The core technologies behind our models and how researchers work with AI.
The hosted, conversational way to reach every model Omphalos and its community build. Ask a question, get a simulation-backed answer, and run experiments without writing code.
The biology-native language and simulation engine LIFABRICA runs on. Learnable by a biologist in under a day, with native syntax for chemistry, units, space, and time.
An open, community-governed library of models and data that LIFABRICA draws on, stewarded by the independent Life Code Foundation. Contributors are credited and compensated for what they add.
AI builds models, runs simulations, and analyzes results. Researchers guide the work and evaluate the science.
Generative AI assembles model components (reaction networks, parameter sets, compartmental structure) from literature and existing open-source models.
A domain expert reviews the logic, assumptions, and parameters directly in L++ before anything is accepted. This is genuine authorship.
The model runs. Plausible-sounding but structurally wrong reactions tend to surface here, visible in the output.
The model is tested against experimental or omics data it was never fitted to, and revised.
The validated model becomes reusable infrastructure: ported, extended, or deployed into a new application.
Escherichia coli, the standard laboratory bacterium. One integrated kinetic simulation, built first-principles from biochemistry and enzyme kinetics: ~40,000 reactions/processes, 4,403 genes expressed genome-wide. Reproduces known experimental results and sustains many clean doublings in live runs.
Acinetobacter baumannii, a drug-resistant hospital pathogen. Derived from the E. coli reference; simulated doubling time closely matches published values. Antibiotic response matches known patterns: effective on the drug-susceptible strain, resistant in the multi-drug-resistant strain, with combination therapy still suppressing its growth.
A Chinese hamster ovary cell model for biomanufacturing advanced therapeutics, from antibodies to cell and gene therapies. An early draft, not yet validated, that we'll advance together with the community.
A comprehensive cellular model of a human cell, built on the same kinetic engine as the microbial models. An early draft, not yet validated, that we'll advance together with the community.
Extends the virtual cell to whole-body scale for integrated PK/PD and ADME-Tox simulation. An early draft, not yet validated, that we'll advance together with the community.
A sample: the same platform extends to other domains that reduce to biological simulation.
