Mechanomics Code - JVT حسب Carlo Vittorio Cannistraci (5854046)

"…At the beginning of the code, there is a help section that explains how to use it.<br></li><li>Python (written by Syed Shafat Ali and tested by Yan Ge): analogous functions of the MATLAB folder. …"

Decoding fairness motivations - repository حسب Sebastian Speer (6489207)

"…</div><div>To obtain neural activation patterns for multivariate analysis individual time series were modeled using a double γ hemodynamic response function in a single trial GLM design using FSL’s FEAT. …"

COI reference sequences from BOLD DB حسب John Sundh (12853901)

"…<br>The file bold_clustered.sintax.fasta.gz is directly compatible with the SINTAX algorithm in vsearch while files bold_clustered.assignTaxonomy.fasta.gz and bold_clustered.addSpecies.fasta.gz are directly compatible with the assignTaxonomy and addSpecies functions from DADA2, respectively. …"

Least Bridges Graphs حسب Richard Frost (14064363)

"…This toolbox was originally created for analysis of values arising in genetic distance measures. The contained algorithms correct errors in commonly used nearest-neighbor and cluster software that are not designed with distances in mind (e.g. nearest-neighbor topology functions currently found in Python, SPSS, etc).…"

Data Sheet 1_Machine learning models integrating intracranial artery calcification to predict outcomes of mechanical thrombectomy.pdf حسب Guangzong Li (16696443)

"…Eleven ML algorithms were trained and validated using Python, and external validation and performance evaluations were conducted. …"

PySilsub—a toolbox for silent substitution حسب Joel Martin (11864048)

"…Device settings that will produce lights to selectively stimulate the photoreceptor(s) of interest can be found using a variety of analytic and algorithmic approaches. …"

Presentation_1_NeuroEditor: a tool to edit and visualize neuronal morphologies.pdf حسب Ivan Velasco (9463019)

"…Moreover, NeuroEditor can be easily extended by users, who can program their own algorithms in Python and run them within the tool. Last, this paper includes an example showing how users can easily define a customized workflow by applying a sequence of editing operations. …"

BrainPepPass: all scripts حسب Ewerton de Oliveira (16033631)

"…</p> <p><br></p> <p>Obs: Among the compressed files, there is the sLE_functions.py script. This script is responsible for providing the necessary functions of the sLE algorithms to run BrainPepPass framework.…"

A paired dataset of multi-modal MRI at 3 Tesla and 7 Tesla with manual hippocampal subfield segmentations on 7T T2-weighted images حسب Shuyu Li (18401358)

"…This dataset is designed to support the development and evaluation of both 3T-to-7T MR image synthesis models and automated hippocampal segmentation algorithms on 3T images. We assessed the image quality using MRIQC. …"

CSPP instance حسب peixiang wang (19499344)

"…</b></p><p dir="ltr">Its primary function is to create structured datasets that simulate container terminal operations, which can then be used for developing, testing, and benchmarking optimization algorithms (e.g., for yard stacking strategies, vessel stowage planning).…"

The software structure. حسب Moritz Hoffmann (6411821)

"…<p><b>(a)</b> Python user interface: Provides a Python binding to the “C++ user interface” with some additional convenience functionality. …"

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

"…This study demonstrates: 1) Description of spatial assets using STAC, 2) Loading heterogeneous data sources into a cube, 3) Spatial projection in xarray using different algorithms offered by the <a href="https://pypi.org/project/PyKrige/" rel="nofollow" target="_blank">pykrige</a> and <a href="https://pypi.org/project/rioxarray/" rel="nofollow" target="_blank">rioxarray</a> packages.…"

VinaLigGen: a method to generate LigPlots and retrieval of hydrogen and hydrophobic interactions from protein-ligand complexes حسب Raghvendra Agrawal (17135479)

"…This paper describes an implementation of an automation technique on the executable programs like ligplot.exe, hbplus.exe and hbadd.exe to obtain the 2D interaction map (LigPlots) of the protein and ligand complex (*.ps) and hydrogen bonds and hydrophobic interactions in *.csv format for molecules to be considered for virtual screening by using some sorting & searching algorithms and python’s file handling functions, and it also mentions the program’s limitations and availability of the program. …"

