DataSheet1_Prostruc: an open-source tool for 3D structure prediction using homology modeling.PDF by Shivani V. Pawar (20355171)

“…</p>Methods<p>Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. …”

DataSheet1_Prostruc: an open-source tool for 3D structure prediction using homology modeling.PDF by Shivani V. Pawar (20355171)

“…</p>Methods<p>Prostruc is a Python-based homology modeling tool designed to simplify protein structure prediction through an intuitive, automated pipeline. …”

Computing speed and memory usage. by David Berling (22170661)

“…<b>(b)</b> Physical memory consumption depending on simulated plane in radial and depth direction. Color coding same as in (a). Memory consumption was recorded as the maximum resident size during simulation monitored with the Python built-in module resource. …”

Workflow of segmentation model creation and application. by Vincent Hickl (16947429)

Replication package for Exploring the relation between source code commit information and SonarQube issues by Liviu Marian Berciu (17797934)

“…<p dir="ltr">This item represents a replication package/dataset for the article `Exploring the relation between source code commit information and SonarQube issues`. …”

R codes and curated dataset for “EnoLEX: A Diachronic Lexical Database for the Enggano Language” by Gede Primahadi Wijaya Rajeg (14592023)

“…</p><blockquote><b><i>EnoLEX</i></b><i> represents a network of independent research materials consisting of a </i><a href="https://doi.org/10.25446/oxford.28295648.v1" rel="noreferrer" target="_blank"><i>source dataset</i></a><i>, this repository of source R codes and the curated data, the </i><a href="https://enggano.shinyapps.io/enolex/" rel="noreferrer" target="_blank"><i>online database</i></a><i>, and a conference </i><a href="https://doi.org/10.25446/oxford.27013864.v1" rel="noreferrer" target="_blank"><i>paper</i></a><i>.…”

Extending the pyAFQ software. by John Kruper (18809386)

Smart contract and interface code for Nature Energy "A general form of smart contract for decentralised energy systems management" by Lee Thomas (19655773)

“…This provides the modelled electricity network cost data, the smart contract code, and the Python interface scripts described in the Nature Energy Paper  "A general form of smart contract for decentralised energy systems management." …”

<b>Data and Code from 'The Perfect and Legitimate Bribe': A Transparent Record of Human-AI Collaboration in Legal Scholarship</b> by Joshua Stern (21748181)

“…</p><p dir="ltr">For optimal viewing of `collated-anonymized.txt`, a text editor that can handle long lines without word wrapping is recommended to preserve the indentation that represents the conversational branching structure.</p><p><br></p><p dir="ltr">### **Running Code/Software**</p><p dir="ltr">The provided scripts (`collator-ipynb.txt` and `sentence-ancestry-ipynb.txt`) are Jupyter Notebooks and require a Python 3 environment to run. …”

Data and code from: Hatchery-reared coho salmon develop less otolith deformities in tanks with alternating water flow directions by Leigh Gaffney (1389855)

“…</li><li>Measurements were generated by manually classifying otolith regions in Adobe Photoshop and calculating pixel coverage using a Python script.</li><li>Representative otolith images and details of the classification workflow are provided in the main manuscript figures and Methods section. …”

Prism and scutoid cell shape. by Sophie Theis (4126453)

Application to Drosophila gastrulation. by Sophie Theis (4126453)

Data and Code repository for the paper: <b>Visual loom caused by self- or object-movement elicits distinct responses in mouse superior colliculus</b> by Stefano Zucca (21686006)

“…Binned rates were transformed into z-scores by normalizing to the mean and standard deviation of firing rate across all stimulus conditions.</p><h2>Code Description</h2><p dir="ltr">Shared code contains both MATLAB and Python functions used in the analysis provided in the study. …”

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. …”

Code and parameter package for long-term mapping and object-based typing of freeze–thaw colluvial deposits (1990–2024) along the Yunnan–Tibet corridor by Hui Ye (22308559)

“…Tested with Python 3.x/ArcGIS Pro (ArcPy) and the GEE Code Editor. …”

The format of the electrode csv file by Joseph James Tharayil (21416715)

“…To enable efficient calculation of extracellular signals from large neural network simulations, we have developed <i>BlueRecording</i>, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. …”

The format of the simulation reports by Joseph James Tharayil (21416715)

“…To enable efficient calculation of extracellular signals from large neural network simulations, we have developed <i>BlueRecording</i>, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. …”

The format of the weights file by Joseph James Tharayil (21416715)

“…To enable efficient calculation of extracellular signals from large neural network simulations, we have developed <i>BlueRecording</i>, a pipeline consisting of standalone Python code, along with extensions to the Neurodamus simulation control application, the CoreNEURON computation engine, and the SONATA data format, to permit online calculation of such signals. …”

High-Throughput Mass Spectral Library Searching of Small Molecules in R with NIST MSPepSearch by Andrey Samokhin (20282728)

“…High-level programming languages such as Python and R are widely used in mass spectrometry data processing, where library searching is a standard step. …”

HCC Evaluation Dataset and Results by Jens-Rene Giesen (18461928)