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Getting started

BioKotlin is published to Maven Central as org.biokotlin:biokotlin. Pick whichever of the following fits how you work.

You need Java 21 or newer

BioKotlin is compiled to Java 21 bytecode, so a JDK 21+ runtime is required. Check yours with java -version.

JupyterLab with the Kotlin kernel

This is the quickest way to try BioKotlin interactively, and it is how the tutorials in this site are written.

  1. Install Java 21 or newer.

  2. Install the Kotlin kernel for Jupyter, either with conda:

    conda install -c jetbrains kotlin-jupyter-kernel

    or with pip:

    pip install kotlin-jupyter-kernel

  3. Install JupyterLab, start it, and create a notebook with the Kotlin kernel.

  4. Load BioKotlin in the first cell:

    %use biokotlin

    The %use line magic resolves BioKotlin from Maven Central and sets up its default imports. To pin a version, write %use biokotlin(1.0.0).

Kotlin script

Add a dependency annotation at the top of a .main.kts file:

@file:DependsOn("org.biokotlin:biokotlin:1.0.0")

import biokotlin.seq.*

val dna = NucSeq("GCAGAT")
println(dna.reverse_complement())

Run it with kotlin my-script.main.kts.

Gradle or Maven project

build.gradle.kts
repositories {
    mavenCentral()
}

dependencies {
    implementation("org.biokotlin:biokotlin:1.0.0")
}

kotlin {
    jvmToolchain(21)
}
build.gradle
repositories {
    mavenCentral()
}

dependencies {
    implementation 'org.biokotlin:biokotlin:1.0.0'
}
pom.xml
<dependency>
    <groupId>org.biokotlin</groupId>
    <artifactId>biokotlin</artifactId>
    <version>1.0.0</version>
</dependency>

All released versions are listed on Maven Central.

Command line tools

The command line interface lives in a separate project, biokotlin-tools. Download an installable tar file from its releases page.

Building from source

git clone https://github.com/maize-genetics/BioKotlin.git
cd BioKotlin
./gradlew build

./gradlew shadowJar produces a fat jar under build/libs/ if you want to load a development build into a notebook with @file:DependsOn.

Next steps