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  1. 2941
    “…However, PathoQC is also available as an open-source Python module that can run as a stand-alone application or can be easily integrated into any bioinformatics workflow. …”
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    PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets
  2. 2942
    “…NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.…”
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    NxRepair: error correction in de novo sequence assembly using Nextera mate pairs
  3. 2943
    “…We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. …”
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    ANNarchy: a code generation approach to neural simulations on parallel hardware
  4. 2944
    por Pernstich, K. P.
    Publicado 2012
    “…The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming.…”
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    Instrument Control (iC) – An Open-Source Software to Automate Test Equipment
  5. 2945
    “…Binaries and source code (java and python) are available from http://sourceforge.net/projects/rambok/.…”
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    RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data
  6. 2946
    por Derrible, Sybil, Ahmad, Nasir
    Publicado 2015
    “…The methodology can be applied to any data set and provides a robust means to uncover meaningful patterns and trends. A free python script and a tutorial are also made available to facilitate the application of the method.…”
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    Network-Based and Binless Frequency Analyses
  7. 2947
    “…The NRGsuite is implemented in Python and C/C++ with an easy to use package installer. …”
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    NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
  8. 2948
    “…The script of MaxReport, which is freely available at http://websdoor.net/bioinfo/maxreport/, is developed using Python code and is compatible across multiple systems including Windows and Linux.…”
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    MaxReport: An Enhanced Proteomic Result Reporting Tool for MaxQuant
  9. 2949
    “…They are implemented in Python and supported on Linux. Contact: shimizu@bi.a.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    Automatic generation of bioinformatics tools for predicting protein–ligand binding sites
  10. 2950
    por Newe, Axel
    Publicado 2016
    “…A reference implementation in Python programming language is available.…”
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    Dramatyping: a generic algorithm for detecting reasonable temporal correlations between drug administration and lab value alterations
  11. 2951
    “…Availability and implementation: Source code is freely available at https://github.com/biodev/HitWalker2 and implemented using Python/Django, Neo4j and Javascript (D3.js and jQuery). …”
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    HitWalker2: visual analytics for precision medicine and beyond
  12. 2952
    por Ye, Hao, Yan, Sunting, Jin, Zhijiang
    Publicado 2016
    “…An extensive parametric study is carried out using Python script and FORTRAN subroutine to investigate the influence of geometric parameters on the collapse behavior under combined loads. …”
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    Collapse of Corroded Pipelines under Combined Tension and External Pressure
  13. 2953
    por Ajeet, Verma, Mansi, Rani, Sangeeta, Kumar, A.
    Publicado 2016
    “…This study has been performed with the help of Chemdraw Ultra 7.0, GUSAR online tool for IC(50) and LD(50) predictions, AutoDock Vina (Python Prescription 0.8), and PaDEL software. Results revealed that ligand-protein interaction affinity of all 10 designed molecules ranges from -5.7 Kcal/mol to -5.2 Kcal/mol, which is approximately comparable to pre-existing GABA(1) inhibitor i.e. phenytoin (CID: 1775, ligand-protein interaction affinity is -6.5 Kcal/mol).…”
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    Antitarget Interaction, Acute Toxicity and Protein Binding Studies of Quinazolinedione Sulphonamides as GABA(1) Antagonists
  14. 2954
    “…Availability and implementation: FILTUS is written in Python and runs on Windows, Mac and Linux. Binaries and source code are freely available at http://folk.uio.no/magnusv/filtus.html and on GitHub: https://github.com/magnusdv/filtus. …”
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    FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector
  15. 2955
    “…To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment—a model for how sector properties might be differentially tuned in members of a protein family. …”
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    Evolution-Based Functional Decomposition of Proteins
  16. 2956
    por Sainudiin, Raazesh, Véber, Amandine
    Publicado 2016
    “…We also describe a continuous-time equivalent of the generating, organizing and deleting processes where tree topology and branch lengths are jointly modelled and provide code in SageMath/Python for these algorithms.…”
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    A Beta-splitting model for evolutionary trees
  17. 2957
    “…Availability. fluff is implemented in Python and runs on Linux. The source code is freely available for download at https://github.com/simonvh/fluff.…”
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    fluff: exploratory analysis and visualization of high-throughput sequencing data
  18. 2958
    “…Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info Contact: phil.ewels@scilifelab.se…”
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    MultiQC: summarize analysis results for multiple tools and samples in a single report
  19. 2959
    “…Given that no general use open source algorithm accessible to the bioinformatics community exists for the purposes of separating the two species data, the proposed Disambiguate tool presents a novel approach and improvement to performing sequence analysis of grafted samples. Both Python and C++ implementations are available and they are integrated into several open and closed source pipelines. …”
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    Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples
  20. 2960
    “…Typically just the ‘best fit’ parameter values are reported in the literature. Here we introduce a Python-based software tool, PyHillFit , and describe the underlying Bayesian inference methods that it uses, to infer probability distributions for these parameters as well as the level of experimental observation noise. …”
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    Hierarchical Bayesian inference for ion channel screening dose-response data
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