content.toml

# JuliaLifeSciences content
# Edit this file to update the site. Each package's `capabilities` list controls
# its filters and tags; values match the IDs in `[[capabilities]]` blocks.
# `paper` and `tutorial` are optional package fields.

[site]
logo = "/JuliaLifeSciencesLogo.svg"
meta_title = "JuliaLifeSciences — One language. Every scale of life."
meta_description = "Discover Julia packages for bioinformatics, biology, health, medicine, imaging, and ecology."
eyebrow = "Explore the Julia life sciences ecosystem"
title = "One language. Every scale of"
accent = "life."
intro = "From DNA and proteins to populations and medical images, discover open-source Julia tools built for ambitious life-science research."
primary_cta = "Explore packages"
secondary_cta = "Meet the communities"
scroll_cue = "Scroll to explore"
topics = ["DNA & RNA", "Proteins", "Medical imaging", "Health", "Ecology"]
proofs = ["Open source", "Composable", "Fast", "Reproducible"]
footer_note = "A community showcase for the tools, people, and possibilities shaping life-science research in Julia."
talks_nav = "JuliaCon talks"

[sections]
capabilities_kicker = "What can you do? · Hand-curated packages"
capabilities_title = "From raw data to discovery."
capabilities_intro = "Explore a focused selection of Julia packages, hand-curated for relevance, practical value, and community adoption across life-science workflows."
organizations_kicker = "The ecosystem"
organizations_title = "Three communities. One shared purpose."
organizations_intro = "Open communities building the foundations for modern biological, health, and ecological research."
testimonials_kicker = "Community stories"
testimonials_title = "Research moves faster in Julia."
testimonials_intro = "The entries below are editable examples. Replace each quote, name, role, and organization with a real community story."
talks_kicker = "From the JuliaCon archive"
talks_title = "Life sciences on stage."
talks_intro = "Watch researchers and community builders share the tools, applications, and ideas advancing biology, health, and ecology in Julia."

[[organizations]]
id = "biojulia"
name = "BioJulia"
focus = "Molecular biology"
description = "Core tools for biological sequences, structures, genomes, and bioinformatics workflows."
url = "https://biojulia.dev"
logo = "https://github.com/BioJulia.png?size=160"
color = "#2d8c5f"
slack_channels = ["#biology", "#sciml-sysbio"]

[[organizations]]
id = "juliahealth"
name = "JuliaHealth"
focus = "Health & medicine"
description = "Open software for medical imaging, clinical data, physiology, and computational medicine."
url = "https://juliahealth.org"
logo = "https://github.com/JuliaHealth.png?size=160"
color = "#c94b47"
slack_channels = ["#health-and-medicine"]

[[organizations]]
id = "ecojulia"
name = "EcoJulia"
focus = "Ecology & evolution"
description = "High-performance tools for biodiversity, ecosystems, phylogenetics, and spatial ecology."
url = "https://github.com/EcoJulia"
logo = "https://github.com/EcoJulia.png?size=160"
color = "#7857a7"

# JuliaCon talks are grouped by organization. Replace any field or add another
# `[[talks]]` block to update the talks page without changing the site code.
[[talks]]
organization = "biojulia"
title = "BioJulia and Bioinformatics in Julia: Past, Present, Future"
speaker = "Ben J. Ward"
year = 2018
youtube_url = "https://www.youtube.com/watch?v=6CpPd6tkokQ"

[[talks]]
organization = "biojulia"
title = "Exploring the State of Machine Learning for Biological Data"
speaker = "Edmund Miller"
year = 2023
youtube_url = "https://www.youtube.com/watch?v=Q9eYgwvJfWE"

[[talks]]
organization = "biojulia"
title = "Structural Bioinformatics with BiochemicalAlgorithms.jl"
speaker = "Jennifer Leclaire"
year = 2024
youtube_url = "https://www.youtube.com/watch?v=vAcAKdfWm64"

[[talks]]
organization = "juliahealth"
title = "Real-Time, I/O, and Multitasking: Julia for Medical Imaging"
speaker = "Niklas Hackelberg"
year = 2022
youtube_url = "https://www.youtube.com/watch?v=chZfGfAAnpE"

[[talks]]
organization = "juliahealth"
title = "What's New with KomaMRI.jl"
speaker = "Carlos Castillo Passi"
year = 2025
youtube_url = "https://www.youtube.com/watch?v=YO-nLLfV27A"

[[talks]]
organization = "juliahealth"
title = "State of JuliaHealth"
speaker = "Jacob Zelko"
year = 2025
youtube_url = "https://www.youtube.com/watch?v=fhMEMNrLUwM"

