SBDI repo overview

The Swedish Biodiversity Data Infrastructure (SBDI) is a collaboration between eleven consortium partners, and will aggregate a variety of tools and open-source software projects. Although most of these will be developed or forked under biodiversitydata-se, some will be hosted by partner organizations or external collaborators. We aim to provide a comprehensive overview of SBDI-related repos below.

Repos hosted elsewhere

The following repos are hosted by SBDI consortium partners or external collaborators:

• ampliseq - Nextflow pipeline for 16S rRNA amplicon sequencing analysis using QIIME2.

• koster_ml - Koster Seafloor Observatory: Object detection model for subsea imagery.

• koster_zooniverse - Koster Seafloor Observatory: Citizen science and database modules.

• nordicmicroalgae - Nordic Microalgae - data layer and API.

• plankton-toolbox - Free tool for phyto- and zooplankton.

Repos grouped by theme

Internal and external SBDI repos can be loosely grouped into the following, non-mutually exclusive categories:

• ALA forks
• Archeological data
• Courses and workshops
• Marine data
• Molecular data
• R
• SBDI information and discussion
• Support
• Systematic monitoring

ALA forks

• ala-map-plugin - Utilities for creating and displaying geographic data for clients of the ecodata services.
• biocollect - Front-end for ecodata, enables entering and retrieving systematic monitoring data (occurences and sites) and managing projects.
• ecodata - Primary data service for the Biocollect application.
• ecodata-client-plugin - Utilities and form rendering for clients of the ecodata services.

Archeological data

Courses and workshops

• workshops - Online material for SBDI courses.

Marine data

• koster_ml - Koster Seafloor Observatory: Object detection model for subsea imagery.

• koster_zooniverse - Koster Seafloor Observatory: Citizen science and database modules.

• nordicmicroalgae - Nordic Microalgae - data layer and API.

• plankton-toolbox - Free tool for phyto- and zooplankton.

Molecular data

• ampliseq - Nextflow pipeline for 16S rRNA amplicon sequencing analysis using QIIME2.

• asvoccur - R tools for ASV occurrence data in SBDI.

• coidb - COI (mitochondrial cytochrome oxidase subunit I) sequences collected from the BOLD database.

• mol-data - Source files for GitHub Pages on molecular data services provided by SBDI.

• mol-mod - Module for handling sequence-based occurrence data in SBDI (ASV portal).

• proxy-ws-mol-mod-docker - A dockerized NGINX reverse proxy for ASV portal.

• sbdi-phylomarkercheck - A pipeline that checks GTDB 16S sequences for phylogenetic signal with Sativa.

• sbdi-gtdb - SBDI Sativa curated 16S GTDB database.

• taxon-build-test - Preprocessing and merging of GBIF taxonomy with GTDB, using Taxonomy builder.

SBDI information and discussion

R

• SBDI4R - R package to access and use Swedish biodiversity data.

• other R resources

• R tools tutorial - tutorial for & demo of SBDI R tools

Support

• sbdi-support - Support issues from the support form and coming in other ways.

Systematic monitoring

• ala-map-plugin - Utilities for creating and displaying geographic data for clients of the ecodata services.
• biocollect - Front-end for ecodata, enables entering and retrieving systematic monitoring data (occurences and sites) and managing projects.
• ecodata - Primary data service for the Biocollect application.
• ecodata-client-plugin - Utilities and form rendering for clients of the ecodata services.