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Naturalis Biodiversity Center

Login: naturalis

Company: null

Location: Leiden, the Netherlands

email:

Blog: http://www.naturalis.nl

Members

Repositories

3d-cetacean-scapulae: null
ai-fann-evolving: Framework to evolve optimal neural networks
algorithm-genetic-diploid: Extensible implementation of a diploid genetic algorithm
apexomes: Scripts and config files for mapping and analyzing exomes of the great apes
arangs: Automated and Reproducible Analysis of Next Generation Sequencing
asterid-phylo-comp: Project repository to infer bayesian phylogenies of Asterids and to perform comparative analysis of state transitions in vascular morphology
basic-checks: null
beamercontrol: Highlevel tool to control beamers via Extron
beelduitwisselaar: Modules and themes of the beelduitwisselaar Drupal application
binford2k-drupal: This is a module that allows you to manage many aspects of a multisite Drupal installation.
bio-info-docs: Documentation about bioinformatics at Naturalis
bio-phylo: Phyloinformatic analysis using Perl
bioportal-dashboard: null
bioportal-php-client: null
bioportal_sitemap_generator: null
biovel-nbc: Naturalis implementations of BioVeL services.
biovel-R-client: An example client showing how to connect to biovel services from within R
bootscript: null
brahms-digi-webapp: Simple pipeline to join BRAHMS CSV records with image analysis
browbrow: Brownian motion in a browser window
Cluster-pipeline: 454 sequence clustering and identification
cobra: null
CourseComparativeMethods: Examples of application of comparative methods in R
cwl-master-project: Source code in Common Workflow Language for sharing pipelines between Rijk Zwaan and Naturalis
DataHackathonLeiden: repository for the pro-eBiosphere hackathon 'Pimp my data'
de-novo-assembly: Contains shell scripts with example usage of NGS assembly tools for mid-size (insect) genomes.
devops-configs: Configs for tools our developers and operators use
dna-barcoding: Scripts, data files and wiki to support dna-barcoding analyses
docker-ab: Run Apache benchmark (ab) and visualize using Kibana.
docker-ccw: Dockerfile and docker-compose for CCW website
docker-galaxy: Docker manifest for galaxy
docker-geneious: Geneious shared database
docker-linnaeusng: Docker related files for deploying linnaeusng
docker-minio: null
docker-nba-ml-mimetype: Mimetype generator for NBA etl module.
docker-openvas: Docker related files for deploying openvas security scanner
docker-salep: Docker related files for deploying salep webcrawler
docker-samba: Samba fileserver docker-compose file
docker-treebase: Dockerfile and docker-compose for treebase
docker-waarneming: Docker related files for deploying waarneming.nl
docs: Documentation about how to use and contribute to Naturalis documentation
DWCAConfig: DWCA Configuratie bestanden om data te downloaden uit ES (NBA)
exhibition-boerhaave: null
Extract_Exons: Bash / python scripts for extracting exons from genomic sequences
fastq-simple-tools: Simple utility scripts for operating on FASTQ files
Find_SNPs: Compare two sets of mapping assemblies and return a list of SNPs (or InDels) that can distinguish the two sets.
FloraDataMining: Source code and data for pilot on FotG data mining and comparative analysis
FlorML: null
FormicID: :ant: Code repository for CNN-based image classification of AntWeb images
Galaxy-Pipeline: Wrappers, scripts and configuration files for running cluster and identification analysis on a Galaxy installation.
galaxy-tool-add-blast-to-otutable: null
galaxy-tool-BLAST_wrapper: null
galaxy-tool-cutadapt: null
galaxy-tool-cutadapt-docker: null
galaxy-tool-flash: null
galaxy-tool-lca: null
galaxy-tool-make-otu-table: null
galaxy-tool-vsearch-pipeline: null
galaxy-tool-worms: null
