2024-03-28T11:53:20Z
https://zenodo.org/oai2d
oai:zenodo.org:159947
2020-01-25T07:25:10Z
user-gcmodeller
software
谢桂纲
關倩倩
2016-10-10
<p>GCModeller provides a set of .NET libraries and CLI tools for processing biological analysis data. Currently GCModeller can provides these productive ready libraries:</p>
<p>1.Basically libraries</p>
<ul>
<li>NCBI data analysis toolkit: Genbank/Taxonomy/nt/nr database</li>
<li>Common Data: FastA database, FastQ, SAM data file I/O class</li>
<li>Biological Data Standard Supports: SBML(level 3), BIOM(level1), PSI, OBO</li>
<li>Biological Pathway Database: MetaCyc, Reactome, KEGG data tools for .NET language</li>
</ul>
<p>2.Biological Data Visualization software API for .NET</p>
<ul>
<li>Circos API(genomic visualizing), Cytoscape DataModel API(Biological network visualizing), SequenceLogo(Molecular motif site visualize)</li>
</ul>
<p>3.Annotation Tools:</p>
<ul>
<li>A complete NCBI localblast toolkit for proteins and nucleotide sequence analysis, includes parallel task library for Win/Linux Server and data analysis protocol.</li>
<li>SNP toolkit</li>
<li>Nucleotide sequence topology feature site analysis toolkit.</li>
<li>RegPrecise database tool and MEME software toolkit for the annotation of bacterial genomics regulation network.</li>
<li>Go(Gene Ontology) annotation tools</li>
</ul>
<p>4.R language hybrids environment for bioinformatics</p>
<ul>
<li>Includes basically R language API, and some R package API from CRAN and Bioconductor</li>
</ul>
<p>5.WebAPI wrapper for KEGG database and RegPrecise Database</p>
<p> </p>
<p><strong>Publications</strong></p>
<p>Here listing the scientific paperworks that based on the analysis services of GCModeller:</p>
<p> </p>
<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>
<p>DOI: 10.1186/s12866-015-0562-x</p>
<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>
https://doi.org/10.5281/zenodo.159947
oai:zenodo.org:159947
Zenodo
https://github.com/SMRUCC/GCModeller/tree/v0.0.1-alpha
https://zenodo.org/communities/gcmodeller
https://doi.org/
info:eu-repo/semantics/openAccess
GNU General Public License v2.0 only
https://www.gnu.org/licenses/old-licenses/gpl-2.0-standalone.html
bacterial
genomics
annotation
localblast
pathway network
Circos
SMRUCC/GCModeller alpha Release
info:eu-repo/semantics/other
oai:zenodo.org:4733445
2021-12-02T04:47:02Z
user-gcmodeller
openaire_data
Kino, Kanon
Okazaki, Atsushi
Cauquoin, Alexandre
Yoshimura, Kei
2021-06-15
<p><strong>Data used in <a href="https://doi.org/10.1029/2021JD035397">Kino et al. (2021, JGR)</a> are stored as <a href="https://numpy.org/doc/stable/reference/generated/numpy.savez.html">NpzFiles</a>.</strong></p>
<ul>
<li>All data (except for sam_jra25.npz and sammon_jra25.npz) resulted from an isotope-enabled atmospheric general circulation model named "iso-MIROC5" <a href="https://doi.org/10.1029/2018JD029463">(Okazaki and Yoshimura, 2019, JGR)</a>.</li>
<li>sam_jra25.npz and sammon_jra25.npz resulted from a long-term global atmospheric reanalysis, named "Japanese 25-year Reanalysis (JRA-25)" <a href="https://doi.org/10.2151/jmsj.85.369">(Onogi et al., 2007, JMSJ)</a></li>
<li>The definition of monthly and daily expanded SAM-index proposed by <a href="https://doi.org/10.1002/2015JD024665">Marshall and Thompson (2016, JGR)</a> was adopted.</li>
<li>Scripts used in <strong><a href="https://doi.org/10.1029/2021JD035397">Kino et al. (2021, JGR)</a></strong> are available in a <a href="https://github.com/kanonundgigue/SAM_DomeFuji">GitHub repository</a>.</li>
</ul>
https://doi.org/10.5281/zenodo.4733445
oai:zenodo.org:4733445
Zenodo
https://github.com/kanonundgigue/SAM_DomeFuji
https://zenodo.org/communities/gcmodeller
https://doi.org/10.5281/zenodo.4733444
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of Geophysical Research, Atmosphere, (2021-06-15)
Contribution of the Southern Annular Mode on variations in water isotopes of daily precipitation at Dome Fuji, East Antarctica
info:eu-repo/semantics/other