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  1. 5021
    “…The program has been tested on Windows, Mac, and Linux operating systems, and is implemented both as an executable JAR file and java WebStart. Program executables, source code, and documentation is available at http://www.bme.ucdavis.edu/facciotti/resources_data/software/.…”
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    JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison
  2. 5022
    “…The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. …”
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    SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology
  3. 5023
    “…To determine the contribution of V(H) replacement products to mouse antibody repertoire, we developed a Java-based V(H) Replacement Footprint Analyzer (V(H)RFA) program and analyzed 17,179 mouse IgH gene sequences from the NCBI database to identify V(H) replacement products. …”
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    Contribution of V(H) Replacement Products in Mouse Antibody Repertoire
  4. 5024
    “…Then, we designed database tables in PostgreSQL database server and developed a Java application to extract data from source files and loaded into database automatically. …”
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    Comparative GO: A Web Application for Comparative Gene Ontology and Gene Ontology-Based Gene Selection in Bacteria
  5. 5025
    “…These can be downloaded from their home pages: http://bamview.sourceforge.net/; http://www.sanger.ac.uk/resources/software/artemis/. Requirements: Java 1.6 or higher.…”
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    BamView: visualizing and interpretation of next-generation sequencing read alignments
  6. 5026
    “…RESULTS: Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. …”
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    Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool
  7. 5027
    “…Towards this end, this paper reports on the development of a prototype analysis module for an automated high-content-analysis (HCA) system, which allows for accurate and fast investigation of in vitro 3D cell culture models for PCa. The Java based program, which we have named PCaAnalyser, uses novel algorithms that allow accurate and rapid quantitation of protein expression in 3D cell culture. …”
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    PCaAnalyser: A 2D-Image Analysis Based Module for Effective Determination of Prostate Cancer Progression in 3D Culture
  8. 5028
    “…A human-curated database was developed using the server side include in Java, JMOL. The results of this functional analysis indicate that the majority of the 124 natural mutants are harmful to the protein structure and thus corroborate the correlation between the reported mutations and fALS. …”
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    Structural and Functional Analysis of Human SOD1 in Amyotrophic Lateral Sclerosis
  9. 5029
    “…Commercial sex plays a significant role in the spread of HIV; therefore, in order to reveal the current HIV prevalence rate among commercial sex workers (CSWs), we conducted an epidemiological study on HIV infection among CSWs residing in Surabaya, the capital of East Java province of Indonesia with large communities of CSWs. …”
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    High Prevalence of HIV-1 CRF01_AE Viruses among Female Commercial Sex Workers Residing in Surabaya, Indonesia
  10. 5030
    “…The QuantWorm software is written in Java and its source code is freely available, so it does not require use of commercial software or libraries. …”
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    QuantWorm: A Comprehensive Software Package for Caenorhabditis elegans Phenotypic Assays
  11. 5031
    por Baier, Herbert, Schultz, Jörg
    Publicado 2014
    “…With its highly modular, JavaEE based design, the implementation of new modules is straight forward. …”
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    ISAAC - InterSpecies Analysing Application using Containers
  12. 5032
    “…Finally a set of dictionaries was implemented to be used via SQL queries or locally via a Java API built upon the Apache Lucene text-search engine. …”
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    Data model, dictionaries, and desiderata for biomolecular simulation data indexing and sharing
  13. 5033
    por Rødland, Einar Andreas
    Publicado 2013
    “…CONCLUSIONS: The kFM-index could replace more memory demanding data structures for storing the de Bruijn k-mer graph representation of sequence reads. A Java implementation with additional technical documentation is provided which demonstrates the applicability of the data structure (http://folk.uio.no/einarro/Projects/KFM-index/).…”
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    Compact representation of k-mer de Bruijn graphs for genome read assembly
  14. 5034
    “…To explore the biological significance of V(H) replacement to the antibody repertoire, we developed a Java-based V(H) replacement footprint analyzer program and analyzed the distribution of V(H) replacement products in 61,851 human IgH gene sequences downloaded from the NCBI database. …”
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    Accumulation of V(H) Replacement Products in IgH Genes Derived from Autoimmune Diseases and Anti-Viral Responses in Human
  15. 5035
    “…Widening inequities between the most developed provinces of Java-Bali and those of other island groupings should be of particular concern for a country embarking on an ambitious plan for universal health coverage by 2019. …”
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    Location Matters: Trends in Inequalities in Child Mortality in Indonesia. Evidence from Repeated Cross-Sectional Surveys
  16. 5036
    “…The software is implemented in C++ and Java, being supported on UNIX and MS Windows.…”
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    A Rank-Based Sequence Aligner with Applications in Phylogenetic Analysis
  17. 5037
    “…We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. …”
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    LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2
  18. 5038
    “…AISO is a freely available Java-based desktop application and runs on multiple platforms. …”
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    AISO: Annotation of Image Segments with Ontologies
  19. 5039
    “…BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. …”
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    BrainBrowser: distributed, web-based neurological data visualization
  20. 5040
    “…RESULTS: We present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. …”
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    VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data
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