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  1. 3501
    “…The package uses the Synchrotron Radiation Workshop (SRW) C/C++ library and its Python binding for numerical wavefront propagation simulations. …”
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    WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations
  2. 3502
    “…National Library of Medicine (NLM). A Python code was used to eliminate duplications in the final bibliography. …”
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    A four-part working bibliography of neuroethics: part 3 – “second tradition neuroethics” – ethical issues in neuroscience
  3. 3503
    “…Finally, IMP is encapsulated within a user-friendly implementation using Python and Docker. IMP is available at http://r3lab.uni.lu/web/imp/ (MIT license). …”
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    IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses
  4. 3504
    “…The current PIPE-chipSAD implementation is written in Python programming language and is freely available at https://github.com/silviamicroarray/chipSAD.…”
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    PIPE-chipSAD: A Pipeline for the Analysis of High Density Arrays of Bacterial Transcriptomes
  5. 3505
    “…DGW is available as an open source Python package.…”
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    DGW: an exploratory data analysis tool for clustering and visualisation of epigenomic marks
  6. 3506
    “…Both algorithms are available in a Python package.…”
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    Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections
  7. 3507
    por Ravignani, Andrea
    Publicado 2018
    “…The annotated onsets and offsets of vocalizations were then imported in a Python script. The script extracted three types of timing information: the duration of calls, the intervals between calls’ onsets, and the intervals between calls’ maximum-intensity peaks. …”
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    Spontaneous rhythms in a harbor seal pup calls
  8. 3508
    “…A software implementation is available as an open-source Python program called JRA at https://bitbucket.org/jointreadalignment/jra-src.…”
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    Jointly aligning a group of DNA reads improves accuracy of identifying large deletions
  9. 3509
    “…The methods are illustrated with data acquired in Cape Range National Park, Western Australia (WA), Australia, orthorectified in Agisoft Photoscan Pro, and processed in Python programming language, scikit-learn, and eXtreme Gradient Boosting (XGBoost) libraries. …”
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    UAVs and Machine Learning Revolutionising Invasive Grass and Vegetation Surveys in Remote Arid Lands
  10. 3510
    “…AVAILABILITY AND IMPLEMENTATION: NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?…”
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    NucliTrack: an integrated nuclei tracking application
  11. 3511
    “…AVAILABILITY AND IMPLEMENTATION: Source code in Julia and Python, and detailed documentation is available at https://github.com/gersteinlab/HiC-spector. …”
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    HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
  12. 3512
    “…MATERIALS AND METHODS: The software was developed using Python programming language and open source libraries. …”
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    Pilot Study of an Open-source Image Analysis Software for Automated Screening of Conventional Cervical Smears
  13. 3513
    “…This paper presents pyBadlands, an open-source python-based framework which computes over geological time (1) sediment transport from landmasses to coasts, (2) reworking of marine sediments by longshore currents and (3) development of coral reef systems. pyBadlands is cross-platform, distributed under the GPLv3 license and available on GitHub (http://github.com/badlands-model). …”
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    pyBadlands: A framework to simulate sediment transport, landscape dynamics and basin stratigraphic evolution through space and time
  14. 3514
    “…This trained potential, simply dubbed “TensorMol-0.1”, is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. …”
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    The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics
  15. 3515
    por Kofler, Robert
    Publicado 2018
    “…AVAILABILITY AND IMPLEMENTATION: SimulaTE is implemented in Python and available at https://sourceforge.net/projects/simulates/. …”
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    SimulaTE: simulating complex landscapes of transposable elements of populations
  16. 3516
    “…These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. …”
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    fastp: an ultra-fast all-in-one FASTQ preprocessor
  17. 3517
    por Budach, Stefan, Marsico, Annalisa
    Publicado 2018
    “…To enable researchers to utilize these networks more easily, we implemented pysster, a Python package for training CNNs on biological sequence data. …”
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    pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks
  18. 3518
    “…We implemented our approach as an open-source Python module called DeCAF (Discrimination, Comparison, Alignment tool for 2D PHarmacophores), freely available at http://bitbucket.org/marta-sd/decaf. …”
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    DeCAF—Discrimination, Comparison, Alignment Tool for 2D PHarmacophores
  19. 3519
    por Kómár, Péter, Kural, Deniz
    Publicado 2018
    “…AVAILABILITY AND IMPLEMENTATION: The Python library geck, and usage examples are available at the following URL: https://github.com/sbg/geck, under the GNU General Public License v3. …”
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    geck: trio-based comparative benchmarking of variant calls
  20. 3520
    “…These techniques, implemented as the Python package KinDA, will allow researchers to predict the kinetic and thermodynamic behaviour of domain-level systems after sequence assignment, as well as to detect violations of the intended behaviour.…”
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    Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems
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