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  1. 1501
    “…To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. …”
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    IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models
  2. 1502
    “…It is implemented in cross-platform C ++ and binary executables are available for Windows, macOS and Linux.…”
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    Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta
  3. 1503
    “…FluxPyt was tested in Microsoft™ Windows 7 and 10, as well as in Linux Mint 18.2. The availability of a free and open (13)C-MFA software that works in various operating systems will enable more researchers to perform (13)C-MFA and to further modify and develop the package.…”
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    FluxPyt: a Python-based free and open-source software for (13)C-metabolic flux analyses
  4. 1504
    “…PyPhi can be installed with Python’s package manager via the command ‘pip install pyphi’ on Linux and macOS systems equipped with Python 3.4 or higher. …”
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    PyPhi: A toolbox for integrated information theory
  5. 1505
    “…Availability: CRAN project page: https://cran.r-project.org/package=BALCONY and our website: http://www.tunnelinggroup.pl/software/ for major platforms: Linux/Unix, Windows and Mac OS X. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2294-z) contains supplementary material, which is available to authorized users.…”
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    BALCONY: an R package for MSA and functional compartments of protein variability analysis
  6. 1506
    “…We then apply those characteristics to four exemplary cases: Linux kernel development, Bitcoin cryptocurrency, the Wikipedia project, and the Linking Open Drug Data repositories. …”
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    Digital sustainability: basic conditions for sustainable digital artifacts and their ecosystems
  7. 1507
    “…CONCLUSIONS: CHERIPIC allows users to rapidly analyse bulk segregant sequence data and we have made it available as a pre-packaged binary with all dependencies for Linux and MacOS and as Galaxy tool. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2515-5) contains supplementary material, which is available to authorized users.…”
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    Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence
  8. 1508
    “…CABS-flex source code, wiki with examples of use and installation instructions for Linux, macOS and Windows are available from the CABS-flex standalone repository at https://bitbucket.org/lcbio/cabsflex.…”
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    CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
  9. 1509
    “…Executables are provided for Windows, MacOS and Linux platforms, together with a comprehensive manual and tutorials illustrating its flexibility. …”
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    QuantiNemo 2: a Swiss knife to simulate complex demographic and genetic scenarios, forward and backward in time
  10. 1510
    “…AVAILABILITY AND IMPLEMENTATION: GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF. …”
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    GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets
  11. 1511
    “…All tools in the GSS are freely available for download under the GPL v3.0 license and can be run locally on Windows, Mac and Linux systems capable of running R and/or Docker. …”
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    The Gene Sculpt Suite: a set of tools for genome editing
  12. 1512
    “…Here, we describe the OMA pipeline available as a standalone program for Linux and Mac. When run on a cluster, it has native support for the LSF, SGE, PBS Pro, and Slurm job schedulers and can scale up to thousands of parallel processes. …”
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    OMA standalone: orthology inference among public and custom genomes and transcriptomes
  13. 1513
    “…CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. …”
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    CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language
  14. 1514
    “…We present an automated pipeline called gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. We compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser. …”
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    gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
  15. 1515
    “…It can be installed to a local Galaxy instance from the ToolShed (https://toolshed.g2.bx.psu.edu/) or locally on a Linux platform via the command line (https://github.com/PGB-LIV/VAPPER). …”
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    VAPPER: High-throughput variant antigen profiling in African trypanosomes of livestock
  16. 1516
    “…The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. …”
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    ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions
  17. 1517
    “…The remote control of the ROV is executed under a graphical user interface developed in Python, which is suitable for different operating systems, such as GNU/Linux, Windows, Android, and OS X. The proposed ROV can reach up to 100 m underwater, thus solving the issue of divers who can only reach 30 m depth. …”
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    Design and Construction of an ROV for Underwater Exploration
  18. 1518
    “…CONCLUSION: The pipeline is available as open-source software for Linux and OS X. Its modular structure, extensive documentation, and ease of deployment using Anaconda facilitate its adoption by researchers and practitioners of single-cell genomics. …”
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    Integrated Computational Pipeline for Single-Cell Genomic Profiling
  19. 1519
    “…The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.…”
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    AncesTree: An interactive immunoglobulin lineage tree visualizer
  20. 1520
    “…AVAILABILITYAND IMPLEMENTATION: The package glmGamPoi is available from Bioconductor for Windows, macOS and Linux, and source code is available on github.com/const-ae/glmGamPoi under a GPL-3 license. …”
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    glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data
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