geogenodist: Data and scripts for the study of global trends in genetic distance by geographic distance.
gif: Overview of devices and collections for the Gif! exhibition
harvest-monitor: Monitoring the medialib CRS harvest errors
Hemiphot: Analysis of hemispherical images
HTS-barcode-checker: Pipeline for BLAST analysis of high-throughput DNA sequencing data.
img-classify-all: Aggregator repository for projects related to image classification
imgpheno: Image feature extraction in Python
iontorrent-backup: Backup script for IonTorrent based on Rsync
KNAW-DANS-NBA-demo: Demo queries for the workshop at KNAW, December 8, 2017
lemmus: High level tool for infrastructure development workflow
lfs-test: null
Lims2-Plugins: null
linnaeus_ng_control: Ansible Playbooks for controlling Linnaeus NG servers
LNG-new-matrix-interface-2015: null
lod-hack: Experiments and documentation for the Linked Open Data mini-Hackathon 25-26 April 2016
logstash_filter: filter part of logstash
mapDamage: mapDamage: testing for damage patterns in ancient DNA sequences
mebioda: Course repository for Methods in Biodiversity Analysis
medialibrary-mediaserver: to serve your media
medialibrary-publisher: to publish your media
mixed-reads-assembly-Erycina: Config files and scripts for assembly of mixed short (Illumina) and long (PacBio) reads
molecularbiodiversity: null
monophylizer: A web tool to assess monophyly in trees as produced by BOLD systems
mycorrhiza: Evolutionary dynamics of mycorrhizal symbiosis in land plant diversification - trait data and analysis
naturalis_data_api: null
naturalis_gbif_node: null
naturalis.github.io: The Naturalis GitHub pages repository
Naturalis-hub: Generic hub template grails app
naturalis-icon-font: A webfont containing much used interface icons in Naturalis style
naturalis-java-development-standards: Documents related to standards, conventions and requirements of Java development at Naturalis
nba-benchmark: Benchmark NBA using apache bench and visualise results
nba-brondata-annex-brahms: null
nba-brondata-bijzcol: Bron data set for NBA on bijzondere collecties
nba-brondata-brahms: null
nba-brondata-col: null
nba-brondata-crs: null
nba-brondata-geo: null
nba-brondata-medialib: null
nba-brondata-nsr: null
nba-brondata-storageunits: null
nba-brondata-testsets: Controlled test data sets for NBA (regression) testing
nba-direct-query-api: null
nba-docs: Netherlands Biodiversity API documentation
nba-dwca-downloader: null
nba-eml: eml bestanden voor Naturalis Biodiversity API
nba-hackaton-team2: null
nba_json_schemas: JSON-schemas for validation of JSON-documents intended for impirt into NDS/NBA
nba-log-parser: Post-processed NBA logs
nbaR: R client library for the Netherlands Biodiversity Api (NBA)
nba_scratchpad: A query scratchpad and management tool for the Netherlands Biodiversity API (NBA)
nba-storageunits-etl: null
nbclassify: Proof of concept demonstrating identification of species images using artificial neural networks.
nbclassify-data: Supplementary data for "OrchID: a Generalized Framework for Taxonomic Classification of Images Using Evolved Artificial Neural Networks"
ndabio: null
nepenthes-3dpca: Pipeline for performing principal component analysis of 3D scans of Nepenthes pitchers
ngs-workflows: Source code, data and documentation to demonstrate automation in NGS data analysis
nl.naturalis.ant.contrib: Ant tasks used in naturalis builds
nl.naturalis.oaipmh: Java framework for expsing OAI-PMH repositories through a REST service
openstack-docs: Documentation resources IT facilities Naturalis
openstack-manuals: null
openstack-resources: Description of resources in openstack
opexpeditie: null
orchid-presentation: LaTeX slides for nbclassify
orchid-report: Report for the automated slipper orchid identification project