[[talks]]
organization = "ecojulia"
title = "EcoJulia: Towards a Framework for Ecological Data Analysis in Julia"
speaker = "Michael Borregaard"
year = 2018
youtube_url = "https://www.youtube.com/watch?v=R4GzK-by0ac"

[[talks]]
organization = "ecojulia"
title = "Analyzing Species Interaction Networks in Julia"
speaker = "Francis Banville"
year = 2020
youtube_url = "https://www.youtube.com/watch?v=2HxWYi2IJb0"

[[talks]]
organization = "ecojulia"
title = "UniversalDiffEq.jl: Applying SciML to Ecology"
speaker = "Jack H. Buckner"
year = 2025
youtube_url = "https://www.youtube.com/watch?v=q7nuB1vcziU"

[[capabilities]]
id = "data-io"
number = "01"
title = "Data I/O"
description = "Read, write, and transform the formats that life-science research depends on."

[[capabilities]]
id = "simulation"
number = "02"
title = "Simulation"
description = "Model complex biological and physical systems efficiently on CPUs and GPUs."

[[capabilities]]
id = "data-analysis"
number = "03"
title = "Data analysis"
description = "Move from experimental data to reproducible statistical and computational insight."

[[capabilities]]
id = "visualization"
number = "04"
title = "Visualization"
description = "Explore high-dimensional results with interactive, publication-ready visual tools."

[[capabilities]]
id = "interoperability"
number = "05"
title = "Interoperability"
description = "Bring trusted libraries from other languages into a fast, composable Julia workflow."

# BioJulia — popular, active life-science packages first.
[[packages]]
name = "BioSequences.jl"
organization = "biojulia"
capabilities = ["data-analysis"]
description = "Efficient data types and operations for DNA, RNA, and amino-acid sequences."
repo = "https://github.com/BioJulia/BioSequences.jl"
tutorial = "https://biojulia.dev/BioSequences.jl/stable/"
stars = 160
featured = true

[[packages]]
name = "BioStructures.jl"
organization = "biojulia"
capabilities = ["data-io", "visualization"]
description = "Read, write, analyze, and visualize macromolecular structures, especially proteins."
repo = "https://github.com/BioJulia/BioStructures.jl"
tutorial = "https://biojulia.github.io/BioStructures.jl/stable/"
paper = "https://doi.org/10.1093/bioinformatics/btaa502"
stars = 106

[[packages]]
name = "BioMakie.jl"
organization = "biojulia"
capabilities = ["visualization"]
description = "Biology-focused plotting and interface tools built on the Makie visualization ecosystem."
repo = "https://github.com/BioJulia/BioMakie.jl"
stars = 71

[[packages]]
name = "GenomeGraphs.jl"
organization = "biojulia"
capabilities = ["data-analysis"]
description = "A modern framework for representing and working with genomic graph data in Julia."
repo = "https://github.com/BioJulia/GenomeGraphs.jl"
stars = 70

[[packages]]
name = "FASTX.jl"
organization = "biojulia"
capabilities = ["data-io"]
description = "Fast parsing and processing for FASTA and FASTQ biological sequence files."
repo = "https://github.com/BioJulia/FASTX.jl"
tutorial = "https://biojulia.dev/FASTX.jl/stable/"
stars = 66

[[packages]]
name = "BioAlignments.jl"
organization = "biojulia"
capabilities = ["data-analysis"]
description = "Pairwise sequence alignment tools and common biological alignment operations."
repo = "https://github.com/BioJulia/BioAlignments.jl"
stars = 65

# JuliaHealth
[[packages]]
name = "KomaMRI.jl"
organization = "juliahealth"
capabilities = ["simulation"]
description = "GPU-accelerated, Pulseq-compatible MRI acquisition simulation for research and education."
repo = "https://github.com/JuliaHealth/KomaMRI.jl"
tutorial = "https://juliahealth.github.io/KomaMRI.jl/stable/"
paper = "https://doi.org/10.1002/mrm.29635"
stars = 215
featured = true

[[packages]]
name = "DICOM.jl"
organization = "juliahealth"
capabilities = ["data-io"]
description = "Read and write Digital Imaging and Communications in Medicine files in Julia."
repo = "https://github.com/JuliaHealth/DICOM.jl"
stars = 59

[[packages]]
name = "BloodFlowTrixi.jl"
organization = "juliahealth"
capabilities = ["simulation"]
description = "Efficient one- and two-dimensional arterial blood-flow simulation using Trixi.jl."
repo = "https://github.com/JuliaHealth/BloodFlowTrixi.jl"
stars = 43

[[packages]]
name = "PubChemCrawler.jl"
organization = "juliahealth"
capabilities = ["data-io"]
description = "Utilities for programmatic access to chemical and compound data from PubChem."
repo = "https://github.com/JuliaHealth/PubChemCrawler.jl"
stars = 28

