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SMRUCC/GCModeller alpha Release

谢桂纲; 關倩倩


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{
  "DOI": "10.5281/zenodo.159947", 
  "abstract": "<p>GCModeller provides a set of .NET libraries and CLI tools for processing biological analysis data.\u00a0Currently GCModeller can provides\u00a0these\u00a0productive ready libraries:</p>\n\n<p>1.Basically\u00a0libraries</p>\n\n<ul>\n\t<li>NCBI data analysis toolkit: Genbank/Taxonomy/nt/nr database</li>\n\t<li>Common\u00a0Data: FastA database, FastQ, SAM data file I/O class</li>\n\t<li>Biological Data Standard Supports: SBML(level 3), BIOM(level1), PSI, OBO</li>\n\t<li>Biological Pathway Database:\u00a0MetaCyc,\u00a0Reactome, KEGG data tools\u00a0for .NET language</li>\n</ul>\n\n<p>2.Biological\u00a0Data\u00a0Visualization\u00a0software API for .NET</p>\n\n<ul>\n\t<li>Circos\u00a0API(genomic visualizing), Cytoscape DataModel API(Biological network visualizing), SequenceLogo(Molecular motif site visualize)</li>\n</ul>\n\n<p>3.Annotation Tools:</p>\n\n<ul>\n\t<li>A\u00a0complete NCBI localblast toolkit for proteins and nucleotide\u00a0sequence\u00a0analysis,\u00a0includes parallel task library for\u00a0Win/Linux Server\u00a0and data analysis protocol.</li>\n\t<li>SNP toolkit</li>\n\t<li>Nucleotide sequence\u00a0topology\u00a0feature site analysis toolkit.</li>\n\t<li>RegPrecise database tool and MEME software toolkit for the\u00a0annotation\u00a0of bacterial genomics regulation network.</li>\n\t<li>Go(Gene\u00a0Ontology) annotation tools</li>\n</ul>\n\n<p>4.R language hybrids environment for\u00a0bioinformatics</p>\n\n<ul>\n\t<li>Includes\u00a0basically R language API, and some R package API from CRAN\u00a0and\u00a0Bioconductor</li>\n</ul>\n\n<p>5.WebAPI wrapper for KEGG database and RegPrecise Database</p>\n\n<p>\u00a0</p>\n\n<p><strong>Publications</strong></p>\n\n<p>Here listing the scientific paperworks that based on the analysis services of GCModeller:</p>\n\n<p>\u00a0</p>\n\n<p>Niu, X.-N., et al. (2015). \"Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola.\" BMC Microbiol 15(1): 1-15.</p>\n\n<p>DOI: 10.1186/s12866-015-0562-x</p>\n\n<p>Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid.</p>", 
  "author": [
    {
      "family": "\u8c22\u6842\u7eb2"
    }, 
    {
      "family": "\u95dc\u5029\u5029"
    }
  ], 
  "id": "159947", 
  "issued": {
    "date-parts": [
      [
        2016, 
        10, 
        10
      ]
    ]
  }, 
  "publisher": "Zenodo", 
  "title": "SMRUCC/GCModeller alpha Release", 
  "type": "article"
}

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