><b>Applications</b></h2><p dir="ltr">The Albumin Degradome Foundation Atlas supports research across multiple biomedical domains:</p><ul><li>Biomarker development in liver disease, kidney dysfunction, inflammation, and systemic disorders</li><li>Mass-spectrometry method development</li><li>Computational proteomics and peptide modelling</li><li>Autoimmunity and neo-epitope analysis</li><li>Protein–peptide interaction studies</li><li>Proteolytic pathway mapping and degradomics</li></ul><h2><b>Versioning and Future Work</b></h2><p dir="ltr">This is <b>Version 1</b> of the Albumin Degradome Foundation Atlas. …"

<b>Tau Degradome Foundation Atlas</b> حسب Axel Petzold (7076261)

"…</li><li><b>Thermodynamic stability</b> is predicted for each peptide, with stable candidates labelled (<code>stable=1</code>), highlighting their suitability for biomarker assay development.…"

MsipNet حسب Nan Song (22280815)

"…<h2><b>MsipNet</b></h2><p dir="ltr">This is a directory for storing the **MsipNet** model code and data. **MsipNet** is a multi-scale representation learning framework for predicting protein-RNA interactions.…"

The Transcriptional Gradient in Negative-Strand RNA Viruses Suggest a Common RNA Transcription Mechanism: Model حسب Jean Peccoud (275555)

"…</p><p dir="ltr">Notebook2 contains the python code for making predictions of transcriptional gradients for gene-shuffled variants.…"

Ambient Air Pollutant Dynamics (2010–2025) and the Exceptional Winter 2016–17 Pollution Episode: Implications for a Uranium/Arsenic Exposure Event حسب Thomas Clemens Carmine (19756929)

"…Includes imputation statistics, data dictionary, and the Python imputation code (Imputation_Air_Pollutants_NABEL.py). …"

SI files for "Addressing Hemolysis-Induced Loss of Sensitivity in Lateral Flow Assays of Blood Samples with Platinum-Coated Gold Nanoparticles and Machine Learning" حسب An Le (20473628)

"…</p><p dir="ltr">2) Model_testing.ipynb: Jupyter Notebook containing Python code for generate predictions for the 112 test strips</p><p dir="ltr">3) Best_model.keras: The final optimized machine learning model saved in Keras format.…"

ncRNA.zip حسب Chongyi Jiang (20987126)

"…<h3><b>ncRNA (non-coding RNA) </b><b>predicted by</b><b> CPC2 (v 0.1) and PINC for 25 </b><b>grassland plant species.…"

DCPR_V1.0 حسب xiao han (21405770)

"…</p><p dir="ltr"><b>DCPR_codes</b>: Source code for DCPR model.</p><p dir="ltr"><b>Visualization</b>: Scripts for data visualization, including circadian curves (cosine model fitting), sample plots (predicted and real time), model performance (CDF curves, and accuracy plots).…"

<b>Rethinking neighbourhood boundaries for urban planning: A data-driven framework for perception-based delineation</b> حسب Shubham Pawar (22471285)

"…</p><p dir="ltr"><b>Input:</b></p><ul><li><code>raw_data/glasgow_open_built/glasgow_open_built_areas.shp</code> - Grid defining sampling points</li></ul><p dir="ltr"><b>Command:</b></p><pre><pre>python svi_module/get_svi_data.py<br></pre></pre><p dir="ltr"><b>Output:</b></p><ul><li><code>svi_module/svi_data/svi_info.csv</code> - Image metadata (IDs, coordinates)</li><li><code>svi_module/svi_data/images/</code> - Downloaded street view images</li></ul><h3>Step 2: Predict Perceptions</h3><p dir="ltr">Use pre-trained deep learning models to predict perceptual qualities (safety, beauty, liveliness, etc.) from street view images.…"

Synthetic Mental Health Survey Dataset حسب Shakil Hossain (22546658)

"…Data were generated using Python code to simulate realistic patterns and scoring based on psychological constructs.This dataset was to develop a machine learning model for predicting severity of multiple mental health disorders & overall Mental Health Status based on survey responses and psychological features.…"

Monte Carlo Simulation for SAPAL Framework: AI-Augmented CI/CD Reliability حسب Rohit Dhawan (22457026)

"…</p><p dir="ltr">Files included: <br>- simulation.py: Python simulation code <br>- README.md: Complete documentation and methodology <br><br>This code supports the paper "AI-Augmented Reliability in Continuous Integration and Deployment: A Conceptual Framework for Predictive, Adaptive, and Self-Correcting Pipelines".…"