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. …”

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…”

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. …”

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

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.…”

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>…”

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. …”

<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. …”

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).…”

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.…”

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.…”

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.…”

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.…”

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. …”

Tasiyagnunpa Migration 2023 by Earth Lab (3386570)

“…<p dir="ltr">This data snippet contains:</p><ol><li>World Wildlife Fund (WWF) ecoregions</li><li>Occurrence data from the Global Biodiversity Information Facility (GBIF) on Tasiyagnunpa (Lakota name for the western meadowlark) in 2023, accessed with the pygbif library</li></ol><p dir="ltr">Data used in the ESIIL Stars program migration coding challenge and published online on the ESIIL Environmental Data Science Learning Portal.…”

Veery Migration 2023 by Earth Lab (3386570)

“…<p dir="ltr">This data snippet contains:</p><ol><li>World Wildlife Fund (WWF) ecoregions for the Veery </li><li>Occurrence data from the Global Biodiversity Information Facility (GBIF) on Veery thrushes (catharus fuscescens) in 2023, accessed with the pygbif library</li></ol><p dir="ltr">Data used in the University of Colorado Boulder Earth Data Analytics -- Foundations graduate certificate program migration coding challenge and published online on the ESIIL Environmental Data Science Learning Portal.…”

A multi-hop example from the BibSQL dataset. by Zhenyu Wang (580934)

“…We further refined SQL generation using a Program-of-Thoughts (PoT) prompting strategy, which guides the LLM to produce more accurate output by first creating Python pseudocode. …”

Detailed statistics of the BibSQL dataset. by Zhenyu Wang (580934)

“…We further refined SQL generation using a Program-of-Thoughts (PoT) prompting strategy, which guides the LLM to produce more accurate output by first creating Python pseudocode. …”

RNACOREX package workflow. by Aitor Oviedo-Madrid (22553399)

“…In this work, we introduce a new Python package called RNACOREX (RNA CORegulatory network EXplorer and classifier). …”