orchids: Scripts and data to analyze and visualize duplication and divergence of the MADS box genes in Orchids
orchid-transcriptome-pipeline: null
pfsense-patches: Pfsense patches
powershell: null
puppet: Collection of puppet manifests
puppet-apachesolr: Puppet Module for Apache Solr running on top on Tomcat (might be configurable)
puppet-apexomes: puppet manifest for the apexomes analysis environment
puppet-arecatools: Puppet module for installing areca tools
puppet-base: Puppet module for server management, installs handy software and ssh keys.
puppet-bhv_cms: Puppet module for cms system Boerhaave
puppet-bioinformatics: many bioinformatic tools
puppet-bioportal: Puppet module for bioportal based on postgres and postgis
puppet-burp: Manage Burp, backup and restore program
puppet-ceph: null
puppet-common: common function library for puppet
puppet-dierendeterminatie: Puppet module for dierendeterminatie.
puppet-duplicitystandalone: Standalone backup module based on duplicity
puppet-elasticsearch_snapshot: puppet resource for creating repositories, creating snaps and restoring snaps.
puppet-fileserver: null
puppet-ftpserver: Puppet manifest for ftp server based on vsftpd
puppet-galaxy: null
puppet-garli: Puppet module for deploying GARLI, Genetic Algorithm for Rapid Likelihood Inference
puppet-geneiouslm: Geneious Floating License Manager
puppet-hermann-herbarium.nl: Puppet modules for website www.hermann-herbarium.nl
puppet-ipt-toolkit: Puppet module for GBIF Integrated Publishing Toolkit
puppet-jira: Puppet module to run docker containers for Jira
puppet-jira-old: (old) Atlassian JIRA Puppet Module
puppet-kiosk: Puppet module to manage and provision kiosk browser
puppet-kiosk-minimal: Puppet module for minimal kiosk functionality
puppet-lemmus: Installs lemmus application
puppet-letsencrypt: A Puppet module to install the Letsencrypt client and request certificates.
puppet-lianas-of-guyana.org: Puppet module for website www.lianas-of-guyana.org
puppet-linnaeusng: Puppet module for Nederlands Soortenregister
puppet-livestream: Puppet module to install livestream viewer
puppet-medatata: Simple puppet manifest that creates facts based on input metadata
puppet-medialibrary: Puppet module for Media Library
puppet-minio: null
puppet-monophylizer: Puppet module for monophylizer
puppet-mrbayes: Puppet manifest for provisioning mrbayes on linux
puppet-naturalislogforwarder: Wrapper around logstash forwarder class
puppet-nba: Puppet deployment for Netherlands Biodiversity API
puppet-nda: null
puppet-nfs: Puppet module for automagic set up of up nfs servers and clients. Storeconfigs is used for propogating configs to clients. Optional nfs4-support.
puppet-novatools: Puppet module for applying nova commands
puppet-orchid: Puppet module for OrchID
puppet-patches: patch the shit out of it!
puppet-pcns: Puppet module for apc powerchute network shutdown
puppet-php: Puppet module to manage PHP
puppet-puppetci: Puppet module for automated testing
puppet-puppetdev: Module for puppet development
puppet-raxml: Puppet module for deploying latest version of raxml: Randomized Axelerated Maximum Likelihood of phylogenetic trees
puppet-role_analytics: null
puppet-role_backup: Backup and Restore role manifest for puppet in a foreman environment.
puppet-role_ccw: Puppet Role manifest for CCW deployments
puppet-role_ceph: null
puppet-role_col: Puppet role module for Catalogue of Life websites and services.
puppet-role_dockertreebase: Docker related files for deploying treebase
puppet-role_drupal: Role definition for drupal manifest.
puppet-role_duplicity: Custom manifest for duplicity
puppet-role_elasticsearch: Role definition for elasticsearch puppet manifest
puppet-role_etlw: Puppet manifest for deployment of ETL Workbench
puppet-role_fileserver: Puppet code for fileserver deployments
