Table 8_MMPred: a tool to predict peptide mimicry events in MHC class II recognition.xlsx by Filippo Guerri (17017524)

“…<p>We present MMPred, a software tool that integrates epitope prediction and sequence alignment algorithms to streamline the computational analysis of molecular mimicry events in autoimmune diseases. …”

Order-flow and long-memory in a simulated financial market by Shane Silverman (22497770)

“…This data does not contain Trader IDs (a way of knowing which trade is associated with which trader) and thus one needs to apply a method for generating synthetic trader IDs for these trades. We used the <a href="https://arxiv.org/abs/2503.18199" rel="noreferrer" target="_blank">Maitrier-Loeper-Bouchaud (MLB)</a> algorithm once we had processed this raw data. …”

ImproBR Replication Package by Anonymus (18533633)

“…**Improve**: Enhance using knowledge retrieval and LLM generation<br><br>## RQ2 Evaluation Pipeline<br>To run the RQ2 evaluation pipeline that compares ImproBR-improved, ChatBR-improved, and raw bug reports against ground truth using similarity analysis on 37 duplicate pairs:<br>```bash<br>cd Modified_ChatBR_Similarity_Codes/RQ2/<br>```<br>Then follow the steps in: [`Modified_ChatBR_Similarity_Codes/RQ2/README.md`](<u>Modified_ChatBR_Similarity_Codes/RQ2/README.md</u>)<br><br><br>## Troubleshooting<br><br>### API Configuration Issues<br><br>**LLM Connection Errors:**<br>- Ensure `AZURE_API_KEY` is valid and not expired<br>- Verify `AZURE_RESOURCE_NAME` matches your Azure OpenAI resource<br>- Check that your deployment name is exactly "gpt-4o-mini"<br>- Confirm you have sufficient quota/credits in your Azure account<br><br>**Knowledge Base Missing:**<br>If you see "Vector store not found" error:<br>```bash<br>python data/build_full_knowledge_base.py<br>```<br><br>### Common Installation Issues<br><br>**ChromaDB Installation Problems:**<br>If ChromaDB fails to install, try:<br>```bash<br>pip install --upgrade pip<br>pip install chromadb==0.4.15 --no-cache-dir<br>```<br><br>Alternative: Install without ChromaDB and use local embeddings<br>```bash<br>pip install -r requirements.txt --exclude chromadb<br>```<br><br>**Requirements Installation Failures:**<br>If requirements.txt fails, install core dependencies first:<br>```bash<br>pip install torch==2.8.0 transformers==4.30.2 sentence-transformers==2.2.2<br>pip install azure-ai-inference==1.0.0b1 openai==1.107.0<br>pip install requests==2.32.5 tqdm==4.67.1 colorama==0.4.6<br>```<br><br>Then install remaining packages:<br>```bash<br>pip install -r requirements.txt<br>```<br><br>**Python Version Compatibility:**<br>- **Minimum**: Python 3.8<br>- **Maximum**: Python 3.11.x<br>- **Recommended**: Python 3.9-3.11<br>- **Known Issues**: Python 3.12+ not supported due to package conflicts<br><br>### Configuration Issues<br><br>**Missing config.py:**<br>Copy template and edit with your API keys:<br>```bash<br>cp config.py.template config.py<br>```<br>Edit config.py with your Azure OpenAI credentials.…”

Raw and derived data: The quantification of downhole fractionation for laser ablation mass spectrometry by Jarred Lloyd (4825671)

“…</p><p dir="ltr">The zip file "DerivedData" contains two CSV files generated by the accompanying Julia code that processes data in preparation for fitting orthogonal polynomials that quantify the dowhnhole fractionation of these analyses and generates the figures for the publication.…”

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

“…Each color represents a distinct cluster.</p><p dir="ltr"><b>Code to generate:</b></p><pre><pre>import geopandas as gpd<br>import matplotlib.pyplot as plt<br><br>gdf = gpd.read_file('.…”

Aluminum alloy industrial materials defect by Ying Han (20349093)

“…</p><p dir="ltr">All code has been tested on Windows computers with Anaconda and CUDA-enabled GPUs. …”

Multi-Offset Synthetic GPR Data by Giacomo Roncoroni (16630053)

“…<p dir="ltr"><b>Overview</b></p><p dir="ltr">This repository contains the data and scripts related to the paper titled "A realistic 2D multi-offset, multi-frequency synthetic GPR data set as a benchmark for testing new algorithms" The data set includes synthetic GPR data generated using gprMax, detailed descriptions of the acquisition geometry, and the required Conda environment for running the associated Jupyter notebooks.…”

Robust Multi-Model Subset Selection by Anthony-Alexander Christidis (6949055)

“…The <a href="https://doi.org/10.1080/10618600.2025.2596057" target="_blank">supplementary material</a> contains all theoretical proofs, additional algorithmic and computational details, and the code and data to reproduce our numerical results.…”

