“…Nanorod lengths were analyzed with a custom-written Python computer script coupled with the Nanorod UI user interface script, thereby generating histograms of particle length. …”
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“…An interactive version of the estimator is at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/ (last accessed 11 March 2022), and we provide a Python module for batch processing. Currently the calculator uses primarily data for antibodies elicited by Wuhan-Hu-1-like vaccination or infection and so is expected to work best for calculating escape from such immunity for mutations relative to early SARS-CoV-2 strains.…”
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“…Our open source software allows easy integration with other Python packages as well as a variety of evolutionary models, including indel models and new hypermutability models that we developed to more realistically represent SARS-CoV-2 genome evolution.…”
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“…Multiplex imaging technologies are increasingly used for single-cell phenotyping and spatial characterization of tissues; however, transparent methods are needed for comparing the performance of platforms, protocols and analytical pipelines. We developed a python software, mplexable, for reproducible image processing and utilize Jupyter notebooks to share our optimization of signal removal, antibody specificity, background correction and batch normalization of the multiplex imaging with a focus on cyclic immunofluorescence (CyCIF). …”
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“…Furthermore, our software framework is implemented in Python to reduce the entrance barrier for future contributions. …”
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“…MATERIALS AND METHODS: Following a model view controller architecture, we developed a web-based tool written in Python 3. RESULTS: Smart Scheduling (SMASCH) system facilitates clinical research and integrated care programs in Luxembourg, providing features to better manage MASPs and speed up management tasks. …”
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“…AVAILABILITY AND IMPLEMENTATION: ATHENA is available as a Python package under an open-source license at: https://github.com/AI4SCR/ATHENA. …”
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“…The pipeline is written in Perl and Python. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.…”
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“…Optocoder is publicly available, open-source and provided as a stand-alone Python package on GitHub: https://github.com/rajewsky-lab/optocoder.…”
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“…The system consists of four python modules that provide rapid access to USEPA inventory data in standard formats and permit filtering and combination of these inventory data. …”
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“…The software was programmed using Python and allowed to import and analyze trajectory data, as well as to export relevant data such as individual and ensemble time-averaged mean square displacements and effective diffusivity, and anomalous transport exponent. …”
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“…In order to make mean-field based analysis tools more accessible, we implemented an extensible, easy-to-use open-source Python toolbox that collects a variety of mean-field methods for the leaky integrate-and-fire neuron model. …”
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“…MATLAB is responsible for data processing and classification, while Python is responsible for communication and real-time transmission between modules, EEG signal collection, and processing. …”
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“…First, 3D scanning and Python are used to measure and fit the radial and ulnar deviation trajectories of healthy participants and patients. 3D printing is then used to manufacture the auxiliary tool for dynamic MRI, and dynamic MRI diagnosis is then conducted to explore the clinical effect. …”
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“…However, using rna-tools requires the installation of a mixture of libraries and tools, basic knowledge of the command line and the Python programming language. To provide an opportunity for the broader community of biologists to take advantage of the new developments in RNA structural biology, we developed rna-tools.online. …”
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“…VisionTool is an open-source python toolbox for semantic features extraction, capable to provide accurate features detectors for different applications, including motion analysis, markerless pose estimation, face recognition and biological cell tracking. …”
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“…This pipeline is coded in Python and is available at https://github.com/fengcong3/HAPPE.…”
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“…FINDINGS: Here, we present spacemake, a modular, robust, and scalable spatial transcriptomics pipeline built in Snakemake and Python. Spacemake is designed to handle all major spatial transcriptomics data sets and can be readily configured for other technologies. …”
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“…Implementation is achieved via a Python library back end and a web application front end built with React and D3.js for visualizations. …”
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“…We found that 1) the genomes of Akkermansia were clustered into four phylogroups with distinct interspecies similarity and different genomic characteristics and 2) A. glycaniphila GP37, a strain of Akkermansia, was isolated from the human gut, whereas previously, it had only been found in python. Amuc III was present in the Chinese population, and Amuc IV was mainly distributed in Western populations. …”
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