Plotting histograms depicting phylogenetic branch lengths (in amino acid substitutions per site) between homeologous gene pairs for 13 tetraploid genomes. by Amjad Khalaf (22470183)

“…<p>Python script used to extract pairwise branch lengths between homeologous gene pairs for 13 tetraploid genomes, and plot them as histograms. …”

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

Supplement Number 1 by Susama Agarwala (21628328)

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

<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.…”

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. …”

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. …”

<b>Data Availability</b> by Bonyad Ahmadi (20750327)

“…</p><p dir="ltr">python scripts documenting the implementation of the Mixture Density Network (MDN) algorithm, including hyperparameter tuning and uncertainty quantification.…”

<b>Data Availability</b> by Bonyad Ahmadi (20750327)

“…</p><p dir="ltr">python scripts documenting the implementation of the Mixture Density Network (MDN) algorithm, including hyperparameter tuning and uncertainty quantification.…”

Artifact for the IJCAI 2024 paper "Solving Long-run Average Reward Robust MDPs via Stochastic Games" by Krishnendu Chatterjee (15367413)

“…<br></pre></pre><h2>Structure and How to run</h2><p dir="ltr">There are four Python files in the repository.</p><pre><pre>(i) `StrategyIteration.py` is the backend code, containing the implementation of the RPPI algorithm described in the paper.…”

Reproducible Code and Data for figures by Bonyad Ahmadi (20750327)

“…</i></p><p dir="ltr">It contains:</p><p dir="ltr">✅ <b>Python Code</b> – Scripts used for data preprocessing, and visualization.…”

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. …”

software code of NeoDesign by Wenqian Yu (19730101)

“…<h2>Implementation and Dependencies</h2><p dir="ltr">neoDesign was developed with python (recommend>3.9) and shell (bash) language. …”

Simulation Code and Raw Data by Melih Özkurt (22278520)

“…<p dir="ltr">Reproducible code (Python) implementing a symmetrized split-step Fourier method (SSFM), with configuration files for all scans. …”

High-throughput chemical genetics screen and titration of hit compounds vinblastine and vincristine. by Emiri Nakamura (21601773)

“…Scale bar = 100μm. (F) Fiji and Python scripts were used to process, analyze, and plot the high-content high-throughput confocal imaging data. …”

Table & Figure.pdfBrainwaves and Higher-Order Thinking: An EEG Study of Cognitive Engagement in Mathematics Tasks by NORLIZA BINTI MOHAMED (20739875)

“…Raw and Processed Data</p> <p><br></p> <p>EEG brainwave recordings (raw and preprocessed signals)</p> <p><br></p> <p>Neurofeedback score datasets ( Neuron-Spectrum.NET )</p> <p><br></p> <p>Statistical analysis data (e.g., SPSS, MATLAB, or Python files)</p> <p><br></p> <p>Cognitive achievement test scores and student performance data</p> <p><br></p> <p><br></p> <p><br></p> <p>2. …”

Raw Data EEG.pdfBrainwaves and Higher-Order Thinking: An EEG Study of Cognitive Engagement in Mathematics Tasks by NORLIZA BINTI MOHAMED (20739875)

“…Raw and Processed Data</p> <p><br></p> <p>EEG brainwave recordings (raw and preprocessed signals)</p> <p><br></p> <p>Neurofeedback score datasets ( Neuron-Spectrum.NET )</p> <p><br></p> <p>Statistical analysis data (e.g., SPSS, MATLAB, or Python files)</p> <p><br></p> <p>Cognitive achievement test scores and student performance data</p> <p><br></p> <p><br></p> <p><br></p> <p>2. …”

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)

“…Convert the aligned homolog groups from fasta format to phylip format using <i>phylpwrtr.py </i>(this script was deposited on this website).</p><p dir="ltr"><i>python /path_DISCO/phylpwrtr.py input.fa output.fa max_number_allowed_in_sequence_head</i></p><p dir="ltr"><i>python ca_disco.py -i a_text_file_includes_all_homolog_trees -o output.phy -a a_text_file_includes_the_path_of_aligned_homologs -t a_list_file_includes_names_of_the_501_samples -m min_number_of_taxon_allowed_for_each_ortholog</i></p><p dir="ltr">a_text_file_includes_all_homolog_trees: each line of this file include one homolog tree.…”

Replication Package by Fatemeh Hadadi (14651705)

“…</p><p dir="ltr"><br>Requirements:</p><p><br></p><ul><li>Python3 (3.12 is recommended)</li></ul><p dir="ltr">Please consult the file README.md for detailed information.…”

Digital Twin for Chemical Sciences by Jin Qian (19339035)

“…Lastly, we use the Figure 4.ipynb notebook in the 3_outputs folder to plot the subfigures in d), e), f). Observing that Basin Hopping performs better than Gaussian Process, we plot the degeneracy result with 0.1 error cutoff to obtain the subfigures in g), h), i). …”

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.</p><p dir="ltr">Bd21-3_Bd21.Rmd:R script (mrkdown) used to run rQTL and generte Supplementary Fig. 3c (Bd21-3 x Bd21)</p><p dir="ltr">.…”