CRC 1535 · SFB MibiNet · Project Z03

Data Management and
Central Database
for CRC MibiNet

CRC MibiNet includes 13 research projects which 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 Research Data Management Dr. Sabrina Zander· 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
Open Research Data
Annotated Research Contexts (ARCs)

All MibiNet datasets published via the DataPLANT / NFDI ARC standard

git.nfdi4plants.org/sfb1535_mibinet
ATPLyzer

ATPLyzer – An advanced ratiometric multi-colour biosensor for long-term monitoring of 1 ATP dynamics

2026
A08 MGlucoMeter2.6

A new series of ultrasensitive and ratiometric genetically encoded nanosensors https://doi.org/10.1101/2025.09.27.678933

A082026
A08 Zoellner2025

The virulence of Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) of rice, critically depends on...

A082026
Kaplunova 2025 TPJ

Artificial Soil (ArtSoil): recreating soil conditions in synthetic plant growth media

2026
Muentjes et al 2025

In vivo online monitoring of intracellular lipid accumulation in Ustilago maydis

2026
CoBiSe

A novel biosensor for ferrous iron developed via CoBiSe - A computational method for rapid biosensor design

2025
IronAndHemeRegulatoryNetworks

The trace element iron is essential for life, but elevated levels can rapidly cause cellular damage through oxidative st...

2025
Witting et al Lab on chip 2025

Quantification of cell growth is central to any study of photoautotrophic microorganisms. However, cellular self-shading...

2025
Devan Sai et al PNAS

Microtubule-dependent endosomal transport is crucial for polar growth, ensuring the precise distribution of cellular car...

2024
GrowthCoupledHemeBiosensor

The iron-containing porphyrin heme is of high interest for the food industry for the production of artificial meat as we...

2024
MibiNet Data Showcases

This ARC presents diverse data from MibiNet members to illustrate the application of MibiNet-specific SWATE templates an...

2024
Sankaranarayanan 2023

Fungal pathogens depend on sophisticated gene expression programs for successful infection. A crucial component is RNA r...

2024
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.