<b>Road intersections Data with branch information extracted from OSM</b> & <b>C</b><b>odes to implement the extraction </b>&<b> I</b><b>nstructions on how to </b><b>reproduce each... by Zihao Tang (19794537)

“…Each script plays a specific role in the overall process:</p><ul><li><b>bufferThin.py</b>: Implements a thinning algorithm to generate a skeleton of buffered road geometry.…”

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

“…Version 3.0 has been deprecated due to the discovery of a data inconsistency in the calculation of net longwave radiation in the source code used to generate the dataset. As a result, there is a general positive bias in potential evapotranspiration (ET₀) and a consequent lower (drier) bias in the Aridity Index (AI) in affected outputs. …”

Supplementary Data: Biodiversity and Energy System Planning - Queensland 2025 by Andrew Rogers (17623239)

“…</p><ul><li>Spatial Resolution: The analysis uses a working spatial resolution of 250-meter grid cells to generate Candidate Project Areas (CPAs).</li><li>Core Tool: CPAs are generated using a custom fork of the source code (released with this Article) supplied by the Multi-criteria Analysis for Planning Renewable Energy (MapRE) initiative.…”

Supporting Data for “All-temperature barocaloric effects at pressure-induced phase transitions” by Zhao Xueting (21796316)

“…The structure search for the low-temperature phase was conducted using the generic evolutionary algorithm implemented in the USPEX code^42–44. …”

Supplementary data for the publication in Clinical Epigenetics, <b>Allelic Expression Patterns of Imprinted and Non-imprinted Genes in Cancer Cell Lines from Multiple Histologies.... by Julia Krushkal (18276223)

“…</p><p dir="ltr">The source code for the pipeline for generating the data is provided in the archive <b>Source_code.zip</b>. …”

MCCN Case Study 2 - Spatial projection via modelled data by Donald Hobern (21435904)

“…All case studies end with generation of an RO-Crate data package including the source data, the notebook and generated outputs, including netcdf exports of the datacubes themselves.…”

Survey Data on NSSI, Stress Response, Emotional Regulation Strategies and gender in Chinese Undergraduates by Yilin Ma (21154754)

“…</li><li>Recommended software: R (packages <b>tidyverse</b>, <b>networktools</b>, <b>devtools</b>, <b>qgraph</b>/<b>bootnet and nodeIdentifyR</b>)</li><li>Considering the simulated generation process of the NIRA algorithm and the randomness of bootstrapping in the Bootnet package, slight variations may occur in the changes of total scores after each silico intervention.…”

3D Deformable cell based model. by Roland M. Dries (6620132)

“…(<b>F</b>) Cell model algorithm, shown as pseudo code.</p>…”

A dataset mapping the temperate savanna in Northeastern China (2022) by Xiaoya Li (19531363)

“…The derived method provides a new insight to explore the extent of regional and global savannain the future.</p><p dir="ltr">The code and generated maps are publicly accessible. …”

Dataset for Partial Parallelism Plot Analysis in Neurodegeneration Biomarker Assays (2010–2024) by Axel Petzold (7076261)

“…<br></p><p dir="ltr">Each dataset entry is annotated with:</p><ul><li>Sample type (serum, plasma, cerebrospinal fluid)</li><li>Assay platform and dilution steps</li><li>Classification of outcome (partial parallelism achieved or not)</li></ul><p dir="ltr"><b>Use cases:</b><br>This dataset is designed to help researchers, assay developers, and meta-analysts to:</p><ul><li>Reproduce figures and analyses from the published review</li><li>Benchmark or validate new assay performance pipelines</li><li>Train algorithms for automated detection of dilutional non-parallelism</li></ul><p dir="ltr"><b>Files included:</b></p><ul><li><code>.csv</code> files containing dilution–response data</li><li>Metadata spreadsheets with assay and sample annotations</li></ul><p></p>…”

Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain by Robert Schnabel (236298)

“…However, the growing appeal of a “universal” algorithm has magnified the unknown impacts when used with non-human species. …”

A Dataset on the Biodiversity Footprints and Sectoral Differences in China by haiyue wang (20803663)

“…It comprises the following components: (1) China’s raw species spatial data, sourced from the IUCN and BirdLife International, with 446 threatened and near-threatened species attributes provided in a CSV file. (2) Biodiversity footprint data of China's 19 economic sectors across 30 provinces (2017), with two versions: Version 1: 352 species (excluding NT species) Version 2: 446 species (including NT species) Stored as “2017 China Provincial Biodiversity Footprint Data” in Shapefile format. (3) Biodiversity footprint data by taxonomic group (Mammal, Amphibian, Reptile, and Bird) across 30 provinces (2017), with two versions as above, stored as “2017 China Taxonomic Biodiversity Footprint Data” in Shapefile format. (4) A procedural demonstration of matrix operations with detailed algorithmic steps for specific species, stored as “An example detailing the computational steps for specific species” in PDF format. (5) Code.…”