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‎BioFSharp.ML.sln

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Microsoft Visual Studio Solution File, Format Version 12.00
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# Visual Studio Version 17
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{D152DA0B-8F60-4611-B613-642379E2B17C}"
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LICENSE = LICENSE
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{8DCCA688-871C-49DD-BC06-4877F714497C}.Release|Any CPU.Build.0 = Release|Any CPU
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‎BioFSharp.XYZ.sln

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@@ -5,12 +5,8 @@ VisualStudioVersion = 17.0.31903.59
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MinimumVisualStudioVersion = 10.0.40219.1
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{7501C4DF-A844-40A0-8742-3343E48E55F1}"
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EndProject
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.XYZ", "src\BioFSharp.XYZ\BioFSharp.XYZ.fsproj", "{BAC97B5C-B9A6-40D6-B533-0A07E12939ED}"
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Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{D152DA0B-8F60-4611-B613-642379E2B17C}"
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EndProject
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.XYZ.Tests", "tests\BioFSharp.XYZ.Tests\BioFSharp.XYZ.Tests.fsproj", "{CB9E38BC-EE86-44EB-AFF5-91D1AF713ADC}"
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EndProject
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.gitignore = .gitignore
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.github\workflows\deploy-docs.yml = .github\workflows\deploy-docs.yml
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.ML", "src\BioFSharp.ML\BioFSharp.ML.fsproj", "{E2E3AA2A-BEEA-4965-A58F-2A3BCDD658D6}"
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Project("{F2A71F9B-5D33-465A-A702-920D77279786}") = "BioFSharp.ML.Tests", "tests\BioFSharp.ML.Tests\BioFSharp.ML.Tests.fsproj", "{9A66D71D-8A9B-4376-85B4-3D5DB8BDDC22}"
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{8DCCA688-871C-49DD-BC06-4877F714497C}.Release|Any CPU.ActiveCfg = Release|Any CPU
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{8DCCA688-871C-49DD-BC06-4877F714497C}.Release|Any CPU.Build.0 = Release|Any CPU
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EndGlobal

‎README.md

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# BioFSharp.XYZ
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# BioFSharp.ML
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![Logo](docs/img/Logo_large.png)
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A template repository for creating an extension package for BioFSharp.
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## Content
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- `src/BioFSharp.XYZ`: The main project folder. Contains a library with BioFSharp core dependency.
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- `tests/BioFSharp.XYZ.Tests`: The test project folder. Contains a XUnit test project
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- `src/BioFSharp.ML`: The main project folder. Contains a library with BioFSharp core dependency.
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- `tests/BioFSharp.ML.Tests`: The test project folder. Contains a XUnit test project
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- `build/build.fsproj`: A FAKE build project that handles building, testing, packaging, publishing, etc.
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- `docs`: the docs folder contains an example index.fsx file with simple documentation boilerplate.
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- Rename some things: Replace `XYZ` with the name of your package
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- `PackageTemplate.sln`
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- `src/BioFSharp.XYZ`
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- `src/BioFSharp.XYZ/BioFSharp.XYZ.fsproj`
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- `src/BioFSharp.ML`
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- `src/BioFSharp.ML/BioFSharp.ML.fsproj`
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- Rename and add nuget package metadata
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- `tests/BioFSharp.XYZ`
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- `tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj`
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- Also make sure to fix the project reference to BioFSharp.XYZ when renamed
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- `tests/BioFSharp.ML`
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- `tests/BioFSharp.ML.Tests/BioFSharp.ML.Tests.fsproj`
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- Also make sure to fix the project reference to BioFSharp.ML when renamed
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- in `build/ProjectInfo.fs`:
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- Set project name:
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```fsharp
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let project = "BioFSharp.XYZ" // replace with the name of your project
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let project = "BioFSharp.ML" // replace with the name of your project
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```
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- Set git owner:
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```fsharp
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```fsharp
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let testProjects =
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[
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"tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj" // replace with the name of your test project
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"tests/BioFSharp.ML.Tests/BioFSharp.ML.Tests.fsproj" // replace with the name of your test project
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]
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```
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- in `.github/workflows/build-and-test.yml`: change codecov slug

