“…XplorSeq integrates and extends several commonly used UNIX-based analysis tools by use of a Macintosh OS-X-based graphical user interface (GUI). …”
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“…Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.…”
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“…The software is available for free online for use on UNIX systems at .…”
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“…High-performance implementations are provided for Unix pipeline integration along with a GUI version for interactive use. …”
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“…The custom-written Perl, Python and Unix shell computer scripts used can be readily modified or adapted to suit many different applications. …”
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“…RESULTS: UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. …”
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“…To address this, we have developed an approach in which, after automatic variant calling on a standard unix pipeline, subsequent variant filtering is performed interactively, using AgileExomeFilter and AgilePindelFilter (http://dna.leeds.ac.uk/agile), tools designed for clinical scientists with standard desktop computers. …”
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“…The GRETNA contains several key features as follows: (i) an open-source, Matlab-based, cross-platform (Windows and UNIX OS) package with a graphical user interface (GUI); (ii) allowing topological analyses of global and local network properties with parallel computing ability, independent of imaging modality and species; (iii) providing flexible manipulations in several key steps during network construction and analysis, which include network node definition, network connectivity processing, network type selection and choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics and assessments of relationship between these network metrics and clinical or behavioral variables of interest; and (v) including functionality in image preprocessing and network construction based on resting-state functional MRI (R-fMRI) data. …”
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“…Moreover, to maximize users’ convenience, its stand-alone version can also be downloaded from http://bioinformatics.hitsz.edu.cn/Pse-in-One/download/, and directly run on Windows, Linux, Unix and Mac OS.…”
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“…The software is implemented in C, Python and shell scripting and is capable of running on Linux/Unix platforms. The source code and installation instructions are available at http://alan.cs.gsu.edu/NGS/?…”
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“…A commercially available, locally applied vibrating device (model UM-30M, Unix Electronics Co. Ltd.) was used, in an on-and-off pattern, together with the CO(2) laser. …”
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“…We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite “pgltools”: a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses. …”
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“…SNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.…”
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“…To annotate a given text, MER only requires: (1) a lexicon (text file) with the list of terms representing the entities of interest; (2) optionally a tab-separated values file with a link for each term; (3) and a Unix shell. Alternatively, the user can provide an ontology from where MER will automatically generate the lexicon and links files. …”
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“…ChromaClade is available for Windows, macOS and Unix or Linux; program executables and source code are available at github.com/chrismonit/chroma_clade.…”
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“…It can easily be run on any UNIX-like system, from local machines to high-performance computing clusters, performing a comprehensive analysis without the requirement for extensive bioinformatics expertise. …”
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“…The GIBBSTHUR software was developed in FORTRAN 90 and can be executed in UNIX, OSX, or WINDOWS environments, and is freely available in a public repository (https://github.com/lvaronaunizar/Gibbsthur). …”
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“…The “Fast Assembly of SMILES Fragments” software is released as open-source at https://github.com/UnixJunkie/FASMIFRA. Experiments regarding speed, training set distribution matching, molecular diversity and benchmark against several other methods are also shown.…”
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“…Inspired by well-established material and pedagogy provided by The Carpentries (Wilson, 2016), we developed a two-day workshop curriculum that teaches introductory R programming for managing, analyzing, plotting and reporting data using packages from the tidyverse (Wickham et al., 2019), the Unix shell, version control with git, and GitHub. …”
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“…We propose that emphasizing modularity and interoperability would lead to a more powerful Unix-like ecosystem of web services for biomedical analysis and data retrieval. …”
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