Comprehensive Metabolic Modeling to Improve Yield and Cell Performance

Use data-driven, genome-scale metabolic models (GEMs) to simulate, optimize, and guide nutrient strategies, strain engineering, and process improvement across industries

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Unlocking Cellular Potential Through In Silico Insights

Metabolic modeling translates biochemical complexity into predictive, actionable insight. Genome-scale metabolic models (GEMs) provide a mechanistic understanding of cellular metabolism across microbial and eukaryotic systems.

At Clarity Bio Systems, we build and validate custom GEMs for novel or less-characterized organisms. By integrating metabolomics, spent media, and omics data, we deliver context-aware simulations and create data-driven models that reflect real cellular behavior.

Our model simulations reveal how cells utilize nutrients, secrete byproducts, and adapt to environmental changes, providing actionable insights for media design and process optimization, strain engineering, and hypothesis generation for a range of industries including biopharma, FMCG, industrial biotech, and cell therapy.

What you get

Curated Genome-Scale Model

Ready-to-use or custom-built GEM tailored to your organism and research goals.

Quantitative Flux Maps

Simulated flux distributions, knockout/overexpression predictions, and nutrient usage patterns.

Data-Integrated Simulations

Models constrained with metabolomics, spent media, and omics data for biologically realistic outcomes.

Targets & Recommendations

Prioritized genes, pathways, or media components to guide process optimization or strain engineering.

Expert Review & Iteration

Scientist-led interpretation sessions to refine strategies and align simulations with experimental data.

Metabolic Models Developed

Chinese Hamster Ovary

No. of genes2441
No. of metabolites4199
No. of reactions6382

Escherichia coli

No. of genes1333
No. of metabolites1944
No. of reactions2768

Chicken Cell

No. of genes2248
No. of metabolites5835
No. of reactions7449
Memote Score88

Homo sapiens

No. of genes2248
No. of metabolites5835
No. of reactions10600
Memote Score86

Saccharomyces cerevisiae

No. of genes905
No. of metabolites1226
No. of reactions1577
Memote Score85

Synechococcus elongatus

No. of genes785
No. of metabolites768
No. of reactions849
Memote Score76

Bacillus subtilis

No. of genes844
No. of metabolites990
No. of reactions1250
Memote Score86

Y. lipolytica

No. of genes1058
No. of metabolites1868
No. of reactions2285

Metabolic Modeling & Optimization is ideal for

Engineering
biopharmaceutical &
microbial production systems

Quantitative
metabolic
flux insights

Bottleneck identification in
metabolic pathways

Design of
nutrient feeding
strategies

Mechanistic understanding
of spent media analysis
results

Early-stage cell line
evaluation in
biomanufacturing

Industry Specific Use Cases

Academic Research

Bioprocess Optimization

Plants & Environment

FMCG & Consumer Health Products

Why choose Clarity for metabolomics

10,000+

Samples Analyzed

40+

Publications & patents

10+

Methods

30+

Clients & collaborators

500+

Metabolites

17

Completed Projects

10,000+

Samples Analyzed

40+

Publications & patents

10+

Methods

30+

Clients & collaborators

500+

Metabolites

17

Completed Projects

FAQs

Yes. We develop GEMs de novo using genomic and phenotypic data, customized to your system and application.

At minimum, genome annotations and growth data. Omics or metabolomics data are ideal for improved accuracy.

We support both steady-state (FBA) and dynamic FBA simulations depending on your needs.

Yes. Our team interprets simulation outputs to identify specific targets for strain engineering or media optimization.

Absolutely. Spent media and intracellular data can be used to constrain and validate model predictions.

Simulate Smarter, Optimize Faster

Whether you’re stuck with noisy results or planning analysis from scratch, our data experts can help you move forward with clarity.

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