‎build/ProjectInfo.fs

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open Fake.Core
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let project = "BioFSharp.XYZ"
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let project = "BioFSharp.ML"
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let testProjects =
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[
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"tests/BioFSharp.XYZ.Tests/BioFSharp.XYZ.Tests.fsproj"
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"tests/BioFSharp.ML.Tests/BioFSharp.ML.Tests.fsproj"
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]
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let solutionFile = $"{project}.sln"

‎docs/index.fsx

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(**
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# BioFSharp.XYZ
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# BioFSharp.ML
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![Logo](./img/Logo_large.png)
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Make sure to load any external references via nuget.
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*)
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#r "nuget: BioFSharp, 2.0.0-preview.3"
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#I @"..\src\BioFSharp.XYZ\bin\Release\netstandard2.0"
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#r "BioFSharp.XYZ.dll"
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#I @"..\src\BioFSharp.ML\bin\Release\netstandard2.0"
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#r "BioFSharp.ML.dll"
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open BioFSharp.XYZ
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open BioFSharp.ML
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let o = BioTalk.helloBio "Kev"
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‎src/BioFSharp.ML/BioFSharp.ML.fsproj

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<Project Sdk="Microsoft.NET.Sdk">
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<PropertyGroup>
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<TargetFramework>netstandard2.0</TargetFramework>
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<GenerateDocumentationFile>true</GenerateDocumentationFile>
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<IncludeSymbols>true</IncludeSymbols>
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<SymbolPackageFormat>snupkg</SymbolPackageFormat>
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</PropertyGroup>
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<PropertyGroup>
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<Authors>Timo Mühlhaus, David Zimmer, Kevin Schneider, F# open source contributors</Authors>
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<Description>Machine learning with BioFSharp and CNTK.Net.</Description>
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<Summary>
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Make your workflow ML ready with BioFSharp.ML.
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Currently contains wrapper functions for CNTK
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and a pre-trained model we used in our publication
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about predicting peptide observability.
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</Summary>
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<PackageLicenseExpression>MIT</PackageLicenseExpression>
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<PackageProjectUrl>https://BioFSharp.github.io/BioFSharp.ML/</PackageProjectUrl>
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<PackageIcon>icon.png</PackageIcon>
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<PackageTags>bioinformatics F# fsharp statistic biostatistics datascience</PackageTags>
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<RepositoryUrl>https://github.com/BioFSharp/BioFSharp.ML</RepositoryUrl>
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<RepositoryType>git</RepositoryType>
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<FsDocsLicenseLink>https://github.com/BioFSharp/BioFSharp.ML/blob/main/LICENSE</FsDocsLicenseLink>
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<FsDocsReleaseNotesLink>https://github.com/BioFSharp/BioFSharp.ML/blob/main/RELEASE_NOTES.md</FsDocsReleaseNotesLink>
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</PropertyGroup>
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<ItemGroup>
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<None Include="..\..\docs\img\icon.png" Pack="true" PackagePath="" />
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<None Include="BioFSharp.ML.fsx" />
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<None Include="CNTKLoadScript.fsx">
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<CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
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</None>
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<Compile Include="CNTK.fs" />
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<Compile Include="DPPOP.fs" />
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<!-- Resources -->
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<EmbeddedResource Include="Resources\Chlamy5Times128.model" />
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<EmbeddedResource Include="Resources\Yeast5Times128.model" />
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<None Include="Scripts\CNTK.fsx" />
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<None Include="Scripts\DPPOP.fsx" />
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</ItemGroup>
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<ItemGroup>
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<PackageReference Include="BioFSharp" Version="2.0.0-preview.3" />
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<PackageReference Include="BioFSharp.IO" Version="2.0.0-preview.3" />
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<PackageReference Include="FSharpAux" Version="2.0.0" />
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<PackageReference Include="FSharpAux.IO" Version="2.0.0" />
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<PackageReference Include="CNTK.CPUOnly" Version="2.8.0-rc0.dev20200201" />
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</ItemGroup>
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</Project>

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