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  1. 3901
    “…To facilitate easy analysis in a single step and support the processing of multiple isolates, BacSeq provides a graphical user interface (GUI) based on the JAVA platform. It is designed to cater to users without extensive bioinformatics skills.…”
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    BacSeq: A User-Friendly Automated Pipeline for Whole-Genome Sequence Analysis of Bacterial Genomes
  2. 3902
    por Mısırlı, Göksel
    Publicado 2023
    “…AVAILABILITY AND IMPLEMENTATION: The libSBOLj3 library is implemented in Java and can be downloaded or used as a Maven dependency. …”
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    libSBOLj3: a graph-based library for design and data exchange in synthetic biology
  3. 3903
    por Wood, Brian M., Jones, James Holland
    Publicado 2015
    “…Pursuit is freely available and can run on any platform that supports Java, including Mac OS, Windows, and Linux.…”
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    Pursuit: A Foraging Simulation Tool for Research and Teaching
  4. 3904
    “…AVAILABILITY AND IMPLEMENTATION: DrForna is a JavaScript project available on Github at https://github.com/ViennaRNA/drforna and deployed at https://viennarna.github.io/drforna…”
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    DrForna: visualization of cotranscriptional folding
  5. 3905
    “…For example, Semgrep performed better considering applications developed using JavaScript technology but had worse results regarding applications developed using PHP technology.…”
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    Comparative Analysis of Open-Source Tools for Conducting Static Code Analysis
  6. 3906
    “…The server generates both VRML and JVX output that can be viewed with a VRML viewer or the JavaView applet, respectively. We show that combining these different features of an alignment into one 3D representation is helpful in identifying correlations between bases and potential RNA and DNA base pairs. …”
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    CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
  7. 3907
    “…The software has been completely re-implemented in Java to enable pure client-side operation as applet and web-start application available at the Bielefeld Bioinformatics Server http://bibiserv.techfak.uni-bielefeld.de/rnamovies…”
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    RNA Movies 2: sequential animation of RNA secondary structures
  8. 3908
    “…It has been written in Java as a plug-in for ImageJ and is distributed as freeware.…”
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    TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy
  9. 3909
    “…YANAsquare comes as an easy-to-setup program package in Java. It is fully compatible and integrates the programs YANA (translation of gene expression values into flux distributions, metabolite network dissection) and Metatool (elementary mode calculation). …”
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    Integrated network reconstruction, visualization and analysis using YANAsquare
  10. 3910
    “…Jobs are submitted from a Java graphical user interface as TOPALi web services to either run remotely on high-performance computing clusters or locally (with multiple cores supported). …”
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    TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops
  11. 3911
    “…Pending the implementation of a dedicated web server, the code accompanying this article, written in JAVA, is available upon request from the contact author.…”
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    Finding 3D motifs in ribosomal RNA structures
  12. 3912
    “…The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. …”
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    OnTheFly: a tool for automated document-based text annotation, data linking and network generation
  13. 3913
    “…Availability and Implementation: QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported. …”
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    QuickGO: a web-based tool for Gene Ontology searching
  14. 3914
    “…And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. …”
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    BioRuby: bioinformatics software for the Ruby programming language
  15. 3915
    “…Recently we developed a user-friendly graphical-interface using JAVA for IMEx to be used as a stand-alone software named G-IMEx. …”
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    G-IMEx: A comprehensive software tool for detection of microsatellites from genome sequences
  16. 3916
    “…The head and neck cancer tissue database system has four interfaces: Web-based, Java API, XML utility, and Web service. The system has been shown to provide robust and programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources.…”
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    caGrid-Enabled caBIG(TM) Silver Level Compatible Head and Neck Cancer Tissue Database System
  17. 3917
    “…Availability: Xwalk is freely available as a web server or stand-alone JAVA application at http://www.xwalk.org. Contact: abdullah@imsb.biol.ethz.ch; aebersold@imsb.biol.ethz.ch Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    Xwalk: computing and visualizing distances in cross-linking experiments
  18. 3918
    “…The Early Cretaceous Greater Ontong Java Event in the Pacific Ocean may have covered ca. 1% of the Earth's surface with volcanism. …”
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    An extraterrestrial trigger for the Early Cretaceous massive volcanism? Evidence from the paleo-Tethys Ocean
  19. 3919
    “…BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. …”
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    BioMAJ: a flexible framework for databanks synchronization and processing
  20. 3920
    “…The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. …”
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    Software support for SBGN maps: SBGN-ML and LibSBGN
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