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. …”

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

“…The samples (SRR36268464, SRR36225071) were retrieved from the NCBI Sequence Read Archive (SRA) and represent publicly available, real-world viral specimens collected during the final month of 2025, <b>the most recent temporal window available at the time of analysis.</b></p><p><br></p><p dir="ltr">Processing was performed using the PEMI-ESC v2.0 bioinformatics pipeline (Python-based, open-source methodology), which includes read quality control (fastp), alignment to NC_045512.2 (BWA-MEM), variant calling (iVar, bcftools), Spike protein reconstruction, and codon-resolved interrogation of five canonical escape positions: R346, S371, K444, F456, and F486.…”

Bayesian Changepoint Detection via Logistic Regression and the Topological Analysis of Image Series by Andrew M. Thomas (712104)

“…The method also successfully recovers the location and nature of changes in more traditional changepoint tasks. An implementation of our method is available in the Python package bclr.…”

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>…”

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

Summary of Tourism Dataset. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Segment-wise Spending Analysis. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Hyperparameter Parameter Setting. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Marketing Campaign Analysis. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Visitor Segmentation Validation Accuracy. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Integration of VAE and RNN Architecture. by Jing Zhang (23775)

“…The model employs robust forecasting of economic impacts, visitor spending patterns, and behavior while accounting for uncertainty through variational inference. The implementation uses Python language on a tourism dataset comprising necessary attributes like visitor numbers, days, spending patterns, employment, international tourism samples over a specific region, and a diverse age group analyzed over a year. …”

Dataset for: Phylotranscriptomics reveals the phylogeny of Asparagales and the evolution of allium flavor biosynthesis, Nature Communications，DOI：10.1038/s41467-024-53943-6 by Xiao-Xiao Wang (2447920)

“…Specifically, run this *.xml file using BEAST six times. Then, output of the six runs was combined and TreeAnnotator was used to summarize divergence time.…”

Supplement Number 1 by Susama Agarwala (21628328)

“…Python files containing the implementation of the graphical calculus on generalized Wilson loop diagrams…”

CNG-ARCO-RADAR.pdf by Alfonso Ladino (21447002)

“…This approach uses a suite of Python libraries, including Xarray (Xarray-Datatree), Xradar, and Zarr, to implement a hierarchical tree-like data model. …”

<b>Anthropogenic nutrient inputs cause excessive algal growth for nearly half the world’s population</b> by Richard McDowell (7311011)

“…</p><p dir="ltr">Models: R code to explore different models for implementation via Python in ArcGIS</p><p dir="ltr">!geotiffs: GeoTIFF raster files at level 6 of HydroBasins for current, zero human effect and the difference between current and zer human effect.…”

Elements: Streaming Molecular Dynamics Simulation Trajectories for Direct Analysis – Applications to Sub-Picosecond Dynamics in Microsecond Simulations by Matthias Heyden (17087794)

“…This eliminates the need for intermediate storage and allows immediate access to high-frequency fluctuations and vibrational signatures that would otherwise be inaccessible. We have implemented this streaming interface in the MD engines NAMD, LAMMPS, and GROMACS</p><p dir="ltr">On the client side, we developed the IMDClient Python package which receives the streamed data, stores into a custom buffer, and provides it to external tools as NumPy arrays, facilitating integration with scientific computing workflows. …”

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

“…</p><p dir="ltr">The Python programming source code used to run the calculation of ET0 and AI is provided and available online on Figshare at:</p><p dir="ltr">https://figshare.com/articles/software/Global_Aridity_Index_and_Potential_Evapotranspiration_Climate_Database_v3_-_Algorithm_Code_Python_/20005589</p><p dir="ltr">Peer-Review Reference and Proper Citation:</p><p dir="ltr">Zomer, R.J.; Xu, J.; Trabuco, A. 2022. …”

NanoDB: Research Activity Data Management System by Lorenci Gjurgjaj (19702207)

“…In a Python environment or as an executable. Ease of Implementation: Using the flexibility of the Python framework all the data setup and algorithm can me modified and new functions can be easily added. …”

Data and some code used in the paper:<b>Expansion quantization network: A micro-emotion detection and annotation framework</b> by Zhou (20184816)

“…</p><p dir="ltr">GPU：NVIDIA GeForce RTX 3090 GPU</p><p dir="ltr">Bert-base-cased pre-trained model: https://huggingface.co/google-bert/bert-base-cased</p><p dir="ltr">python=3.7，pytorch=1.9.0，cudatoolkit=11.3.1，cudnn=8.9.7.29.…”

The codes and data for "Lane Extraction from Trajectories at Road Intersections Based on Graph Transformer Network" by Chongshan Wan (19247614)

“…</li></ul><h2>Codes</h2><p dir="ltr">This repository contains the following Python codes：</p><ul><li>`data_processing.py`: Contains the implementation of data processing and feature extraction. …”