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.…”

3D PD-Controlled Nanorobot Swarm Simulation for Targeted Cancer and BBB Therapy by Umar Tabbsum (22058780)

“…</p><p dir="ltr">Implemented in Python (NumPy, Matplotlib, 3D visualization), the framework is fully annotated and reproducible. …”

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. …”

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

“…The full implementation is detailed in the accompanying Python script (Imputation_Air_Pollutants_NABEL.py). …”

The artifacts and data for the paper "DD4AV: Detecting Atomicity Violations in Interrupt-Driven Programs with Guided Concolic Execution and Filtering" (OOPSLA 2025) by zixuan yuan (17602152)

“…</p><pre><pre>sudo apt-get install -y wget git build-essential python3 python python-pip python3-pip tmux cmake libtool libtool-bin automake autoconf autotools-dev m4 autopoint libboost-dev help2man gnulib bison flex texinfo zlib1g-dev libexpat1-dev libfreetype6 libfreetype6-dev libbz2-dev liblzo2-dev libtinfo-dev libssl-dev pkg-config libswscale-dev libarchive-dev liblzma-dev liblz4-dev doxygen libncurses5 vim intltool gcc-multilib sudo --fix-missing<br></pre></pre><pre><pre>pip install numpy && pip3 install numpy && pip3 install sysv_ipc<br></pre></pre><h4><b>Download the Code</b></h4><p dir="ltr">Download <b>DD4AV</b> from the Figshare website to your local machine and navigate to the project directory:</p><pre><pre>cd DD4AV<br></pre></pre><h4><b>Configure Environment and Install the Tool</b></h4><p dir="ltr">For convenience, we provide shell scripts to automate the installation process. …”

Void-Center Galaxies and the Gravity of Probability Framework: Pre-DESI Consistency with VGS 12 and NGC 6789 by 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. …”

<b>DeepB3Pred</b> by Saleh Musleh (22263718)

“…MCTD is the implementation of composition-transition and distribution, and GSFE is the implementation of graphical and statistical-based feature engineering.…”

DeepB3Pred - code by Saleh Musleh (22263718)

“…MCTD is the implementation of composition-transition and distribution, and GSFE is the implementation of graphical and statistical-based feature engineering.…”

DeepB3Pred_source_code by Muhammad Arif (17012472)

“…Testing dataset TS_BB includes BBB_pos and BBB_neg testing samples</p><p dir="ltr">**Feature_Extraction: CPSR is the implementation of component protein sequence representation. mctd is the implementation of composition-transition and distribution, GSFE is the implementation of Graphical and statistical-based feature engineering.…”

SEPARATE Code Repository by Gyuri Kim (21424973)

“…<p dir="ltr">Python implementation of the SEPARATE, which enables three-dimensional multiplexed fluorescence imaging by pairing proteins based on their spatial expression patterns and computationally unmixing signals using deep learning.…”

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

“…<p dir="ltr">NanoDB is a Python-based application developed to optimize the management of experimental data in research settings. …”

MSc Personalised Medicine at Ulster University by Steven Watterson (100045)

“…</b> This module introduces the techniques needed to be able to work with high dimensional data (big data) and the mathematics that underpins the fundamental data science. Coding in Python, we learn how to analyse data and explore machine learning/AI based analysis</p><p dir="ltr">· <b>MPM708: Research Project (60 credits).…”

Optimized Bayesian regularization-back propagation neural network using data-driven intrusion detection system in Internet of Things by Ashok Kumar K (21441108)

“…The proposed DIDS-BRBPNN-BBWOA-IoT method is implemented using Python. The performance of the DIDS-BRBPNN-BBWOA-IoT approach is examined using performance metrics like accuracy, precision, recall, f1-score, specificity, error rate; computation time, and ROC. …”

Supplementary Material by Aris Shahbazian (22464325)

“…The supplementary material includes the full Python-based implementation of the AI-driven optimization framework described in the manuscript. …”

Soulware-Lite by Abhiram Gnyanijaya (21572942)

“…It operates as middleware to intercept user inputs and LLM outputs, performing real-time semantic auditing, belief-state tracking, introspective alignment scoring (KRW, deltaΨ), and automated self-correction.…”

Microscopic Detection and Quantification of Microplastic Particles in Environmental Water Samples by Derek Lam (11944213)

“…Image processing algorithms, implemented in Python using adaptive thresholding techniques, were applied to segment particles from the background. …”

Data Sheet 1_COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices.pdf by Rafael Pereira Lemos (9104911)

“…Here, we introduce COCαDA (COntact search pruning by Cα Distance Analysis), a Python-based command-line tool for improving search pruning in large-scale interatomic protein contact analysis using alpha-carbon (Cα) distance matrices. …”

adnus by Mehmet Keçeci (14301782)

“…<p dir="ltr">adnus (AdNuS): Advanced Number Systems</p><p dir="ltr">adnus is a Python library that provides an implementation of various advanced number systems. …”

Gene Editing using Transformer Architecture by Rishabh Garg (5261744)

“…</p><p dir="ltr">Once TASAG detects a deviation from a reference sequence (e.g., the H-Bot sequence), it facilitates on-screen gene editing, enabling targeted mutations or the insertion of desired genes. Implementation requires Python and deep learning frameworks like TensorFlow or PyTorch, with optional use of Biopython for genetic sequence handling. …”

Computational performance analysis script. by Le Qi (8859521)

“…<p>Python implementation for computational performance evaluation and timing analysis.…”