[WARNING] This project is a work in progress and is not recommended for production use.
GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
Microsoft Azure Cloud
Development: Microsoft VisualStudio 2017 | VisualBasic.NET
Runtime environment: sciBASIC# v2.1.5 beta &
.NET Framework 4.6 (or
VS2017 is required of compiles this project. After the source code have been clone using git, just open solution file /src/GCModeller.sln, and when restore nuget packages finished, then you are good to go of compile GCModeller project.
NOTE: Due to the reason of this project is using git submodule for manage some runtime component, so that please do not directly download the project source code from github by using the
Donwload Zip button. The internal github client in the VisualStudio is recommended using for download the project source code.
GCModeller is an open source cloud computing platform for the geneticist and systems biology. You can easily build a local computing server cluster for
GCModeller on the large amount biological data analysis.
GCModeller platform is original writen in
VisualBasic.NET language, a feature bioinformatics analysis environment that .NET language hybrids programming with R language was included, which its SDK is available at repository:
R language hybrids programming environment just provides some
bioconductor API for the analysis in
GCModeller is a set of utility tools working on the annotation of the whole cell system, this including the whole genome regulation annotation, transcriptome analysis toolkits, metabolism pathway analysis toolkits. And some common bioinformatics problem utils tools and common biological database I/O tools is also available in GCModeller for the .NET language programming.
- /GCModeller : The location of GCModeller compile output, I have config all of the project output in the path
- /src/GCModeller : GCModeller basic library and analysis protocols
- /src/interops : GCModeller tools that dependent on the external programs
- /src/R.Bioconductor : R language hybrids environment
- /src/repository : GCModeller data repository system
- /src/runtime : Third part library and VisualBasic runtime source code
- GCModeller supports the
BIOMdata standards for exchanges the analysis and model data with other bioinformatics softwares.
PSIdata for the biological interaction network model
OBOdata for ontology database like
Modules & Functions
GCModeller provides a set of .NET libraries and CLI tools for processing biological analysis data. Currently GCModeller can provides these productive ready 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)
- 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
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.
Visit our project home: http://gcmodeller.org
Here are some released library of the
GCModeller is published on nuget, then you can install these library in
VisualStudio from Package Manager Console:
# Install Microsoft VisualBasic sciBASIC# runtime via nuget: # https://github.com/xieguigang/sciBASIC/ PM> Install-Package sciBASIC -Pre # The GCModeller core base library was released: # https://github.com/SMRUCC/GCModeller.Core PM> Install-Package GCModeller.Core # The NCBI localblast analysis toolkit: # https://github.com/SMRUCC/ncbi-localblast PM> Install-Package NCBI_localblast
The GCModeller demo script and data for user tutorials can be download from these public data repository:
genome map plot of Xanthomonas campestris pv. campestris 8004
Copyleft © SMRUCC genomics 2016. All rights reversed.