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NBIS -- National Bioinformatics Infrastructure Sweden

Login: NBISweden

Company: null

Location: Sweden

email:

Blog: https://nbis.se

Members

Repositories

agda: The BILS Tools Portal engine
annie: annie = ANNotation Information Extractor
AssemblyValidation: Assembly Validation
B2SAFE-core: B2SAFE service core code for EUDAT project
backup2nrm: Backup script for transferring UPPMAX files to NRM.
catfasta2phyml: Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file
Check_MD5SUMS: Check md5 sums for all *.md5 files found in directory tree
clihp: Command Line Help - to - Common Workflow Language Parser
CopyNumber450kCancer: Base line correction for copy number calling data from methylation 450k array
course_chipseq: null
workshop-common: Common configuration of githubpages for workshops
workshop-common: Common configuration of githubpages for workshops
course-course-tutorial: How to manage materials for a course given by NBIS.
course-ngs-test: null
workshop-howto: Howto setup a workshop
workshop-howto: Howto setup a workshop
cwltool: Common Workflow Language reference implementation
data-management-gym: Repository for Data Management training session modules
development-guidelines: Small repository, this one. Contains a single document (README.md) describing guidelines for the development of software within NBIS.
dist-ensembl: distributed ensembl
dockercommon: Base images for docker. The docker container can be started with any user and solved the owership of the mounted volume as well as the home dir
doi-bils-site: doi-bils-site PHP and XSLT code to generate index page of issued DOI's and landing pages for each DOI
doi-bils-site-data: Pointers to data download urls for issued DOIs
ds-km: ELIXIR Data Stewardship Knowledge Model
ds-wizard: Data Stewardship Wizard for the questions from DS Knowledge Model
Easy_webshare_on_UPPMAX: Easy websharing of files on UPPMAX
efasta2fasta: Convert extended fasta (efasta) to fasta
ega-api-key: Encryption Key server: abstract encryption key management.
ega-config-server: Spring (Netflix) Configuration Server
ega-data-api-dockerized: null
ega-data-api-v3-access: User Access (Edge) Service (Part of EGA Data API v3)
ega-data-api-v3-cipher: Collection of cipher and related code
ega-data-api-v3-config: Spring Configuration Service (Part of EGA Data API v3)
ega-data-api-v3-dataedge: User Data/Download (Edge) Service (Part of EGA Data API v3)
ega-data-api-v3-downloader: Downloader (Database) Service (Part of EGA Data API v3)
ega-data-api-v3-eureka: Spring Eureka Discovery Service (Part of EGA Data API v3)
ega-data-api-v3-key: Simple Encryption Key Provider Service (Part of EGA Data API v3)
ega-data-api-v3-res_mvc: Re/Encryption Provider Service (Part of EGA Data API v3)
ega-data-api-v3-zuul: ZUUL Reverse Proxy front end for EGA Data API v3
ega-dataedge: EGA API Edge service: enforces access control and provides public API functions
ega-eureka-service: Spring (Netflix) Eureka Discovery Server
ega-filedatabase-service: An abstraction layer microservice providing database functionality to other API microservices.
ega-htsjdk: A fork of HTSJDK with EGA specific enhancements
ega-res: A Cryptographic service to Access encrypted archived files and return a variety of formats (plain, encrypted AES 128/256, GPG Public Key, etc..). CPU/Memory Intensive.
ega-stream-collection: A collection of useful EGA cryptographic/caching streams
ega-zuulproxy: A front end for the EGA data API. Required for ELIXIR integration. Provides Load Balancing, Traffic Shaping, Automated Retries.
EMBLmyGFF3: An efficient way to convert gff3 annotation files into EMBL format ready to submit.
ena-metadata-forms: Javascript forms to generate XML files for submissions to ENA
ENA-submission: Tool for easing the submission of data to the ENA
ensembl-ensembl-pipeline: Job management for the Ensembl Genebuild pipeline
Ensembl-public-plugins: Plugins for an Ensembl website
ETTLIMS: A Lab Information Management System for Metagenomic and Single Cell Sequencing developed for the Ettema Lab
first-assignment-viklund: first-assignment-viklund created by GitHub Classroom
fts3: fts3
GAAS: Will contain all development done by the GAAS (Genome Assembly Annotation Service).
github-admin: null
GRSworkflow: Repository for development of workflow for use case 1.1
homo-horreum: null
human-data-beacon: null
IgDiscover: Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads
irods-b2safe-vagrant: A Vagrant "box" config with iRODS 4.x, B2SAFE, on a CentOS 6.5 64bit VirtualBox VM
K9-WGS-Pipeline: Nextflow pipeline for standardised variant calls on canine genomes
kanki-irodsclient: Cross-Platform iRODS GUI Client
Knox: Knox Documentation
Knox-ePouta: Connection between Knox (Sweden) and ePouta (Finland)
KubeNow: Deploy Kubernetes. Now!
LEGA-another-simplemicroservice: A testing microservice for the Local-EGA project
LEGA-common-jpa: Classes related to JPA
