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  1. 4001
    por Curtis, Ross E, Goyal, Anuj, Xing, Eric P
    Publicado 2012
    “…GenAMap and Auto-SAM are implemented in JAVA; binaries for GenAMap can be downloaded from http://sailing.cs.cmu.edu/genamap.…”
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    Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system
  2. 4002
    “…Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. …”
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    CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions
  3. 4003
    “…CONCLUSIONS: Vanted is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org.…”
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    VANTED v2: a framework for systems biology applications
  4. 4004
    “…Availability: DoRIS, a Java implementation of the proposed method, and its source code are freely available at http://www.cs.columbia.edu/∼pier/doris. …”
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    Inference of historical migration rates via haplotype sharing
  5. 4005
    “…Implementation: The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. …”
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    Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
  6. 4006
    “…Here, we describe a new Java-based architecture for the widely used protein function prediction software package InterProScan. …”
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    InterProScan 5: genome-scale protein function classification
  7. 4007
    “…GASOLINE has been developed in Java, and is available, along with all the computed alignments, at the following URL: http://ferrolab.dmi.unict.it/gasoline/gasoline.html.…”
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    GASOLINE: a Greedy And Stochastic algorithm for Optimal Local multiple alignment of Interaction NEtworks
  8. 4008
    “…With initial implementations in C++ and Java, BioC provides libraries of code for reading and writing BioC text documents and annotations. …”
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    BioC implementations in Go, Perl, Python and Ruby
  9. 4009
    “…The results along with the implemented Java tool, serve as useful resources to elucidate the mechanism of lysine acetylation and facilitate hypothesis-driven experimental design and validation.…”
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    Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features
  10. 4010
    “…RESULTS: jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. …”
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    jvenn: an interactive Venn diagram viewer
  11. 4011
    “…We implemented a prototype interactive static analysis tool as a plug-in for Java in Eclipse. Our technical evaluation of our prototype detected multiple zero-day vulnerabilities in a large open source project. …”
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    Supporting secure programming in web applications through interactive static analysis
  12. 4012
    “…Such patterns of geographic trait distribution cannot be simply explained by clinal geographic variation of Homo erectus between northern China and Java, and suggests survival of multiple evolutionary lineages among archaic hominins before the arrival of modern humans in the region.…”
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    The first archaic Homo from Taiwan
  13. 4013
    “…. • Methods and Results: MatrixConverter is an open source program written in Java; a platform-independent binary executable, as well as sample data sets and a user’s manual, are available at https://github.com/gburleigh/MatrixConverter/tree/master/distribution. …”
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    MatrixConverter: Facilitating construction of phenomic character matrices(1)
  14. 4014
    “…The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. …”
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    (PS)(2): protein structure prediction server version 3.0
  15. 4015
    “…SimFluVar is developed in C++, and Java RCP is used as a distribution package. SimFluVar, including the associated documentation, manuals, and examples, is publicly available at http://lcbb.snu.ac.kr/simfluvar.…”
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    A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups
  16. 4016
    “…We have adapted an existing JavaScript library (Cubism) that implements Horizon Charts for the time series domain so that it works effectively with genomic datasets. …”
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    DNAism: exploring genomic datasets on the web with Horizon Charts
  17. 4017
    “…A toolbox, including C++ and Java source code and executable files on both Windows and Linux platforms together with a user instruction, is downloadable from the website for academic purpose at https://sourceforge.net/projects/kakscalculator2/.…”
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    KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies
  18. 4018
    por de Almeida, João M.G.C.F.
    Publicado 2010
    “…To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. …”
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    BiDiBlast: Comparative Genomics Pipeline for the PC
  19. 4019
    “…The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. …”
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    TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life
  20. 4020
    “…It provides simple access to microarray data over the Internet and uses only HTML and JavaScript to display graphic and annotation information. …”
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    GeneXplorer: an interactive web application for microarray data visualization and analysis
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