Pathway-Guided Pruning Reconstruction of Genome-Scale Metabolic Models
The consensus GEM for Streptomyces coelicolor -
Cellular agriculture × AI: end-to-end Claude Agent SDK app that composes cell-culture media (Sardine framework) and validates against CHO genome-scale metabolic models + readouts (Hamster framework) in one loop. 10 custom tools: KEGG, Ensembl, EuropePMC, arXiv, BiGG, ChEBI, caail, yields calculator, notes r/w.
A validated, genome-scale metabolic model of the HEK293 human cell line - prospective, falsifiable predictions, held-out validation only.
GEM for Aurantiochytrium sp. T66
A. niger curated CCM virtual-microbe pilot (VitaMind series). Real BIOMASS reaction, verifiable carbon guardrail (28 rxn / 24 met / 17 gene), and the phosphate-switch citrate phenotype (citrate 6 -> 12). MIT licensed.
Lernprojekt zum Umgang mit dem **CellNetAnalyzer (CNA)** in MATLAB. Ziel ist es, den Import und die Analyse eines stöchiometrischen Modells zu demonstrieren.
Unified Aspergillus niger virtual-microbe pilot: two model scales (iJB1325 genome-scale BiGG + in-house curated CCM) plus an annotation crosswalk, with one fail-closed verify.py covering all three layers (12 hard checks). MIT for code/CCM; iJB1325 under the BiGG non-profit licence.
Minimal reproducible S. cerevisiae (ecYeastGEM) pilot: real GECKO-constrained FBA + carbon guardrail, licence-clean. Second entry of the virtual-microbe series (E. coli: ijb1325-ecoli-pilot).
Real Escherichia coli (iML1515, BiGG) virtual-microbe pilot: reproducible COBRApy FBA + carbon guardrail + fail-closed species-assertion gate (7/7 verify PASS). VitaMind series.
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