Archive of data and code associated with the publication "<b>Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes</b>" by Beckwith, Brunner, e... by Kai Sandvold Beckwith (19646290)

“…</p><p dir="ltr">run_LE_sim.ipynb: Jupyter notebook containing code examples to run 1D loop extrusion simulations to be used as input for dynamic polymer simulations.</p><p dir="ltr">run_polychrom_LE.py: Executable python program to run dynamic polychrom simulations based on the 1D loop extrusions. …”

Code for AOP-DB v3 by Brandy Wilkinson (20827586)

Spectral inclusion and pollution for a class of dissipative perturbations - data by Alexei Stepanenko (19655629)

“…The datasets are numpy array (Python programming language) saved as pickle files and can be opened using the pickle package  (see https://docs.python.org/3/library/pickle.html).…”

CpG Signature Profiling and Heatmap Visualization of SARS-CoV Genomes: Tracing the Genomic Divergence From SARS-CoV (2003) to SARS-CoV-2 (2019) by Tahir Bhatti (20961974)

“…</p><p dir="ltr">Tools and Libraries</p><p dir="ltr">The following tools and libraries were used in this analysis:</p><p dir="ltr">Programming Language :</p><p dir="ltr">Python 3.13</p><p dir="ltr">Libraries :</p><p dir="ltr">pandas: For data manipulation and cleaning.…”

Fusion API (Supplementary Information 3) from GrowCAD: Bioinspired Mathematical Design for Additive Manufacturing by Nasim Mahmoodi (11535135)

“…This Python program generates a 3D body using nonguided loft function from cloud points data…”

Fusion API (Supplementary Information 2) from GrowCAD: Bioinspired Mathematical Design for Additive Manufacturing by Nasim Mahmoodi (11535135)

“…This Python program generates a 3D body using a guided rails loft function from cloud points data…”

The Improved Hydro-Sediment Numerical Model and Machine Learning Models by Yuning Tan (20580932)

“…The hydro-sediment model was implemented in the C# programming language using Visual Studio, while the machine learning models were developed in Python.…”

ML-UrineQuant by Warren Hill (20108487)

“…<p dir="ltr">ML-UrineQuant is a machine learning program written in Python for identifying and quantifying mouse urine on absorbent paper. …”

MPCID: A new high-resolution multi-precipitation concentration indicators dataset for mainland China by 栋洋 张 (20515496)

“…</li><li>Data Format<br>CSV files: The station - based annual data in CSV format can be easily opened and analyzed using spreadsheet software like Microsoft Excel or programming languages such as Python with libraries like Pandas.…”

software code of NeoDesign by Wenqian Yu (19730101)

“…Before running the program, it is necessary to check or download python packages and local functions as follow:</p><ul><li>gor4</li><li>mhcflurry</li><li>NetMHCpan4.1</li><li>NetChop3.1</li><li>pepsickle</li><li>hmmer(>3.4)</li></ul><h3>See the read.md file for instructions on how to use the code.…”

Fuzzing: On Benchmarking Outcome as a Function of Benchmark Properties by Dylan Wolff (13565191)

“…Also contains some pre- and post-processing scripts for gathering data</p><p dir="ltr"><code>final-data-analysis</code> -- An R Jupyter notebook and Python scripts used to generate the figures in the paper, along with the cleaned and aggregated data in CSV files</p><p dir="ltr"><code>delay</code> -- Python scripts used to generate the figures for e0 (injecting delays) in the paper</p><p dir="ltr"><code>raw-data</code> -- The raw files output by Fuzzbench for our experiments</p><p dir="ltr">The notebook and scripts should be runnable on the CSV files in that directory without modification. …”

Projected HST/STIS images of Jupiter's FUV aurora by Jonathan Nichols (17840543)

“…The images are in kR projected onto a stereographic projection and, like the NIRCam images, can be read using the accompanying Python code in hstimage.py:</p><p dir="ltr">im = HSTProjImage(filename)</p><p dir="ltr">im.readHSTFile()</p><p dir="ltr">im.tvPolar()</p>…”

Cheyenne River Flood Frequency by Earth Lab (3386570)

