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.
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.
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-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.
- workshops - Online material for SBDI courses.
-
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.
-
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.
-
SBDI4R - R package to access and use Swedish biodiversity data.
-
R tools tutorial - tutorial for & demo of SBDI R tools
- sbdi-support - Support issues from the support form and coming in other ways.
- 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.