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  1. 4841
    “…Availability: InCroMAP is freely available as Java™ application at www.cogsys.cs.uni-tuebingen.de/software/InCroMAP, including a comprehensive user’s guide and example files. …”
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    Online Artículo Texto
    InCroMAP: integrated analysis of cross-platform microarray and pathway data
  2. 4842
    “…This new problem variant generalizes the standard (one-to-one) weighted bipartite matching problem, and can be solved using network flows. The resulting Java-based tool, called SAGE (Scoring function for Assembled GEnomes), is freely available upon request. …”
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    Evaluating genome architecture of a complex region via generalized bipartite matching
  3. 4843
    “…We succeeded in implementing libSBMLSim as a platform-independent library that can run on most common operating systems (Windows, MacOSX and Linux) and also provides several language bindings (Java, C#, Python and Ruby). Availability: The source code of libSBMLSim is available from http://fun.bio.keio.ac.jp/software/libsbmlsim/. …”
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    LibSBMLSim: a reference implementation of fully functional SBML simulator
  4. 4844
    “…This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. …”
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    VisANT: an online visualization and analysis tool for biological interaction data
  5. 4845
    “…METHODS: Agent-based template development was performed in java-based computer simulation suite AnyLogic Professional 6.6. …”
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    Online Artículo Texto
    An Agent-Based Modeling Template for a Cohort of Veterans with Diabetic Retinopathy
  6. 4846
    “…Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. …”
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    Genome Maps, a new generation genome browser
  7. 4847
    “…IMPLEMENTATION: CURE Soft is a desktop application developed in JAVA. It has two modes of operation, 1) Online real-time monitoring decision support and, 2) Offline for user education purposes, auditing, or reviewing patient care. …”
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    The Clinical Utilisation of Respiratory Elastance Software (CURE Soft): a bedside software for real-time respiratory mechanics monitoring and mechanical ventilation management
  8. 4848
    “…RESULTS: We present Circular Interaction Graph for Proteomics (CIG-P), which generates circular diagrams for visually appealing final representation of AP-MS data. Through a Java based GUI, the user inputs experimental and reference data as file in csv format. …”
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    CIG-P: Circular Interaction Graph for Proteomics
  9. 4849
    “…METHODS: Active tuberculosis was measured prospectively among 1900 consecutive antiretroviral treatment (ART)-naïve adult patients entering care in a clinic in West Java. Prevalence of LTBI was determined cross-sectionally in a subset of 518 ART-experienced patients using an interferon-gamma release assay. …”
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    Active and latent tuberculosis among HIV-positive injecting drug users in Indonesia
  10. 4850
    “…We identified three deep lineages in Platerodrilus occurring predominantly in (1) Borneo and the Philippines, (2) continental Asia, and (3) Sumatra, the Malay Peninsula and Java. We document limited ranges of all species of Platerodrilus and complete species level turnover between the Sunda Islands and even between individual mountain regions in Sumatra. …”
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    Molecular Phylogeny Reveals High Diversity, Geographic Structure and Limited Ranges in Neotenic Net-Winged Beetles Platerodrilus (Coleoptera: Lycidae)
  11. 4851
    “…The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. …”
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    Follicle Online: an integrated database of follicle assembly, development and ovulation
  12. 4852
    “…In this study, we introduced the open source Java implementation of MedEx, an existing high-performance medication information extraction system, based on the Unstructured Information Management Architecture (UIMA) framework. …”
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    Extracting and standardizing medication information in clinical text – the MedEx-UIMA system
  13. 4853
    “…Allele distribution patterns in Bali and Java differed in relation to cervical carcinoma risk, with four ERAP1 SNPs and one TAP2 SNP in the Javanese population showing significant association with cervical carcinoma risk, while in the Balinese population, only one TAP2 SNP showed this association. …”
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    Differences in genetic variation in antigen-processing machinery components and association with cervical carcinoma risk in two Indonesian populations
  14. 4854
    por Alvare, Graham, Gordon, Richard
    Publicado 2015
    “…RESULTS: We have successfully implemented CT Brush in Java and made it available publicly, requesting crowdsourced feedback on improving the open source code. …”
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    CT brush and CancerZap!: two video games for computed tomography dose minimization
  15. 4855
    “…METHODS: We developed the Genetic Merging & Editing (Genetic ME) program, an open source Java application built on top of CraneFoot and Ghostscript, to support comparing, editing and merging of pedigrees collected from multiple sources in a visually-oriented manner. …”
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    Genetic ME–a visualization application for merging and editing pedigrees for genetic studies
  16. 4856
    “…METHODS: We conducted in-depth, semistructured interviews with pharmacists working in community health centers (Puskesmas, n=5) and community pharmacies (apotek, n=15) in East Java Province. We interviewed participating pharmacists using Bahasa Indonesia to explore facilitators and barriers to their practice in chronic disease management. …”
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    Challenges in the management of chronic noncommunicable diseases by Indonesian community pharmacists
  17. 4857
    “…METHODS: We calculated the cost of providing HIV care and treatment in a main referral hospital in West Java, Indonesia from 2008 to 2010, differentiated by initiation of treatment at different CD4 cell count levels (0–50, 50–100, 100–150, 150–200, and >200 cells/mm(3)); time of treatment; HIV care and opportunistic infections cost components; and the costs of patients for seeking and undergoing care. …”
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    Costs of HIV/AIDS treatment in Indonesia by time of treatment and stage of disease
  18. 4858
    “…Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Contact: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online.…”
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    BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements
  19. 4859
    “…Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. …”
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    NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles
  20. 4860
    “…The isolated strains were grouped into different phylotypes according to the presence of chuA, yjaA and TSPE4.C2 genes. Then, the prevalence of stx gene subtypes was evaluated in the B(1) phylotypes. …”
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    Distribution of Shiga toxin genes subtypes in B(1) phylotypes of Escherichia coli isolated from calves suffering from diarrhea in Tehran suburb using DNA oligonucleotide arrays
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