“…Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.…”
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“…CONCLUSIONS: ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net. …”
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“…Finally, fastGEAR correctly identified many known recombination hotspots and pointed to potential new ones. Matlab code and Linux/Windows executables are available at https://users.ics.aalto.fi/~pemartti/fastGEAR/ (last accessed February 6, 2017).…”
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“…The combination of chemalot and chemalot_knime not only facilitates the compilation and maintenance of sequences of command line programs but also allows KNIME workflows to take advantage of the compute power of a LINUX cluster. RESULTS: Use of the command line programs is demonstrated in three different workflow examples: (1) A workflow to create a data file with project-relevant data for structure–activity or property analysis and other type of investigations, (2) The creation of a quantitative structure–property-relationship model using the command line programs via KNIME nodes, and (3) The analysis of strain energy in small molecule ligand conformations from the Protein Data Bank database. …”
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“…The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. …”
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“…Webserver at http://diversity.ncl.res.in/; standalone (Mac OS X/Linux) from https://github.com/NarlikarLab/DIVERSITY/releases/tag/v1.0.0.…”
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“…CONCLUSIONS: Finally, we implemented the proposed method into R and tested extensibility and usability on Windows, MacOS, and Linux operating systems. The method, MySort, is wrapped as the Galaxy platform pluggable tool and usage details are available at https://testtoolshed.g2.bx.psu.edu/view/moneycat/mysort/e3afe097e80a.…”
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“…Our evaluations indicate that i2b2 containers function successfully on the Linux platform. Our results demonstrate that the containerized components work out-of-the-box, with minimal configuration. …”
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“…RESULTS: We have successfully generated executables for Linux, Mac, and Windows from a single code-base, and we have shown that performance need not be completely sacrificed when building a cross-platform application. …”
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“…NGmerge is available on GitHub (https://github.com/harvardinformatics/NGmerge) under the MIT License; it is written in C and supported on Linux. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2579-2) contains supplementary material, which is available to authorized users.…”
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“…The source code is freely available, and is implemented in Windows and Linux operation system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2670-3) contains supplementary material, which is available to authorized users.…”
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“…CONCLUSIONS: svist4get is implemented in Python 3 and runs on Linux. The command-line interface of svist4get allows for easy integration into bioinformatics pipelines in a console environment. …”
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“…CONCLUSION: The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/. …”
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“…VCF2CNA is a tool (Linux commandline or web-interface) for copy-number alteration (CNA) analysis and tumor purity estimation of paired tumor-normal VCF variant file formats. …”
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“…However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment. MAIN BODY: Here, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. …”
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“…Written in Python 3, EMULSION runs on Linux, MacOS, and Windows. It is released under Apache-2.0 license. …”
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“…AVAILABILITY AND IMPLEMENTATION: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. …”
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“…As a Perl script, there is no obstacle to running PGsim on any version of the MAC OS or Linux systems, and no libraries, packages, interpreters, compilers, or other dependencies need to be installed in advance. …”
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“…CONCLUSION: SEQing is written in Python3 and runs on Linux. The web-based access makes iCLIP data easily accessible, even with mobile devices. …”
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“…The software is written using the NextFlow framework for parallelization and portability, and relies on Linux containers such as Docker and Singularity for achieving better reproducibility. …”
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