“…It is compatible with Mac, Windows and Unix operating systems, requiring version >1.45 of ImageJ and Java 8. …”
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“…In this article, we present a novel bioinformatics pipeline called LAZYPIPE for identifying both previously known and novel viruses in host associated or environmental samples and give examples of virus discovery based on it. LAZYPIPE is a Unix-based pipeline for automated assembling and taxonomic profiling of NGS libraries implemented as a collection of C++, Perl, and R scripts.…”
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“…It works with Windows, Macintosh, and UNIX-based systems. Source code, standalone versions, user manual, sample images, video tutorial and further documentation are freely available at: https://sourceforge.net/p/cometanalyser.…”
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“…We evaluated Watcher in a Unix system programming class for 96 students. The results showed that Watcher improves the quality of the coding experience for students through Web-IDE, and it offers instructors valuable data that can be used to analyze the various coding activities of individual students.…”
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“…AVAILABILITY AND IMPLEMENTATION: LIQUORICE is freely and openly available as a Python package and command-line tool for UNIX-based systems from bioconda. Documentation, examples and usage instructions are provided at http://liquorice.computational-epigenetics.org. …”
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“…AVAILABILITY AND IMPLEMENTATION: MiCellAnnGELo employs the cross-platform (Mac/Unix/Windows) Unity game engine and is available under the MIT licence at https://github.com/CellDynamics/MiCellAnnGELo.git, together with sample data. …”
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“…Moreover, specifications for institutional Cloud resources proposed by Worldwide LHC Computing Grid (WLCG), mainly by the High Energy Physics Unix Information Exchange (HEPiX) group, have been taken into account. …”
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“…Availability: MTMDAT can be downloaded from the following page: http://www.cms.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat by clicking on the corresponding links (windows- or unix-based) together with the manual and example files. …”
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“…Availability: SAMStat is open source and freely available as a C program running on all Unix-compatible platforms. The source code is available from http://samstat.sourceforge.net. …”
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“…In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. …”
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“…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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“…It can be executed as an application from the UNIX command line, or as a set of Java classes called from a script or a Java application. …”
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“…GFF-Ex package consists of several UNIX Shell and PERL scripts. CONCLUSIONS: Compared to other available GFF parsers, GFF-Ex is a simpler tool, which permits sequence retrieval based on additional inferred features. …”
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“…Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. …”
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“…Availability and implementation: RADIS is written in perl, designed to run on Linux and Unix platforms. RADIS and its manual are freely available from http://www1.montpellier.inra.fr/CBGP/software/RADIS/. …”
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“…BeatBox is a free software written in C language to be run on a Unix-based platform. It provides the whole spectrum of multi scale tissue modelling from 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations, with run time measurements including cardiac re-entry tip/filament tracing, ECG, local/global samples of any variables, etc. …”
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“…With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. …”
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“…BacPipe is integrated in EBI-SELECTA, a project-specific portal (H2020-COMPARE), and is available as an independent docker image that can be used across Windows- and Unix-based systems. BacPipe offers a fully automated “one-stop” bacterial WGS analysis pipeline to overcome the major hurdle of WGS data analysis in hospitals and public-health and for infection control monitoring.…”
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“…This high degree of flexibility also comes with a high degree of complexity, which may present an obstacle for researchers not trained in programming or the UNIX command line. The Galaxy platform provides a user-friendly browser-based graphical interface incorporating a broad range of “wrapped” command line tools to facilitate accessibility. …”
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“…AVAILABILITY AND IMPLEMENTATION: LRez is implemented in C++, supported on Unix-based platforms and available under AGPL-3.0 License at https://github.com/morispi/LRez, and as a bioconda module. …”
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