Results for diamond_tool

Lightning-fast CLI for stacked pull requests

The is a boilerplate creating tool for diamond standard, it covers diamond standard with Hardhat(JavaScript), Hardhat(Type Script), Foundry, Foundry + Hardhat and the Modular flavour of all this code base.

Local-first drawing tool

Encrypted terminal note-taking app

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.