Software Open Access

SMRUCC/GCModeller alpha Release

谢桂纲; 關倩倩


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<oai_dc:dc xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:oai_dc="http://www.openarchives.org/OAI/2.0/oai_dc/" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai_dc/ http://www.openarchives.org/OAI/2.0/oai_dc.xsd">
  <dc:creator>谢桂纲</dc:creator>
  <dc:creator>關倩倩</dc:creator>
  <dc:date>2016-10-10</dc:date>
  <dc:description>GCModeller provides a set of .NET libraries and CLI tools for processing biological analysis data. Currently GCModeller can provides these productive ready libraries:

1.Basically libraries


	NCBI data analysis toolkit: Genbank/Taxonomy/nt/nr database
	Common Data: FastA database, FastQ, SAM data file I/O class
	Biological Data Standard Supports: SBML(level 3), BIOM(level1), PSI, OBO
	Biological Pathway Database: MetaCyc, Reactome, KEGG data tools for .NET language


2.Biological Data Visualization software API for .NET


	Circos API(genomic visualizing), Cytoscape DataModel API(Biological network visualizing), SequenceLogo(Molecular motif site visualize)


3.Annotation Tools:


	A complete NCBI localblast toolkit for proteins and nucleotide sequence analysis, includes parallel task library for Win/Linux Server and data analysis protocol.
	SNP toolkit
	Nucleotide sequence topology feature site analysis toolkit.
	RegPrecise database tool and MEME software toolkit for the annotation of bacterial genomics regulation network.
	Go(Gene Ontology) annotation tools


4.R language hybrids environment for bioinformatics


	Includes basically R language API, and some R package API from CRAN and Bioconductor


5.WebAPI wrapper for KEGG database and RegPrecise Database

 

Publications

Here listing the scientific paperworks that based on the analysis services of GCModeller:

 

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.

DOI: 10.1186/s12866-015-0562-x

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.</dc:description>
  <dc:identifier>https://zenodo.org/record/159947</dc:identifier>
  <dc:identifier>10.5281/zenodo.159947</dc:identifier>
  <dc:identifier>oai:zenodo.org:159947</dc:identifier>
  <dc:relation>url:https://github.com/SMRUCC/GCModeller/tree/v0.0.1-alpha</dc:relation>
  <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
  <dc:rights>http://www.opensource.org/licenses/GPL-3.0</dc:rights>
  <dc:subject>bacterial</dc:subject>
  <dc:subject>genomics</dc:subject>
  <dc:subject>annotation</dc:subject>
  <dc:subject>localblast</dc:subject>
  <dc:subject>pathway network</dc:subject>
  <dc:subject>Circos</dc:subject>
  <dc:title>SMRUCC/GCModeller alpha Release</dc:title>
  <dc:type>info:eu-repo/semantics/other</dc:type>
  <dc:type>software</dc:type>
</oai_dc:dc>

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