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

“…</p><p dir="ltr"><b>Note:</b></p><p dir="ltr">Analysis was performed using a custom Python-based bioinformatics pipeline developed for <b>high-throughput surveillance of pemivibart (VYD2311) escape mutations in SARS-CoV-2</b>. …”

<b>Challenges and Strategies for the Management of Quality-Oriented Education Bases in Universities under Informatization Background</b> by Yang Yanxi (21571568)

“…Final codes, together with basic demographic attributes supplied by the institutions’ HR offices, were exported to Excel and cleaned in Python 3.10 using pandas 2.2.1 and numpy 1.26. …”

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. …”

<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.…”

Oka et al., Supplementary Data for "Development of a battery emulator using deep learning model to predict the charge–discharge voltage profile of lithium-ion batteries" by Kanato Oka (20132185)

“…(<b>DOI:</b> 10.1038/s41598-024-80371-9 )<br><br>A zip file contains following data and codes.</p><p dir="ltr"><br></p><p dir="ltr">01_lstm_model_making.py</p><p dir="ltr">This file is a Python script for reading battery charge-discharge data and training an LSTM model. …”

Supplementary file 1_ParaDeep: sequence-based deep learning for residue-level paratope prediction using chain-aware BiLSTM-CNN models.docx by 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.…”

Social media images of China's terraces by Song Chen (19488280)

“…Geo-tagged images were collected using Weibo cookies and Python-based scraping tools (available at: https://github.com/dataabc/weibo-search). …”

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

“…This file can be used together with the analysis code (link to be added upon publication) to generate all figures.…”

MCCN Case Study 3 - Select optimal survey locality by Donald Hobern (21435904)

“…</p><p dir="ltr">This is a simple implementation that uses four environmental attributes imported for all Australia (or a subset like NSW) at a moderate grid scale:</p><ol><li>Digital soil maps for key soil properties over New South Wales, version 2.0 - SEED - see <a href="https://esoil.io/TERNLandscapes/Public/Pages/SLGA/ProductDetails-SoilAttributes.html" target="_blank">https://esoil.io/TERNLandscapes/Public/Pages/SLGA/ProductDetails-SoilAttributes.html</a></li><li>ANUCLIM Annual Mean Rainfall raster layer - SEED - see <a href="https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-rainfall-raster-layer" target="_blank">https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-rainfall-raster-layer</a></li><li>ANUCLIM Annual Mean Temperature raster layer - SEED - see <a href="https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-temperature-raster-layer" target="_blank">https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-temperature-raster-layer</a></li></ol><h4><b>Dependencies</b></h4><ul><li>This notebook requires Python 3.10 or higher</li><li>Install relevant Python libraries with: <b>pip install mccn-engine rocrate</b></li><li>Installing mccn-engine will install other dependencies</li></ul><h4><b>Overview</b></h4><ol><li>Generate STAC metadata for layers from predefined configuratiion</li><li>Load data cube and exclude nodata values</li><li>Scale all variables to a 0.0-1.0 range</li><li>Select four layers for comparison (soil organic carbon 0-30 cm, soil pH 0-30 cm, mean annual rainfall, mean annual temperature)</li><li>Select 10 random points within NSW</li><li>Generate 10 new layers representing standardised environmental distance between one of the selected points and all other points in NSW</li><li>For every point in NSW, find the lowest environmental distance to any of the selected points</li><li>Select the point in NSW that has the highest value for the lowest environmental distance to any selected point - this is the most different point</li><li>Clean up and save results to RO-Crate</li></ol><p><br></p>…”

Electrical Tactile Dataset (Piezoelectric and Accelerometer) for textures by Dexter Shepherd (13238508)

“…</p><p dir="ltr">X shape: (Number, frame, sensor index)</p><p dir="ltr">y shape: (Number,)</p><p dir="ltr">All files are in compressed numpy format. Python users can load in the dataset using the code provided in the ReadMe.…”

Phylogenomics of aquatic bacteria by Krzysztof Jurdzinski (12519700)

“…</p> <p><br></p> <p>all_MSG_ids.txt - a text file with names of all the representative MAGs within all the MSG pairs.</p> <p><br></p> <p>filter_MSGs.py - a Python script to extract the MAGs from within the MSGs (given all_MSG_ids.txt) from a folder containing a larger set of sequences.…”

Optical Tactile (TacTip) Dataset for texture classification by Dexter Shepherd (13238508)

“…</p><p dir="ltr">X shape: (Number, frame, h, w)</p><p dir="ltr">y shape: (Number,)</p><p dir="ltr"><br></p><p dir="ltr">All files are in compressed numpy format. Python users can load in the dataset using the code provided in the ReadMe.…”

Improving the calibration of an integrated CA-What If? digital planning framework by CA What If? (21381170)

“…</p><p dir="ltr">This dataset includes (1) all required data for reproducing the materials within the manuscript, (2) detailed Python codes of the proposed CA-What If? model, and (3) a step-by-step instruction document.…”

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

“…</p> <p><strong>Processing environment</strong></p> <p>This research has been conducted using Python for ESRI ArcGIS Pro version 3.2.1 and the TensorFlow package. …”

PepENS by Abel Chandra (16854753)

“…<br><br>Download and Use</p><p dir="ltr">The codes for Datasets 1 and 2 are found in the respective folders of this repository.…”

<b>Engineered Muscle-Derived Extracellular Vesicles Boost Insulin Sensitivity and Glucose Regulation</b> by Hagit Shoyhet (21090650)

“…</p><p dir="ltr"><b>miR_path_target_enrichment.csv</b></p><p dir="ltr"><b>Description:</b> KEGG pathway enrichment analysis results of shared mRNA targets of miRNAs miR-16-5p, miR-122-5p and miR-486-5p ranked by their interaction score defined in our paper. this includes the pathway name, the enrichment p-value, number of genes found in the term and number of miRNAs targeting these genes</p><p dir="ltr"><b>Code/software</b></p><p dir="ltr">Data were analyzed using R-V4.0.4, Python-V3.9.2 and GraphPad software. miRNA analyses were run in R-V4.0.4 Differential expression analysis was conducted using the “DEseq2” package and corrected for multiple hypotheses by FDR. …”

Chromosomal rearrangements among clade A pathogenic <i>Cryptococcus</i> species. by Marco A. Coelho (7353659)

“…<p>(A) Synteny comparisons between <i>C. neoformans</i> strain 125.91 (reference) and representative strains from 7 other clade A species (8 species total). …”