Discover naturalis/orchids Open Source project

Species Distribution Modelling using Deep Learning

sdmdl

Course repository for Methods in Biodiversity Analysis

mebioda

Ecological Niche Modelling Using Deep Learning

trait-geo-diverse-dl

Jupyter Notebook

Hemiphot

Analysis of hemispherical images

imgpheno

Image feature extraction in Python

CNN-based image classification of AntWeb images

FormicID

Convert markdown documentation to SCORM

markdown2scorm

JavaScript

brassicaceae-hybseq-pipeline

Pipeline for BLAST analysis of high-throughput DNA sequencing data.

HTS-barcode-checker

Find for your input taxonomy the taxonomy from an other database

galaxy-tool-taxonmatcher

Phylogenomic analysis on the CIPRES REST portal

bio-cipres

galaxy-tool-lca

Automated and Reproducible Analysis of Next Generation Sequencing

arangs

Contains shell scripts with example usage of NGS assembly tools for mid-size (insect) genomes.

de-novo-assembly

Ontology-mediated refinement of bulk segregant analyses

brassica-snps

Naturalis implementations of BioVeL services.

biovel-nbc

Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - trait data and analysis

mycorrhiza

Pipeline for building topologically-constrained phylogenies from DNA barcode data

barcode-constrained-phylogeny

Comparative analysis of abiotic niches in Ungulates

trait-geo-diverse-ungulates

img-classify-all

Aggregator repository for projects related to image classification

docker-treepl

Dockerfile for treePL

Dockerfile

seshat-trait-data-domesticates

Repository for aggregating comparative trait data for Ungulates and Poaceae and preparing for submission to the SESHAT database

3d-cetacean-scapulae

RiseAndFall

Data repository for the Rise and Fall of Species

Config files and scripts for assembly of mixed short (Illumina) and long (PacBio) reads

mixed-reads-assembly-Erycina

Documentation about bioinformatics at Naturalis

bio-info-docs

lab-rdm-in-github

Research data management in GitHub

big-data-for-bees

Repository to collect data sets, notes, and prototypes of integration

nbclassify

Proof of concept demonstrating identification of species images using artificial neural networks.

Standardized validation of barcodes

barcode_validator

Captures insect counts on sticky traps by image analysis. Docker image.

trap-cap

Dockerfile

Custom-databases-DNA-sequences

Bioinformatics project B19017-555

Wrappers, scripts and configuration files for running cluster and identification analysis on a Galaxy installation.

Galaxy-Pipeline

Use a python script to utilize either the Global Names api or the TNRS api to collect accepted taxonomic names.

galaxy-tool-synonym-checker

Project directory for the analysis of ancient tomato DNA

tomatogenome

A web tool to assess monophyly in trees as produced by BOLD systems

monophylizer

Pipelines for analyzing fungal diversity

mycodiversity

DWCA Configuratie bestanden om data te downloaden uit ES (NBA)

DWCAConfig

Data and scripts for a research collaboration with the Vlinderstichting

butterflies

Morphological, behavioral, and life history traits for the comparative analysis of Ungulates

naturalis-galaxy-tutorials

trait-organismal-ungulates

apexomes

Scripts and config files for mapping and analyzing exomes of the great apes