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“…Availability:  DREAMTools is a Python package. Releases and documentation are available at http://pypi.python.org/pypi/dreamtools. …”
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“…This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. …”
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“…Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. …”
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“…We explored potential for spillover and spillback of lung parasites infecting Burmese pythons (Python bivittatus) in their invasive range (Florida). …”
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“…AVAILABILITY AND IMPLEMENTATION: ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org. …”
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“…RESULTS: We introduce cyvcf2, a Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. …”
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“…We present an open-source Python package to compute information-theoretical quantities for electroencephalographic data. …”
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“…It can also be difficult to keep pace with rapidly expanding biological knowledge, which often results in daily changes to any of the over 47,000 gene ontologies that describe biological knowledge. GOATOOLS, a Python-based library, makes it more efficient to stay current with the latest ontologies and annotations, perform gene ontology enrichment analyses to determine over- and under-represented terms, and organize results for greater clarity and easier interpretation using a novel GOATOOLS GO grouping method. …”
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“…RESULTS: PyCoTools is a Python package aimed at providing a high level interface to COPASI tasks with an emphasis on model calibration. …”
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“…refnx is a model-based neutron and X-ray reflectometry data analysis package written in Python. It is cross platform and has been tested on Linux, macOS and Windows. …”
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“…[Image: see text] Using the modern object-oriented programing language Python (e.g., tkinter and pandas modules) and a chemoinformatics open-source library (RDKit), the classic Joback and Reid group contribution method was revisited and written into a graphical user interface program, JRgui. …”
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“…RESULTS: Here, we present Glycosylator, a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its application programming interface (API) or through its graphical user interface (GUI). …”
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“…Here the strategy has been implemented as a Python program for microcrystal data assembly (PyMDA). …”
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“…In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. …”
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“…Aside from the need for high efficiency, there is no package for screening endogenous genes available in Python. Here, we introduce ERgene, a Python library for screening endogenous reference genes. …”
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“…Pipelines can be customized by integrating new Python code, third-party programs, or Python libraries. …”
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“…In this work, we implemented DKI in the Diffusion in Python (DIPY) project—a large collaborative open-source project which aims to provide well-tested, well-documented and comprehensive implementation of different dMRI techniques. …”
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“…In this context, Computational Strain Optimization (CSO) plays a relevant role by putting forward mathematical approaches able to identify potential metabolic modifications to achieve the defined production goals. We present MEWpy, a Python workbench for metabolic engineering, which covers a wide range of metabolic and regulatory modelling approaches, as well as phenotype simulation and CSO algorithms. …”
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