“…This work includes the development and presentation of a new, publicly available mathematics curriculum for the bootcamp on select mathematics topics, including calculus, linear algebra, functions, differential equations, statistics, and coding in Python, aiming at improving students’ confidence and learning experiences in graduate quantum mechanics and statistical physics courses. …”
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“…AVAILABILITY AND IMPLEMENTATION: We have created a Python package that can be installed using the following command: pip install interpretable_tsne. …”
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“…To address these issues, we introduce OpenABC, a software package that greatly simplifies the setup and execution of coarse-grained condensate simulations with multiple force fields using Python scripting. OpenABC seamlessly integrates with the OpenMM molecular dynamics engine, enabling efficient simulations with performance on a single GPU that rivals the speed achieved by hundreds of CPUs. …”
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“…To facilitate implementation and reproducibility, we have made all of our software available through the open-source ChemSpaceAL Python package.…”
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“…The pipeline is implemented with the Nextflow workflow manager using Python and R scripts. It will remain available for at least two years following publication and will be regularly updated and upgraded. …”
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“…We imaged dually labeled (nuclear tdTomato and cytoplasmic GCaMP7s) transgenic Hydra and developed an open-source Python platform (TraSE-IN) for the Tracking and Spike Estimation of Individual Neurons in the animal during behavior. …”
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“…It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. …”
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“…In addition to these new capabilities, RAW has undergone significant technical updates, such as adding Python 3 compatibility, and has entirely new documentation available both online and in the program.…”
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“…Graphical networks resembling real world networks are an important requirement for these studies. Python packages NetworkX and OSMnx are probably the most popular approaches in industry for creating and analyzing real world graphical networks using ESRI Shapefiles (Geospatial Vector Data). …”
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“…MATERIALS AND METHODS: We refactored R-iCARE into a Python package (Py-iCARE) then compiled it to WebAssembly (Wasm-iCARE): a portable web module, which operates entirely within the privacy of the user’s device. …”
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“…Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples. …”
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“…To facilitate the application of this method, we have implemented it in an open-source Python toolbox called physio. This toolbox includes essential functionalities for processing electrocardiogram (ECG) and respiratory signals, while also introducing this new approach for RSA analysis. …”
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“…PyCalibrate can be accessed either by executing the Python code locally or via a user-friendly web portal to further improve accessibility when moving between locations and machines. …”
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“…CSPOT is robust to artifacts that commonly afflict tissue imaging and can replace conventional gating. The end-to-end Python implementation of CSPOT can be integrated into cloud-based image processing pipelines to substantially improve the speed, accuracy, and reproducibility of single-cell spatial data.…”
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“…AVAILABILITY AND IMPLEMENTATION: The corresponding Python package, entitled Nunchaku, is available at PyPI: https://pypi.org/project/nunchaku.…”
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“…Source code in C, Java, and C#, and integration instructions for Perl and Python are provided. CONCLUSION: The uShuffle tool surpasses existing implementation of the Euler algorithm in both performance and flexibility. …”
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“…Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API). …”
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“…Exposure most likely occurred in the Python Cave (Maramagambo Forest), which harbors bat species that elsewhere in Africa have been found positive for Marburg virus. …”
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“…Availability: GimmeMotifs is implemented in Python and runs on Linux. The source code is freely available for download at http://www.ncmls.eu/bioinfo/gimmemotifs/. …”
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“…This approach allows us to use high-level programming languages such as Python, because with vectorized operations, the computational cost of interpretation represents a small fraction of the total cost. …”
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