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  1. 3481
    “…Availability: BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/.…”
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    POWRS: Position-Sensitive Motif Discovery
  2. 3482
    “…Availability and implementation: 13CFLUX2 is implemented in C++ (ISO/IEC 14882 standard) with Java and Python add-ons to run under Linux/Unix. A demo version and binaries are available at www.13cflux.net. …”
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    13CFLUX2—high-performance software suite for (13)C-metabolic flux analysis
  3. 3483
    “…Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. …”
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    The PARIGA Server for Real Time Filtering and Analysis of Reciprocal BLAST Results
  4. 3484
    “…The same approach can be applied to any system in which reactions (or metabolites) can be assigned a score based on some biological observation, without the limitation of predefined pathways. A Python implementation of ambient is available at http://www.theosysbio.bio.ic.ac.uk/ambient.…”
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    AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response
  5. 3485
    “…Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one.…”
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    Vobi One: a data processing software package for functional optical imaging
  6. 3486
    “…ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. …”
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    ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research
  7. 3487
    “…Our approach comprises a semi-automated stage, where actual surface topographic parameters, obtained using an atomic force microscope, are imported into Maya via a custom Python script, followed by a ‘creative stage', where the bacterial cells and their interactions with the surfaces are visualized using available experimental data. …”
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    Three-dimensional visualization of nanostructured surfaces and bacterial attachment using Autodesk® Maya®
  8. 3488
    “…Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. …”
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    Open Source Software to Control Bioflo Bioreactors
  9. 3489
    “…The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. …”
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    Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm
  10. 3490
    “…We solve this problem through the NeuroElectro project: a Python library, RESTful API, and web application (at http://neuroelectro.org) for the extraction, visualization, and summarization of published data on neurons' electrophysiological properties. …”
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    NeuroElectro: a window to the world's neuron electrophysiology data
  11. 3491
    “…Availability and implementation: The Galaxy Data Manager framework is implemented in Python and has been integrated as part of the core Galaxy platform. …”
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    Wrangling Galaxy’s reference data
  12. 3492
    “…We illustrate Chimera's use of web services with an example workflow that interleaves use of these services with interactive manipulation of molecular sequences and structures, and we provide an example Python program to demonstrate how easily Opal-based web services can be accessed from within an application. …”
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    Enhancing UCSF Chimera through web services
  13. 3493
    “…Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. …”
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    Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial
  14. 3494
    “…The new MMFF functionality can be accessed through a C++/C#/Python/Java application programming interface (API) developed along the lines of the one already available for UFF in the RDKit. …”
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    Bringing the MMFF force field to the RDKit: implementation and validation
  15. 3495
    “…The whole pipeline of methods is implemented in Python and makes use of Pylearn2 and modified parts of Scikit-learn. …”
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    Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images
  16. 3496
    “…RESULTS: For this reason we have developed an intuitive framework-independent Python tool to automate analyses common to a variety of modelling approaches. …”
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    Automatising the analysis of stochastic biochemical time-series
  17. 3497
    “…Availability and implementation: Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de. …”
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    Oasis: online analysis of small RNA deep sequencing data
  18. 3498
    “…These resources were developed within the context of the NanoPUZZLES EU project and include data collection templates, corresponding business rules that extend the generic ISA-TAB-Nano specification as well as Python code to facilitate parsing and integration of these datasets within other nanoinformatics resources. …”
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    An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology
  19. 3499
    “…Tools are provided to perform this method online using the CysBar web-tool (http://CysBar.science.latrobe.edu.au) and offline (python script available from http://github.com/ts404/CysBar). …”
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    Structural homology guided alignment of cysteine rich proteins
  20. 3500
    “…Availability and implementation: SUPER-FOCUS was implemented in Python, and its source code and the tool website are freely available at https://edwards.sdsu.edu/SUPERFOCUS. …”
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    SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
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