Develop with GCModeller
GCModeller is not only an R# scripting environment — every module is also published as a .NET package. Add the sciBASIC NuGet feed to Visual Studio, reference SMRUCC.genomics.* from your project, and build bioinformatics applications directly on top of the framework in VB.NET, C# or F#.
sciBASIC NuGet Feed
Browse the 93 packages tagged gcmodeller, with versions, descriptions and download links.
nuget.scibasic.net · tag=gcmodeller ↗GitHub Repository
Full source of every module, including the reference command line projects you can copy from.
github.com/SMRUCC/GCModeller ↗.NET API Reference
The CLR type documentation for every namespace, generated from the assemblies you install.
gcmodeller.org/vignettes ↗Docker & R# Route
Prefer scripting inside the container environment? Start from the Install page instead.
install.html →Register the sciBASIC package source
Tools ▸ Options ▸ NuGet Package Manager ▸ Package Sources
# click (+), fill in the two fields below, then Update → OK
Name: sciBASIC
Source: https://nuget.scibasic.net/v3/index.jsonThe feed is a standard NuGet v3 service, so the official Visual Studio client talks to it without any extra tooling. Package downloads are anonymous; publishing to the feed is a separate, authenticated operation and is not needed to consume GCModeller.
Browse and install the packages
# right-click the project → "Manage NuGet Packages…"
# switch the package source dropdown to sciBASIC, then search:
Package source: sciBASIC
Search: SMRUCC.genomics
# 93 packages currently carry the gcmodeller tag, for example:
SMRUCC.genomics.core # 10.5.3.8911 · foundation library
SMRUCC.genomics.annotation # GFF / PTF annotation models
SMRUCC.genomics.annotation.prodigal # gene prediction
SMRUCC.genomics.analysis.hts.gsea # gene set enrichment
SMRUCC.genomics.analysis.metagenome # 16S / OTU community analysisThe complete, always up-to-date listing lives on the gcmodeller tag page of the sciBASIC feed — check it first when you are unsure which module provides the algorithm you need. Dependencies are resolved automatically, so installing a high-level module such as SMRUCC.genomics.analysis.hts.gsea also pulls in SMRUCC.genomics.core and the shared data models.
Command line & NuGet.config
# register the feed once, then add packages as usual
$ dotnet nuget add source https://nuget.scibasic.net/v3/index.json -n sciBASIC
$ dotnet add package SMRUCC.genomics.core --source sciBASIC
# or, from the Package Manager Console inside Visual Studio:
PM> Install-Package SMRUCC.genomics.core -Source sciBASIC<?xml version="1.0" encoding="utf-8"?>
<configuration>
<packageSources>
<add key="sciBASIC" value="https://nuget.scibasic.net/v3/index.json" />
</packageSources>
</configuration>A checked-in NuGet.config is the most reliable option for teams and CI pipelines: every restore resolves GCModeller from the sciBASIC feed without any per-machine setup.
Your first GCModeller program
The snippet below is real production code taken from the Bifrost gene-prediction command line tool of GCModeller (annotations/Bifrost/Bifrost/Program.vb). It exposes two CLI verbs — prodigal for ab-initio prokaryotic gene calling and metaeuk for homology-based eukaryotic prediction — and shows the typical shape of a GCModeller program: import a namespace, read a FASTA file, run a worker, export the result. The same program is shown in all three .NET languages.