[[packages]]
name = "Thunderbolt.jl"
organization = "juliahealth"
capabilities = ["simulation"]
description = "A high-performance framework for multiscale cardiac multiphysics simulation."
repo = "https://github.com/JuliaHealth/Thunderbolt.jl"
stars = 26

[[packages]]
name = "NeuroAnalyzer.jl"
organization = "juliahealth"
capabilities = ["data-analysis", "visualization"]
description = "A toolbox for analysis and visualization of neurophysiological signals and recordings."
repo = "https://github.com/JuliaHealth/NeuroAnalyzer.jl"
stars = 21

# EcoJulia
[[packages]]
name = "SpatialEcology.jl"
organization = "ecojulia"
capabilities = ["visualization"]
description = "Data types and utilities for spatial ecological analysis and community datasets."
repo = "https://github.com/EcoJulia/SpatialEcology.jl"
stars = 60
featured = true

[[packages]]
name = "Microbiome.jl"
organization = "ecojulia"
capabilities = ["data-analysis"]
description = "Tools for analysis of microbiome and microbial-community abundance data."
repo = "https://github.com/EcoJulia/Microbiome.jl"
stars = 48

[[packages]]
name = "EcoSISTEM.jl"
organization = "ecojulia"
capabilities = ["simulation"]
description = "A computational framework for simulating ecosystems, biodiversity, and environmental change."
repo = "https://github.com/EcoJulia/EcoSISTEM.jl"
stars = 46

[[packages]]
name = "Phylo.jl"
organization = "ecojulia"
capabilities = ["visualization"]
description = "Create, manipulate, simulate, and visualize phylogenetic trees and traits."
repo = "https://github.com/EcoJulia/Phylo.jl"
stars = 37

[[packages]]
name = "Diversity.jl"
organization = "ecojulia"
capabilities = ["data-analysis"]
description = "Measure and partition alpha, beta, and gamma diversity across ecological communities."
repo = "https://github.com/EcoJulia/Diversity.jl"
paper = "https://doi.org/10.48550/arXiv.1404.6520"
stars = 35

[[packages]]
name = "RasterDataSources.jl"
organization = "ecojulia"
capabilities = ["data-io"]
description = "Download and use common global raster datasets in ecological Julia workflows."
repo = "https://github.com/EcoJulia/RasterDataSources.jl"
stars = 25

# Interoperability — these packages keep their own repository organization
# metadata so the ecosystem section remains focused on the three communities.
[[packages]]
name = "PythonCall.jl"
organization = "juliapy"
capabilities = ["interoperability"]
organization_name = "JuliaPy"
organization_logo = "https://avatars.githubusercontent.com/u/22030672?v=4"
organization_color = "#4063d8"
description = "Call and share data with Python from Julia, with automatic conversion and CondaPkg integration."
repo = "https://github.com/JuliaPy/PythonCall.jl"
tutorial = "https://juliapy.github.io/PythonCall.jl/stable/"
stars = 1064
featured = true

[[packages]]
name = "RCall.jl"
organization = "juliainterop"
capabilities = ["interoperability"]
organization_name = "JuliaInterop"
organization_logo = "https://avatars.githubusercontent.com/u/20260648?v=4"
organization_color = "#9558b2"
description = "Call R from Julia and move values between both languages in the same workflow."
repo = "https://github.com/JuliaInterop/RCall.jl"
tutorial = "https://juliainterop.github.io/RCall.jl/stable/"
stars = 337

[[packages]]
name = "JuliaCall"
organization = "juliainterop"
capabilities = ["interoperability"]
organization_name = "JuliaInterop"
organization_logo = "https://avatars.githubusercontent.com/u/20260648?v=4"
organization_color = "#9558b2"
description = "Embed Julia in R and call Julia functions through a seamless R package interface."
repo = "https://github.com/JuliaInterop/JuliaCall"
tutorial = "https://juliainterop.github.io/JuliaCall/"
paper = "https://doi.org/10.21105/joss.01284"
stars = 287

# [[testimonials]]
# quote = "Now that I run my analysis in Julia, the same pipeline is 20× faster — without splitting it across three languages."
# name = "Add a researcher name"
# role = "Research scientist"
# organization = "Add their organization"

# [[testimonials]]
# quote = "Our simulation went from an overnight job to something we can explore interactively during a meeting."
# name = "Add a researcher name"
# role = "Computational scientist"
# organization = "Add their organization"

# [[testimonials]]
# quote = "We kept the readable code our students need and gained the performance our production workflow demands."
# name = "Add a researcher name"
# role = "Lab lead"
# organization = "Add their organization"