Data_Sheet_1_MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence.docx حسب Mehdi Foroozandeh Shahraki (9555317)

"…MCIC is freely available as a python package and standalone toolkit for Windows and Linux-based operating systems with several functions to facilitate the screening and thermal and pH dependence prediction of cellulases.…"

Barro Colorado Island 50-ha plot aerial photogrammetry orthomosaics and digital surface models for 2018-2023: Globally and locally aligned time series. حسب Vicente Vasquez (13550731)

"…We first computed a grid of co-registration point using arosics.COREG_LOCAL function and used the highest reliability point position to globally align to the closest date orthomosaics. …"

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

"…</p><p dir="ltr"><b>Input:</b></p><ul><li><code>perception_module/output_data/glasgow_perception.nc</code> - Perception scores from Step 2</li></ul><p dir="ltr"><b>Command:</b></p><pre><pre>python cluster_module/cluster_perceptions.py<br></pre></pre><p dir="ltr"><b>Output:</b></p><ul><li><code>cluster_module/output_data/clusters.shp</code> - Shapefile of neighbourhood boundaries</li></ul><h2>Quick Test</h2><p dir="ltr">To test the clustering module with demo data:</p><pre><pre>python cluster_module/cluster_perceptions.py<br></pre></pre><p dir="ltr">This uses the pre-computed embeddings from <code>perception_module/pred_output/20250626_*_embedding_efficientnet.nc</code>.…"

Polygon vector map distortion for increasing the readability of one-to-many flow maps: data and codes حسب Laetitia Viau (14057463)

"…This directory contains: </p> <p>- README file,</p> <p>- server.py: can be run from the command line to create a local server (`python3 server.py or python server.py`). This is not mandatory, it is possible to use any other solution to create a local server. …"

UMAHand: Hand Activity Dataset (Universidad de Málaga) حسب Eduardo Casilari (3333906)

"…</p><p dir="ltr">Finally, the SCRIPTS subfolder comprises two scripts written in Python and Matlab. These two programs (named Load_traces), which perform the same function, are designed to automate the downloading and processing of the data. …"

Expression vs genomics for predicting dependencies حسب Broad DepMap (5514062)

"…"dim_0" holds the row/index names as an array of strings, "dim_1" holds the column names as an array of strings, and "data" holds the matrix contents as a 2D array of floats. In python, these files can be read in with:</p><p dir="ltr"><br></p><p dir="ltr"> import pandas as pd</p><p dir="ltr"> import h5py</p><p dir="ltr"><br></p><p dir="ltr"> def read_hdf5(filename):</p><p dir="ltr"> src = h5py.File(filename, 'r')</p><p dir="ltr"> try:</p><p dir="ltr"> dim_0 = [x.decode('utf8') for x in src['dim_0']]</p><p dir="ltr"> dim_1 = [x.decode('utf8') for x in src['dim_1']]</p><p dir="ltr"> data = np.array(src['data'])</p><p dir="ltr"><br></p><p dir="ltr"> return pd.DataFrame(index=dim_0, columns=dim_1, data=data)</p><p dir="ltr"> finally:</p><p dir="ltr"> src.close()</p><p dir="ltr"><br></p><p>##################################################################</p><p dir="ltr">Files (not every dataset will have every type of file listed below):</p><p>##################################################################</p><p dir="ltr"><br></p><p dir="ltr">AllFeaturePredictions.hdf5: Matrix of cell lines by perturbations, with values indicating the predicted viability using a model with all feature types.…"

Skeletal_ Muscle_MRI_Registration حسب Lucia Fontana (9435020)

"…</p> <p>wxPython library was employed to develop the GUI, which is composed by two main windows – initial window and registration window – and 5 secondary frames for support functionalities. 3D images are presented with three views – axial, coronal and sagittal – with three sliders to adjust maximum value, minimum value, and gamma correction.…"