“…<p dir="ltr">Streamflow data retrieved from the USGS National Water Information Service (NWIS) with the <code>dataretrievals</code> library with the following query: </p><ul><li>Cheyenne River near Wasta site (site number 06423500)</li><li>Starting 1934-10-01</li><li>Ending 2024-09-30</li></ul><p dir="ltr">Data used in the ESIIL Stars program flood frequency coding challenge and published online on the ESIIL Environmental Data Science Learning Portal.…”

<b>Analysis of Cost Leadership Strategy in Low-Cost Airline Enterprises with Deep Learning Method</b> by ZEHRA YARDI (20284389)

“…The tweets of Ryanair were processed using a program called Knime, which is one of the useful programs. …”

DevCMG: Developer-Centric Automated Commit Message Generation by ZN (21452111)

“…<br><br>---<br><br>## **Datasets**<br>The `dataset` folder contains all 2,683 commits used in this study, covering the following five programming languages:<br>- C++<br>- C#<br>- Java<br>- JavaScript<br>- Python<br><br>---<br><br>## **Baselines**<br>### **State-of-the-Art (SOTA):**<br>- KADEL<br>- OMEGA<br>- DeepSeek-V3<br><br>### **Other Tools:**<br>- GPT-3.5<br>- CmtGen<br>- CoRec<br>- NMT<br>- NNGen<br>- Ptr-net<br><br>---<br><br>## **Experiments**<br><br>### **RQ1: Effectiveness of DevCMG**<br>Commands to run the experiments:<br>python message_generation.py<br>python llm_judge_metrics.py<br><br>## **RQ2: Ablation Study Results**<br><br>| **Approach**                  | **Reasonableness** | **Comprehensiveness** | **Succinctness** | **Normativity** | **Weighted Average** |<br>|-------------------------------|--------------------|-----------------------|------------------|-----------------|-----------------------|<br>| Baseline                      | 3.36              | 2.99                 | 3.32             | 2.18            | 2.9445                |<br>| Without behavior clustering   | 3.39              | 3.37                 | 2.61             | 2.22            | 2.919                 |<br>| Without CCS classification    | 3.59              | 3.18                 | 3.33             | 3.20            | 3.3725                |<br>| **Our approach**              | **3.99**          | **3.91**             | **3.65**         | **3.87**        | **3.891**             |<br><br>---<br><br># **RQ3: Rankings from Different Evaluators**<br><br>| **Evaluator**     | **Ranking**                                                                                                  |<br>|-------------------|------------------------------------------------------------------------------------------------------------|<br>| **Gemini-2.5**    | DevCMG, Zero-Shot, GPT-3.5, OMEGA, KADEL, NNgen, Ptr-net, CmtGen, CoRec, NMT                               |<br>| **GPT-4o**        | DevCMG, Zero-Shot, OMEGA, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **DeepSeek-R1**   | DevCMG, Zero-Shot, OMEGA, GPT-3.5, KADEL, NNgen, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **Qwen-3**        | DevCMG, Zero-Shot, GPT-3.5, OMEGA, KADEL, NNgen, Ptr-net, CoRec, NMT, CmtGen                               |<br>| **ChatGLM-4**     | DevCMG, OMEGA, Zero-Shot, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **Human**         | DevCMG, Zero-Shot, OMEGA, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br><br>## **RQ4: User Study Results**<br><br>The user study results are available in the `/experiments/RQ4` folder. …”

The perceived wealth and physical disorder scores prediction dataset for urban China by Yanji Zhang (22363905)

“…They can be processed using GIS software such as ArcGIS and QGIS, as well as Python programming language packages such as Rasterio. …”

HISTORECO: Historical Spanish transition database on climate, geography, and economics of the 20th-21st Century by Guillermo Rodríguez López (19872589)

“…</p><p dir="ltr">The dataset combines information from twenty sources (databases/articles), harmonizing and downscaling them to the municipal level using GIS and programming tools (mainly QGIS, R, and Python). …”

FANDANGO: Evolving Language-Based Testing by José Antonio Zamudio Amaya (17288821)

“…In FANDANGO, constraints can use the whole Python language and library. This expressiveness gives testers unprecedented flexibility in shaping test inputs. …”

Data and code for: A century of reforestation reduced anthropogenic warming in the eastern United States by Mallory Barnes (9756051)

“…</p><p>All the data can be processed using open-source programs such as R or Python. </p>…”

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. …”