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  1. 2001
    “…FINDINGS: The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. …”
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    The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
  2. 2002
    “…Here we present StochPy (Stochastic modeling in Python), which is a flexible software tool for stochastic simulation in cell biology. …”
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    StochPy: A Comprehensive, User-Friendly Tool for Simulating Stochastic Biological Processes
  3. 2003
    “…Availability and implementation: Poretools is an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface. …”
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    Poretools: a toolkit for analyzing nanopore sequence data
  4. 2004
    “…The decon1d program is freely available as a downloadable Python script at the project website (https://github.com/hughests/decon1d/).…”
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    Deconvolution of Complex 1D NMR Spectra Using Objective Model Selection
  5. 2005
    “…Previous ecological investigations of large ERB colonies inhabiting Python Cave and Kitaka Mine, Uganda revealed that argasid ticks (Ornithodoros faini) are hematophagous ectoparasites of ERBs. …”
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    No evidence for the involvement of the argasid tick Ornithodoros faini in the enzootic maintenance of marburgvirus within Egyptian rousette bats Rousettus aegyptiacus
  6. 2006
    por Tsuji, Junko, Weng, Zhiping
    Publicado 2016
    “…DNApi is compatible with Python 2 and 3, and is available at https://github.com/jnktsj/DNApi. …”
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    DNApi: A De Novo Adapter Prediction Algorithm for Small RNA Sequencing Data
  7. 2007
    “…However, facultative parthenogenesis occurs in some Squamata, such as Komodo dragon (Varanus komodoensis) and Burmese python (Python bivittatus). Here, we report facultative parthenogenesis in the green anaconda (Eunectes murinus). …”
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    Facultative parthenogenesis validated by DNA analyses in the green anaconda (Eunectes murinus)
  8. 2008
    “…In this respect, the CoLoMoTo Interactive Notebook provides a joint distribution of several logical modeling software tools, along with an interactive web Python interface easing the chaining of complementary analyses. …”
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    Prediction of Mutations to Control Pathways Enabling Tumor Cell Invasion with the CoLoMoTo Interactive Notebook (Tutorial)
  9. 2009
    por Lopin, Prattana, Lopin, Kyle V.
    Publicado 2018
    “…To control the device, a graphical user interface (GUI) was developed in the python programming language. Python is open source, with a style that makes it easy to read and write programs, making it an ideal choice for open source projects. …”
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    PSoC-Stat: A single chip open source potentiostat based on a Programmable System on a Chip
  10. 2010
    “…We present SBEMimage, an open-source Python-based application to operate serial block-face electron microscopy (SBEM) systems. …”
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    SBEMimage: Versatile Acquisition Control Software for Serial Block-Face Electron Microscopy
  11. 2011
    “…SUMMARY: CABS-flex standalone is a Python package for fast simulations of protein structure flexibility. …”
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    CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
  12. 2012
    “…Readers can investigate the R and Python tutorials interactively in the browser using Binder by Project Jupyter.…”
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    Raincloud plots: a multi-platform tool for robust data visualization
  13. 2013
    “…To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. …”
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    iHam and pyHam: visualizing and processing hierarchical orthologous groups
  14. 2014
    “…Method: Instructions on installation of libraries for R and Python, source codes and links to census data are provided in a notebook format to enhance experience with running the software. …”
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    An Introduction to Software Tools, Data, and Services for Geospatial Analysis of Stroke Services
  15. 2015
    “…Links to additional resources, tutorials and package documentation are provided in the 'Python package' section of the website. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    Rhapsody: predicting the pathogenicity of human missense variants
  16. 2016
    “…AVAILABILITY AND IMPLEMENTATION: TreeSAPP was developed in Python 3 as an open-source Python package and is available on GitHub at https://github.com/hallamlab/TreeSAPP. …”
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    TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
  17. 2017
    por Kryś, Justyna D, Gront, Dominik
    Publicado 2021
    “…RESULTS: VisuaLife is a Python library that provides a new approach to visualization in a web browser. …”
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    VisuaLife: library for interactive visualization in rich web applications
  18. 2018
    “…Here we present CytoPy, a Python framework for automated analysis of cytometry data that integrates a document-based database for a data-centric and iterative analytical environment. …”
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    CytoPy: An autonomous cytometry analysis framework
  19. 2019
    “…The runtime of the gpuZoo implementation in MATLAB and Python is up to 61 times faster and 28 times less expensive than multi-core CPU implementation of the same methods. gpuZoo is available in MATLAB through the netZooM package https://github.com/netZoo/netZooM and in Python through the netZooPy package https://github.com/netZoo/netZooPy.…”
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    gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit
  20. 2020
    “…AVAILABILITY AND IMPLEMENTATION: GEnView is implemented in Python 3. Instructions for download and usage can be found at https://github.com/EbmeyerSt/GEnView under GLP3. …”
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    GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids
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