puppet-role_foreman_proxy: Customisation module for foreman_proxy
puppet-role_geneious: null
puppet-role_ids: null
puppet-role_iontorrent: Puppet manifest for managing iontorrent backup and monitoring
puppet-role_lamp: Puppet module for LAMP stack
puppet-role_limsoaipmh: word of many words
puppet-role_logging: role of logging
puppet-role_minio: null
puppet-role_mysql: Install and manage mysql
puppet-role_nbcdata: Puppet Role manifest for installation of nbcdata server(s)
puppet-role_openstack: null
puppet-role_openvas: Puppet manifest for deploying dockerbased openvas
puppet-role_openvpn: Wrapper module thejandroman/puppet-openvpn_client
puppet-role_oradb: Puppet module for custom settings for the oradb module
puppet-role_resourcespace: Puppet manifest for deployment of resourcespace
puppet-role_reverseproxy: null
puppet-role_rsyslog: null
puppet-role_salep: Puppet deployment scripts for deploying salep webcrawler
puppet-role_sensu: Role for deploying Sensu
puppet-role_simplelb: Basic loadbalancer role manifest based on Nginx loadbalancer
puppet-role_snmp: null
puppet-role_solr: puppet module for provisioning solrcloud
puppet-role_storage-analytics: Puppet manifest supporting installation of storage-analytics software
puppet-role_waarneming: null
puppet-role_waarnemingcms: Puppet deployment scripts for Waarneming.nl CMS
puppet-role_waarnemingforum: Puppet deployment scripts for Waarneming.nl Forum
puppet-role_xenocanto: Puppet deployment manifest for Xeno Canto
puppet-samba: Puppet module to manage Samba Server
puppets-bioinformatics: puppet manifests for bioinformatics tasks
puppet-scirius: null
puppet-security: null
puppet-security_updates: Manifest for unattended security updates
puppet-sensuclient: Puppet module for sensu standalone client
puppet-simple_nfs: simple nfs server, module wrapper arround https://forge.puppet.com/derdanne/nfs
puppet-solr: A puppet module for setting up a multi-core solr instance
puppet-sqlplus: null
puppet-squid: Squid proxy puppet manifest for reverse proxy setups
puppet-stresstest: Puppet module for stress testing linux systems.
puppet-suricata: null
puppet-user: null
puppet-vmwaretools: null
puppet-wildfly: Puppet model for installing and configuring WildFly
puppet-windows_oradb: null
puppet-windows_role_oradb: null
puppet-wingid: Puppet module for WingID
puppet-zookeeper: Puppet manifest for deploying apache zookeeper
RBIEN: Tools for accessing the Botanical Information and Ecology Network (BIEN) database
role_treebase: Puppet module for treebase
rs-lng-plugins: null
selenium-tests-crs: A set of Java Selenium tests for functional and regression testing of the web interface of the Naturalis CRS system
sff2fastq: extract 454 Genome Sequencer reads from a SFF file and convert them into a FASTQ formatted output
Simple-LCA: A tool to find the lowest common ancestor of BLAST results
Split_on_Primer: Split a FASTQ or FASTA file into sub files based on the primers used.
Split_sequence: Split a sequence file into sub files based on the tags or primers used
storage-analytics: null
supersmart: Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
surrogacy_analysis: Clone from http://sourceforge.net/projects/surrogacy/
svn2gitignore: Simple script to migrate SVN ignores to .gitignore file
swagger-ui: swagger-ui costomised for NBA endpoint reference documentation
tolomatic-java: Port of MapReduce pruner to Java/Hadoop
tomatogenome: Project directory for the analysis of ancient tomato DNA
treebase-artifact: Treebase binaries for deployment
trexintown: Overview of devices and collections for the T.rex in Town exhibition
trexontour: Configuration for T.rex on Tour
wgs2ncbi: Toolkit for preparing genomes for submission to NCBI
windows-openstack-imaging: null

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.