Search Results - python interfaces _ reference format*

imzML Writer: An Easy-to-Use Python Pipeline for Conversion of Continuously Acquired Raw Mass Spectrometry Imaging Data to imzML Format by Monaghan, Joseph, Nguyen, Kiera, Woytowich, Nicholas, Keyowski, Alora, Duncan, Kyle D

“…). Here, we present imzML Writer, an easy-to-use Python application with a graphical…”
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SBML2HYB: a Python interface for SBML compatible hybrid modeling by Pinto, José, Costa, Rafael S, Alexandre, Leonardo, Ramos, João, Oliveira, Rui

“… The tool supports a user-friendly export interface with an internal format validator. Two case studies illustrate the use of the sbml2hyb tool…”
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VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions by Freeman, Peter J., Hart, Reece K., Gretton, Liam J., Brookes, Anthony J., Dalgleish, Raymond

“…‐source hgvs Python package (https://github.com/biocommons/hgvs) provides a programmatic interface for parsing, manipulating, formatting, and validating of variants according to the HGVS recommendations, but does not provide a user…”
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Empowering High-Throughput High-Content Analysis of Microphysiological Models: Open-Source Software for Automated Image Analysis of Microvessel Formation and Cell Invasion by Wiggin, Noah, Cook, Carson, Black, Mitchell, Cadena, Ines, Rahal-Arabi, Salam, Asnes, Chandler L., Ivanova, Yoanna, Hettiaratchi, Marian H, Hind, Laurel E, Fogg, Kaitlin C

“…Purpose The primary aim of this study was to develop an open-source Python-based software for the automated analysis of dynamic cell behaviors in microphysiological models using non-confocal microscopy…”
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A fast and efficient python library for interfacing with the Biological Magnetic Resonance Data Bank by Smelter, Andrey, Astra, Morgan, Moseley, Hunter N. B.

“…s. It is primarily maintained and accessed in a flat file ASCII format known as NMR-STAR. While the format is human readable, the size of most BMRB entries makes computer…”
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DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation by Dohmen, Elias, Aubel, Margaux, Eicholt, Lars A, Roginski, Paul, Luria, Victor, Karger, Amir, Grandchamp, Anna

“… Results This work presents a standardized annotation format to document the methodology of de novo gene datasets in a reproducible way…”
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jmzTab-M: A Reference Parser, Writer, and Validator for the Proteomics Standards Initiative mzTab 2.0 Metabolomics Standard by Hoffmann, Nils, Hartler, Jürgen, Ahrends, Robert

“…mzTab 2.0 for metabolomics (mzTab-M) is the most recent standard format developed in collaboration by the Proteomics and Metabolomics Standards Initiatives including contributions by the recently founded Lipidomics Standards Initiative…”
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Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments by Ingargiola, Antonino, Laurence, Ted, Boutelle, Robert, Weiss, Shimon, Michalet, Xavier

“…We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors…”
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Sensortoolkit—A Python Library for Standardizing the Ingestion, Analysis, and Reporting of Air Sensor Data for Performance Evaluation by Kumar, Menaka, Frederick, Samuel G., Barkjohn, Karoline K., Clements, Andrea L.

“… The library compares the collocated air sensor against reference monitor data and includes procedures to reformat both datasets into a standardized format using an interactive setup module…”
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Enhancing RDM in Galaxy by integrating RO-Crate by De Geest, Paul, Coppens, Frederik, Soiland-Reyes, Stian, Eguinoa, Ignacio, Leo, Simone

“…) to enable FAIR and reproducible data analysis. RO-Crate (Soiland-Reyes et al. 2022) is a generic packaging format containing datasets and their description using standards for FAIR Linked Data…”
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pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning by Cordes, Jonas, Enzlein, Thomas, Hopf, Carsten, Wolf, Ivo

“… pyM2aia provides interfaces to its parent application M2aia, which offers interactive capabilities for exploring and annotating MSI data in imzML format…”
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Pythonic Black-box Electronic Structure Tool (PyBEST). An open-source Python platform for electronic structure calculations at the interface between chemistry and physics by Boguslawski, Katharina, Leszczyk, Aleksandra, Nowak, Artur, Brzęk, Filip, Żuchowski, Piotr Szymon, Kędziera, Dariusz, Tecmer, Paweł

“… The package provides an efficient and reliable platform for electronic structure calculations at the interface between chemistry and physics using unique electronic…”
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Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python by Kuehl, Malte, Wong, Milagros N, Wanner, Nicola, Bonn, Stefan, Puelles, Victor G

“… Here we present pytximport, a Python implementation of the tximport R package that supports a variety of input formats, different modes of bias correction, inferential replicates, gene-level…”
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Scalable adaptive assessment framework for collaborative eLearning: a service-oriented AI approach by Hadyaoui, Asma, Cheniti-Belcadhi, Lilia

“… An experimental study involving 250 participants in an online Python programming course demonstrated its effectiveness. SOFIA achieved 92…”
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pvlib iotools—Open-source Python functions for seamless access to solar irradiance data by Jensen, Adam R., Anderson, Kevin S., Holmgren, William F., Mikofski, Mark A., Hansen, Clifford W., Boeman, Leland J., Loonen, Roel

“… However, lack of standardization in data formats and access interfaces across providers constitutes a major barrier to entry for new users. pvlib…”
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QuTiP 2: A Python framework for the dynamics of open quantum systems by Johansson, J.R., Nation, P.D., Nori, Franco

“…We present version 2 of QuTiP, the Quantum Toolbox in Python. Compared to the preceding version [J.R. Johansson, P.D. Nation, F. Nori, Comput. Phys. Commun. 183 (2012) 1760…”
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Bite-Size Python: An Introduction to Python Programming by Speight, April

“…Introduce children to the popular Python programming language through relatable examples and fun projects…”
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Digital signal processing with python programming by Charbit, Maurice

“…The parameter estimation and hypothesis testing are the basic tools in statistical inference.These techniques occur in many applications of data processing.,…”
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Free Analysis and Visualization Programs for Electrochemical Impedance Spectroscopy Coded in Python by SUZUKI, Tohru S., KOBAYASHI, Kiyoshi

“…New programs for fitting using an equivalent circuit model and data visualization of electrochemical impedance spectroscopy were developed using Python and its open-source libraries…”
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An Open and Customizable Software Suite for Systems Engineering and Data Management by Adam, Fabian, Losch, Caroline, Muntinaga, Hauke

“…). In particular, we aim for open interfaces, extensibility and ease of use, with a "single source of truth" data model, to provide a wide range…”
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