CRC 1535 · SFB MibiNet · Project Z03

Data Management and
Central Database
for CRC MibiNet

CRC MibiNet spans 11 microorganisms and 13 research projects generating data from microfluidics, live-cell imaging, biosensors, biochemistry, and structural biology. Z03 INF ensures all experimental output is FAIR-compliant through the DataPLANT ARC standard.

Principal Investigator Prof. Dr. Björn Usadel · Institut für Biological Data Science, HHU Düsseldorf
Saccharomyces cerevisiae · DIC microscopy
© Masur / Wikimedia Commons · Public Domain
F
Findable

Persistent DOI identifiers; indexed in DataPLANT and NFDI registries

A
Accessible

ARC format retrieval via open, standardised protocols; elabFTW integration

I
Interoperable

ISA-XLS metadata, CWL workflows, standard formats (bam, fastq, SBML)

R
Reusable

Rich provenance records; templates tailored to each MibiNet subproject

Growth Media Explorer
MibiGro
DSMZ + MibiNet Curated Media Database
Open MibiGro
Growth Media — The Foundation of Microbial Reproducibility

Every carbon source, nitrogen source, trace element, and vitamin shapes cell physiology — and thereby the outcome of every experiment. Inconsistent media formulations are a leading cause of irreproducible results in microbiology.

MibiGro makes media FAIR: machine-readable recipes with CAS-referenced ingredients, searchable by organism or compound, linked to MibiNet-specific MBN-xxx media and the DSMZ — world's largest biobank.

Microbial colonies on agar plate · Public Domain · NOAA / Wikimedia Commons
3,324
DSMZ media
40
MibiNet media
1,235
Ingredients
1,498
Solutions
  • Full DSMZ Media Browser
    Complete Leibniz Institute database — 3,324 media with full recipe trees, ingredient details, and solution compositions.
  • Curated MibiNet Media (MBN-xxx)
    40 lab-verified entries for CRC organisms — annotated and linked to experimental protocols.
  • LLM Protocol Extraction Pipeline
    AI-powered extraction from 45,000+ public protocols. Expands coverage beyond formal databases.
  • AI Knowledge Assistant
    Semantic search + LLM Q&A about growth conditions, ingredient functions, organism requirements.
Coverage across CRC organisms
S. pombeP. putidaS. cerevisiaeC. glutamicumSynechocystis sp.S. elongatusR. capsulatusH. boliviensis
87
Total sensors
64
Z01 (login)
23
Public
45+
Analytes
  • Sensor Selection Wizard
    Guided multi-step filter by analyte, organism, and spectral range.
  • 3D Protein Structure Viewer
    MolStar-powered visualisation of sensor structures directly in the browser.
  • AI Knowledge Assistant
    On-device Qwen3.5-0.8B via WebGPU. Answers biosensor design questions from MibiNet literature.
  • Sensor Analytics & Comparison
    Side-by-side excitation/emission spectra and dynamic range comparison.
Key organisms measured
C. glutamicumP. putidaS. cerevisiaeS. pombeSynechocystis sp.R. capsulatus
Biosensor Database Portal
MibiSens
Z01 Project Sensors & Public Collection
Open MibiSens
Genetically Encoded Biosensors for Metabolite Detection

Biosensors are molecular tools — built from fluorescent proteins (GFP, RFP) or FRET pairs — that report metabolite concentrations in real-time inside living cells.

In MibiNet they track iron homeostasis, carbon flux, itaconic acid, and signalling molecules across bacteria, yeast, and cyanobacteria. MibiSens centralises the Z01 sensor collection so researchers reuse validated sensors rather than building new ones.

Fluorescent protein membrane markers (RFP/GFP) in yeast · CC BY-SA 3.0 · Masur / Wikimedia
Z03 INF — Mandate
Four Core Objectives
of the INF Project

Z03 operates across all CRC subprojects, ensuring that experimental data from Area A (intracellular interactions) and Area B (intercellular interactions) is captured, structured, and preserved for long-term reuse.

01 / 04
Data Stewardship & Training

Ongoing training and consultations for all CRC members. Guidance on storage, curation, and FAIR-compliant archiving.

02 / 04
Templates & Forms

Metadata templates for MibiNet experiments — microfluidics, fermentation, biosensor assays, structural biology.

03 / 04
NFDI & Cluster Liaison

Integration with DataPLANT, NFDI, EOSC, ELIXIR. Synergy with CEPLAS II, TRR341, CRC1208.

04 / 04
elabFTW Integration

Linking HHU's electronic laboratory notebook to the ARC framework for automatic FAIR data chaining.