LEGA-common-messaging: null
LEGA-common-mongo: Mongo common classes
LEGA-config-microservice: null
LEGA-core-microservice: Core components of a microservice
LEGA-crypto-microservice-stub: null
LEGA-ingestion: Local EGA ingestion microservice
LEGA-ingestion-microservice: null
LEGA-session-microservice: null
LEGA-sftp-inbox: null
LEGA-simple-microservice: A testing microservice for the Local-EGA project
LEGA-swagger-documentation-constants: null
LEGA-worker-microservice: null
LocalEGA: NBIS repository for the Local EGA code
LocalEGA-auth: Authentication of EGA users
LocalEGA-cryptor: PGP Encryption
Makeblock-Libraries: Arduino Library for Makeblock Electronic Modules, learn more from Makeblock official website
mdc-file-export: Export tool for images from microscope
MLST-Blast: Scripts for conducting multi-locus sequencing typing against the pubmlst.org database using blast.
mosler-micro-mosler: null
mosler-openstack-fairshare-scheduler: Mosler Fairshare Scheduler for Openstack
mosler-openstack-foreman: Foreman on Openstack
mosler-openstack-puppet-modules: puppet modules shared between packstack and foreman
mosler-system-scripts: null
MrBayes: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
NBIS-template-outreach: null
NBIS-template-support-reports: null
NBIS-UtilityCode: null
NGScourse: Introduction to Bioinformatics Using NGS Data
november: A wiki engine written in Perl 6
opencb-sweden: OpenCB installation in sweden
outreach_templates: null
pipelines: Pipelines developed within NBIS through different pipeline frameworks.
PlotSimMap: R script for plotting output from SIMMAP's ancestral state reconstructions
pouta-blueprints: Pouta Blueprints is a frontend to manage cloud resources and lightweight user accounts.
project_template: null
proteomics-servers: Ansible scripts for installation of proteomics servers
PythonCourse: null
python-irodsclient: A python API for iRODS
RaukR: Course and presentation R Markdown templates for RaukR course
Rcourse: R Programming Foundations for Life Scientists
redmine_anonymous_authors: Update of Redmine Anonymous Authors plugin to work with redmine v3+.
redmine_anonymous_watchers: Update of Redmine Anonymous Watchers plugin to work with redmine v3+.
redmine_semipublic: Semipublic - public but hard-to-guess links - issue views for redmine.
redmine_timetables: Redmine plugin for displaying users schedules.
redmine_wiki_showrevision: Redmine plugin: Add wiki macro for revision information.
reformatKML: Reformat KML files. Script used in Stephan Nylinder et al. "On the Biogeography of Centipeda: A Species Tree Diffusion Approach". Syst. Biol.
ReprRes_J_Lehtio_1411: Reproducible Research resources for NBIS LT project j_lehtio_1411
rmclient: Simple redmine command line client.
Robo-Cup-2017: Template Code for the 2017 Robotic tournament at NBIS retreat
Robo-Cup-2017-viklund: null
sftp-squid: Commandline program to transfer files between two sftp servers.
shiny-baseline-correction-Cancer-CN: R Shiny app for Baseline Correction for Copy Number Data from Cancer Samples
swefreq: Swedish Frequency resource for genomics website
swefreq-browser: Browser for swefreq data
testing-eslint-config: null
test-nextflow: Testing nextflow stuff
toolsinfo: Contains YML files with content for tools section of NBIS website.
ucscBeacon: A GA4GH Draft Beacon implementation
uirods: A proof-of-concept for a super-lightweight web interface for iRODS (http://irods.org). These days, you should probably check out GoRods (https://github.com/jjacquay712/GoRODS) instead.
vcf2cytosure: Convert VCF with structural variations to CytoSure format
virtual-fallback-cluster: Compute resources for training
web_common_backend: A generic backend framwork for sequence prediction web-servers using WSDL API
webdocker-website: null
web_pconsc3: A django based web-server platform suitable for schedualling time consuming jobs only at the remote computational node
web_prodres: Web server for PRODRES: Fast protein searches using a protein domain-reduced database.
web_proq3: null
web_scampi2: Web server for SCAMPI2
web_subcons: Web server for SubCons: a new ensemble method for improved subcellular localization predictions
web_topcons2: web-server implementation for topcons2
wgs-structvar: Whole Genome Sequenceing Structural Variation Pipelines
workflows: Community maintained workflows & tools (with examples)
workflow-tools-evaluation: Evaluating workflow tools and formats, such as the Common Workflow Language (CWL) for possible use within NBIS
workshop-common: Common configuration of githubpages for workshops
workshop-common: Common configuration of githubpages for workshops
workshop-howto: Howto setup a workshop
workshop-howto: Howto setup a workshop
workshop-in-the-cloud: A cloud solution for providing workshops
workshop-scRNAseq: Single cell RNA sequencing analysis course
xferticket: transient storage service

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.