Alignment abstraction for gapsmith: blast/diamond/mmseqs2 runners + precomputed TSV ingestion.
Command-line interface for gapsmith.
Core types for gapsmith: Model, Reaction, Metabolite, StoichMatrix, GPR.
Loaders for gapseq's reference data tables (SEED, MNXref, biomass JSON, pathway tables).
Draft model construction for gapsmith (port of src/generate_GSdraft.R + helpers).
FBA / pFBA / gap-filling via good_lp + HiGHS for gapseq
Pathway/reaction finder for gapsmith: selects pathways, orchestrates alignment, classifies hits, scores completeness.
I/O helpers for gapsmith: model (de)serialization (CBOR/JSON), paths, TSV/FASTA utilities.
Rule-based medium inference — port of gapseq's predict_medium.R
Streaming SBML L3V1 + FBC2 + groups writer for gapsmith.
Transporter detection for gapsmith (port of src/transporter.sh + analyse_alignments_transport.R).
Metabolizer is a Rust library to transform Gesttalt gardens into deployable units.
This is an ActiveRecord Model & mixin to add meta data to any AR object
ATP-like cognitive energy system with metabolic cycles, catabolism, and anabolism for brain-modeled agentic AI
MetsAdvisor helps users estimate weekly METs based on activity input, supporting health maintenance.