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  1. 5221
    “…CONCLUSIONS: The results show that the second approach efficiently enumerates minimal precursor sets taking stoichiometry into account, and allows for broad in silico studies of strains or species interactions that may help to understand e.g. pathotype and niche-specific metabolic capabilities. sasita is written in Java, uses cplex as LP solver and can be downloaded together with all networks and input files used in this paper at http://www.sasita.gforge.inria.fr. …”
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    Enumeration of minimal stoichiometric precursor sets in metabolic networks
  2. 5222
    “…Demographic history inference under isolation and migration (IM) model detected substantial gene flow from the Sri Lanka populations to the populations in the Java Island. Moreover, multi-locus sequence analysis indicated that S. lanceolata was most closely related to the Indian Ocean populations of S. caseolaris and the divergence time between them was 2.057 MYA, coinciding with the onset of the Pleistocene glaciation. …”
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    Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata
  3. 5223
    “…RESULTS: We developed a JavaScript to determine the codon frequencies of aligned nucleotide sequences. …”
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    Does antiretroviral treatment change HIV-1 codon usage patterns in its genes: a preliminary bioinformatics study
  4. 5224
    “…We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). …”
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    ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour
  5. 5225
    “…METHODS: A cluster-randomized controlled trial will be conducted in 106 patients in four hospitals in Bandung, West Java, Indonesia. Data will be collected at baseline (pre-assessment), 7 days after the intervention (post-assessment), and at 3 months (follow-up assessments). …”
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    A protocol for a cluster-randomized controlled trial of a self-help psycho-education programme to reduce diagnosis delay in women with breast cancer symptoms in Indonesia
  6. 5226
    “…The induction algorithm is called VC-DomLEM; it has been implemented as software package called jMAF (http://www.cs.put.poznan.pl/jblaszczynski/Site/jRS.html), based on java Rough Set (jRS) library. In the studied group, there were 148 patients (78 boys and 70 girls), and the mean age was 85 months. …”
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    With a little help from a computer: discriminating between bacterial and viral meningitis based on dominance-based rough set approach analysis
  7. 5227
    “…Image processing was done with Fiji (an open source Java image processing program by Fiji contributors) using 10% to 90% phase images of CCTA; and tissue displacement (MLM shift) was shown on the resulting images. …”
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    Influences of cardiac motion on computed tomography-guided biopsy of lung nodules located near the heart
  8. 5228
    “…In addition, the search results are shown in interactive JavaScript chart framework using DC.js. The analysis of quality scores across major public genome databases find that around 68% of the genomes are of acceptable quality for many uses. …”
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    dBBQs: dataBase of Bacterial Quality scores
  9. 5229
    “…Bi-Force is implemented in Java and integrated into the open source software package of BiCluE. …”
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    Bi-Force: large-scale bicluster editing and its application to gene expression data biclustering
  10. 5230
    “…AVAILABILITY AND IMPLEMENTATION: RG was implemented in Java, source code and binaries are freely available for non-commercial use at https://github.com/popitsch/wtchg-rg/. …”
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    ReliableGenome: annotation of genomic regions with high/low variant calling concordance
  11. 5231
    “…The code, written in Google Earth Engine's implementation of JavaScript, is provided as Supporting Information for its use in any other AOI without particular technical knowledge or access to topographical data. © 2017 The Authors. …”
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    Multi‐scale relief model (MSRM): a new algorithm for the visualization of subtle topographic change of variable size in digital elevation models
  12. 5232
    “…Among the shared DEGs, ATP6V1E1, GNG3, NDUFV2, GOT1, USP14, and NAV2 have been previously found in both normal aging individuals and AD patients. Furthermore, using Java Enrichment of Pathways Extended to Topology (JEPETTO) analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we determined that changes in aging-related KEGG annotations may contribute to the aging-dependence of AD risk. …”
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    Low expression of aging-related NRXN3 is associated with Alzheimer disease: A systematic review and meta-analysis
  13. 5233
    “…In the interest of accessibility, we developed this new toolbox as a series of JavaScript procedures that can be utilized as either server side resources (easily packaged as web services) or as client side scripts (web applications running in the browser). …”
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    Kinomics toolbox—A web platform for analysis and viewing of kinomic peptide array data
  14. 5234
    “…PATIENTS AND METHODS: Study population was people living in endemic areas in Pekalongan district, Central Java Province. This was a cross-sectional study. …”
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    Perceived threat and benefit toward community compliance of filariasis’ mass drug administration in Pekalongan district, Indonesia
  15. 5235
    “…Here, we release the first large scale assessment of the megadiverse insect groups that occur in the Mount Halimun-Salak National Park, one of the largest tropical rain-forest ecosystem in West Java, with a focus on Hymenoptera, Coleoptera, Diptera and Lepidoptera collected with Malaise traps. …”
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    The Mt Halimun-Salak Malaise Trap project - releasing the most species rich DNA Barcode library for Indonesia
  16. 5236
    “…RESULTS: We present a Java desktop application called GOPHER (Generator Of Probes for capture Hi-C Experiments at high Resolution) that implements three strategies for CHC probe design. …”
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    GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution
  17. 5237
    “…We developed the tool (PolyMorphPredict) using Perl, R, Java and launched at Apache which is available at http://webtom.cabgrid.res.in/polypred/. …”
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    PolyMorphPredict: A Universal Web-Tool for Rapid Polymorphic Microsatellite Marker Discovery From Whole Genome and Transcriptome Data
  18. 5238
    “…METHODS AND RESULTS: The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non‐parametric statistics for various crop traits. …”
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    STABILITYSOFT: A new online program to calculate parametric and non‐parametric stability statistics for crop traits
  19. 5239
    “…Canopy fogging on 28 trees was undertaken at two different sites, Cikaniki and Gunung Botol, in the south-eastern area of the Gunung Halimun-Salak National Park in West Java, Indonesia. In total, 7,447 specimens of Coleoptera were processed, of which 3,836 specimens produced DNA barcode sequences that were longer than 300 bp. …”
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    DNA barcoding data release for Coleoptera from the Gunung Halimun canopy fogging workpackage of the Indonesian Biodiversity Information System (IndoBioSys) project
  20. 5240
    “…METHODS: TeamDoc mobile app for Android and Apple smartphones was developed using 3 languages: C++, Qt Modeling Language, and JavaScript. For the server-side connectivity, Hypertext Preprocessor (PHP) was used as it is a commonly used cross-platform language. …”
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    Design, Development, and Evaluation of an Injury Surveillance App for Cricket: Protocol and Qualitative Study
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