These are DECIDE subprojects taken end-to-end the FAIR way — our show-off examples of good scientific practice. Where a project is FAIR-ready, its Data, Documentation and Analysis are one click apart: the cloud folder, the protocols and metadata, and the runnable notebook — so you can go straight from data to reproducing the result. Access is governed by Nextcloud’s fine-grained permissions; some links are on the university network only (VPN).
Catalogues
Public data catalogue
Browse DECIDE's openly available datasets, organised by subproject — each project's public data is appended here as it is released.
Science Club knowledgebase
The Science Club's shared knowledgebase in the cloud — talks, materials and resources collected by the community.
Showcase use cases — CRC projects
Triple RNA-seq · neonatal skin
Colonisation vs infection at the newborn skin–microbiota interface, with data sharing and HPC setup.
Co-infection · decision nodes
Molecular decision nodes in a C. difficile / B. theta co-infection model (epithelial / HT29), prepared for FAIR publication.
Butyrate & infection · organoid
Testing whether butyrate explains infection-related phenotypes — a C. difficile organoid comparison arm to the co-infection model.
Chlamydia host–pathogen interaction
Dissecting the Chlamydia–host interface.
Dual RNA-seq · lung
Host and pathogen transcriptomes captured in parallel in lung infection.
Coming soon
Showcase in preparation — topic being finalised.
Platform & data services — Z02 / INF
CellWhisperer — talk to your data
Talk to your sequencing data: query single-cell datasets in natural language.
cycleHCR spatial imaging
Highly multiplexed spatial imaging, analysed collaboratively on the HPC.
Infection Atlas
An integrated single-cell expression landscape for DECIDE RNA-seq and single-cell studies.
Metadata engine / catalogue
Standardises and enriches metadata across DECIDE datasets — the connective tissue for FAIR.
The "ask the bot" link opens a Nextcloud Talk assistant trained on consortium literature. Analysis links (JupyterHub, port 8000 / CellWhisperer, port 5005) run on the HPC and require the university network (VPN).
Bioinformatics tools
Analysis tools & pipelines
Network and omics analysis tools from the Würzburg Bioinformatics group — dynamic network and enzyme analysis (Prosimat), Boolean network simulation (JimenaE), metabolic analysis (YanaSquare), and RNA-seq analysis (RNAanalyzer), plus semi-automated omics and integrated-network pipelines.
Need help while working in the VRC? See the Support & FAQ — real answers from VRC support on transfers, sync, cloud documents, and FAIR analysis.
New subprojects are added here as they reach FAIR-ready state. To list yours, contact the cRDM helpdesk. Related: How to start a project · JupyterHub · External RDM Resources.