Repositories list

• msl_api

  Public
  PHP

  •1•0•0•8•Updated Aug 29, 2025Aug 29, 2025

• FSW-Openshift

  Public
  CSS

  •0•0•0•5•Updated Aug 29, 2025Aug 29, 2025

• yoda-ruleset

  Public
  iRODS ruleset and policies for Yoda: https://github.com/UtrechtUniversity/yoda

  pythonyodairods

  Python

  •

  GNU General Public License v3.0

  •13•9•0•2•Updated Aug 29, 2025Aug 29, 2025

• campylobacter-crisprscape

  Public
  Exploring the diversity of CRISPR spacers in Campylobacter jejuni & coli

  bioinformaticssnakemakecampylobacter+ 2crispr-cas-systemsbacterial-genomics

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•10•0•Updated Aug 29, 2025Aug 29, 2025

• yoda

  Public
  A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.

  ansibledataresearch+ 4yodairodsautomated-deploymentutrecht-university

  HTML

  •

  GNU General Public License v3.0

  •24•51•53•1•Updated Aug 29, 2025Aug 29, 2025

• yoda-clienttools

  Public
  Client-side Yoda tools - mainly intended for data managers and key users

  yoda

  Python

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated Aug 28, 2025Aug 28, 2025

• cd2-ansible

  Public
  Ansible scripts for the deployment of the CD² metadata catalogue

  Jinja

  •

  GNU Affero General Public License v3.0

  •1•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• ETAIN-webmap

  Public
  JavaScript

  •0•0•0•0•Updated Aug 28, 2025Aug 28, 2025

• containerplatform-docs

  Public
  Container Platform public documentation

  Dockerfile

  •4•1•0•0•Updated Aug 28, 2025Aug 28, 2025

• irods-consistency-check

  Public
  Check consistency between irods resource and on-disk vault.

  checksumirods

  Python

  •

  GNU General Public License v3.0

  •3•2•0•0•Updated Aug 28, 2025Aug 28, 2025

• researchcloud-items

  Public
  Installation scripts for SURF ResearchCloud catalog components

  ansible-roleresearch-cloud

  Jinja

  •

  GNU General Public License v3.0

  •4•7•31•4•Updated Aug 27, 2025Aug 27, 2025

• SRC-molecule

  Public
  A set of molecule configuration files to faciliate testing of SURF Research Cloud items.

  0•0•3•2•Updated Aug 27, 2025Aug 27, 2025

• ibridges-ansible

  Public
  Ansible modules for syncing data with iRODS using iBridges.

  Python

  •

  MIT License

  •0•1•4•2•Updated Aug 27, 2025Aug 27, 2025

• SRC-test-workspace

  Public
  Packer definitions and scripts for generating containers and VMs mimicking SURF Research Cloud workspaces.

  research-cloud

  HCL

  •

  MIT License

  •0•3•7•2•Updated Aug 27, 2025Aug 27, 2025

• src-component-galaxy

  Public
  Galaxy Workflow manager for SURF Research Cloud

  Jinja

  •

  GNU Lesser General Public License v2.1

  •4•1•6•3•Updated Aug 26, 2025Aug 26, 2025

• davrods

  Public
  An Apache WebDAV interface to iRODS

  yodawebdavirods+ 1davrods

  C

  •

  GNU Lesser General Public License v3.0

  •15•26•12•0•Updated Aug 26, 2025Aug 26, 2025

• irods-uu-microservices

  Public
  Miscellaneous iRODS microservices developed or modified by Utrecht University.

  yodairods

  C++

  •

  GNU Lesser General Public License v3.0

  •3•2•0•0•Updated Aug 25, 2025Aug 25, 2025

• yoda-portal

  Public
  Web portal for Yoda: https://github.com/UtrechtUniversity/yoda

  pythonflaskyoda+ 1irods

  JavaScript

  •

  GNU General Public License v3.0

  •13•10•0•0•Updated Aug 22, 2025Aug 22, 2025

• PoC-scoping-review

  Public
  Scoping review of the methods to compute the "Probability of Causation (PoC)" or assigned share of an exposure as the cause of a multi-causal disease.

  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• yoda-external-user-service

  Public
  A service that provides for external user enrollment and external user management via a HTTP API for Yoda: https://github.com/UtrechtUniversity/yoda

  pythonyoda

  Python

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Aug 20, 2025Aug 20, 2025

• icat-database-checker

  Public
  script to check the iRODS ICAT database for inconsistencies and unusual situations

  irods

  Python

  •

  MIT License

  •1•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• mimosa

  Public
  MIMOSA: Integrated Assessment Model for global cost-benefit analysis of climate policy

  Python

  •

  GNU General Public License v3.0

  •6•7•0•1•Updated Aug 20, 2025Aug 20, 2025

• yoda-web-mock

  Public
  Mocks for web services that Yoda depends on.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 20, 2025Aug 20, 2025

• yoda-moai

  Public
  Yoda OAI-PMH endpoint: https://github.com/UtrechtUniversity/yoda

  oai-pmh

  Python

  •

  Other

  •21•1•0•0•Updated Aug 20, 2025Aug 20, 2025

• ivt-pipeline-noresm-arctic_cordex

  Public
  Python

  •0•0•0•0•Updated Aug 18, 2025Aug 18, 2025

• S23

  Public
  Computer lab exercises of Utrecht Summer School S23 "Advanced course on using Mplus"

  TeX

  •1•1•1•0•Updated Aug 18, 2025Aug 18, 2025

• PoC-Asbestos

  Public
  Code and documentation for the calculation of a cut-off asbestos exposure value for the compensation of workers who develop lung cancer as a result of asbestos exposure, taking into account confounding and statistical uncertainties. The calculation uses the probability of causation (PoC) principle.

  Rich Text Format

  •

  MIT License

  •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• MEGAISurv-Namaste

  Public
  Nanopore Metagenomic Antibiotic Resistance and Taxonomy Screening

  snakemakemetagenomicsantibiotic-resistance+ 2taxonomic-classificationnanopore-sequencing

  R

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

• vre-docs

  Public
  User documentation for Research Cloud tailored at UU researchers

  Lua

  •

  MIT License

  •2•1•13•0•Updated Aug 13, 2025Aug 13, 2025

• yoda-zabbix

  Public
  Zabbix files for Yoda: https://github.com/UtrechtUniversity/yoda

  zabbixyodazabbix-agentd

  Shell

  •

  GNU General Public License v3.0

  •2•0•0•0•Updated Aug 13, 2025Aug 13, 2025