Imports Microsoft.VisualBasic.CommandLine
Imports Microsoft.VisualBasic.CommandLine.Reflection
Imports SMRUCC.genomics.Annotation.MetaEuk
Imports SMRUCC.genomics.Annotation.Prodigal
Imports SMRUCC.genomics.SequenceModel.FASTA
Module Program
Public Function Main(args As String()) As Integer
Return GetType(Program).RunCLI(App.CommandLine)
End Function
<ExportAPI("prodigal")>
Public Function Prodigal(args As CommandLine) As Integer
Dim MAGs As String = args("--contigs")
Dim outprefix As String = args("--output")
Dim predicts = ProdigalWorker.GenePrediction(FastaFile.Read(MAGs)).ToArray
Call ProdigalWorker.ExportResult(predicts, outprefix)
Return 0
End Function
<ExportAPI("metaeuk")>
Public Function MetaEuk(args As CommandLine) As Integer
Dim config As New MetaEukConfig With {
.ReferenceFile = args("--reference"),
.ContigsFile = args("--contigs"),
.OutputPrefix = args("--output")
}
Dim predicts As GenePrediction() = MetaEukWorker.Predict(config).ToArray
Call MetaEukWorker.ExportResult(predicts, config)
Return 0
End Function
End Moduleusing Microsoft.VisualBasic.CommandLine;
using Microsoft.VisualBasic.CommandLine.Reflection;
using SMRUCC.genomics.Annotation.MetaEuk;
using SMRUCC.genomics.Annotation.Prodigal;
using SMRUCC.genomics.SequenceModel.FASTA;
public static class Program
{
public static int Main(string[] args)
{
return typeof(Program).RunCLI(App.CommandLine);
}
[ExportAPI("prodigal")]
public static int Prodigal(CommandLine args)
{
string MAGs = args["--contigs"];
string outprefix = args["--output"];
var predicts = ProdigalWorker.GenePrediction(FastaFile.Read(MAGs)).ToArray();
ProdigalWorker.ExportResult(predicts, outprefix);
return 0;
}
[ExportAPI("metaeuk")]
public static int MetaEuk(CommandLine args)
{
var config = new MetaEukConfig {
ReferenceFile = args["--reference"],
ContigsFile = args["--contigs"],
OutputPrefix = args["--output"]
};
GenePrediction[] predicts = MetaEukWorker.Predict(config).ToArray();
MetaEukWorker.ExportResult(predicts, config);
return 0;
}
}open Microsoft.VisualBasic.CommandLine
open Microsoft.VisualBasic.CommandLine.Reflection
open SMRUCC.genomics.Annotation.MetaEuk
open SMRUCC.genomics.Annotation.Prodigal
open SMRUCC.genomics.SequenceModel.FASTA
module Program =
let Main (args: string[]) : int =
typeof<Program>.RunCLI(App.CommandLine)
[<ExportAPI("prodigal")>]
let Prodigal (args: CommandLine) : int =
let MAGs = args.["--contigs"]
let outprefix = args.["--output"]
let predicts = ProdigalWorker.GenePrediction(FastaFile.Read(MAGs)) |> Seq.toArray
ProdigalWorker.ExportResult(predicts, outprefix)
0
[<ExportAPI("metaeuk")>]
let MetaEuk (args: CommandLine) : int =
let config = MetaEukConfig(
ReferenceFile = args.["--reference"],
ContigsFile = args.["--contigs"],
OutputPrefix = args.["--output"])
let predicts : GenePrediction[] = MetaEukWorker.Predict(config) |> Seq.toArray
MetaEukWorker.ExportResult(predicts, config)
0Every type and function used above — FastaFile, ProdigalWorker, MetaEukWorker, GenePrediction — is documented with its full signature in the CLR API reference. GCModeller itself is written in VB.NET, so the VB.NET flavour is always the reference implementation; C# and F# consume the very same assemblies.
Which package do I need?
Core
SMRUCC.genomics.core — the foundation library: biological file I/O streams and the shared data models every other module builds on. Install it first.
Annotation
SMRUCC.genomics.annotation, .annotation.prodigal, .annotation.metaeuk — gene prediction and genome annotation file models (GFF, PTF, GO / KO / Pfam mapping).
Analysis
SMRUCC.genomics.analysis.* — enrichment (.go, .kegg, .analysis.hts.gsea), expression (.hts.rnaexpression), network inference (.hts.wgcna), FBA and metagenomics.
Data & repositories
SMRUCC.genomics.data.* — readers for BioCyc / MetaCyc, KEGG, Reactome, UniProt, RCSB PDB and the regulon databases.